Highlights of Biological Physics (DBIO) Talks @ APS 2024 March Meeting
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TABLE 1: Highlights of Biological Physics (DBIO) Talks @ APS 2024 March Meeting
| Paper | Author(s) | |
|---|---|---|
| 1 | Phylogeny Structures Species’ Interactions in Experimental Ecological Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we propose a novel framework to test whether phylogeny influences the patterns of coexistence and abundance of species assemblages, and apply it to analyze data from large biodiversity-ecosystem functioning experiments. |
Stefano Allesina ; Paula Lemos-Costa ; Zachary Miller; |
| 2 | Species Interactions Alter The Impact of Mutations in Predictable Ways Across Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work suggest that species interactions can predictably impact the effect of mutations, in turn suggesting that evolution may ultimately be predictable in multi-species communities. |
William Harcombe ; Jeremy Chacón ; Jonathan Martinson; |
| 3 | Fundamental Metabolic Strategies of Heterotrophic Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work reveals how the evolution of bacterial genomes is structured by fundamental constraints rooted in metabolism. |
Matti Gralka ; Otto Cordero ; Shaul Pollak; |
| 4 | Global Patterns in Gene Content of Soil Microbiomes Emerge from Microbial Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions. |
Karna Gowda ; Kyle Crocker ; Kiseok Lee ; Milena Chakraverti-Wuerthwein ; Zeqian Li ; Mikhail Tikhonov ; Madhav Mani ; Seppe Kuehn; |
| 5 | Multi-stressor Responses Across The Ecological Hierarchy – from Equilibrium to Non-equilibrium Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Fluctuations in primary productivity create a series of novel C-R cycles based on distinct cycle characteristics that change drastically across time scales of environmental variation. |
Carling Bieg; |
| 6 | A Novel Type of Self-avoiding Walk Revealed By Influenza A’s Motion on Coverslips Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a model that elucidates the underlying ‘burnt-bridge’ Brownian ratchet mechanism, effectively transforming stochastic binding, unbinding, and cleaving events into directed motion. |
Siddhansh Agarwal ; Boris Veytsman ; Daniel Fletcher ; Greg Huber; |
| 7 | Cycle Kinetic of Molecular Motors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the talk I will discuss coarse-graining of cycle descriptions of molecular motors, the influence of an opposing force and the level of coarse-graining on the expected entropy production, and the energy cost of accuracy. |
Stefan Klumpp; |
| 8 | Learning from Failed Steps of Molecular Walkers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In recent work, we developed a mesoscopic model for kinesin stepping on a microtubule that can be simulated efficiently with Brownian dynamics simulations. |
Jutta Luettmer-Strathmann ; Matthew Murrow; |
| 9 | Machines on Genes: A Single-Molecule Perspective Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will describe the research program developed in my laboratory that employs single-molecule biophysical methods to visualize and manipulate the behavior of protein machines on DNA and chromatin. |
Shixin Liu; |
| 10 | Multiple Conserved States Characterize The Twist Landscape of The Bacterial Actin Homolog Mre Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show that MreB double protofilaments can adopt multiple twist states during microsecond-scale MD simulations. |
Kerwyn Huang; |
| 11 | Maximum-likelihood Analysis of Single-Molecule Data on Elongation in An In Vitro Eukaryotic Translation System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These mechanisms have been studied extensively in prokaryotic organisms, but eukaryotic elongation is less well understood. We applied single-molecule fluorescence resonance energy transfer to this problem. |
Clark Fritsch ; Arpan Bhattacharya ; Martin Ng ; Hong Li ; Philip Nelson ; Barry Cooperman ; Yale E. Goldman; |
| 12 | Dynamics of Nuclear Pore Complexes: A Computational Insight Into Macromolecular Traffic Regulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we employ a structure-based computational approach to build molecular simulations for the human NPC. |
Ananya Mondal ; Vinicius Contessoto ; Paul Whitford ; Jose Onuchic; |
| 13 | Specificity and Tunability of Bacterial Efflux Pumps: A New Role for The Proton Motive Force? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Motivated by experimentally determined information about the properties of various cellular pumps, we construct a series of models treating their operation as a Markov jump process between states associated with different protein conformations and bound ligands. We derive an expression for the efflux rate, demonstrating its specific dependence on the parameters characterizing conditions in the cell. |
Matthew Gerry ; Duncan Kirby ; Dvira Segal ; Anton Zilman; |
| 14 | RNA Translocation Through Protein Nanopores: Unfolding of Secondary and Tertiary Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: The translocation of RNA is greatly influenced by secondary and tertiary structures, making it challenging to track the structural changes during translation. We open up a new … |
Minglun Li ; Murugappan Muthukumar; |
| 15 | Proposal for A High-efficiency Voltage Converter Using Semiconductor Electrochemistry Inspired By Biological Electron Bifurcation Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Life invented many marvelous molecular machines. Electron bifurcating enzymes harvest electrons from a two-electron donor, using the resulting electrons to reduce separate … |
Jonathon Yuly; |
| 16 | Controlling The Dynamics of Artificial Nucleic Acid Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss our work toward developing artificial biomolecular condensates whose dynamics of formation and dissolution can be controlled through chemical reactions or external inputs. |
Elisa Franco; |
| 17 | Traveling Bands of Liquid Droplets from Stoichiometrically Skewed Binary Condensation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By monitoring the interface between a P nanostar solution and a Q nanostar solution, we observe stoichiometry-dependent kinetics in the band of liquid condensate droplets that form. |
Connor Chatfield ; Deborah Fygenson; |
| 18 | Versatile DNA Origami Subunit Design for Self-assembled Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By contrast, we introduce a design principle, exploiting a modularity concept, to make a versatile subunit that can target an abundant variety of self-assembled structures. |
Wei-Shao Wei ; Daichi Hayakawa ; Rupam Saha ; Thomas Videbaek ; W. Benjamin Rogers ; Seth Fraden; |
| 19 | Exploiting Floppy Modes in Geometrically-frustrated Assemblies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose how alternative designs such as triangular building blocks on a Kagome lattice may lead to further improvements to size. |
Michael Wang ; Gregory Grason ; Sourav Roy ; Christian Santangelo; |
| 20 | How Does A DNA Motor Turn Around A Corner on DNA Origami? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study reveals the intricate nanomechanical effects of motor-origami performance for complex motion, thus contributing to the advancement of DNA nanorobotics. |
Hon Lin Too ; Pei Yang ; Winna Siti ; Zhisong Wang; |
| 21 | Performing Isothermal Molecular Amplification in Nanocavities with Tunable Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, using a device approach based on pneumatic actuation of a thin membrane lid to seal an embedded nanocavity in a nanoslit, we demonstrate key steps necessary for single cavity molecular amplification. |
Walter Reisner ; Imman Hosseini ; Vahid Hamidi ; Zezhou Liu ; Xavier Capaldi ; Sara Mahshid; |
| 22 | Physics of Single-molecule Electrokinetically Driven Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a device that can perform molecular confinement electrically and allows direct loading of dsDNA from bulk solution. |
Matheus Pessôa ; Han Cao ; Michael Austin ; Sara Mahshid ; Walter Reisner; |
| 23 | Equilibrium Dynamics and Organization of Two Cavity-confined Polymers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that the tendency for polymers to segregate is enhanced by increasing polymer width. |
James Polson ; Desiree Rehel; |
| 24 | Ni-DNA-based Thin-film NDR Device Development Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we developed a flexible gold nano thin-film device by sputtering the gold on a PET substrate. |
Yu-Chun Lin ; Meng-Wei Hsieh ; Kuan-Cheng Lu ; Chia-Yu Chang ; Wen-Bin Jian ; Yu-Chang Chen ; Chia-Ching Chang; |
| 25 | Specific Ion Effects and Solvation at Metastable Biomimetic Interfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show, using surface specific vibrational spectroscopy, how specific ion effects and associated changes to interfacial hydrogen bonding networks can play a key role in the formation of metastable assemblies responsible for memcapacitive behaviors and long-term potentiation in biomimetic membranes. |
Benjamin Doughty ; Haden Scott ; Dima Bolmatov ; Uvinduni Premadasa ; Jan-Michael Carrillo ; Robert Sacci ; Maxim Lavrentovich ; John Katsaras ; Charles Collier; |
| 26 | Coherent Lipid Acyl Tail Correlation Dynamics Measured Using Polarized Quasi-elastic Neutron Scattering Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Lipid molecules self-assemble in aqueous environment to form bilayers. Although the elastic and viscous properties of the bilayers are controlled by molecular orientations and … |
Michihiro Nagao ; Antonio Faraone ; Elizabeth Kelley ; Gøran Nilsen ; Victoria Garcia-Sakai; |
| 27 | Physical Response of Pseudomonas Aeruginosa Outer Membrane to Signaling Molecule Insertion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using an accurate in silico model, this work explores how PQS interaction varies physical properties of P. aeruginosa outer membrane. |
Xin Yong ; Emad Pirhadi; |
| 28 | Biological Tuning of The Membrane Phase Transition Facilitates Plasma Membrane Organization and Function Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Isolated cell plasma membranes are biologically tuned to be in a single phase at growth temperature but close to a critical point of the membrane phase transition. This talk will explore several consequences of this biological tuning through experiments in model and intact cell membranes. |
Sarah Veatch; |
| 29 | Myosin-driven Mechanical Stress Triggers Curvature-dependent Membrane Phase Separation Within Cell-like Model Blebs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study sheds light on membrane phase behaviors regulated by cytoskeletal forces in mammalian cells. |
Ryota Sakamoto ; Michael Murrell; |
| 30 | Localization of Lipid Density-sensing Proteins in Fluctuating Biomembranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: As an initial step to model this lipid defect sensing, we model a diffusing membrane protein with an energetic preference for a particular local lipid density, as well as bending and compressibility moduli that differ from the host membrane. This extends our earlier work on continuum simulations of fluctuating membrane height and lipid density using Fourier Space Brownian Dynamics. |
Indrajit Badvaram ; Brian Camley; |
| 31 | Membrane Fusion As A Pathway to Fission Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work investigates the mechanisms and pathways for the fission of phospholipid membranes, in particular double-membrane fission as it occurs in mitochondrial division. |
Russell Spencer ; Marcus Müller; |
| 32 | Interplay Between Elastic and Structural Properties in Cholesterol-rich Lipid Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our results clearly show that cholesterol stiffens all studied membranes, irrespective of chain unsaturation. More importantly, by mapping these observations to those from small-angle X-ray scattering studies, we find that the measured changes in κ<! |
Teshani Kumarage ; Sudipta Gupta ; Fathima Doole ; Milka Doktorova ; Haden Scott ; Laura Stingaciu ; John Katsaras ; George Khelashvili ; Michael Brown ; Rana Ashkar; |
| 33 | Polysaccharide Functionalization Reduces Lipid Vesicle Stiffness Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Typically, synthetic polymers like polyethylene glycol are used to increase vesicle stability but polysaccharides are much less explored. Here, we report a general method to functionalize lipid vesicles with polysaccharides by binding them to cholesterol. |
Kevin Jahnke ; David Weitz; |
| 34 | X-ray Standing-Wave Fluorescence Study of The Transverse Distribution of Cholesterol Within A Supported Phospholipid Bilayer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: X-ray Standing-Wave Fluorescence study of the transverse distribution of cholesterol within a supported phospholipid bilayer. |
Jonathan Maloney; |
| 35 | The Effects of Propofol, Sevoflurane and Isoflurane on Lipid Membrane Fluidity at Clinic Concentrations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we compare the effects of three clinically significant anesthetic drugs: propofol, sevoflurane and isoflurane, on lipid membrane fluidity. |
MUHAMMAD SIDDIQUE ; Juyang Huang ; Ulrich Bickel ; Ehsan Nozohouri; |
| 36 | Scattering Simulations from Laterally Heterogeneous Lipid Vesicles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Combining SANS measurements with simulations, we determine the morphology and composition of lipid domains on spherical lipid vesicles composed of biological and engineered lipid species. |
Nicholas Morris ; Teshani Kumarage ; Rana Ashkar; |
| 37 | Dynamics of The CRISPR Array Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work focused on Type 1E CRISPR/Cas system expressed from synthetic constructs in Escherichia coli. |
James Boedicker; |
| 38 | From Epigenetic Landscape to Genetic Assimilation: Revisiting Waddington’s Experiments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our model captures Waddington’s picture of developmental paths in a canalized landscape, with alternative paths that can be controlled by either external signals or internal variables. |
Archishman Raju ; BingKan Xue ; Stanislas Leibler; |
| 39 | Quantifying Sample Collection Time Uncertainty Improves Epidemiological Modeling of SARS-CoV-2 Evolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk I will present results from our simulations that validate this method, as well as applications to real-world viral case data. |
Elizabeth Finney ; John Barton ; Brian Lee; |
| 40 | Emergent Structure Enables Lab-evolved Multicellular Organisms to Overcome Nutrient Diffusion Limits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Over ~5,000 generations of selection for large size, these clonal yeast clusters evolved to grow exponentially to millimeter sizes in both still and shaken media, growing far larger than previously-demonstrated uptake limits. In this project, we explore how the internal structure of these multicellular clusters facilitates fluid flow through them. |
Emma Bingham ; William Ratcliff ; Peter Yunker; |
| 41 | Robustness of Collectively Encoded Genomic Information Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we demonstrate the suppression of mutations through cooperation among oligomers. |
Leon Zhou ; Martin Falk ; Yoshiya Matsubara ; Kabir Husain ; Jack Szostak ; Arvind Murugan; |
| 42 | Inferring Time-varying Selection for HIV Escape from T Cell Responses Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we extend the marginal path likelihood [1] method to disentangle the time-varying effects of escaping CD8 + T cell-mediated immunity, which we model as a binary trait, from other contributions to fitness. |
Yirui Gao ; Brian Lee ; John Barton; |
| 43 | Evolutionary Adaptation of Dense Microbial Colonies to Surface Associated Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Future work will investigate the physical and mechanical changes evolved at both the single-cell and colony scales that enable faster expansion and modulation of the evolutionary dynamics at play in the colony. |
Katie Randolph ; Marco Fumasoni ; Andrea Giometto; |
| 44 | Mass Extinctions & Evolutionary Lineages: A Coalescent-Theory Approach in An Agent-Based Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In an agent-based model of evolutionary dynamics, which has been shown to undergo a nonequilibrium phase transition from extinction to survival, we apply principles of coalescent theory to investigate the responses of population lineages to simulated mass extinctions of various depths and durations. |
Emily Vastola ; William Hayes ; Joseph Milliano ; Tyler Hanke ; Ian Heye ; Dawn King ; Sonya Bahar; |
| 45 | The Prebiotic Emergence of Biological Evolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using evolutionary invasion analysis, we develop a universal framework for describing any origin story for evolutionary dynamics. |
Charles Kocher ; Ken Dill; |
| 46 | Population Structure, Information, and Growth in Randomly Fluctuating Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk I will show how population structure encodes the information about the history of environmental change and guides population growth. |
Antun Skanata; |
| 47 | Landscape-Enhanced Mutant Survival Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using an Eden model, we simulate population spatial expansion through a landscape of hotspots with deleterious mutations arising at a fixed rate. |
Jimmy Gonzalez Nunez ; Daniel Beller; |
| 48 | Using Time-series Genomic Data for Early Detection of Novel SARS-CoV-2 Variants with Increased Transmissibility Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we develop an epidemiological model that describes the evolution of a pathogen population over time. |
Brian Lee; |
| 49 | Bistable Cellular Fate Commitment in Developmen Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, unless their parameters are quantitatively determined, it is unclear if positive autoregulatory modules found within developmental gene regulatory networks are actually bistable. We combined in vivo live imaging with mathematical modeling to study the fruit fly pair-rule gene fushi tarazu ( ftz), which activates its own expression in a positive feedback loop. |
Hernan Garcia ; Jiaxi Zhao ; Mindy Perkins; |
| 50 | Contact Mediated Spatial Patterning of The Early Human Neocortex Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discuss the implications of fate-patterning and early glial fate restriction. |
Alexandru Bacanu ; Sharad Ramanathan; |
| 51 | Temporal Dynamics of Epithelial Cell Development in The Early Fetal Lung Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore the developmental dynamics of epithelial cells within the human fetal lung from gestational weeks 10 to 19 with single cell RNA sequencing and spatial transcriptomics. |
Spencer Farrell ; Henry Quach ; Sidhartha Goyal ; Amy Wong; |
| 52 | Control of Cellular Phenotype in A Human Stem Cell-derived Smooth Muscle Cell Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To address mechanically induced modulation of vSMC phenotype switching, we have developed a human induced pluripotent stem (iPS) cell-derived vSMC model. |
Melissa Kissling ; Chen-Yu Huang ; Yi-Wen Chen ; Stanley Chun Ming Wu ; Alexander Arking ; Harrison Yezzi ; Shankar Sivarajan ; Kenneth Boheler ; Daniel Reich; |
| 53 | A Computational Method for Inferring Reversible and Irreversible Single Cell State Transitions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we devise a new computational method, named state transition inference using cross-cell correlations (STICCC), for inferring reversible and irreversible cell state transitions by using single cell gene expression data and a gene regulatory network. |
Daniel Ramirez ; Mingyang Lu; |
| 54 | Graph-Dynamo: Learning Stochastic Cellular State Transition Dynamics from Single Cell Data Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Modeling cellular processes in the framework of dynamical systems theories is a focused area in systems and mathematical biology, but a bottleneck to extend the efforts to genome-wide modeling is lack of quantitative data to constrain model parameters. |
Jianhua Xing; |
| 55 | Oral: Self-Regulated Symmetry Breaking Model for Stem Cell Differentiation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, a mean-field model for stem cell populations that considers the interplay between cell-to-cell cooperativity, variability, and finite-size effects is presented. |
Nikolaos Voulgarakis ; Madelynn McElroy ; Kaylie Green; |
| 56 | Machine Learning Approaches for Classifying Temporal Patterns and Tracing Causality in RNA-Seq Datasets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have analyzed a genome-wide RNA-Seq time series dataset from an in-vitro macrophage-neutrophil differentiation process. |
Nimasha Samarawickrama ; Yen Lee Loh ; Manu Manu ; Andrea Repele; |
| 57 | Challenges in Describing The ‘simple’ Sporulation-versus-quiescence Differentiation Decision in Budding Yeast Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The external parameters representing nutrients modify the shape of the landscape, leading to new transitions. Combining experimental data and statistical inference, we provide a model explaining these transitions. |
Sahand Rahi ; Maxime Scheder; |
| 58 | Stabilizing Protein Networks: A Method to Extend Lifespan? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: (1) We analyze the bifurcations and stability of all possible 3- and 4-node regulatory motifs across biologically realistic parameter values to determine which network sub-components are at risk of destabilizing the system. |
Christian Anderson; |
| 59 | Invited Speaker: Carl-Phillipp HeisenbergFriction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes Upon Fertilization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we show that in ascidian oocytes the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. |
Carl-Philipp Heisenberg; |
| 60 | Cilia in Focus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, I will discuss the organization of ciliated organs from a physics perspective, whereby I attempt to untangle the intricate interplay between morphology, activity, and mechanics that lead to robust biological function. |
Eva Kanso; |
| 61 | Nonlinear Elasticity and Rheological Response in Epithelial Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In contrast, our study integrates both aspects using a 2D active vertex model of confluent tissue. |
Dapeng Bi ; Suzanne Fielding ; Michael Hertaeg; |
| 62 | I Have Many Questions About How The Mechanics and Microstructure of Biofilm Infections Impact Interactions with The Immune System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using abiotic gels as models to recreate biofilm mechanics, we have shown that the success of human neutrophils at engulfing things out of the gel is impacted by gel viscoelasticity and toughness. |
Vernita Gordon; |
| 63 | Mechanical Phase Transitions in Articular Cartilage Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Crucially, how extracellular matrix constituents determine mechanical performance, particularly in shear, remains poorly understood. Here, I will describe experiments and theory in support of a rigidity percolation framework that quantitatively describes the structural origins of cartilage’s shear properties and how they arise from the mechanical interdependence of the collagen and aggrecan networks making up its extracellular matrix. |
Itai Cohen; |
| 64 | Sticky Enzymes: Increasing Metabolic Efficiency Via Substrate-dependent Enzyme Clustering Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe how phase-separating enzymes can self-organize into nearly-optimally sized and spaced clusters – provided their “stickiness” is allosterically regulated by local substrate availability. |
Ned Wingreen; |
| 65 | Deriving A Genetic Regulatory Network from An Optimization Principle Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Nevertheless, optimization as a predictive principle has only been applied in very simplified setups. Here, in contrast, we explore a mechanistically detailed class of models for the gap gene network of the Drosophila embryo, and determine its 50+ parameters by optimizing the information that gene expression levels convey about nuclear positions, subject to physical constraints on the number of available molecules. |
William Bialek ; Thomas Gregor ; Thomas Sokolowski ; Gasper Tkacik; |
| 66 | Typicality in High-dimensional Gene Regulation Out of Equilibrium Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using graph theory, we explore how multiple transcription factors modulate the expression of genes through their transcription rates, in or out of equilibrium. |
Gabriel Salmon ; Sara Mahdavi ; Patill Daghlian ; Hernan Garcia ; Rob Phillips; |
| 67 | Energetic Costs for Information Processing with Ion Channels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we extend this framework towards estimating energetic bounds for information processing tasks. |
Jose Betancourt ; Isabella Graf ; Benjamin Machta; |
| 68 | Universal Thermodynamic Bounds on Symmetry Breaking in Living Systems: from Error Correction to Pattern Formation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using our framework, we recover the thermodynamic constraints in kinetic proofreading. |
Shiling Liang ; Paolo De Los Rios ; Daniel Maria Busiello; |
| 69 | Signatures of Energy Dissipation in Bacterial Chemotaxis Signaling Pathways Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Second, cells can spontaneously switch between active and inactive states, but the switch to inactivity takes longer, signifying time-reversal symmetry-breaking. In each case, we show that these measurements are inconsistent with equilibrium mechanisms. |
Yuhai Tu ; David Hathcock ; Qiwei Yu; |
| 70 | Jensen Bound for The Entropy Production Rate in Stochastic Thermodynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we extend the Jensen bound to far greater generality, encompassing position-dependent diffusion, underdamped dynamics, and non-multipartite dynamics. |
David Sivak ; Matthew Leighton; |
| 71 | A Minimal Scenario for The Origin of Non-equilibrium Order Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work suggests the intriguing possibility that non-equilibrium order can arise more easily than assumed, even before that order is directly functional, with consequences impacting the evolution of mutation rates and kinetic traps in self-assembly to the origin of life. |
Riccardo Ravasio ; Kabir Husain ; Constantine Evans ; Rob Phillips ; Marco Ribezzi-Crivellari ; Jack Szostak ; Arvind Murugan; |
| 72 | In There Any Speed-accuracy Tradeoff for Various Non-cognate Species in Nucleotide Substrate Incorporation and Selection of RNA Polymerase Elongation? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The study can be applied to the template-based synthesis in the central dogma. |
Jin Yu; |
| 73 | Limits on The Accuracy of Contact Inhibition of Locomotion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a theoretical model where cells recognize the presence of another cell by binding the protein ephrin with the Eph receptor. |
Wei Wang ; Brian Camley; |
| 74 | Efficiency-noise Trade-offs in Biomolecular Assembly Processes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While biochemical systems are often sparsely characterized, bounds on such fluctuations can be derived for broad classes of stochastic systems. Using such an approach, previous work established a universal trade-off between the efficiency of complex formation and subunit abundance fluctuations. |
Brayden Kell ; Andreas Hilfinger; |
| 75 | Diffusion of Nanoparticles in A Potential Energy Well Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we focus on the case in which the potential energy below the presynaptic bouton is lower than the extrasynaptic membrane and the diffusion constant is identical in the whole system. |
Ho Tin Cheung ; Hyokeun Park ; K.Y. Michael Wong; |
| 76 | Tradeoffs in Concentration Sensing in Dynamic Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We model a eukaryotic cell sensing a chemical secreted from bacteria (e.g. folic acid). |
Brian Camley ; Aparajita Kashyap ; Wei Wang; |
| 77 | Fast Is Hot: Energetics of Information Erasure and The Overhead to Landauer’s Bound at Low Dissipation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use as one-bit memory an underdamped micro-mechanical oscillator confined in a double-well potential created by a feedback loop. |
Ludovic Bellon ; Sergio Ciliberto ; Salambô Dago ; Jorge Pereda ; Nicolas Barros; |
| 78 | Optimal Encoding of Information Enables Net Work Extraction from A Partially Observable Szilard Engine Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: In the classical Szilard engine, a Maxwell demon makes perfect measurements, and all stored information leads to work extraction. However, a real system may produce ambiguous … |
Prithviraj Basak ; John Bechhoefer; |
| 79 | Thermodynamics of Periodic Processes with Unidirectional Transitions and Stochastic Finishing Times — The Case of Digital Computers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Developing a thermodynamic theory of computation is a challenging task that requires addressing difficulties such as stochastic halting times, unidirectional (possibly deterministic) transitions, and restricted initial conditions, features common in real-world computers. Here, we present a framework which tackles these difficulties by extending martingale theory of non-equilibrium thermodynamics to non-stationary Markovian dynamics with broken local detailed balance and absolute irreversibility. |
David Wolpert ; Édgar Roldán ; Gonzalo Manzano Paule ; Gülce Kardes; |
| 80 | Controlling Stochastic Logic Circuits Subject to Thermodynamic Tradeoffs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore tradeoffs among speed, accuracy, and dissipation in a thermodynamically consistent model of complementary logic gates to understand the fundamental bounds and design principles for computing near thermal energy scales. |
Songela Chen ; Phillip Helms ; David Limmer; |
| 81 | The Stochastic Thermodynamics of Communication Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we analyze how the channel information capacity – a property of communication systems that is fundamental to modern information theory – is related to the entropy production in a communication channel. |
Abhishek Yadav ; David Wolpert; |
| 82 | Thermodynamically Optimal Information Gain in Finite Time Measurement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will show the finite-time enegy cost for measurement process by incorporating optimal transport theory, which has attracted attention as a theory that provides tight bounds on the energy cost required for finite-time processes. |
Rihito Nagase ; Takahiro Sagawa; |
| 83 | Trade-offs Between Cost and Information in Cellular Prediction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This constitutes a universal upper bound on prediction accuracy. Using existing experimental data, we show that E. coli cells are far below this upper bound for signals typically encountered during chemotaxis. |
Age Tjalma ; Vahe Galstyan ; Nils Becker ; Pieter Rein ten Wolde; |
| 84 | Bit-driven Active Matter: Measurement Turns Noise Into Motive Power Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The result is a fluid comprised of microscopic controllers carrying out feedback loops that can use environmental noise as a source of motive power. We demonstrate how such a system, when simulated, can create patterns that are immune to noise. |
Bryan VanSaders ; Vincenzo Vitelli; |
| 85 | Thermodynamic Cost of Molecular Computation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss a thermodynamic limit on computation. |
Milo Lin ; Easun Arunachalam; |
| 86 | Connecting Dynamical Coherent Structures to Thermodynamics in Nonequilibrium Reaction Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We consider a range of dynamical regimes by applying nonequilibrium forcing via chemostats. |
Charles Young ; Alexander White ; Sergei Tretiak ; Galen Craven; |
| 87 | Information Processing First and Second Laws for Maxwellian Ratchets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We then show how stochastic thermodynamics’ integral fluctuation theorems take the first law equality to second law inequalities, thus recovering, extending, and ultimately tightening previous results for nonequilibrium steady-state ratchets which violate detailed balance—the case for a great number of complex biological and biophysical processes. In this talk, we will present the information processing first and second laws and then apply them to an example ratchet designed to tunably violate detailed balance in its effective dynamics. |
Mikhael Semaan; |
| 88 | Effect of Localized Active Fluctuations in Conformation and Dynamics of Chromosomal DNA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we introduce a mathematical framework that integrates the spatial and temporal patterns of the fluctuations on a flexible polymer to different observables that describe the dynamics and conformations of the polymer. |
Andrew Spakowitz; |
| 89 | Microtubule Self-assembly Is Controlled By The Topological Activity of Ring and Linear DNA in Microtubule-DNA Composites Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the time-dependent structural and mechanical properties of similar DNA-microtubule composites, undergoing in situ enzymatically-driven linearization and fragmentation of DNA rings, to determine the impact of DNA digestion on the self-assembly of the microtubule network. |
Karthik Reddy Peddireddy ; Mehdi Shafiei Aporvari ; Juexin Marfai ; Rae Robertson-Anderson; |
| 90 | Effective Interactions Between Double-stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Umbrella sampling simulations were performed, and effective potentials have been computed by employing the weighted histogram analysis method. |
Terpsichori Alexiou ; Christos Likos; |
| 91 | The Underappreciated Role of Nonspecific Attractions in Crystallization of DNA-coated Colloids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will show that other non-specific attractive interactions do in fact alter the structure of DNA-programmed colloidal crystals and how changes in the particle synthesis can tune the strength of non-specific interactions. |
Hunter Seyforth ; Manodeep Mondal ; Thomas Videbaek ; William Rogers; |
| 92 | SAT-assembly: A Method for Model-driven Inverse Design of Self-assembling 3D Lattices, Capsids, and Polycubes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The goal of inverse design problem is hence to find a set of blocks that reliably assemble in high yield into a target structure while avoiding kinetic traps and alternative competing states. We present here design method “SAT-assembly”, which solves this problem by mapping the design problem in terms of different building block types and interactions between them to Boolean Satisfiability problem (SAT). |
Petr Sulc; |
| 93 | Sliding Tubules: Adding Additional Degrees of Freedom to Anneal Self-assembled DNA Origami Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Introducing new degrees of freedom can alleviate these kinetic traps. In this talk, I will describe how we apply these ideas to reduce polymorphism in self-assembled tubules. |
Thomas Videbaek ; Daichi Hayakawa ; William Rogers; |
| 94 | Scaling Down Bioreactor Processes to Create Unimolecular Supercoiled, Cyclic, and Linear DNA for Study of Topology Effects in Soft Materials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We report up to 100 mg/mL solutions of unimolecular DNA. |
Nathan Oldenhuis; |
| 95 | Deformation of Kinetoplast DNA in Microfluidic Racetracks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Found in the mitochondria of the trypanosome parasite, kDNA are comprised of topologically interconnected small loops of DNA which create an effectively two-dimensional catenated network. In this work we examine the flow-induced deformation in kinetoplast as they translate through a microfluidic racetrack. |
Alexander Klotz ; Nicholas Cuomo; |
| 96 | Single-molecule Dynamics of Tethered DNA in Shear Flow: The Effect of Viscosity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine experiment and simulation to study the effect of buffer viscosity on DNA flow-stretching and DNA fluctuations. |
Andreas Hanke ; Fatema Zohra ; Huda Al-Zuhairi ; Daniel Leon ; Hyeongjun Kim; |
| 97 | Characterizing The Nucleation and Crystal Growth of DNA Origami Nanoparticles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will describe our experimental approach to quantifying the nucleation and growth of crystals formed from octahedral DNA origami nanoparticles.In particular, we study crystallization of DNA origami confined to monodisperse water-in-oil droplets made via microfluidics. |
Myeonggon Park ; Shenkai Li ; Hunter Seyforth ; William Rogers; |
| 98 | Force-induced Structural Transitions in DNA Nanostructures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we investigate the deformation of the building blocks of DNA nanostructures, linear dsDNA chains and circular rings, in elongational flow. |
Arjav Shah ; Beatrice Soh ; Patrick Doyle; |
| 99 | DNA-Functionalized Nanoparticles in Mixed Electrolytes: Salting In, Out, and Beyond Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we analyze how interactions between nanoparticles grafted with non-base-pairing DNA change with the composition of the surrounding electrolyte. |
Roger Reinertsen ; Sumit Kewalramani ; Monica Olvera De La Cruz ; Michael Bedzyk; |
| 100 | Trainable Control of Active Nematic Defect Dynamics Using Imperfect Feedback and Artificial Intelligence Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by advances in training neural networks using imperfect error signal propagation, we introduce an imperfect, thermodynamically-motivated learning algorithm for controlling non-equilibrium systems. |
Carlos Floyd ; Aaron Dinner ; Suriyanarayanan Vaikuntanathan; |
| 101 | Dynamic Remodeling Biopolymer Networks Achieve Mechanical Homeostasis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work offers important insight into how the interplay between polymerization and depolymerization during turnover contributes to the rigidity of the cytoskeleton. |
Marco Aurelio Galvani Cunha ; John Crocker ; Andrea Liu; |
| 102 | Residue-specific Coarse-grained Model of Actin Filaments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed a coarse grained molecular dynamics model of actin filaments that incorporates residue-specific interactions through the C-alpha implicitsolvent model of Kim and Hummer (KH), modified to account for experimentally-determined actinactin interactions. |
Dimitrios Vavylonis ; Shuting Zhang; |
| 103 | Cytoskeletal Response to External Forces: Contractile to Extensile Transition Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we employ a simplified and coarse-grained agent-based description of the actin cytoskeleton using polar filaments and motors to understand it’s response to the external forces. |
Deb Banerjee ; Alexandra Lamtyugina ; Yuqing Qiu ; Suriyanarayanan Vaikuntanathan; |
| 104 | Stress Relaxation of Actin Networks and Solutions Via Severing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop computational models to predict specific signatures in stress relaxation due to severing in both limits. By introducing mechano-chemical feedback of stress on severing, we study its implications on the network topology and the effects on the onset of floppy to rigid transition based on the network connectivity and the applied shear strain. |
Prathamesh Kulkarni ; Frederick MacKintosh ; Anatoly Kolomeisky; |
| 105 | Active Deformation and Self-organization in Elastic Fiber Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These properties emerge from the collective response of individual fibers to external stress as well as to intrinsic active stresses created by myosin motors. In this presentation, we consider how such actively generated forces are transmitted through the network and how this depends on fiber stiffness and connectivity. |
Kinjal Dasbiswas; |
| 106 | Role of Fiber Bending in The Macroscopic Active Contraction of Model Cytoskeletal Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We characterize the strain distribution and normal forces at the boundaries of the network for different configurations of dipoles. |
Abhinav Kumar ; David Quint ; Kinjal Dasbiswas; |
| 107 | Myosin-I Enhances The Force Generation of Arp2/3-mediated Branched Actin Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We site-specifically coupled various densities of myosin-Is to the bead surface and assessed their effects on actin polymerization, network architecture, and symmetry breaking. |
Mengqi Xu ; David Rutkowski ; Luther Pollard ; Grzegorz Rebowski ; Malgorzata Boczkowska ; Roberto Dominguez ; Dimitrios Vavylonis ; Michael Ostap; |
| 108 | Confined Actin Ring Assembly Through Bundle Coarsening Prior to Kinetic Arrest Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We used the high-performance, open-source software aLENS where a constraint method enforces hard-core repulsion between rigid spherocylinders and crosslinking forces in a unified implicit solver. |
Dimitrios Vavylonis ; Adam Lamson ; David Rutkowski ; Bryce Palmer ; Bryce Palmer ; Michael Shelley; |
| 109 | Lévy Distributed Fluctuations and Cytoquakes in The Actomyosin Cortex Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we report low noise, high statistical power measurements of lateral fluctuations in the cortex of multiple cell types, using arrays of flexible microposts. |
Shankar Sivarajan ; Yu Shi ; Katherine Xiang ; Clary Rodriguez-Cruz ; Christopher Porter ; Geran Kostecki ; Leslie Tung ; John Crocker ; Daniel Reich; |
| 110 | Bio-realistic Multiscale Modeling of Cortical Circuits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A central question in neuroscience is how the structure of brain circuits determines their activity and function. To explore this systematically, we developed a 230,000-neuron model of mouse primary visual cortex (area V1). |
Anton Arkhipov; |
| 111 | Memory-induced Long-range Order in Neural Activity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate the relation between memory (time non-locality) and long-range order (LRO) in neuronal dynamics. |
Chesson Sipling ; Jay Ke-Chieh Sun ; Massimiliano Di Ventra; |
| 112 | Generalized Cortical Branching Model: A Minimal Functional Network of Brain Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a generalized CBM (GCBM) to include inhibitory neurons. |
Naruepon Weerawongphrom ; Jeremy Goetz ; Rashid Williams-Garcia ; John Beggs ; Gerardo Ortiz; |
| 113 | Discoveries with Hierarchy of Mean-Field Models of Cellular Automaton Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To gain an understanding of the brain we use a stochastic cellular automata archetype called the Generalized Cortical Branching Model(GCBM) to simulate the activity of excitatory and inhibitory neurons with various interactions between the neurons. |
Jeremy Goetz ; Naruepon Weerawongphrom ; John Beggs ; Gerardo Ortiz ; Rashid Williams-García; |
| 114 | Cocaine Diminishes Functional Network Robustness and Destabilizes The Energy Landscape of Neuronal Activity in The Medial Prefrontal Cortex Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using an underlying modern Hopfield model as a description for the neuronal network, combined with a machine learning approach, we compute the underlying functional connectivity of the neuronal network. |
J. M. Schwarz ; Ahmad Borzou ; Sierra Miller ; Jonathan Hommel; |
| 115 | Ion-channel-based Complete Synchronization Between Neurons Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Communication between neurons may therefore also be possible by the electrical influence of surrounding neurons on the nonlinear dynamics of ion channels. We have achieved complete synchronization between both Hodgkin-Huxley and FitzHugh-Nagumo neurons by assuming the above interaction. |
Seido Nagano; |
| 116 | A Century of The Alpha Rhythm and Its Relatives: A Unified Theory at Last Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we show that just 4 corticothalamic activity eigenmodes can explain the key features of alpha, mu, and tau rhythms, including their frequency structure and topography. |
Peter Robinson ; Rawan El-Zghir ; Natasha Gabay; |
| 117 | Connecting The Eye to The Brain: Retina Structure Shapes Neuron Function in Drosophila Motion Vision Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Finally, we identified and reconstructed the complete set of self-motion neurons in the same EM volume. Using the T4 PD map, we computationally predicted the receptive fields of these self-motion neurons and the body motion they encode. |
Arthur Zhao ; Eyal Gruntman ; Aljoscha Nern ; Nirmala Iyer ; Ed Rogers ; Sanna Koskela ; Marisa Dreher ; Igor Siwanowicz ; Miriam Flynn ; Connor Laughland ; Ludwig Henrique ; Alex Thomson ; Cullen Moran ; Bruck Gezahgen ; Mert Erginkaya ; Ruchi Parekh ; Judith Hoeller ; Sandro Romani ; Eugenia Chiappe ; Davi Bock ; Michael Reiser; |
| 118 | Emergence of A Coherent Bursting State with Scale-free Avalanches from Collective Dynamics of Neuronal Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We observe three distinct dynamical states in the parameter space of g E and g I: (I) incoherent spiking (II) coherent bursting and (III) incoherent bursting. |
Emily S.C. Ching ; Lik Chun Chan ; Tsz Fung Kok; |
| 119 | Collective Entropy in Differing Astrocyte Signaling Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Astrocytes are integral non-neuronal cells that process information uniquely in the brain. In order to understand this unique information processing, we employ symbolization to quantify the dynamics encoding in active, signaling astrocytes. |
Nicholas Mennona ; Barbara Barile ; Hoony Kang ; Kate O’Neill ; Valentina Benfenati ; Grazia Nicchia ; Wolfgang Losert ; Wolfgang Losert; |
| 120 | Periodic Spiking Response to High-Frequency Stimulation in Cortical Cultures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The goal of this study is to examine whether periodic stimulation of a cortical network results in a temporal spiking response within the network. |
Kathryn Hagen; |
| 121 | Large Scale Collective Biological Neural Network Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Neural networks in vivo operate on a range of scales, with information thought to be carried by groups of neurons, and often traveling in waves of activity, such as gamma and delta waves. In this presentation we investigate which aspects of this collective behavior neural cells can recapitulate when they self-assemble into a network in vitro. |
Anna Emenheiser; |
| 122 | Collagen Organisation Regulates Morphogenesis and Cell Fate in Mesenchymal Cell Collectives in Vivo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides a mechanism for coordinated motion that does not rely upon the cytoskeletal dynamics of cell migration. |
Jacqueline Tabler; |
| 123 | Morphogenesis of The Transport Network in Jellyfish Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We model the growth of the gastrovascular canal network, studying how the hydrodynamic effects (pressure in the canals [2]) and elasticity of the tissue [1] interplay in governing the growth of the network. |
Stanisław Żukowski ; Annemiek Cornelissen ; Stéphane Douady ; Piotr Szymczak; |
| 124 | Spatial Patterning of Mitochondrial Energy Production in Mouse Oocytes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: At this non-equilibrium steady state, there exists a spatial gradient of mitochondrial metabolism with distance from the meiotic spindle, but the causes and consequences of this gradient are unknown. To decipher the physical mechanism underlying the origin of this gradient, I am integrating quantitative microscopy with biochemical and mechanical perturbations, with the aim of interpreting the data using the lens of continuum biophysical theory. |
Yash Rana ; Xingbo Yang ; Daniel Needleman; |
| 125 | Competing Adhesions Rigidify The Vertebrate Body Axis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose that the cadherin mutants experience increased integrin-based interactions between cells and the extracellular matrix (ECM) that partially rescues tissue integrity. |
Andrew Ton; |
| 126 | Lateral Cell-cell Contact Remodeling in The Mouse Neural Plate Epithelium Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides a basis for linking tissue shape changes to the dynamics of cell-cell contacts in three dimensions in a broad class of epithelial sheets. |
Sassan Ostvar ; Xiaoyun Liu ; Alyssa Lesko ; Bianca Dumitrascu ; Ann Sutherland ; Karen Kasza; |
| 127 | Mechanical Control of Anisotropic Tissue Growth and Oriented Cell Divisions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we propose a cell-level model for anisotropic growth based on mechanical feedback between cell motility, mechanical pressure, and division rates. |
Xinzhi Li ; Shiladitya Banerjee; |
| 128 | Interplay Between Elasticity and Order in 2D Biological Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Most theoretical treatments of ordered biological tissues are based on fluid models, however there are examples of tissues, such as hydra, which are not freely flowing but which are, nonetheless, often modeled as such. With this motivation, we have developed a Foppl-van Karman model for an active elastic sheet with nematic order, inspired by nematic elastomers, which couples in-plane passive and active stresses to bending and order. |
Sergey Sokolovskiy ; Arthur Hernandez ; Fridtjof Brauns ; M Cristina Marchetti; |
| 129 | Morphogenesis and Chiral Dynamics in Epithelial Organoids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Altogether, our work reveals the role of topological defects in determining collective cell behavior, with implications in morphogenesis of complex 3D organoids. |
Tzer Han Tan ; Aboutaleb Amiri ; Irene Seijo-Barandiarán ; Michael Staddon ; Marko Popovic ; Anne Grapin-Botton ; Frank Jülicher; |
| 130 | Recording Morphogen Signals Reveals Origins of Gastruloid Symmetry Breaking Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study defines a mechanism through which aggregates of stem cells can form a patterning axis even in the absence of external spatial cues. |
Harold McNamara ; Sabrina Solley ; Britt Adamson ; Michelle Chan ; Jared Toettcher; |
| 131 | Electric Stimulation Induces Morphogenetic Elongation in A 3D Embryo Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present preliminary data characterizing key molecular and mechanical pathways of ‘electro-elongation’ using a combination of knock-out mutations and pharmacological inhibition and explore the role of electrostatic stresses by modeling the gastruloids using a modified Taylor-Melcher leaky dielectric model. |
Isaac Breinyn ; Evan Underhill ; Jared Toettcher ; Daniel Cohen; |
| 132 | Proliferation of Model Protocells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we discover a collective proliferation mode that enables model protocells to flourish throughout prolonged incubation periods. |
Yisen LI ; Yilin Wu; |
| 133 | Continuous Evolution of Dynamic, Multi-state, and Computational Protein Functionalities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a continuous, in vivo directed evolution approach for evolving proteins with multiple conformations. |
Vojislav Gligorovski ; Sahand Rahi; |
| 134 | Unveiling Heterogeneity in Optogenetic Circuit Dynamics Via Single-Cell Time-Lapse Imaging Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we perform time-lapse imaging of single mammalian cells engineered with chemical and light-inducible negative feedback gene circuits, allowing us to quantify individual cell expression kinetics. |
Joshua Azukas ; Rafal Krzyszton ; Gabor Balazsi ; Helmut Strey; |
| 135 | Efficient Design of Stochastic Molecular Circuits with Differentiable Programming Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Developing more general and efficient techniques would have a significant impact on many fields, including synthetic biology, developmental biology, and tissue engineering. In this work, we explore the use of general gradient-based optimization approaches to tackle this problem. |
Francesco Mottes ; Ramya Deshpande ; Michael Brenner; |
| 136 | Construction of A Stably Integrated Mammalian Toggle Switch from Bacterial Components Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Initial induction experiments showed that the circuit was responsive to Dox, but not DAPG, likely due to cellular uptake issues with DAPG. Mathematical modeling suggested solutions to overcome this issue. |
Julia Petreczky ; Rafal Krzyszton ; Kai Wahlin ; Yiming Wan ; Gabor Balazsi; |
| 137 | Unraveling Transcriptional Dynamics in Mammalian Cells Using A Synthetic Reporter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In future work, we aim to leverage the rules learned from our platform to advance our ability to engineer complex gene circuitry in mammalian cells. |
Zheng Diao ; Oleg Igoshin ; Caleb Bashor; |
| 138 | Adaptive DNA Amplification of Synthetic Gene Circuit Opens New Way to Overcome Cancer Chemoresistance Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Drug resistance remains a formidable barrier to the efficacy of cancer treatments, underscoring the necessity for experimental model systems that are comprehensive yet streamlined to allow the identification of the underlying mechanisms and corresponding countermeasures that can be applied across various cancer types. To address this need, we investigated a collection of engineered mammalian cell lines with synthetic gene circuits integrated into their genome that evolved resistance to Puromycin. |
Yiming Wan ; Quanhua Mu ; Rafal Krzyszton ; Joseph Cohen ; Damiano Coraci ; Christopher Helenek ; Christopher Tompkins ; Annie Lin ; Kevin Farquhar ; Erin Cross ; Jiguang Wang ; Gabor Balazsi; |
| 139 | Non-disruptive Characterization of Cell-free Synthesized Membrane Interacting-proteins with A Quartz Microbalance Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present a new method in which we used a cell-free transcription-translation (TXTL) to recreate the natural biogenesis of membrane proteins and non-disruptively measure their incorporation into supported lipid bilayers (SLB) with a quartz crystal microbalance with dissipation (QCMD). |
Aset Khakimzhan ; Ziane Izri ; Seth Thompson ; Oleg Dmytrenko ; Chase Beisel ; Vincent Noireaux; |
| 140 | Flexible PEG-LifeAct Crosslinkers Tune Actin Network Structure and Mechanics in A Contour Length Dependent Manner Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: In vitro studies of actin filament networks dynamically crosslinked with binding proteins enable direct probing of cytoskeletal mechanics as well as inspire new adaptive materials … |
Tyler Jorgenson ; Kashmeera Baboolall ; Cristian Suarez ; David Kovar ; Margaret Gardel ; Stuart Rowan; |
| 141 | Microeconomics of Metabolism: A Linear Response Theory of Evolved Metabolic Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we focus on the responses of metabolic systems to environmental perturbations, rather than their metabolic states themselves, and theoretically demonstrate a universal property of the responses independent of the systems’ details. |
Jumpei Yamagishi ; Tetsuhiro Hatakeyama; |
| 142 | Enzyme Diffusion Watched in Real Time Directly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A limitation, in the controversial study of enhanced enzyme diffusion, is that the experiments were too indirect and controversial. |
Qi Pan ; Steve Granick; |
| 143 | Durotaxis and Frictiotaxis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Durotaxis and Frictiotaxis Cells migrate along gradients of substrate stiffness — a process called durotaxis. Here, I will show that this process relies on different physical mechanisms that operate in different contexts. |
Ricard Alert; |
| 144 | Chemorepulsion and Chemoattraction of Malignant T Cells in CCL19 Gradients of Various Strengths Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use Monte Carlo simulations to model the stochastic binding and unbinding of CCL19 to receptors, as well as the desensitization, internalization, and recycling of receptors. We propose that the sensed concentrations of CCL19 regulate these processes. |
Grace Luettgen ; Brian Camley; |
| 145 | Characterizing 3D Trajectories of Immune Cells in Live Larval Zebrafish Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We examined innate immune cells – neutrophils and macrophages – in larval zebrafish, a model vertebrate. |
Piyush Amitabh ; Jonah Sokoloff ; Julia Ngo ; Raghuveer Parthasarathy; |
| 146 | Inferring Directionality of Diffusive Sources from Short Time Fluxes to Membrane Receptors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We consider the scenario of a single cell seeking the directionality of a point source of diffusing molecules. |
Alan Lindsay ; Andrew Bernoff ; Alexandra Jilkine ; Adrián Hernández; |
| 147 | Mammalian Sperm Thermotaxis Is Driven By Modulation in Flagellar Beating Patterns Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this paper, we develop a microfluidics assay to study bovine sperm thermotaxis in detail. |
Vasily Kantsler; |
| 148 | Physical Limits to Mechanical and Chemical Sensing of Fluid Flow Direction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop a global framework that describes the sensory precision of multiple types of directional sensing from a statistical mechanics perspective. |
Louis Gonzalez ; Bumsoo Han ; Andrew Mugler; |
| 149 | Bacterial Motility Patterns Adapt in Response to Spatial Confinement and Disorder Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a simple microfluidics device to examine how interactions with spatially complex mechanical cues shape bacterial motility. |
Haibei Zhang ; Miles Wetherington ; Hungtang Ko ; Cody FitzGerald ; Jasmine Nirody; |
| 150 | How Bacteria Navigate Through Complex Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In contrast to E. coli, our research reveals the transient subdiffusion of bacteria in agar, primarily due to intermittent trapping. |
Agniva Datta ; Sönke Beier ; Veronika Pfeifer ; Robert Großmann ; Carsten Beta; |
| 151 | Physical Limits on Galvanotaxis Via Transmembrane Protein Electrophoresis Is Dependent on Cell Morphology and Orientation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, they also experience greater variation in their estimation of the field direction along this axis. Our model predicts that if cells estimate the field direction by taking the average of all the protein locations, this introduces a bias towards the short axis. |
Ifunanya Nwogbaga ; Brian Camley; |
| 152 | A New Way for Quantifying Bacterial Chemotaxis with The Three Channels Microfluidic Chip Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We aim to understand the role of surfaces in the migration of bacteria towards the favorable environment. |
Adam Gargasson ; Harold Auradou ; Peter Mergaert ; Carine Douarche; |
| 153 | Repulsion from Slow-diffusing Molecules Improves Chemotactic Capture of Moving Sources Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a new explanation for why microbes may be repulsed by certain nutrients. |
Blox Bloxham ; Hyunseok Lee ; Jeffrey Gore; |
| 154 | Measuring The Torque Produced By The Flagellar Motor in Pseudomonas Aeruginosa Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The aim of this work is to experimentally measure the motion of P. aeruginosa near a surface to compute the torque required to rotate the flagellum. |
Victoria Torres ; Orrin Shindell ; Hoa Nguyen ; Frank Healy ; Bruce Rodenborn; |
| 155 | Silver Ions Inhibit Bacterial Movement and Stall Flagellar Motor Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report our study on how Ag + ions affect the motility of E. coli bacteria using swimming, tethering, and rotation assays. |
Yong Wang ; Benjamin Russell ; Ariel Rogers ; Ryan Yoder ; Matthew Kurilich ; Venkata Rao Krishnamurthi ; Jingyi Chen; |
| 156 | Incorporating Local Secondary Structure Information Into Coarse-grained Simulations of IDPs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe efforts to incorporate helical and sheet structure in a sequence-dependent manner into implicit solvent coarse-grained models. |
Robert Best; |
| 157 | All at The Surface: Exploring The Surface Thermodynamics of Polymer Clusters Through Minimal Molecular Modelling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite the importance of these droplets, through their association with disease, and even bacterial antibiotic resistance, the key molecular mechanisms underpinning their formation remain rather incomplete. Here, we explore the role of the interface of these droplets and present novel simulation techniques to explore the thermodynamics of these systems (such as surface tension and excess free energy) from coarse-grained molecular dynamics simulations, based on modern statistical mechanics and polymer physics. |
Luke Davis ; Philip Pearce; |
| 158 | Fine Structures of Intrinsically Disordered Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduced the Wilson charge index to capture charge interactions and their distribution in the sequence space and a skewness parameter to monitor the change in the gyration radii distribution with charge patches and charge asymmetry. |
Aniket Bhattacharya ; Brandon Stine ; Swarnadeep Seth; |
| 159 | Conformational Ensembles of The Human Intrinsically Disordered Proteome Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Through bioinformatics analyses, we explored the relationship between the compaction of the IDRs and the biological function and cellular localization of the proteins. |
Giulio Tesei ; Anna Ida Trolle ; Nicolas Jonsson ; Johannes Betz ; Frederik Knudsen ; Francesco Pesce ; Kristoffer Johansson ; Kresten Lindorff-Larsen; |
| 160 | Accelerating Missense Mutation Identification in Intrinsically Disordered Proteins Using Deep Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We report simulation studies of 2000–5000 random IDPs of length 30–400 amino acids of disparate hydropathy and net charge per residue obtained from the Disprot database using a coarse-grained (CG) model that predicts the radius of gyration of the IDPs rather accurately 1. |
Swarnadeep Seth ; Aniket Bhattacharya; |
| 161 | Comparison of Results from Different Coarse-grained Models of Intrinsically Disordered Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present simulation results from three different CG models 1,2,3,4 (HPS1, HPS2, and SOP-IDP). |
Brandon Stine ; Swarnadeep Seth ; Aniket Bhattacharya; |
| 162 | Minimum Dissipation Approximation: A Fast Algorithm for The Prediction of Diffusive Properties of Intrinsically Disordered Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, this approach fails when the disordered protein contains structured domains. To provide quantitative predictions in such cases, we present a rapid predictive methodology for the estimation of the diffusion coefficients of intrinsically disordered proteins irrespectively of the presence of structured domains. |
Maciej Lisicki ; Radost Waszkiewicz ; Agnieszka Michas ; Michal Bialobrzewski ; Barbara Klepka ; Maja Cieplak-Rotowska ; Zuzanna Staszalek ; Bogdan Cichocki ; Anna Niedzwiecka ; Piotr Szymczak; |
| 163 | The Effects of Ionic Strength on The Morphology, Scattering, and Mechanical Response of Neurofilament-derived Protein Brushes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the effect of ionic strength, phosphorylation, and sequence modification on the morphology of protein brushes using a continuous-space self-consistent field theory. |
Takashi Yokokura ; Chao Duan ; Erika Ding ; Sanjay Kumar ; Rui Wang; |
| 164 | Magnetic Field Effects in Biology from The Perspective of The Radical Pair Mechanism Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have suggested an explanation based on the radical pair mechanism, which involves the quantum dynamics of the electron and nuclear spins of transient radical molecules. |
Christoph Simon; |
| 165 | Weak Magnetic Field Effects on Pigmentation in Tadpoles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work contributes to the growing body of evidence supporting the involvement of weak magnetic fields in biological processes and underscores the importance of the RPM as a key explanatory framework. |
Hadi Zadeh Haghighi ; Gabriel Bertolesi ; Christoph Simon ; Sarah McFarlane; |
| 166 | Radical Pair Mechanism As A Potential Quantum Mechanical Explanation for Superoxide-mediated Low-intensity Magnetic Field Effects in Biology Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In many of these processes, it has been observed that magnetic field effects act via the changes in reactive oxygen species, mainly superoxide. This presentation will discuss radical pair mechanisms based on flavin-superoxide radical pair as a potential explanation for two such phenomena, namely, detrimental effects of hypomagnetic field on adult hippocampal neurogenesis in mice and magnetic field effects on stem cell-mediated growth in planaria. |
Rishabh Rishabh ; Hadi Zadeh-Haghighi ; Dennis Salahub ; Christoph Simon; |
| 167 | Study Photosynthesis A Single Photon at A Time with Quantum Light Spectroscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We report the observation of individual single-photon absorption and emission events in spatially distinct regions in photosynthetic systems. |
Quanwei Li ; Kaydren Orcutt ; Robert Cook ; Javier Sabines-Chesterking ; Ashley Tong ; Gabriela Schlau-Cohen ; Xiang Zhang ; Graham Fleming ; Birgitta Whaley; |
| 168 | Infrared Probes of Ion Specificity in Signaling Metalloproteins and Model Ion-binding Compounds Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Ion-sensing proteins play critical and varied roles in hundreds of biological signaling pathways that are essential to human health and implicated in diseases ranging from cardiac … |
Sean Edington ; Emily Armlin ; Diotima Bose ; Sara Forcina ; Kira Gusciora ; Harrison Vedrani; |
| 169 | Searching The Genome for New Genetic Markers, Associations, and Combinations Related to Disease, Using An AI Assisted Simulation Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The original computer model (Fall 2021 NES 66,9 B01.00003, March 2023 APS JJ05.00007) has been enhanced with AI extensions and modified to generalize the insights gained in our studies of Type 1 Diabetes. |
Robert Goshen ; Harriet Papernick; |
| 170 | Understanding The Mechanobiology of Cell Competition During Cancer Initiation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We found that when the matrix becomes stiffer, it impairs the body’s ability to defend against the mutant cells. |
Tamal Das; |
| 171 | Mechanical Characterization of Neural Organoids Using Ferrofluid Droplets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To extract Calcium signals in 3D at high spatiotemporal resolution, we have constructed a custom lightsheet microscope. |
Friedhelm Serwane ; Elijah Shelton ; Michael Frischmann ; Achim Brinkop ; Teresa Rogler ; Paulina Wysmolek ; Rebecca James ; Filippo Kiessler ; Sebastian Willenberg; |
| 172 | Cell-level Modelling of Active Forces in Early-stage Development Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, using the vertex model for cell-level description of epithelial tissues, we will discuss how various active processes, such as mechano-chemical feedback, cell growth, division, ingression, etc. couple to cell mechanics and lead to pattern formation and flows in model tissues. |
Rastko Sknepnek ; Cornelis Weijer ; Silke Henkes ; Jan Rozman ; Sravana Chaithanya Kanala Venkata ; Julia Yeomans ; Andrej Kosmrlj; |
| 173 | Stress Management: Dissecting How Epithelial Tissues Flow and Fold Inside Developing Embryos Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: During embryonic development, groups of cells reorganize into functional tissues with complex form and structure. Tissue reorganization can be rapid and dramatic, often occurring … |
Karen Kasza; |
| 174 | Cellular Sumo Wrestling: Emergent Dynamics Following Heterotypic Monolayer Collisions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present our group’s ongoing work showing a novel biophysical behavior following the heterotypic collision of two monolayers with distinct biophysical phenotypes. |
Jennifer Mitchel; |
| 175 | Early Career Award for Biological Physics Research: Shaping Living Matter Through Mechanochemical Feedback Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk I will discuss our recent work on mechanochemical modeling of morphogenetic processes in cells that integrates theory with tractable biophysical measurements. |
Shiladitya Banerjee; |
| 176 | Elucidating The Role of Filament Turnover in Cortical Flow Using Simulations and Representation Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We obtain formulas that can be used to fit data from simulations and microscopy experiments. Our work provides insights into the mechanisms of contractility that contribute to cortical flows and how they can be controlled quantitatively. |
Yuqing Qiu ; Elizabeth White ; Edwin Munro ; Suriyanarayanan Vaikuntanathan ; Aaron Dinner; |
| 177 | Noisy Microbial Population Growth Carries An Imprint of Initial Conditions in Its First-passage-time Statistics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In several stochastic models of exponential growth we show power-law relationships that relate variability in the time required to reach a threshold population size to growth rate and inoculum size. |
Eric Jones ; Joshua Derrick ; Roger Nisbet ; Will Ludington ; David Sivak; |
| 178 | A Bifurcation Integrates Information from Many Noisy Ion Channels and Allows for Milli-Kelvin Thermal Sensitivity in The Snake Pit Organ Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Single nerve fibers innervating the organ robustly respond to milli-Kelvin changes in temperature, even though the opening probability of each individual temperature-sensitive ion channel only changes by 0.1%. Here, we propose a mechanism for the integration of this noisy molecular information into an amplified response. |
Isabella Graf ; Benjamin Machta; |
| 179 | Award for Outstanding Doctoral Thesis Research in Biological Physics: Fundamental Limits to Cell Replication in Extreme Heat and Cold Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: An important challenge is explaining how myriad cellular processes together dictate a "pace" at which a cell’s life progresses. |
Diederik Laman Trip ; Hyun Youk; |
| 180 | Optimal Mechanical Interactions Direct Multicellular Network Formation on Elastic Substrates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By combining a linear elastic model for substrate-mediated cell-cell mechanical interactions and an agent-based model for cell movement, we show that force dipoles modeling contractile cells on elastic substrates form branched networks that percolate when the interactions are sufficiently strong. |
Patrick Noerr ; Jose Zamora Alvarado ; Farnaz Golnaraghi ; Kara McCloskey ; Ajay Gopinathan ; Kinjal Dasbiswas; |
| 181 | Temperature Compensation and Scaling in Vertebrate Segmentation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we study temperature scaling and developmental compensation in the context of vertebrate segmentation. |
Viktoriia Mochulska ; Carina Vibe ; Sapna Chhabra ; Thomas Thumberger ; Joachim Wittbrodt ; Paul Francois ; Alexander Aulehla; |
| 182 | Catch Your Breath: Time-dependent Bacterial Turbulence in The Presence of Oxygen Diffusion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use confocal microscopy to image the bacterial turbulent flow in a cylindrical well where the top surface is in contact with ambient air. |
Dipanjan Ghosh ; Xiang Cheng; |
| 183 | Modelling Cell Fate Transitions with Signal-driven Attractor Network Bifurcations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, no models currently bridge the gap between signal-driven bifurcations in an abstract cell fate landscape and the dynamics of gene expression. To address this, we introduce a new model for cell fate transitions that combines modern Hopfield networks with geometric landscapes and bifurcations. |
Maria Yampolskaya ; Pankaj Mehta; |
| 184 | Glioma Cells in Vitro Display Liquid Crystal Characteristics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This also impacts local cell density, with about 40% fewer cells at the trefoil core compared to elsewhere in the culture. Future work aims to study this phenomenon in 3D, utilizing a gel platform to allow for the hypothesized migration upwards at defect sites. |
Anna Argento ; Syed Faisal ; Carles Blanch-Mercader ; Pedro Lowenstein; |
| 185 | Clone Size Statistics of Tumor-inhabiting Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we develop a mechanistic understanding of the microecological dynamics of tumor-inhabiting bacteria. We present a physical model that captures the observed statistics with simple assumptions and explains the uniqueness of this observation to the tumor environment. |
Motasem ElGamel ; Serkan Sayin ; Amir Mitchell ; Andrew Mugler; |
| 186 | Self-organization, Criticality and Collective Information Processing in Animal Groups Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a spatially-explicit schooling model, we will investigate the optimal collective response at the transition between order and disorder, and individual-level evolutionary adaptation as a mechanisms for self-organization towards criticality [4]. |
Pawel Romanczuk; |
| 187 | Collective Mechanics of Shoaling Fish Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Classic examples of this include the flocking of birds and the schooling of fish, where local interactions between individuals lead to large scale collective behavior. To learn more about how these groups behave and whether we can exhibit control or programmability, we experimentally observe shoals of fish within the lab and use image analysis techniques to identify and track fish within dynamic groups. |
Pasha Tabatabai; |
| 188 | Feedback Motifs for Robust Signal Amplification and Critical Behavior Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How do these systems find the critical manifold in the high-dimensional parameter space? Here we present an information theoretic perspective on this question and argue how critical behavior might occur naturally in high-dimensional systems. |
Benjamin Machta ; Isabella Graf; |
| 189 | Large Signal Amplification in Bacterial Chemosensing Due to A Non-equilibrium Phase Transition with Zero-order Ultrasensitivity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Motivated by the arrangement of receptors and kinases in a tight signaling array, we propose a new model where receptor and kinase states are distinct and live on edges and vertices of a lattice, respectively. |
Derek Sherry ; Thierry Emonet ; Isabella Graf ; Benjamin Machta; |
| 190 | Constraints on Active Processes in Cochlear Hair Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a model with feedback where dissipation is cancelled at each location for the resonant frequency mode. |
Asheesh Momi ; Isabella Graf ; Benjamin Machta; |
| 191 | Does Nematic Order Allow Groups of Elongated Cells to Sense Electric Fields Better? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study we focus on the impact of anisotropy in cell shape and local cell alignment on the collective response to electric fields. |
Kurmanbek Kaiyrbekov ; Brian Camley; |
| 192 | Ionic (electric) Cell-cell Signaling During Wound Healing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report that the epithelial system raises the tissue-scale grand movements to overcome the complexity of problems when the local damage becomes no longer single, but multiple and distant from each other using micro-patterned laser irradiation. |
Sun-Min Yu ; Steve Granick; |
| 193 | Enhanced Communication During Prolonged Stimulation Is Detrimental to The Synchronization of Neural Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our previous study, we demonstrated that temporal signals from the environment, in conjunction with the level of intercellular communication, guide the self-organization and communication dynamics of multicellular systems.In this project, we aim to utilize the micropatterning technique for precise control over the shape of the KTaR-1 cell monolayer, creating ’barriers’ that prevent the formation of gap junctions. |
Guanyu Li ; Bo Sun ; Andrew Mugler ; Ryan LeFebre ; Patrick Chappell ; Alia Starman; |
| 194 | Dilute Swarmers Have Different Run-and-Tumble Motility Than Planktonic Swimmers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we compare the run-and-tumble behavior of SM3 as planktonic swimmers and as swarmers diluted in motility buffer. |
Silverio Johnson ; Jay Tang ; Brian Freedman; |
| 195 | Filaments of Collectively Moving Nematode T. Aceti in Viscous Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the collective motion of nematodes in oils of different molecular weight and viscosity. |
Anton Peshkov ; Alyssa Agarie ; Ashley Robinson ; Christina Ceballos; |
| 196 | Emergent Phenomena in Anisotropic and Chiral Dense Active Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will present two new types of collective phenomena that emerge in dense active systems of components displaying anisotropy and asymmetry that can be found in real-world systems. |
Amir Shee ; Guozheng Lin ; Zhangang Han ; Silke Henkes ; Cristian Huepe; |
| 197 | The Effect of Interaction Radius on Vicsek Particles in The Presence of Geometrical Constraints Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we will present our study which investigates the influence the particle’s interaction radius has on the collective behavior that can be attained in the presence of geometric obstacles. |
Eighdi Aung ; Nicole Abaid ; James McClure; |
| 198 | Modeling Collective Dynamics of Biological Systems in Curved Space Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recently, numerical approaches have been developed that solve differential equations for the evolution of continuum fields on arbitrarily curved surfaces; these have been used to study familiar phenomena such as flocking or epithelial relaxation dynamics. Complementing such continuum approaches, we present a molecular dynamics-like framework for performing agent-based simulations on surfaces of arbitrary curvature. |
Toler Webb ; Daniel Sussman; |
| 199 | Warmer Temperatures Favor Slower-growing Bacteria in Natural Marine Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, analyzing the distribution of fast- and slow-growing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperature-dependent growth rates differentially modulate the impact of mortality on species abundances. |
Martina Dal Bello ; Clare Abreu ; Jeffrey Gore ; Carina Bunse ; Jarone Pinhassi; |
| 200 | How Realistic Features Effect Steady State Stability of An Arctic Marine Food Web Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that including realistic characteristics into the model, like predator-specific foraging traits or habitat constraints increases food-web stability. |
Renate Wackerbauer ; Stefan Awender ; Greg Breed; |
| 201 | Emergent Simplicity in Microbial Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we propose an information-theoretic framework for quantifying emergent simplicity in empirical data based on the ability of simple models to predict community-level functional properties. |
Mikhail Tikhonov; |
| 202 | Selection for Coexistence May Help Explain Smooth Functional Landscapes of Microbial Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Species in experiments are typically chosen to favor their ability to coexist, while in nature evolution selects for communities that coexist. Here, we adopt a simulation-based approach to test the likely impact of such species selection on the smoothness of community functional landscapes, and find that, at least in our model, filtering species for coexistence rendered the landscapes smoother. |
Lucas Graham ; Mikhail Tikhonov; |
| 203 | A Universal Geometry Governs The Response of Ecosystems to Environmental Perturbations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a theoretical framework for calculating the linear response of ecosystems to environmental perturbations in generalized consumer resource models. |
Akshit Goyal ; Jason Rocks ; Pankaj Mehta; |
| 204 | The Ecological Consequences of Microbial Metabolic Strategies in Fluctuating Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Microbes adopt a variety of metabolic strategies to consume resources in fluctuating environments, but most work has focused on understanding these strategies in the context of … |
Zihan Wang ; Akshit Goyal ; Sergei Maslov; |
| 205 | Timescale of Environmental Fluctuations Determines Dimensionality of Microbial Community Response Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use a consumer-resource model framework to demonstrate that communities assembled in rapidly fluctuating environments exhibit low-dimensional community structure in which species with similar phenotypes have correlated abundances, whereas in slowly fluctuating environments, abundances of similar phenotypes are anti-correlated. |
Kyle Crocker ; Abigail Skwara ; Arvind Murugan ; Seppe Kuehn; |
| 206 | Growing Phylometabolic Trees from Metabolic Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce and apply a computational framework for a classification scheme of species that compares metabolic networks using distance metrics on linear subspaces of stoichiometric matrices. |
Jorge Reyes ; Jorn Dunkel; |
| 207 | Macroecological Patterns in Coarse-grained Microbial Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that measures of biodiversity at a given scale can be consistently predicted using a minimal model containing zero free parameters, the Stochastic Logistic Model of growth (SLM). |
William Shoemaker ; Jacopo Grilli; |
| 208 | Electromechanical Enhancement of Live Jellyfish for Ocean Exploration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent work has demonstrated the feasibility of externally stimulating live jellyfish swimming via implanted microelectronics. We present a robotic platform that leverages this external electrical swimming control, while also using a passive mechanical attachment to streamline the jellyfish shape and significantly enhance the payload capacity of the biohybrid robotic jellyfish. |
John Dabiri ; Simon Anuszczyk; |
| 209 | Mechanical Characterization of Bio-inspired Flagella Interaction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a characterization map of propulsive force based on various elastic flagella interactions by varying their number, spacing distance, and motion pattern. |
Zhuonan Hao ; Sangmin Lim ; Siddharth Zalavadia ; Darren Chin ; Sumukh Johri ; Vinay Nagappala ; Khalid Jawed; |
| 210 | Wave Propagation in A Basally-actuated Robotic Filament Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a simple realisation of enhanced wave propagation in a macroscale robophysical model of a cilium. |
Rebecca Poon ; Clément Moreau ; Benjamin Walker ; Daniel Soto ; Christopher Pierce ; Eamonn Gaffney ; Daniel Goldman ; Kirsty Wan; |
| 211 | Octopus Arms Chasing in Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine a 3D computational model of an octopus arm, created from medical imaging and biomechanical data, with sensory feedback control inspired by motion camouflage. |
Arman Tekinalp ; Tixian Wang ; Ilia Nasiriziba ; Udit Halder ; Prashant Mehta ; Mattia Gazzola; |
| 212 | Crawling on Waves with A Soft Foot Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by the adhesive locomotion of snails, we have developed a bioinspired soft robot equipped with a single-soft foot. |
Saravana Prashanth Murali Babu ; Ali Sahafi ; Jose Bonilla ; Ahmad Rafsanjani; |
| 213 | Learning to Track Flows Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work emphasizes the importance of both sensor location and sensor type and has implication on other source seeking control problems with traveling-wave characteristic. |
Haotian Hang ; Yusheng Jiao ; Sina Heydari ; Feng Ling ; Eva Kanso; |
| 214 | DiSMech: A Simulator for Soft Robots and Flexible Structures Based on Discrete Differential Geometry Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this research, we present DiSMech, an open-source simulator for intricate soft robots and structures that can be modeled as flexible rods, shells, or interconnected elements thereof. |
Radha Manoj Lahoti ; Andrew Choi ; Mohammad Khalid Jawed; |
| 215 | Plant-inspired Mechano-sensing Soft Robot Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: More specifically, we used a biocompatible strain-softening material, Ecoflex©, to design a skin perforated with channels filled with a liquid that we implemented on a homemade 3D-printed arm and connected to a pressure sensor. |
Tofayel Ahammad Ovee ; JEAN-FRANÇOIS LOUF ; Eftakhar Ahmed Arnob; |
| 216 | Rubble Traversal Experiments of A Vine Robot Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we developed a low-cost vine robot and studied how well it can grow into simulated rubble. |
Zheyu Zhou ; Yaqing Wang ; Elliot Hawkes ; Chen Li; |
| 217 | Shape Morphing Structures with Shrinky Dink and 3D Printed Kirigami Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present an equipment-frugal method of creating 3D free-forms from Shrinky Dink sheets, a well-known children’s toy, and 3D printed ABS plastic. |
Mrunmayi Mungekar ; M. Ravi Shankar ; Mohammad Khalid Jawed; |
| 218 | TBD Related Papers Related Patents Related Grants Related Venues Related Experts View |
Mo Khalil; |
| 219 | Engineering Synthetic Allostery for Phosphorylation-Based Protein Circuits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides insights into allostery design principles and the systematic development of phosphorylation-based protein circuits with composable engineered kinases. |
Meryl Liu ; Michael Elowitz ; Dongyang Li; |
| 220 | The Effect of MicroRNA on Protein Variability and Gene Expression Fidelity Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Small regulatory RNA molecules such as microRNA modulate gene expression through inhibiting the translation of mRNA. Such post-transcriptional regulation has been recently … |
Andreas Hilfinger ; Raymond Fan; |
| 221 | Impact of Mitochondrial Dynamics on Diffusive Spread of Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To explore how protein spread is controlled by mitochondrial dynamics, we developed quantitative models of mitochondrial fission and fusion dynamics and protein diffusion via the network. |
Prabha Chuphal ; Aidan Brown; |
| 222 | Size Scaling of Phase-separated Domains and Mesoscale Clusters That Precede Liquid-liquid Phase Separation (LLPS): Theory and Experiment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discuss observations* of large (10’s-100 nm’s) protein assemblies in the one-phase regime that precedes LLPS, using an analytical theory of these protein assemblies based on analogies with other mesoscale structures in amphiphilic systems with core-shell assemblies. |
Gonen Golani; |
| 223 | Polymer Dynamics Relates Chromosome Mixing to Temporal Changes in Biological Contact Maps Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce the chromosome mixing index, which quantifies the mixing of distinct chromosomes in the nucleus. |
Gaurav Bajpai; |
| 224 | Dissipation and Recovery in Collagen Fibrils Under Cyclic Loading: A Molecular Dynamics Study Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we modify an existing coarse-grained molecular dynamics model for collagen fibril with initially cross-linked collagen molecules, which is known to reproduce the response to uniaxial strain, by incorporating reformation of cross-links to allow for possible recovery of the fibril. |
Amir Suhail ; Anuradha Banerjee ; R. Rajesh; |
| 225 | Temperature-dependent Shear Moduli in Shape-based Models of Dense Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we investigate the temperature dependence of the shear modulus in the Voronoi cell model—a computational shape-based model often used to describe epithelial sheets. |
Chengling Li ; Daniel Sussman; |
| 226 | Mean-field Elastic Moduli of A Three-dimensional, Cell-based Vertex Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we focus on a mean field approach to obtain the elastic moduli, within linear response, for an ordered, three-dimensional vertex model using the space-filling shape of a truncated octahedron and whose energy functional is characterized by a restoring surface area spring and a restoring volume spring. |
Kyung Eun Kim ; Tao Zhang ; J. M. Schwarz; |
| 227 | Graph Vertex Model of 3D Cell Aggregates and The Early Fly Embryo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Since these transitions are not yet mathematically properly formulated, the 3D vertex model is difficult to implement and the few existing implementations rely on highly customized and virtually non-reproducible software solutions. To solve this, we propose Graph Vertex Model (GVM), a reformulation of the vertex model, which stores the topology of the cell network into a knowledge graph. |
Matej Krajnc ; Tanmoy Sarkar ; Tomer Stern ; Jack Deuser ; Urban Zeleznik; |
| 228 | Mechanical Signatures of Structural Disorder in The Drosophila Germband Epithelium Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the origins of structural disorder in epithelia and what roles it might play in morphogenesis are not understood. We study this question in the Drosophila germband epithelium, which undergoes dramatic changes in internal structure as cell rearrangements drive elongation of the embryo body axis. |
Christian Cupo ; Cole Allan ; Vikram Ailiani ; Andrew Cupo ; Sassan Ostvar ; Karen Kasza; |
| 229 | A Dynamic 3D Vertex Model of Stratified Epithelia Predicts Biomechanical Drivers of Cell Delamination Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We perform simulations of a 3D Vertex model extended to represent stratified epithelia. |
Somiealo Azote epse Hassikpezi ; Clementine Villeneuve ; Elizabeth Lawson-Keister ; Matthias Rübsam ; Carien M. Niessen ; Sara A. Wickström ; M. Lisa Manning; |
| 230 | Dietary Conditions Affect The Invasion and Mechanics of Engineered Tumors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we took advantage of a microfluidics strategy to mimic all three properties simultaneously, which we used to investigate how tumor growth and invasion are influenced by the dietary conditions of the patient. |
Maryam Kohram ; Molly Brennan ; Carolina Trenado Yuste ; Susan Leggett ; Jasmine Hao ; Bharvi Chavre ; Sherry Zhang ; Celeste Nelson; |
| 231 | The Origin of Yield-stress and Plasticity in Tissue Monolayers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: As such, gaining insights into the factors that determine a tissue’s yield stress is essential for understanding both tissue development and the onset of tumorigenesis. To investigate this, we employed a multifaceted approach that combines agent-based computational simulations with mean-field theoretical models. |
Anh Nguyen ; Dapeng(Max) Bi ; Junxiang Huang; |
| 232 | Epithelial Layer Fluidization By Curvature-induced Unjamming Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we investigate the role of surface curvature on tissue plasticity and cellular migration using a vertex model embedded on a spherical surface. |
Margherita De Marzio ; Amit Das ; Jeffrey Fredberg ; Dapeng Bi; |
| 233 | How Cells Communicate During Tissue Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will discuss experimental evidence, a computational model verified with experimental observations and hypothesized principles linking tissue growth driven changes in morphology and signal output patterns. |
Abdul Malmi Kakkada; |
| 234 | Signatures of Jamming in A Potts Model of Cellular Migration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore glassy behavior and the jamming transition in an equilibrium Cellular Potts Model (CPM) as a function of confinement, cell adhesion, and cell shape. |
Alex Devanny ; Daniel Lee ; Lucas Kampman ; Laura Kaufman; |
| 235 | Beyond 2D Tissue Modeling: A 3D Continuum Shell Theory of Epithelial Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Two-dimensional (2D) models for confluent tissues correlate the mechanical state of monolayers to morphological indicators such as the shape of their cellular components. We show that such an approach, relying on perimeter elasticity and adhesion of the cells, proves inadequate when applied to in-vitro cultured MDCK epithelia, and that this discrepancy is a consequence of the response of epithelial cells to localized stresses exerted by actin fiber bundles at their basal faces and by a diffuse actin cortex at their apical face. |
Jairo Martin Rojas Huamaní ; Mayisha Nakib ; William Brieher ; Sascha Hilgenfeldt; |
| 236 | Self-Assembly and Stability of 3D Printed Cell Structures in Jammed Microgel Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we will present work on the spatiotemporal evolution of 3D-printed Madin Darby Canine Kidney (MDCK) cell populations in a microgel support medium. |
Vignesh Subramaniam ; Thomas Angelini; |
| 237 | Modeling Cephalic Furrow Architecture in The Drosophila Melanogaster Embryo Using An Automated Multi-node Lateral Vertex Model Approach Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The cell-shape changes that are produced by active modifications of the apical, lateral, and basal membrane lengths require a complex balance between the cortical membrane tension forces and cellular pressure forces in a system of mechanically coupled cells. To investigate this force balance and its role in the invagination process, we have developed an advanced two-dimensional multi-node lateral vertex model that includes a multi-node representation of cellular membranes. |
Redowan Ahmed Niloy ; Michael Holcomb ; Jeffrey Thomas ; Jerzy Blawzdziewicz; |
| 238 | Ginestra BianconiLearning The Topology of Complex Systems from Their Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we reveal how non-linear dynamical processes can be used to learn the topology, by defining Topological Kuramoto model and Topological global synchronization. |
Ginestra Bianconi; |
| 239 | Uncovering The Microscopic Mechanism of The Devil’s Staircase in The Kuramoto Model with Inertia Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We originally propose a phase diagram of the synchronization transitions of the second order Kuramoto oscillator system. |
Jinha Park ; Cook Hyun Kim ; Young Jin Kim ; Byung nam Kahng; |
| 240 | Shortest-path Percolation on Complex Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we present our results obtained from extensive Monte Carlo simulations on synthetic networks and discuss the results. |
Minsuk Kim ; Filippo Radicchi; |
| 241 | Extra Annealing Dimensions for Improved Performance in Physical Optimizers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The former expands the space of states by providing access to each unit’s full complex phase space, while the latter expands the space of connections by making the network a directed graph. Each extension introduces an extra annealing parameter that can be tuned through novel dynamical regimes, recovering conventional CIM operation at one end of its domain. |
Daniel Wennberg ; Hideo Mabuchi; |
| 242 | Opinion Dynamics Entropy Generation Via Complex Network Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work explores the social entropy production of majority-vote opinion dynamics in complex networks, including Erdös-Rényi random graphs, scale-free and small-world networks via Monte Carlo simulations and mean-field analysis. |
Igor Oliveira ; Chao Wang ; Gaogao Dong ; André Vilela ; L.; |
| 243 | Temperature As A Measure of Complexity in Games and Social Hierarchies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Examining data sets from a variety of settings we find that sports and games generically have a higher temperature than human social hierarchies, which in turn have a higher temperature than animal social hierarchies. |
Maximilian Jerdee ; Mark Newman; |
| 244 | StructuralGT V2.0: Graph Theoretic Characterization and Modeling of Complex Networked Materials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Structural analysis of networked materials is a fundamental component in understanding their mechanical, electrical and optical properties. We introduce StructuralGT 2.0 – a graph theoretic software package for analyzing complex networked materials – and demonstrate its applicability to self-assembled nanostructures. |
Alain Kadar ; Wenbing Wu ; Ahmet Emre ; Sharon Glotzer ; Nicholas Kotov; |
| 245 | Scale-Free Networks Beyond Power-Law Degree Distribution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Both models show promising accuracy by fitting only one model parameter each when modeling real-world networks. |
XIANGYI MENG ; Bin Zhou; |
| 246 | The Role of Network Structure in Circadian System Adaptation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We focus on the phenomenon of jet lag as an example: adjusting to a new time-zone after flying westward is generally easier than flying eastward. |
Sneha Kachhara ; Rosemary Braun; |
| 247 | The Counter-intuitive Network Features of Optimal Diffusive Navigation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Traditionally, it has been assumed that small-world architectures with numerous shortcuts between distant nodes are ideal. Counter-intuitively, for diffusive exploration of spatially embedded networks, we find that the addition of a link can worsen the total search time between all pairs of nodes, akin to the well-known Braess paradox where increasing a system’s capacity reduces its efficiency. |
Georgios Gounaris ; Eleni Katifori; |
| 248 | Strange States of "thinking Matter" Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Herds of sheep, flocks of birds, swarms of insects… animal collectives often exhibit large-scale properties that are reminiscent of traditional, passive matter. This is … |
Raphael Sarfati; |
| 249 | Decoding Stride Variability in A Galloping Sled Dog Team Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using custom animal-borne sensors, we collected multi-sensor movement data from a team of sled dogs to investigate their collective locomotion. |
Benjamin Seleb ; Matthew Bull ; Saad Bhamla; |
| 250 | Fire Ant Raft Morphology and Energetics Under Water Wave Forcing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Surprisingly, after 15 minutes (at 20 Hz and 0.6 g), the rate returned to the nonperturbed rate. We hypothesize that the animals achieve this collective reduction in energy expenditure via the discovery of suitable passive mechanical binding. |
Hosain Bagheri ; Michael Goodisman ; Daniel Goldman; |
| 251 | Treadmilling and Protrusion Dynamics in Fire Ant Rafts Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This presentation will discuss our recent work on the collective behaviors of the red imported fire ant that forms a buoyant raft, entirely out of their own bodies, to escape flooding. |
Zachary White ; Robert Wagner ; Franck Vernerey; |
| 252 | Global Coordination Using Local Information in Fire Ant Pontoon Bridges Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Fire ants ( S. invicta) are known to collectively entangle to create free-floating rafts as a survival mechanism upon nest flooding. Here we demonstrate that they can also create structures which allow foraging across a water surface. |
Noah Egan ; Haolin Zeng ; Ram Avinery ; Hosain Bagheri ; Takao Sasaki ; Daniel Goldman; |
| 253 | Self-Organized Floating of Aquatic Worms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesize that the emergence of worm buoys is intricately linked to the degree of entanglement influenced by oxygen levels, which we test by systematically monitoring DO at various population densities. |
Harry Tuazon ; Emily Kaufman ; Vishal Patil ; Tuhin Chakrabortty ; Saad Bhamla; |
| 254 | Interfacial Latch of Aquatic Worms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we explore how blackworms remain suspended at the underside of the interface. |
Harry Tuazon ; Soohwan Kim ; Ishant Tiwari ; Hossam Ismail ; David Hu ; Saad Bhamla; |
| 255 | Afloat Together: Aquatic Worms Utilization of Duckweed for Collective Locomotion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we explore the multifaceted roles played by duckweed and blackworms in their ecology. |
Harry Tuazon ; Ivy Li ; Hossam Ismail ; Saad Bhamla; |
| 256 | Tunnel Remodeling in Fire Ant (S. Invicta) Collectives Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we monitor material flow by creating quasi-2D “ant farms” with 6 layers of colored sand (particle size 75-400 μm, saturated with water 10% by mass). |
Laura Treers ; Daniel Soto ; Michael Goodisman ; Daniel Goldman; |
| 257 | Peering Inside Honeybee Swarms: Adaptive Responses to Temperature Changes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using x-ray computed tomography, we characterize the internal structure of honeybee swarms at varying ambient temperatures. |
Danielle L. Chase ; Olga Shishkov ; Pedro Albuquerque-Lemos ; Anna Simone ; Maridith Stading ; Olaya Garcia-Grau ; Rick Yang ; Orit Peleg; |
| 258 | Investigating The Role of Individual Ant Behaviours on The Collective Movement of Bidirectional Ant Trails Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use detailed experimental analyses of extant data combined with agent based modelling to explore individual ant trajectories and properties that make up the collective colony movement. |
Kimberly Bowal ; L Mahadevan; |
| 259 | Phase Transitions in A Kinetic Mean-field Game Model for Self-propelled Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we study the stability of coherent states in a MFG model of self-propelled agents with a biologically inspired cost function. |
Piyush Grover ; Mandy Huo; |
| 260 | Tunable Rotating Active Nematic States in The Collective Motions of Self-propelled, Chiral Filaments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In gliding assay experiments on microtubules and kinesin motors, microtubules at sufficient density form a long-range-ordered active nematic state whose director rotates counterclockwise. We investigate the emergence of this bulk rotation and its connection to the microtubule structure using Brownian dynamics simulations of self-propelled, semiflexible filaments with chiral activity. |
Madhuvanthi Athani ; Nathan Prouse ; Patrick Noerr ; Niranjan Sarpangala ; Ondrej Kucera ; Kinjal Dasbiswas ; Ajay Gopinathan ; Daniel Beller; |
| 261 | Using Electric Fields to Control Brain Activity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk I will present our recent research on TACS/TMS mechanisms and how to develop more effective stimulation protocols using concurrent brain measurements. |
Alexander Opitz; |
| 262 | Towards A Comprehensive Understanding of The Neural Circuits Controlling Drosophila Flight Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To unravel the fly’s navigation program, we harness genetic fly lines, some of which we helped generate, to optogenetically target specific neuronal populations within the flight motor and sensory systems. By measuring their response to such neuronal perturbations in free flight, we shed light on the neuromuscular underpinning of the fly’s motor control. |
Itai Cohen ; B. Kemper Ludlow ; Han Kheng Teoh ; Abby Leung ; Samuel Whitehead; |
| 263 | Measuring The Amount of Computation Done in C.elegans Brain Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce a novel approach, and use it to quantify the amount of computation done in the joint dynamics of the neurons in a C.elegans. |
Junang Li ; Matthew Creamer ; Andrew Leifer ; David Wolpert; |
| 264 | Natural Visual Input Implies Estimation Biases in A Blowfly Motion Sensitive Neuron Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrated that an optimal motion estimator constructed using scenes captured by the FlEye camera has naturally appearing correlator-like motion estimation properties at low signal-to-noise ratios. |
Charles Edelson ; Robert de Ruyter ; Sima Setayeshgar ; William Bialek; |
| 265 | State-dependent Behavioral Strategies in C. Elegans Olfactory Navigation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Animals can dynamically adjust their behavioral response depending on the odor environment, their internal states, and learned experiences. To understand these behavioral dynamics, we study olfactory learning and navigation strategies in the roundworm C. elegans. |
Kevin Chen ; Jonathan Pillow ; Andrew Leifer; |
| 266 | Behavioral Variability of Drosophila Larva Under Uni- and Multi-sensory Stimulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To study the larva’s information-processing algorithms, we present blue light to stimulate larva’s visual system and red light to optogenetically activate CO 2 receptor neurons. |
Yiming Xu ; Mirna Mihovilovic Skanata; |
| 267 | Internal States Vs. External Cues in Crawling Insect Larvae Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A Markov model of behavioral states shows a switch to weaker responses after repeated stimulus pulses, and we characterize distinct time constants for de-sensitization and re-sensitization, and other features that build a framework for studying behavior in strongly adaptive animals. |
Mason Klein; |
| 268 | Lattice Boltzmann Simulations Reveal Complementary Function of Different Waste Clearance Mechanisms in The Brain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Both of these mechanisms are found within the brain vasculature and they provide redundancy for eliminating waste with different efficacy at high and low concentrations. In this study, we have developed a Lattice Boltzmann code to simulate the brain tissue including its arteries, veins, and capillaries, permitting the selective activation or deactivation of each pathway. |
Reza Yousofvand ; Jeff Tithof; |
| 269 | Unraveling The Influence of Geometry, Binding and Diffusion on Proteins in The Presynaptic Region Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our work we use simulations to disentangle the interplay of the aforementioned factors. |
Simon Dannenberg ; Sarah Mohammadinejad ; Stefan Klumpp; |
| 270 | A Flexible Idealized Model for Investigating Extracellular Solute Transport in The Brain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We analytically formulate an axisymmetric model of fluid flow exchange between the PVS of a penetrating arteriole and the surrounding brain parenchyma modeled as a porous medium. |
Saikat Mukherjee ; Jeff Tithof; |
| 271 | In Search of Emergent Problem Solving in Intelligent Active Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We can call this dumb active matter. We are developing a form of intelligent active matter where the agents communicate with each other over extended distances, have memories and code running internally where their actions are based on previous experiences and their internal records of changing environments which both sustain them and are hostile. |
Robert Austin; |
| 272 | Reprogrammable Microscopic Robots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For instance, we successfully wrote and implemented programs for gradient climbing, sensor value reporting, and gait control. |
Maya Lassiter ; Jungho Lee ; Kyle Skelil ; William Reinhardt ; Lucas Hanson ; Li Xu ; Dennis Sylvester ; David Blaauw ; Marc Miskin; |
| 273 | Material Disturbance During Collective Construction with Soft Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Instead of the deterministic approach that humans and other robot swarms employ, construction by invertebrate collectives is subject to uncertainty due to challenges in transport and cohesion of soft materials, agent interactions during collisions and crowding, and material disturbances from external and internal perturbations. Using a robophysical swarm, we seek to discover principles by which collectives can mitigate such challenges and form reliable, repeatable structures composed of soft materials. |
Joonha Hwang ; Laura Treers ; Daniel Soto ; Michael Goodisman ; Daniel Goldman; |
| 274 | Mind in Vitro: A Complementary Approach to Physical Intelligence Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In order to aid dissecting principles of neural computations, pertinent to locomotion and beyond, here we discuss potential opportunities afforded by a ‘Mind in Vitro’ approach, whereby in vitro living processing architectures may be realized and operated by spatially distributing and connecting neural populations of various nature onto input/output/actuation substrates. |
Mattia Gazzola; |
| 275 | The Median Statistics and Velocity Dependence of Multi-contact Dry Friction Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, recent experiments and simulation have revealed that multi-legged animals and robots exhibit dynamics that are consistent with speed-dependent interaction forces when walking [1], [2]. In this work we provide a simple demonstration of how this speed dependence arises in multi-contact frictional systems with heterogeneous contact velocities. |
Nick Gravish ; Rohan Shah; |
| 276 | The Chaotic Milling Behaviors of Interacting Swarms After Collision Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In particular, recent analysis of the transient dynamics of two colliding swarms has revealed the existence of a critical transition whereby the collision results in a combined milling state about a stationary center of mass. In the present work, we show that the collision dynamics of two swarms that form a milling state transitions from periodic to chaotic motion as a function of the repulsive force strength and its length scale. |
Sayomi Kamimoto ; Jason Hindes ; Ira Schwartz; |
| 277 | Excluded Volume of Polytopes and The Geometry of Inaccessible Configurations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using the relevant theoretical tools from convex geometry we describe the excluded region and excluded volume concepts through the elementary yet practical perspective of convex polytopes. |
Trevor Teague ; Sharon Glotzer; |
| 278 | Stigmeric Coverage with A Robotic Collective for Surface Micro-patterning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we parallelize surface coverage with multiple decentralized robotic agents that indirectly communicate through stigmergy, a principle of coordination through altering and detecting signatures left by other agents in an environment. |
Annalisa Taylor ; Malachi Landis ; Yaoke Wang ; Ping Guo ; Todd Murphey; |
| 279 | Pulse Coupled Oscillators for Micromachines Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Achieving this coordination, however, presents a formidable challenge, primarily centered around the need for a scalable synchronization strategy—a crucial hurdle to overcome for enabling collective behaviors in multiple autonomous microscopic robots. In this context, we introduce pulse-coupled CMOS oscillators as a practical solution for achieving scalable synchronization. |
Milad Taghavi ; Wei Wang ; Itai Cohen ; Alyssa Apsel; |
| 280 | Mechanically Transduced Soft Magnetic Rollers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a novel soft active robotic system composed of functionalized ferromagnetic rollers. |
Joshua Steimel ; Nicholas Brown ; Joseph Harrison ; Alfredo Alexander-Katz; |
| 281 | Differential Drive Kinematics from A Microscopic Robot Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a robot three times smaller than a period of print that obeys the same kinematics, allowing us to import well developed control laws to the microscale. |
William Reinhardt ; Lucas Hanson ; Maya Lassiter ; Tarunyaa Sivakumar ; Scott Shrager ; Marc Miskin; |
| 282 | Modeling of Elastically Coupled Robots Locomoting on An Elastic Membrane Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To gain insight into the dynamics, we develop a numerical model with several important features. |
James Lewis ; Hussain Gynai ; Shengkai Li ; Gongjie Li ; Daniel Goldman; |
| 283 | ‘Mind in Vitro’ Open Hardware: From Versatile, Robust Single-unit Neural Interfaces to Robot-assisted Mini-clusters Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Motivated by the unexplored potential of in vitro neural systems for computing, control, and sensing, and by the corresponding need of versatile, scalable interfaces for multimodal interaction, we present accurate, modular, fully customizable and portable recording/stimulation solutions that can be easily fabricated, robustly operated, and broadly disseminated. |
Xiaotian Zhang ; Zhi Dou ; Seung Hyun Kim ; Gaurav Upadhyay ; Hongbo Yuan ; Zhantao Song ; Daniel Havert ; Kimia Kazemi ; Scott Lee ; Sehong Kang ; Onur Aydin ; Taher Saif ; Nancy Amato ; Hyun Joon Kong ; John Beggs ; Mattia Gazzola; |
| 284 | Prize Talk: Max Delbruck Prize in Biological PhysicsGeometry and Genetics Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: The application of quantitative methods to biological problems faces the choice of how much detail to include and the generality of the conclusions. The middle ground entails some … |
Eric Siggia; |
| 285 | Mechanics of Embryonic Self-organization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present a study of avian gastrulation, in which we have shown that the forces driving morphogenesis self-organize and impinge on gene expression in the establishment of the embryonic axis. |
Francis Corson; |
| 286 | Modulating Signals to Pattern Complex Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Can we pattern these cells by learning and establishing the correct spatiotemporal boundary conditions to generate complex human tissues? We will address this question using a combination of statistical inference approaches and experiments on human embryonic stem cells. |
Sharad Ramanathan; |
| 287 | Imaging Protein Translation from Micron to Atomic Scales Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To study translation at the atomic scale, we employed High Resolution Template Matching (HRTM) to examine ribosomes at different stages of peptide elongation in cryo-EM images of intact human cells. |
Jennifer Lippincott-Schwartz; |
| 288 | Loop Extrusion, Chromatin Crosslinking, and The Geometry, Topology and Mechanics of Chromosomes and Nuclei Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our group uses biophysical and mathematical approaches to study chromosome structure and dynamics. |
John Marko; |
| 289 | Using Machine Learning to Extract Models from Observations of Biological Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss data-driven biophysical modeling approaches we are developing to learn the mechanical behavior of adherent cells. |
Margaret Gardel; |
| 290 | Biological Tissues Can Fluidize By Tuning Their Internal Degrees of Freedom Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that as we introduce the preferred cell perimeters as transient degrees of freedom, the system can find a lower energy state, so that the rigidity transition occurs at a lower average value of the perimeter. |
Sadjad Arzash ; Indrajit Tah ; Andrea Liu ; M. Lisa Manning; |
| 291 | Design Principles of Fate, Form, Forces, and Function: from Embryogenesis to Synthetic Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe work involving machine learning to mine a morphodynamic atlas of Drosophila development and formulate verifiable hypotheses from which we build a mathematical model that captures how protein dynamics govern morphogenesis. |
Sebastian Streichan; |
| 292 | A Single-cell Model for Oxygen Distribution System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These cells can be imaged in both live and fixed tissues, and in a wide range genetic and environmental conditions. I will report on our ongoing experimental and theoretical efforts to reverse-engineer the natural algorithm responsible for the morphogenesis of these remarkable cells, focusing on the scaling laws that connect the structure of the terminal cells to the area of the oxygenated tissue. |
Stanislav Shvartsman ; Tatyana Gavrilchenko ; Tanner Simpson ; Lena Barrett; |
| 293 | A Structural Basis of Cell Fate Precision Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Can cells learn to perform certain functions in response to global cues propagated in the tissue they are embedded in? We address this top-down regulation of cell functions by using a physics-guided quantitative developmental biology approach combined with tailored in vivo engineering. |
Nicoletta Petridou ; Camilla Autorino ; Bernat Corominas-Murtra; |
| 294 | Early Career Award for Biological Physics Research: Microswimmer Behavior in Complex Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss our ongoing work in modeling and simulations that aim to understand the motion of micro-swimmers such as bacteria, micro-algae, spermatozoa or active colloids in complex environments. |
Enkeleida Lushi; |
| 295 | Chemotactic Aggregation of Micro-swimmers in Brinkman Flows Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a parameter phase space for the distinct types of dynamics we can expect in the case of chemotactic pusher swimmers. |
Yasser Almoteri ; Enkeleida Lushi; |
| 296 | Controlled Transport of Passive Beads By Phototactic Swimming Microorganisms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our experimental work, we study how passive beads are moved by directionally swimming microorganisms. |
Gabriel Amselem ; Julien Bouvard ; Mojtaba Jarrahi ; Taha Laroussi; |
| 297 | Three-dimensional Characterization of Rippling Behavior in Dense Colonies of Myxococcus Xanthus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we characterize the properties of rippling in three dimensions within dense populations of M. xanthus. |
Aaron Bourque ; Joshua Shaevitz; |
| 298 | FREE BOUNDARY PROBLEMS FOR SWARMS OF MAGNETOTACTIC BACTERIA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The mechanism we describe represents a new approach to describing the dynamics of free boundary problems related to swarms of magnetotactic bacteria, caused by the influence of active stress on the free boundary. |
Andrejs Cebers ; Malo Marmol ; Damien Faivre ; Cecile Cottin-Bizonne ; Cristophe Ybert ; Andris Stikuts; |
| 299 | Run-and-tumble Bacterial Chemotaxis in Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a run-and-tumble model for confined bacterial motion model coupled to the chemical gradient of externally-supplied exygen gradient which affects the bacterial motility. |
SHANG-HUAN CHIU ; Yasser Almoteri ; Enkeleida Lushi; |
| 300 | Chemotactic Response of Bacteria to Nutrient Plumes in Heterogenous Flow Fields Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate how the interplay between flow and chemotaxis leads to the preferential accumulation of bacteria around the hydrogel obstacles. |
Akash Ganesh ; Amir Pahlavan; |
| 301 | Memory Effects in The Phototactic Behaviour of Chlamydomonas Reinhardtii Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our work, we study the phototactic behavior of suspensions of C. reinhardtii confined within shallow cylindrical wells, and exposed to directional light stimuli of various intensities. |
Taha Laroussi ; Mojtaba Jarrahi ; Gabriel Amselem; |
| 302 | Bacterial Diffusion in Disordered Media, By Forgetting The Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we theoretically study bacterial diffusion in a model of disordered porous media. |
Henry Mattingly; |
| 303 | Collective Phases of Motile Sperm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report that a transient pulse of ordering fluid flow was able to generate a long-lived flocking phase. |
Chih-Kuan Tung ; Charles Packard ; Shobitha Unnikrishnan ; Shiva Phuyal ; Soon Hon Cheong ; M Lisa Manning ; Daniel Sussman; |
| 304 | Up, Up, and Away: Entrainment By Biogenic Bubbles Enables Long-range Microbial Dispersal Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The sequential entrainment by the train of rising bubbles ultimately culminates in the formation of a conduit within the matrix, encapsulating the colony and giving rise to a distinct columnar morphology. Our study provides a quantitative insight into the entrainment process driven by biogenic bubbles and demonstrates its connection to microbial spreading. |
Babak Vajdi Hokmabad ; Hao Nghi Luu ; Meera Ramaswamy ; Sujit Datta; |
| 305 | Single-cell Dynamics in Bacterial Active Turbulence Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we developed a high-resolution single-cell and flow-tracking technique to study the microscopic dynamics in bacterial active turbulence. |
Yuhao Wang ; Yilin Wu; |
| 306 | Romualdo Pastor-SatorrasOpinion Depolarization Transtions in Interdependent Topics on Heterogeneous Social Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present an analytically tractable model of opinion dynamics in a space of two interdependent topics, the so-called "Social Compass Model" (SCM). |
Romualdo Pastor-Satorras ; Michele Starnini ; Jaume Ojer; |
| 307 | Phase Transitions in The Potts Model with Hidden States: Potential Application to A Shy Voter Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we analytically demonstrate that the Potts model with hidden states exhibits a rich phase diagram comprising various types of phase transitions and critical points with different natures. |
Byung nam Kahng; |
| 308 | Direct Measurements of The Effects of Complex Time Delay in A Simple Scattering Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our earlier work has related the real and imaginary parts of CTD to the zeros and poles in the complex energy plane of the scattering matrix. |
Steven Anlage ; Isabella Giovannelli ; Nadav Shaibe; |
| 309 | Network Science Ising States of Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work reveals the important insights that network science can bring to the characterization of phases of matter. |
Hanlin Sun ; Marcello Dalmonte ; Ginestra Bianconi ; Rajat Kumar Panda ; Alex Rodriguez ; Roberto Verdel; |
| 310 | Title: Persistence of Chimera States and The Challenge for Synchronization in Real-world NetworksOral Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Based on a pattern formation mechanism, in this paper, we shed light on the role that non-normality, a ubiquitous structural property of real networks, has in the emergence of several diverse dynamical phenomena, e.g., amplitude chimeras or oscillon patterns. |
Malbor Asllani; |
| 311 | Swift Consensus Formation on Scale-Free Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We examine the processes that underlie opinion formation, transition, and consensus-building by investigating the short-time dynamics of the majority-vote evolution on scale-free networks. |
Giuliano Porciúncula ; A. J. de Souza ; Kenric Nelson ; André Vilela ; L.; |
| 312 | Epistasis in Allosteric Mechanical Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Elastic networks of springs can be pruned to create a response between distant pairs of nodes that mimics allosteric behavior in proteins. We create pairs of such responses: one in which the source and target respond in phase with each other (+) and one in which they respond out-of-phase (-). |
Samar Alqatari ; Sidney Nagel; |
| 313 | D-Mercator: Multidimensional Hyperbolic Embedding of Real Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce D-Mercator, a model-based embedding method that produces multidimensional maps of real networks into the (D+1)-hyperbolic space, where the similarity subspace is represented as a D-sphere. |
Robert Jankowski ; Antoine Allard ; Marian Boguña ; M. Angeles Serrano; |
| 314 | Characterizing Universal Intrinsic Mesoscale Heterogeneity in The Structure and Fluctuation Correlations of Equilibrium Amorphous Solids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Both cases have been addressed using a replica Landau-Wilson description of amorphous solidification [3] and, in the latter case, the Goldstone branch of low-energy fluctuations dictated by the pattern of spontaneous symmetry breaking [2]. We extend this Landau-Wilson-Goldstone approach to obtain a universal statistical characterization of the intrinsic mesoscale structure and fluctuations in the amorphous solid state. |
Boli Zhou ; Ziqi Zhou ; Paul Goldbart; |
| 315 | Spatial Symmetry Breaking in Optimal Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We consider the simpler problem of a distribution of points in the plane and ask for the fast layer network of a given length that minimizes the average time to reach a central node. |
Siddharth Patwardhan ; Sirag Erkol ; Santo Fortunato ; Marc Barthelemy ; Filippo Radicchi; |
| 316 | Social Interaction Radius Effects on Three-state Consensus Resilience Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work investigates collective decision-making processes via a three-state opinion formation model within the continuous network framework. |
Mateus F. B. Granha ; Chao Wang ; Gaogao Dong ; Luiz Felipe Pereira ; André Vilela ; L.; |
| 317 | Analyzing Local Information in Trainable Materials with Internal Prestress Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We model amorphous materials via disordered elastic network models to understand the complex mechanics of non-crystalline systems and their use as platforms for training in function. |
Ayanna Matthews ; Sidney Nagel ; Margaret Gardel; |
| 318 | Nonlinear Dynamics of Belief Formation Over Social Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the presented work, we investigate how social effects shape belief formation and social decisions using a new agent-based nonlinear model of belief formation dynamics. |
Anastasia Bizyaeva ; Naomi Leonard ; Alessio Franci; |
| 319 | Dynamic Risk and Decision Making in Markov Models of Wildfire Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce and analyze a birth-death-suppression Markov process as a model of controlled culling of an abstract dynamic population. |
Jean Carlson ; George Hulsey ; David Alderson; |
| 320 | Cognitive Biases Can Move Opinion Dynamics from Consensus to Chaos Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We straightforwardly generalize the model used by economists to describe Bayesian updating so that the likelihood of a piece of data depends on ground truth and, potentially, the alignment of the receiver’s beliefs with the sender’s beliefs and the data point itself. |
Sarah Marzen ; Emily Dong; |
| 321 | Dynamics of Innovation: From Particles to Ideas Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we propose that innovation processes share analogous characteristics, all regulated by a common mechanism related to the creation and annihilation of particles through collisions. |
Carlo daCunha ; Guilherme Giardini ; John Hardy; |
| 322 | Is Groundbreaking Research Controversial During Peer Review? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In these situations, negative opinions from experts can impede innovative research, delay scientific progress, and derail promising careers in science. We explore this effect by combining data analytics from anonymized referee databases with case studies of classic papers. |
Manolis Antonoyiannakis; |
| 323 | Understanding The Scaling of Social Organizations Using Reddit Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These results suggest the presence of underlying interaction networks that drive the formation and behavior of organizations, similar to the role of networks in biological systems and cities, where various scaling laws are also observed. We aim to understand how the structural properties of these networks relate to the behavior of the organizations, which could enable us to develop a mechanistic model for the formation and efficiency of social organizations. |
Anna Stephenson ; Guillaume Falmagne ; Simon Levin; |
| 324 | Learning About Early Warning Signals and The Structure of Collaborations with A Large-scale Experiment on Reddit Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We studied the transitions in these compositions (i.e. their replacement by another drawing), which could provide general insights on transitions in socio-ecological systems. To build a warning system for these transitions, we use gradient-boosted decision trees to combine multiple time-dependent variables in each composition. |
Guillaume Falmagne ; Anna Stephenson ; Simon Levin; |
| 325 | Humans Efficiently Predict in A Sequence Learning Task Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: But how well and how human participants efficiently predict non-naturalistic sequences. We use three highly artificial stimuli to answer these questions. |
Sarah Marzen ; Vanessa Ferdinand ; Amy Yu; |
| 326 | Physicalization of Social Experiments: Harnessing Large Language Models for Automated Exploration of Emergent Behaviors in Simulated Social Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present a computational framework and platform that simulates the entire social scientific process, leveraging Large Language Models (LLMs) to study human actors within social systems. |
Kehang Zhu ; Benjamin Manning ; John Horton; |
| 327 | The Impact of Bias on The Accuracy of Early and Late Deciders in Groups Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How does a decision made quickly differ from a more deliberate one? In this talk, we answer this question for a large heterogeneous population of independent agents and show how initial bias influences the accuracy of early and late deciders. |
Samantha Linn ; Sean Lawley ; Bhargav Karamched ; Zachary Kilpatrick ; Kreso Josic; |
| 328 | Musical Rhythm and Meter As An Ordered Phase of Sound Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The temporal patterns of events associated with rhythm and meter can be viewed as a reduced symmetry state as compared to non-musical sound. Motivated by this, we apply methods from statistical mechanics to explore how musical rhythm and meter can emerge from fundamental assumptions about human psychology. |
Jesse Berezovsky ; Robert St. Clair; |
| 329 | Extreme Outbreak Statistics in Stochastic Populations: Large and Small Fluctuations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we consider the general problem of calculating the dynamics and likelihood of extensive large transient fluctuations in general stochastic populations for a large class of population models, including outbreaks in the susceptible-infected-recovered (SIR) model and intensity fluctuations in class B lasers. |
Ira Schwartz ; Michael Assaf ; jason hindes; |
| 330 | Action at A Distance Along The Microtubule Couples Kinesin MotorsMeredith D Betterton Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, modeling of motor-protein motion along microtubules predicted an unexpected long-range interaction. |
Meredith Betterton ; Shane Fiorenza ; Sithara Wijeratne ; Radhika Subramanian; |
| 331 | Building Cytoskeletal Circuits with Branched Microtubule Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Specifically, by forming branched MT networks in Xenopus egg extract within microfabricated channels, we built a nanotechnology platform to engineer robust MT architectures on a chip. |
Meisam Zaferani ; Ryungeun Song ; Sabine Petry ; Howard Stone; |
| 332 | Pushing or Pulling? A 2D Model of The Mitotic Spindle Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These models have proven difficult to distinguish using experimental manipulation. We are therefore building a minimalistic computational model in 2D to test how these possibilities could affect spindle dynamics and daughter cell positioning. |
Alikhan Yeltokov ; Dan Bergstralh; |
| 333 | Assembly Processes Leading to The Formation of The Z-ring in Escherichia Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The sequence of steps on how FtsZ protofilaments assemble into the Z-ring is not yet understood. Here, we investigate how this energy-driven phase transition occurs in Escherichia coli model using high temporal and spatial resolution imaging and computer modeling. |
Jaan Mannik; |
| 334 | In-situ CryoET of The Metaphase Human Mitotic Spindle Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The development of biophysical models of how the collective behavior of these microtubules and motors shapes the spindle, generates forces, and ultimately segregates chromosomes has been severely limited by the resolution of traditional fluorescence microscopy, which cannot resolve individual microtubules and motors in the densely packed spindle. To overcome this, we employed in-situ cryo-electron tomography to image microtubules in the metaphase mitotic spindle in their native context. |
William Conway ; Daija Bobe ; Adam Lamson ; Abhilash Sahoo ; Sonya Hanson ; Pilar Cossio ; Daniel Needleman ; Mykhailo Kopylov ; Michael Shelley ; Alex De Marco ; Stefanie Redermann; |
| 335 | Dynamic Behavior of Microtubules Around The Critical Temperature and The Effect of The Electric Field Generated By These Vibrations on Their Environment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this paper, we study the microtubule as a ferroelectric system. |
NGANFO YIFOUE WILLY ANISET; |
| 336 | Entropy Production and Cytoskeletal Avalanches in Cytoskeletal Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The cytoskeleton endues cells with their instantaneous shapes, providing a machinery for cells to move around, generate forces and also integrate both chemical and mechanical signaling. To investigate the fundamental principles behind the self-organization of these networks, we have developed a detailed physico-chemical, stochastic model (MEDYAN, http://medyan.org) of the cytoskeletal dynamics, where the mechanical rigidity of filaments and their corresponding deformations under internally and externally generated forces are taken into account. |
Garegin Papoian; |
| 337 | Regulating Actin Assembly Microstructure Through Cross-linkers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate actin assembly microstructures as a function of cross-linker length using fluorescence and transmission electron microscopy. |
Carolyn Feigeles ; Kimberly Weirich; |
| 338 | Physical Phase Field Model for Phagocytosis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose and study a simple, physical model for phagocytosis, i.e. the active, actin-mediated uptake of micron-sized particles by biological cells. |
Benjamin Winkler ; Falko Ziebert ; Mohammad Hamed ; Alexander Nepomnyashchy; |
| 339 | An Integrated Experimental and Theoretical Approach to Investigate Endothelial Cell Alignment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our in vitro approach employs a sparse endothelial cell colony, distinctly tagged for myosin-II, F-actin, and focal adhesion proteins. |
Waleed Mirza ; Alejandro Sánchez ; Maria Bernabeu ; Matt Govendir; |
| 340 | Dynamics of Vimentin Intermediate Filament Enabled By The Unique Molecular Nature of The Protein Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Such dynamics also heavily depend on the phosphorylation level of the vimentin. We propose that such unique dynamics of the filament are enabled by the molecular nature of the vimentin. |
Sijie Sun ; qiaoling Huang ; David Weitz; |
| 341 | Microbial Community Dynamics In-silico, In-vitro, and In-vivo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will discuss how the statistical properties of environmental variability can give rise to regularities in community variation. |
Jacopo Grilli; |
| 342 | Noisy Environments Select for Privatized Growth in Complex Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: But it is not clear what conditions lead to such dynamic coexistence. Here we use a broad range of models to show that such successive growth is naturally selected for in ecosystems assembled in fluctuating environments. |
Milena Chakraverti-Wuerthwein ; Yoshiya Matsubara ; Finnegan Roach ; Avaneesh Narla ; Terence Hwa ; Arvind Murugan; |
| 343 | Diversity Begets Stability: Sublinear Growth and Competitive Coexistence Across Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Whereas conventional wisdom and empirical observation suggest that stability increases with diversity, ecological theory has long made the opposite prediction, leading to the longstanding "diversity-stability debate". |
Onofrio Mazzarisi ; Ian Hatton ; Ada Altieri ; Matteo Smerlak; |
| 344 | Phase Transition to Chaos in Complex Ecosystems with Non-reciprocal Species-resource Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the effects of non-reciprocity in the context of theoretical ecology by analyzing a generalization of MacArthur’s consumer-resource model with asymmetric interactions between species and resources. |
Emmy Blumenthal ; Pankaj Mehta ; Jason Rocks; |
| 345 | Evolution of Division of Labor in A Response Threshold Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work explores the evolving division of labor in a response threshold model. |
Paulo Campos ; José Fontanari ; Viviane Oliveira; |
| 346 | Linear Response Theory for Eco-evolutionary Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Ecological and evolutionary processes often unfold on overlapping timescales, making an integrated theory of eco-evolutionary dynamics indispensable. |
Zhijie Feng ; Akshit Goyal ; Emmy Blumenthal ; Pankaj Mehta; |
| 347 | Horizontal Transfer of Phage-defense Genes Can Stably Maintain Their Diversity in A Microbial Pan-genome Despite Continuous Extinction and Turnover of Genomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we formulate a Lotka-Volterra type model of a host/phage system interacting via a combinatorial variety of defense/anti-defense systems and show that HGT enables stable maintenance of diverse defense/anti-defense genes in the microbial pan-genome even when individual microbial strains inevitably undergo extinction leaving only few descendants that survive thanks to immunity acquired through HGT. |
Wenping Cui ; Jemma Fendley ; Sriram Srikant ; Boris Shraiman; |
| 348 | Computing Macroscopic Reaction Rates in Reaction-diffusion Systems Using Monte Carlo Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce an algorithmic approach using Monte Carlo simulations to evaluate the macroscopic reaction rates by counting how many events occur per simulation timestep. |
Mohamed Swailem ; Uwe C. Täuber; |
| 349 | A Framework for The Interaction Between Wildlife and Spatial Hazards Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop a general theory for the interactions between a moving agent and a hazardous domain. |
Benjamin Garcia de Figueiredo ; Ricardo Martinez-Garcia; |
| 350 | Tweets Vs Pathogen Spread: A Case Study of COVID-19 in American States Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In response, we initially propose a null model that couples two Susceptible-Infectious-Recovered (SIR) dynamics and analyze it using a mean-field approach. Subsequently, we explore the parameter space to quantify the effects of this mutual influence on various observables. |
Sara Shabani ; Sahar Jafarbegloo ; Sadegh Raeisi ; Fakhteh Ghanbarnejad; |
| 351 | Quantifying Noise Effects on Networked Epidemic Transmission Through Structural Predictability Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we established a dual equivalence between epidemic dynamics stability to noise and network structural predictability. |
En XU ; Tao Zhou ; Qianyuan Tang ; Liang TIAN ; Jiming Liu; |
| 352 | Morphodynamics of Bacterial Communities Proliferating in Three Dimensions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use two different strains of E. coli suspended in a transparent jammed packing of microgel particles to investigate the morphodynamics of communities with multiple cell types proliferating in 3D. |
Meera Ramaswamy ; Carolina Trenado-Yuste ; Alejandro Martinez-Calvo ; Ned Wingreen ; Sujit Datta; |
| 353 | Affordances of Animals and Machines Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present a brief account of work in my lab over the past decade that attempts to develop an abstracted, compositional view of environmental features suitable for reasoning about their possible role as affordances to be exploited by appropriate compositions of templates – abstracted behavioral features of a robot’s architecture. |
Daniel Koditschek; |
| 354 | Geometry of Contact: Contact Planning for Multi-legged Robots Via Spin Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study develops an analytic tool to explore the high-dimensional search space in multi-legged systems. |
Baxi Chong ; Di Luo ; Tianyu Wang ; Gabriel Margolis ; Zhaocheng Xu ; Massimiliano Iaschi ; Pulkit Agrawal ; Marin Soljacic ; Daniel Goldman; |
| 355 | Characterizing Mechanical Properties of Natural Deformable Substrates with A Direct-Drive Robotic Leg Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we created a direct-drive (i.e., gearless) robotic leg with the ability to accurately sense contact forces and measure terrain characteristics, without the need for additional sensor payload. |
John Bush ; Yifeng Zhang ; Jake Futterman ; John Ruck ; shipeng liu ; Ethan Fulcher ; Douglas Jerolmack ; Kenton Fisher ; Ryan Ewing ; Feifei Qian; |
| 356 | Gait Switching Enables Body Pitch Modulation During Legged Burrowing in Granular Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work introduces EMBUR 2.0—an updated self-burrowing robot capable of body pitch control. |
Amber Young ; Laura Treers ; Hannah Stuart; |
| 357 | Tactile Feedback Enhances Multi-legged Locomotion on Rugged Landscapes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, it remains unclear if foot-level tactile information could contribute to overall locomotion via high-level centralized, intra-leg processing. To address this, we developed a centipede-like multi-legged robophysical model (L= 60 to 160 cm, 3 to 8 segments each with four degrees of freedom for limb and body movement) with point-like feet and tested it on rugose terrains. |
Juntao He ; Baxi Chong ; Zhaochen Xu ; Esteban Flores ; Daniel Soto ; Daniel Goldman; |
| 358 | Combined Machine and Human Learning Facilitates Fast Robot Turns on Steep Granular Slopes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Granular slopes are prone to flow under small disturbances, making rover traversal challenging. To discover principles by which a new class of four legged and wheeled rover (able to lift, sweep, and spin its wheels, see Srivastava et al, 2020) can effectively turn in place on granular slopes without toppling over or sliding down the slope, we studied in the laboratory a 30 cm long robophysical rover model on a granular medium of poppy seeds. |
Malone Hemsley ; Deniz Kerimoglu ; Daniel Soto ; Joseph Brunner ; Sehoon Ha ; Tingnan Zhang ; Daniel Goldman; |
| 359 | Proprioceptive Sensing to Aid with Locomotion Adaptation in Mud Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To enable terrestrial robots to effectively determine mud properties and flexibly adapt their locomotion strategies accordingly, in this study we explore proprioceptive terrain-sensing methods for robots to estimate substrate mechanical properties through joint torques during locomotion. |
shipeng liu ; Shravan Pradeep ; Sen Gao ; Douglas Jerolmack ; John Bush ; Siyuan Meng ; Jiaze Tang ; John Ruck ; Feifei Qian; |
| 360 | Anisotropic Body Compliance Facilitates Robotic Sidewinding in Complex Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by control simplification achieved via mechanical intelligence in lateral undulation [Wang et al 2023], which offloads feedback control to passive body mechanics, we developed a new kind of sidewinding limbless robophysical model. |
Velin Kojouharov ; Tianyu Wang ; Matthew Fernandez ; Jiyeon Maeng ; Daniel Goldman; |
| 361 | A Robophysical Study of Active Force Sensing for Least-resistance Traversal of Cluttered Large Obstacles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our recent work on cockroaches and their robophysical models showed that such transitions are strenuous barrier-crossing transitions across basins of a potential energy landscape. Because a potential energy landscape’s gradients are conservative forces, we hypothesize that a robot can sense its obstacle contact forces to infer landscape gradients, reconstruct the landscape, and seek saddle points between basins to transition with least resistance. |
Yaqing Wang ; Ling Xu ; Chen Li; |
| 362 | Making Every Step An Experiment: Proprioceptive Sensing During Locomotion for Enhanced Mobility and Data Collection in Earth and Planetary Explorations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent advancements in direct-drive actuators have enabled the development of individual robotic legs with the ability to measure contact forces and terrain characteristics through actuator phase current. The goal of our study is to extend this novel capability from stationarily mounted individual legs to dynamic quadrupedal robots, and develop platforms that can rapidly assess substrate strength and rheology during continuous locomotion. |
Yifeng Zhang ; Ethan Fulcher ; Diego Caporale ; shipeng liu ; John Bush ; John Ruck ; Daniel Koditschek ; Douglas Jerolmack ; Feifei Qian; |
| 363 | Gait Design and Mechanical Intelligence Facilitate Open-loop Limbless Obstacle Aided Locomotion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we test the efficacy of elliptical gaits in OAL, using geometric mechanics to generate novel undulatory templates. |
Tianyu Wang ; Baxi Chong ; Anushka Bhumkar ; Velin Kojouharov ; Christopher Pierce ; Daniel Goldman; |
| 364 | Comparative Biological and Robophysical Study of Amphibious Fishes Moving on Mud of Variable Strength Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The bichir’s and the ropefish’s performance did not change, and they lifted parts of the body, likely to reduce drag. To understand these observations, we are developing a robophysical model. |
Divya Ramesh ; Gargi Sadalgekar ; Hongbo Zhang ; Jiangqi Tan ; Dami Kim ; Alex Nath ; Qiyuan Fu ; Zachary Souders ; Lei An ; Chen Li; |
| 365 | Mechanical Intelligence Facilitates Limbless Locomotion in Cluttered Aquatic Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Motivated by the remarkable control scheme simplification that mechanical intelligence (MI, purely passive, mechanically controlled body-environment interactions) offers limbless systems in highly damped environments [Wang et al. 2023], we hypothesize that MI could also play a role in cluttered aquatic locomotion. |
Nishanth Mankame ; Tianyu Wang ; Matthew Fernandez ; Christopher Pierce ; Daniel Goldman; |
| 366 | Coordinating Adhesion with Repulsion: How Cells Leverage Hyaluronan Glycocalyx Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Previously, we have shown that this bulky glycocalyx significantly weakens cell adhesion and tunes cell migration speed in a predictable, adhesion-dependent fashion. Building on these results, I will present new and consistent data quantifying the impact of hyaluronan expression in neural crest cell migration in vivo and ex vivo. |
Jennifer Curtis; |
| 367 | Using 3D Discrete Fiber Models to Investigate Cell-Mediated Extracellular Matrix Remodeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a coarse-grained computational model of collagen matrix rearrangement by one or more cells, focusing on the changes in the matrix and comparing the results to experimental observation. |
Adam Ley ; Lauren Bersie-Larson ; Ryan Collanton ; Sabin Adhikari ; Robert Tranquillo ; Kevin Dorfman ; Victor Barocas; |
| 368 | Cell Collision Outcomes in Suspended Fiber Environments As Controlled By Physical and Geometric Factors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by experiments, we use a phase-field model to numerically simulate two-cell collisions in fiber geometries, especially the effects of cellular mechanics and geometric factors on their outcomes. |
Yongtian Luo ; Brian Camley; |
| 369 | Collective Cell Migration Driven By Mechanical Coupling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will discuss experimental evidence, a computational model verified with experimental observations and hypothesized principles linking collective cell migration to cell-substrate mechanical coupling. |
Abdul Malmi Kakkada; |
| 370 | Dynamics of Early Cell Spreading with Hyaluronan Glycocalyx Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we will compare the dynamics of isotropic spreading MCF-7 cells with and without glycocalyx during early cell adhesion. |
Jennifer Curtis ; Yu Jing ; Jianqiao Li ; Emma Poma ; Mariela Lopez Gonzalez; |
| 371 | Cell Motility Self-regulated By Secreted Footprints Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study highlights the potential of cells to self-regulate their motility using footprints and provides insight into the mechanisms guiding cell migration. |
Emiliano Perez Ipiña ; Joseph d’Alessandro ; Benoît Ladoux ; Brian Camley; |
| 372 | Myxococcus Xanthus Colony Expansion Depends on Substrate Stiffness and Surface Coating Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using polyacrylamide hydrogels of tunable stiffness, we found that wild-type M. xanthus spreads faster on stiffer substrates. |
Nuzhat Faiza Nufa ; Alison Patteson ; Roy Welch; |
| 373 | Effect of Cell Softness and Polydispersity on The Viscosity of Non-confluent Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using agent(particle)- based simulations of three-dimensional tissue, we showed that depending on the cell elasticity and the size dispersity, the tissue exhibits fluid-like, glass-like, and glass-like dynamics followed by a viscosity saturation. |
Rajsekhar Das ; Xin Li ; Sumit Sinha ; Devarajan Thirumalai; |
| 374 | Multi-dimensional, Multi-scale Memory During Fruit Fly Social Communication Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Social communication requires continually updating one’s memory of what has been said before, often over multiple timescales, yet how the brain solves this is unknown. We address this question in fly courtship, a social behavior in which the male courts the female via a long, variable song. |
Rich Pang ; William Bialek ; Mala Murthy ; Jonathan Pillow ; Christa Baker; |
| 375 | A Geometric Explanation of Hippocampal Remapping Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that a place like coding strategy allows one to locally decode both context and location robustly. |
Spencer Rooke ; Ron DiTullio ; Zhaoze Wang ; Vijay Balasubramanian ; Shai Abramson ; Dori Derdikman; |
| 376 | Spontaneous Brain Activity Emerges from Pairwise Interactions in The Larval Zebrafish Brain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Calcium imaging provides access to in vivo recordings of whole-brain activity at single-neuron resolution and, therefore, allows the study of how large-scale brain dynamics emerge from local activity. In this study, we used a statistical mechanics approach – the pairwise maximum entropy model (MEM) – to infer microscopic network features from collective patterns of activity in the larval zebrafish brain, and relate these features to the emergence of observed whole-brain dynamics. |
Arian Ashourvan ; Richard Rosch ; Christopher Lynn ; Dominic Burrows; |
| 377 | Exactly Solvable Statistical Physics Models for Large Neuronal Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The best choice is the one that provides the greatest reduction in entropy, defining a "minimax entropy" principle. This principle becomes tractable if we restrict attention to correlations among pairs of neurons that link together into a tree; we can find the best tree efficiently, and the underlying statistical physics models are exactly solved. |
Christopher Lynn ; Qiwei Yu ; Rich Pang ; William Bialek ; Stephanie Palmer; |
| 378 | Minimax Entropy Principle and Dimensionality Reduction in Neural Data Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Statistical physics offers robust tools for addressing this challenge via simple models, such as maximum entropy models that match pairwise correlations, which have shown remarkable predictive accuracy for populations of N~100 neurons. But these methods are hindered by under-sampling at larger N. To address this issue, we employ the recently rediscovered "minimax entropy" principle [arXiv:2310.10860] to extract a low-dimensional representation of the neural population activity, providing a principled way to reduce the number of model parameters to a range that matches the number of available samples. |
Luca Di Carlo ; Francesca Mignacco ; William Bialek; |
| 379 | Parameter Estimation from An Ornstein-Uhlenbeck Process with Measurement Noise with Applications in Neuroscience Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work aims to investigate the impact of noise on parameter fitting for an Ornstein-Uhlenbeck process, focusing on the effects of multiplicative and thermal noise on the accuracy of signal separation. |
Helmut Strey ; Simon Carter; |
| 380 | A Comprehensive Large-Scale Model of The Primary Visual Cortex (V1) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The majority of mean-field models of the primary visual cortex (V1) are limited in their capacity to represent local features adequately or are unable to reconcile key experimental observations within a single framework. In this work, we introduce a comprehensive retinotopic model of V1 that surmounts these limitations. |
Shivang Rawat ; David Heeger ; Stefano Martiniani; |
| 381 | Branching FBM As A Model of Serotonergic Axons Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we introduce branching events in an fBM trajectory to improve the model. |
Angela Rayle ; Gaurav Khairnar ; Reece Beattie-Hauser ; Jonathan House ; Thomas Vojta; |
| 382 | How Does The Brain Fold, and What Does It Fold Into? Searching for A New Morphological Syntax for The Cerebral Cortex Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The same law also applies across healthy humans [2] and cortical regions [3]. Here, we show that, despite all this diversity, cortical shape can be universally and explicitly expressed as the hierarchical composition of folded structures of different sizes. |
Bruno Mota ; Yujiang Wang ; Karoline Leiberg; |
| 383 | Memory-induced Spontaneous Symmetry Breaking Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use robotic active matter to investigate how decisions based on individual memories can influence their collective behavior. |
Shengkai Li ; Trung Phan ; Gao Wang ; Ramzi Khuri ; Liyu Liu ; Robert Austin; |
| 384 | Locality of Critical Thresholds in Spin Glasses Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the response of other bonds’ $JC$ to the $J_{ij}$ change is not as drastic: specifically, it typically decays with the distance between the target bond’s $JC$ and the changed $J_{ij}$. Utilizing this characteristic, we have designed a method to assess the accuracy of locally computing the ground state in Edwards-Anderson spin glasses. |
Mutian Shen ; Zohar Nussinov ; Zhiqiao Dong ; Gerardo Ortiz ; Martin Weigel; |
| 385 | Tunning Magnetic Phases of Ising Systems on Continuous Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore the fundamental concepts of the Ising model on a continuous substrate of variable particle density and interaction radius. |
André L. M. Vilela ; Gilvania Da Silva Vilela ; Chao Wang ; Gaogao Dong ; Ruijin Du; |
| 386 | Photon Counting Detection and Phase Imaging For Multi-Contrast Deep Bioimaging Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe methods that involve extracting information from wave nature of X-rays with novel imaging system designs to generate additional contrast types. |
Mini Das; |
| 387 | Visualuzing and Actuating Biology with Living Magnetic Contrast Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Biomineralization of iron by magnetotactic bacteria leads to living cells with integrated magnetic signals that can be imaged by magnetic resonance imaging (MRI) and magnetic particle imaging (MPI). We have been developing these bacteria as magnetoendosymbionts, to live in the cytoplasm of mammalian cells and exert desired effects with magnetothermal energy as an actuator of biological change. |
Christopher Contag ; Ashley Makela; |
| 388 | Non-linear Organic Fluorophores for Detecting Transmembrane Protein Aggregation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will discuss some of our recent work in developing functional imaging agents for multi-wavelength and multi-photon live-cell imaging, focusing on recent molecular designs performed using density functional theory as well as in vitro studies. |
Andrea Armani; |
| 389 | 6D Single-Molecule Orientation-Localization Microscopy: Fundamental Limits for Visualizing The Dynamic Organization of Biomolecule Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, I will introduce the concept of 6D single-molecule orientation-localization microscopy (SMOLM), in which the dipole-spread function (the image of a dipole-like emitter) is specifically engineered to enable sensitive measurements of the 3D position and 3D orientation of any fluorescent emitter. |
Matthew Lew; |
| 390 | Computational Imaging Through Scatter Using Synthetic Waves Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk discusses how diversity in illumination wavelength can be utilized to circumvent the problem of phase randomization in scattered light fields. |
Florian Willomitzer; |
| 391 | Rational Design of Multicomponent Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will describe recent theoretical and computational advances towards the goal of designing fully programmable, synthetic multiphase condensates. |
William Jacobs; |
| 392 | Coacervate Vesicles and Double Emulsions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study investigates the formation of vesicles and double emulsions of polyelectrolyte coacervates. |
Aman Agrawal ; Anusha Vonteddu ; Alamgir Karim; |
| 393 | Phase Separation of A Heterogeneous DNA Nanostar System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we consider mixtures of multiple, distinct NS particle species and investigate the effect on the phase behavior of the system. |
Aria Chaderjian ; Sam Wilken ; Omar Saleh; |
| 394 | Dynamic Swarms Regulate The Growth and Morphology of Membrane Domains Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These structures frequently merge and break up, leading to arrested domain growth. In this work, we combine the Toner-Tu equation for flocking dynamics with a phase field model to study such systems of activity-mediated phase separation. |
Aakanksha Gubbala ; Daniel Arnold ; Sho Takatori; |
| 395 | Directed Movement of Condensates By Reaction-driven Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate that organelle movement within cellular domains can naturally arise from biochemical reactions, which are driven by a chemical fuel and produce waste. |
Gregor Häfner ; Marcus Müller; |
| 396 | Modeling The Effects of HU Proteomic Interactions in The Genome Configuration of A Minimal Cell Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we investigate the effect of the HU proteomic interactions on chromosomal configuration. |
Gesse Roure ; Vishal Sankar Sivasankar ; Roseanna Zia; |
| 397 | Spatial Organization of DNA Liquids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the dynamics and long-range structures formed by a model phase-separating DNA system. |
Sam Wilken; |
| 398 | A Background Enzymatic Active Bath Affects Liquid-Liquid Phase Separation (LLPS) of Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will use urease, an exothermic and kinetically fast enzyme that converts urea to carbon dioxide and ammonia, as the background enzyme. |
Kevin Ching ; Anthony Estrada ; Sarthak Gupta ; J. M. Schwarz ; Jennifer Ross; |
| 399 | Are Phases An Appropriate Description for Cells? – Fluctuation Dominated Regime in Finite Systems with Many Components Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a toy model, I will show that what we consider "large systems" is largely subjective and dependent on details in multicomponent systems. |
Martin Girard; |
| 400 | Impact of The Substrate on The Phase Transitions Properties in Supported Lipid Bilayers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work highlights the importance of external membrane contacts to control the composition and biophysical properties of bacterial membranes. |
Nicolò Tormena ; Kislon Voitchovsky ; Teuta Pilizota; |
| 401 | Spatio-temporal Control of Optically Responsive Compressible Isotropic Active Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we explore how compressible isotropic active fluids respond to different light patterns. |
Yu-Chuan Cheng ; Liang Zhao ; Seungwoo Shin ; Zvonimir Dogic; |
| 402 | Learning The Emergent Order of Living Matter from Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk we will introduce several physical mechanisms that give rise to spatiotemporal order in diverse bacterial populations, including bacterial colonies, biofilms, and generic bacterial suspensions. |
Yilin Wu; |
| 403 | A Multi-layer Neural Network Model to Predict The Quorum Sensing Behavior of A Heterogeneous Community of Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here bacterial communication given the added complexity of multiple species exchanging multiple types of signals is modeled as a multilayer neural network. |
Soumya Das; |
| 404 | Interface-mediated Three-dimensional Microbe Expansion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: . We characterized the growth and interaction dynamics of this unique process by high resolution imaging. |
Zheyi Wang ; Yilin Wu; |
| 405 | Migration of Living Droplets: A Novel Paradigm for Chemotaxis of Multicellular Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we propose a continuum, coarse-grained, active fluid model to study how physical interactions affect the complex spatiotemporal dynamics of cell swarms’ collective chemotaxis in response to self-generated chemical gradients. |
Giulia Celora ; Jonathan Chubb ; Philip Pearce ; Mohit Dalwadi ; Hugh Ford ; Benjamin Walker; |
| 406 | Effects of Cell Density on Swarming SM3 Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate the swarming behavior of Enterobacter sp. |
Danielle Germann ; Jay Tang; |
| 407 | Categorizing Spatiotemporal Dynamics of Bacterial Swarms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use a spectral dimensionality reduction framework to quantitatively characterize the spatiotemporal patterns that emerge and reveal correlations between cellular and collective properties. |
Alasdair Hastewell ; Hannah Jeckel ; Andreea-Oana Chelban ; Gabriel Rodriguez-Roig ; Knut Drescher ; Jorn Dunkel; |
| 408 | Pattern Formation By Bacteria-phage Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The interactions between bacteria and phages—viruses that infect bacteria—play critical roles in agriculture, ecology, and medicine; however, how these interactions influence the spatial organization of both bacteria and phages remain largely unexplored. Here, we address this gap in knowledge by developing a theoretical model of motile, proliferating bacteria that aggregate via motility-induced phase separation (MIPS) and encounter phage that infect and lyse the cells. |
Alejandro Martinez-Calvo ; Ned Wingreen ; Sujit Datta; |
| 409 | Cell Scale Mechanics of Super Competition in Epithelial Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we develop a Cellular Potts Model framework to predict the patterns of cell proliferation and elimination within a tissue comprised of normal wild type cells and mutations. |
Logan Carpenter ; Shiladitya Banerjee; |
| 410 | Collective Motion in Vascular Endothelium Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Related in vitro investigations have shown that unconfined endothelial cell layers exhibit a unique form of collective motion, with cells moving in antiparallel streams when cultured on anisotropic micro-grooved substrates. In this presentation, we examine this emergent behavior through a SPV model which not only reproduces experimental findings but also provides deeper insights into how this form of collective motion manifests within cells under different physical and physiological conditions. |
Prakhar Bandil ; Claire Leclech ; Abdul Barakat ; Franck Vernerey; |
| 411 | Intercellular Friction and Motility Drive Orientational Order in A Model Cell Monolayer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use a multiphase field model of deformable, motile cells to study numerically the role of intercellular friction in tissue dynamics. |
Austin Hopkins ; Michael Chiang ; Benjamin Loewe ; Davide Marenduzzo ; M Cristina Marchetti; |
| 412 | Surfing A Signaling Wave for Whole-body Regeneration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using planarian flatworms capable of whole-body regeneration, we report that injury induces Erk activity wave to travel at a speed 10-100 times faster than those in other multicellular tissues. |
Bo Wang ; Yuhang Fan ; Chew Chai ; James Ferrell; |
| 413 | Engineering Emergent Morphogenetic Properties of Cell Clusters with Differentiable Programming Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we use differentiable programming to optimize over physical models of cells, learning local decision functions to drive collective behavior. |
Ramya Deshpande ; Francesco Mottes ; Ariana Dalia-Vlad ; Michael Brenner ; Alma Dal Co; |
| 414 | Physical Insights Into The Evolutionary Dynamics of Viruses Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I’ll tell you about our recent efforts to use ideas from physics to understand the evolutionary dynamics of pathogens like these. |
John Barton; |
| 415 | Quantifying Microbial Fitness Under Conceptual Uncertainty Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we develop such an argument, based on a single first principle: relative fitness measures must have the function to predict strain frequencies in the upcoming time window. From this axiom, we characterize the set of possible fitness metrics (it is large!) |
Justus Wilhelm Fink ; Michael Manhart; |
| 416 | Correlations Between Mutations Under Recurrent Genetic Hitchhiking Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we will describe a forward-in-time approach that stratifies the dynamics of variants by their present-day frequencies, which provides new opportunities to predict the multi-site effects of recurrent hitchhiking. |
Zhiru Liu ; Jamie Blundell ; Daniel Fisher ; Benjamin Good; |
| 417 | Strong Environmental Memory Revealed By Experimental Evolution in Static and Fluctuating Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that fitness in fluctuating environments indeed often deviates from the expectation based on static components, leading to fitness non-additivity. |
Clare Abreu ; Shaili Mathur ; Dmitri Petrov; |
| 418 | Detectability of Epistasis from Temporal Genetic Data Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we inferred epistasis from simulated temporal genetic data with different types of epistasis and recombination rates. |
Kai Shimagaki ; John Barton; |
| 419 | Noise Robustness and Metabolic Load Determine The Principles of Central Dogma Regulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To explore the consequences of noise in the expression of hundreds of essential genes, we build a minimal model where the trade-off between metabolic cost and growth robustness can be analyzed analytically. |
Paul Wiggins ; James Choi ; Dean Huang ; Teresa Lo; |
| 420 | The Distribution of The Time to The Most Recent Common Genetic Ancestor of A Pair of Genomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Basic evolutionary theory predicts that the marginal distribution of the TMRCA for each gene is exponential with a mean proportional to the population size, but the joint distribution across genes is unknown. |
Zehui Zhao ; Rohan Mehta ; Daniel Weissman; |
| 421 | Impact of Crowding on The Diversity of Expanding Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study highlights the importance of cellular crowding for the emergence of rare genetic variants. |
Carl Schwendinger-Schreck ; Oskar Hallatschek ; Marie-Cecilia Duvernoy ; Jona Kayser ; Jona Kayser ; Stephen Martis ; Yuya Karita ; Diana Fusco; |
| 422 | Predicting Influenza Evolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These simplifications undermine methods’ predictability. To address this gap, we developed a physics-inspired method that accounts for the full evolutionary history and genetic background to estimate the fitness advantage of influenza mutations and predict strains that are most likely to be dominant in the future. |
Edwin Rodriguez ; John Barton; |
| 423 | A Hike Through The Protein Evolutionary Landscape Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a scheme to calculate the masked residue profile for the entire sequence in a single forward pass with unmasked residue embeddings. |
Pranav Kantroo ; Ben Machta ; Gunter Wagner; |
| 424 | Emergence of Meaning in The Sensor Evolution of Anteorganisms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we apply the framework of Semantic Information Theory to a model of an anteorganism whose behavior is chemotactic, a sensorless forager. |
Damian Sowinski ; Adam Frank ; Gourab Ghoshal; |
| 425 | Statistical Machine Learning for Learning Representations of Embryonic Development Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will describe statistical machine learning frameworks aimed at understanding how tissue level mechanical and morphometric information impact gene expression patterns in spatio-temporal contexts. |
Bianca Dumitrascu; |
| 426 | TubULAR: Tracking in Toto Deformations of Dynamic Tissues Via Constrained Maps Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present the Tube-like sUrface Lagrangian Analysis Resource (TubULAR), an analysis framework that builds in toto maps of tissue deformations by following tissue parcels in a static material frame of reference. |
Noah Mitchell ; Dillon Cislo; |
| 427 | Distinguishing Between Stereotyped Patterns and Developmental Noise in Drosophila Wing Cell Sizes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we share initial results of analyzing patterns of cell size. |
Avik Mondal ; Daniel McCusker ; Dalmiro Blanco-Obregon ; Pierre Leopold ; David Lubensky; |
| 428 | Local and Collective Cellular Forces Driving Neural Tube Closure Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we utilize live-imaging data in mouse embryos to construct a cell-based computational model of hindbrain neuropore gap closure, shedding light on the underlying physical mechanisms. |
Fernanda Pérez Verdugo ; Eirini Maniou ; Gabriel Galea ; Shiladitya Banerjee; |
| 429 | Direct Application of Tissue-scale Tension to Epithelia Reveals Mechanical Coupling of Germ Layers and Multi-scale Mechanical Properties in The Developing Chick Embryo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Exploiting the size and accessibility of the developing chick embryo, here we describe a simple technique to quantitatively apply exogenous forces on the order of microNewtons to the endoderm. |
Panagiotis Oikonomou ; Lisa Calvary ; Helena Cirne ; Andreas Welch ; Nandan Nerurkar; |
| 430 | Bilateral Cellular Flows Initiate Left-right Asymmetry During Early Gastrulation in Amniotes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The first sign of L-R asymmetry was observed at a later stage when genetic regulatory programs took over and at the beginning of organogenesis. In this work, we investigate these early-stage gastrulation cell flows before the activation of laterality genes and quantify the cellular speeds and vorticity using the Particle Image Velocimetry (PIV) technique. |
Shubham Sinha ; Rieko Asai ; Vivek Prakash ; Takashi Mikawa; |
| 431 | Mechanical and Molecular Self-organization Principles in Chick Gastrulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We derive a continuum model that couples tissue flows, stress-dependent myosin activity, and actomyosin cable orientation. |
Mattia Serra; |
| 432 | A Mechano-chemical Mechanism for Symmetry Breaking and Patterning of The Early Chick Embryo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discover a differential cell division rate between the embryonic and extraembryonic tissue, which generates mechanical anisotropy and, in turn, specifies the orientation of the intercalation. |
Sreejith Santhosh ; Manli Chuai ; Cornelis Weijer ; Mattia Serra; |
| 433 | Embryonic Area Homeostasis in Avian Gastrulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a self-organizing mechanochemical model wherein mechanosensitive contractile actomyosin activity in the embryo resists expansion to keep the embryo’s size constant. |
Alex Plum ; Guillermo Serrano-Najera ; Cornelius Weijer ; Mattia Serra; |
| 434 | Low Dimensionality of Phenotypic Space As An Emergent Property of Coordinated Teams in Biological Regulatory Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose that team-based topology in biological networks is critical for generating a cell-fate canalization landscape. |
Anantha Samrajya Shri Kishore Hari ; Mohit Kumar Jolly ; Pradyumna Harlapur ; Aashna Saxena ; Herbert Levine ; Aishwarya Girish ; Kushal Haldar ; Tanisha Malpani; |
| 435 | Multistability Towards Reprogrammable Mechanical Devices Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Notably, the multi-welled energy landscape of the linkages can be easily modified through geometry adjustments triggered by environmental energy inputs, enabling autonomous adaptation. As a practical demonstration of this platform, we create a four-degree-of-freedom robot capable of navigating mazes and avoiding obstacles — all without the need for computational intelligence and utilizing only a single actuator. |
Leon Kamp ; Katia Bertoldi; |
| 436 | Identifying Traces of Learning in Physical Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Functionality in these systems emerges from a dual optimization: a simultaneous minimization in a learning and a physical landscape. Here we study this interplay within functional linear resistor networks, a paradigmatic model for physical learning systems. |
Marcelo Guzmán ; Felipe Martins ; Andrea Liu; |
| 437 | Neural Computation Without Neurons Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work suggests that exploiting ubiquitous physical phenomena, such as nucleation, is an underexplored powerful route to neural computation without neurons. |
Arvind Murugan; |
| 438 | Physics for Neuromorphic Computing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have performed simulations and experiments to demonstrate quantum neuromorphic computing with superconducting circuits. |
Danijela Markovic; |
| 439 | Physical Neural Networks Trained with A Physics-aware Backpropagation Algorithm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a version of backpropagation suited to experimental physical systems, we have demonstrated physical neural networks based on nonlinear optics, analog electronics, mechanics, and coupled oscillators [Wright, Onodera et al., Nature (2022)]. In this talk, I will review this and our recent work on physical neural networks, primarily with optical systems. |
Logan Wright; |
| 440 | Dynamic Symphonies: Spatio-Temporal Pattern Formation in Tissue Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our theoretical framework, we examine the dynamics of a one-dimensional generic isotropic active viscoelastic continuum that adheres to a substrate. |
Arkayan Laha; |
| 441 | Metabolic Effects of Glutamine on Glycolysis in Kidney Cancer Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, multiple trials of the glycolytic effects of the absence or presence of 5-, 10-, and 20-mM glutamine in complete media was examined in the culture of A498 and Caki-1 kidney cancer cells. |
Melaud Elahi ; Lloyd Lumata; |
| 442 | Metabolic Competition of Glucose and Mannose in SK-N-SH Neuroblastoma Cancer Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this project, two hexose sugars glucose and the structurally similar mannose were investigated as metabolic fuels for the proliferation and growth of SK-N-SH neuroblastoma cancer cells. |
Faiez Qureshi ; Lloyd Lumata; |
| 443 | Temporal Dynamics of Spo0A Control The B. Subtilis Cell Fate Decision of Entering Starvation or Biofilm Formation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Studies have shown that these mechanisms are activated by the same molecule, Spo0A. We investigate how Spo0A triggers these two mutually exclusive cell-fates using optogenetics, microscopy, flow cytometry, and mathematical modeling. |
Cristina Palma ; Daniel Haller ; Jeffrey Tabor ; Oleg Igoshin; |
| 444 | Inferring Biochemical Reaction Rates from Stochastic Fluctuations in Growing and Dividing Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present numerical examples in which non-stationary system fluctuations were used to successfully infer rate functions between stochastically interacting components. |
Linan Shi ; Andreas Hilfinger; |
| 445 | How Plankton Can Exploit Hydrodynamic Cues for Vertical Migration: A Deep Reinforcement Learning Approach Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How can they exploit these hydrodynamic cues to migrate more efficiently? We use deep reinforcement learning to address this question. |
Aurore Loisy ; Selim Mecanna ; Christophe Eloy; |
| 446 | A Novel Electrochemical High-performance Non-enzymatic Glucose Sensor Based on Face-centred Cubic FeCoNiMnCr High Entropy Nano Alloys Grafted NCNTs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: High entropy alloys (HEAs) have gained sweeping attention in recent years in terms of their excellent mechanical properties, corrosion resistance and so on but is fairly less projected in terms of their electrochemical sensing properties. Here in we are reporting a FeCoNiMnCr HEA based non enzymatic glucose sensor along with its comprehensive OER kinetic studies both experimentally and theoretically. |
Gokul Raj; |
| 447 | Computationally Efficient and Accurate Exchange-correlation Functionals for QEDFT Calculations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we extend our previous findings by incorpo- rating the anisotropy and cavity modified-dispersion corrections of the polaritonic systems. |
Cankut Tasci ; Johannes Flick; |
| 448 | Machine Learning Nucleation Collective Variables with Graph Neural Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we discuss the development of a graph-based model for the approximation of one or more nucleation CVs, which enables orders-of-magnitude gains in computational efficiency in the on-the-fly evaluation of nucleation CVs. |
Florian Dietrich ; Gianpaolo Gobbo ; Michael Bellucci ; Matteo Salvalaglio; |
| 449 | 3D Imaging of Extracellular Matrix Analogues Via Fluorescence Correlation Spectroscopy Super-Resolution Optical Fluctuation Imaging (fcsSOFI) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we have taken a step further to extend this approach, employing fcsSOFI in conjunction with light sheet microscopy to reconstruct the three-dimensional structure of the matrix in various specific extracellular matrix analogues. |
Stephanie Kramer ; Benjamin Wellnitz ; Jeanpun Antarasen ; Surajit Chatterjee ; Albert Kim ; Lydia Kisley; |
| 450 | Hyperspectral Imaging of Head and Neck Tumors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A clinical study involving human patients with BCC, SCC, and benign skin lesions in the head and neck region will be presented. |
Matija Milanic ; Aljosa Krt ; Črt Keber ; Tadej Tomanic ; Jost Stergar ; Bostjan Markelc ; Ales Groselj ; Gregor Sersa; |
| 451 | Robustness of Machine Learning Techniques for CT26 Colon Carcinoma Classification Based on Hyperspectral Images Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we utilized hyperspectral imaging (HSI) to monitor CT26 colon carcinoma tumors subcutaneously grown on the back of BALB/c mice. |
Tadej Tomanic ; Jost Stergar ; Tim Bozic ; Bostjan Markelc ; Simona Kranjc Brezar ; Gregor Sersa ; Matija Milanic; |
| 452 | Quantum Photonic Micro/Nanolaser for Rapidly Assessing Overall Health of Cells and Organelles Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Healthy respiration of cells and organelles requires a stable proton pump in the inner mitochondrial membrane to regulate the membrane potential and internal biomolecular … |
Paul Gourley; |
| 453 | Theoretical Explorations of Quantum Neurosurgery Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Thus, the ambition here is to undertake a rigorous theoretical exploration into the potential possibilities of implementing quantum theory into a Neurosurgical setting. |
Juan Diego Garcia; |
| 454 | Ultrasound Luminescence Chemical Imaging for Implant Infection Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a hybrid ultrasound luminescent chemical imaging (ULCI) technique to probe the chemical environment on an implant surface. |
Sriparna Bhattacharya ; Gretchen Schober ; Unaiza Uzair ; Morgan Reel ; Vigjna Abbaraju ; Herbert Behlow ; Apparao Rao ; Jeffrey Anker; |
| 455 | Enhancing The Photodeactivation Efficiency of Pathogens in Prosthetic Joint Infection with Methylene Blue and Silver Nanoparticles Through Efflux Pump Inhibition Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This research adopts a synergistic approach, combining the efflux pump inhibitor (EPI) , reserpine, with silver nanoparticles (Ag NPs) and methylene blue (MB) to enhance PDT efficiency. |
Yaran Allamyradov ; Justice ben Yosef ; Inomjon Majidov ; Zikrulloh Khuzhakulov ; Simran Banga ; Mahmood Ateyeh ; Alper Er ; Ali Oguz Er ; Salizhan Kylychbekov; |
| 456 | Hydroxyapatite Coatings on Ti6Al4V and Si(100) Surfaces By Pulsed Laser Deposition Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this research, the effect of substrate temperature and ablation mechanism on the properties of hydroxyapatite (HA) coatings were investigated. |
Ali Er ; Salizhan Kylychbekov ; Yaran Allamyradov ; Justice ben Yosef ; Liviu Duta ; Inomjon Majidov ; Zikrulloh Khuzhakulov ; Simran Banga; |
| 457 | Deep Dive Into Optical Properties of SiliGlass Tissue Phantoms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this contribution, we present a detailed study of a polymer-based, stable, and affordable phantom, based on the SiliGlass polymer, black pigment, and glass microspheres. |
Jost Stergar ; Matija Milanic; |
| 458 | Active Response of Metabolically Intact Isolated Nuclei to Compression Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: The nucleus is generally considered to be the stiffest part of the cell with an apparent Young’s modulus of ~10 kPa, but cells deform their nuclei as they move through much softer … |
Fitzroy Byfield ; Alison Patteson ; Paul Janmey; |
| 459 | Complex Rheology in Single Cells: Compression Stiffening But Shear Softening Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, I have identified the relative contribution of actin and vimentin intermediate filaments in uniaxial compression experiments on single fibroblasts. |
James Conboy ; Pouyan Boukany ; Gijsje Koenderink; |
| 460 | Stoichiometric Model for The Microtubule-mediated Dynamics of Centrosome and Nucleus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we extend the original Stoichiometric Model to incorporate (1) overlap in the cortical motors, and (2) the dependence of velocity in the detachment rate of MTs from the cortical motors. |
Yuan-Nan Young ; Reza Farhadifar ; Michael Shelley ; Justin Maramuthal ; Libin Liu ; Alex Barnett; |
| 461 | In Situ Single-cell Mechanics of Mouse Preimplantation Embryos Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we use microrheology to monitor the evolution of mechanical properties of mouse preimplantation embryos at single-cell resolution. |
Haiqian Yang ; Ehsan Habibi ; Anubhav Sinha ; Aviv Regev ; Fei Chen ; Ming Guo; |
| 462 | On The Topology and Dynamics of Breast Cancer Cell Morphologies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Since we are dealing with biological systems, these morphological realizations are governed by the expression of phenotypes, which will endow the phase space with a particular topology. To better understand this natural topology, we employed the use of an adversarial autoencoder, a neural network, to reduce the dimensionality and better understand the phase space’s topology. |
Christian Cunningham ; Bo Sun; |
| 463 | Cancer Cell Footprinting and Exploration in Micropatterned Fibrinogen Mazes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we placed MDA-MB-231 cancer cells onto 2-dimensional micropatterned fibrinogen coated coverslips with circular maze structure. |
Trevor Reid ; Bo Sun; |
| 464 | Deciphering Tumor Heterogeneity in Triple-Negative Breast Cancer: The Crucial Role of Dynamic Cell-Cell and Cell-Matrix Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Overall, our work enables the systematic interrogation of breast tumor heterogeneity in the context of dynamic cell-cell and cell-matrix interactions, providing insight into the physical basis of TNBC progression. |
Susan Leggett ; Ian Wong ; Celeste Nelson ; Molly Brennan ; Mohak Patel ; Christian Franck ; Sophia Martinez ; Joe Tien ; Lena Gamboa ; Thomas Valentin ; Amanda Khoo ; Evelyn Williams; |
| 465 | Fluidization of Jammed Epithelia By Noninvasive Carcinoma in A Heterogeneous Tumor Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use spheroids, tumor approximations, composed of isogenic cell lines to investigate jamming across the epithelial to mesenchymal transition. |
Karen Yu ; Alex Devanny ; Laura Kaufman; |
| 466 | Modeling Nonlinear Dynamics of Cells in Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By contrast, healthy MCF10A cells plated on two-state micropattern can be described as bistable, with only noise-induced hopping between the two states [1]. Can we explain these different behaviors with a single model of cell-extracellular matrix interaction? |
Pedrom Zadeh; |
| 467 | Long-Wavelength Interface Fluctuations Between Different Cell Populations Are Suppressed By Friction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In these cellular systems, another general feature is the high dissipation due to friction between cells and their environment. In this study, we use vertex model to simulate the interface between two groups of deformable cells moving under Brownian Dynamics and show that the interface fluctuation spectrum for these friction-dominated systems is qualitatively different from the prediction of CWT, with fluctuations in the long-wavelength regime being suppressed. |
Haicen Yue ; Daniel Sussman; |
| 468 | Model of Cell-cell Adhesions As Cytockeleton-to-cytoskeleton Linkers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand how tissues behave mechanically and how forces are propagated between cells, we present a model of cell-cell coupling that takes into explicit account the dynamics of adhesion molecules and their interaction with the cytoskeleton. |
XinXin Du ; Michael Shelley; |
| 469 | Microrheology of Suspended Cells Using Optical Traps Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We here report on measurements of viscoelastic properties as well as non-equilibrium fluctuations of both, suspended cells and isolated cell nuclei, using optical traps. |
Mingru Li ; Paul Janmey ; Siyan He ; Brenton Hoffman ; Fitzroy Byfield ; Christoph Schmidt; |
| 470 | Combinatorial Role of Mechano-chemical Cues in Cell Mechanics and State Transitions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our present work will explore a combinatorial mechano-chemical phase space that influences the mechanical state of cells and regulates cell state transitions. |
M Sreepadmanabh ; Ashitha Arun ; Nandhu Babu ; Nivedita Chaudhary ; Dasaradhi Palakodeti ; Tapomoy Bhattacharjee; |
| 471 | Shaping Dynamical Neural Computations Using Spatiotemporal Constraints Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Thus, in this work, we examine how spatial patterns of cortical organization affect the computational dynamics of RNNs. |
Linden Parkes ; Bart Larsen ; Jason Kim; |
| 472 | Multi-stage Cortical Recurrent Circuit Implementing Normalization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Communication is supported by long-range reciprocal connections and, crucially, feedback connections have been hypothesized to influence perception by mediating attentional modulation. Here, we present a hierarchical recurrent neural circuit model with feedback that implements divisive normalization exactly at each stage of its hierarchy. |
Asit Pal ; Shivang Rawat ; David Heeger ; Stefano Martiniani; |
| 473 | Neurodivergent Behavior Gives Insight to Neural Noise Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work builds a new class of motion models using a dynamic phase-space optimization principle of the discrepancy between planned and observed states that both better predict participants’ motions for a wider range of scenarios. |
Nicholas Parris ; Jorge Jose; |
| 474 | Synchronization in Model Plastic Neuronal Networks Through Synaptic Re-organization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show that the numbers of pre- and post-synaptic partners depend on the firing rates of the neurons. |
Kanishk Chauhan ; Alexander Neiman ; Peter Tass; |
| 475 | Topological Synchronization of Coupled Nonlinear Oscillators Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: On another front, synchronization of nonlinear oscillators can be found throughout nature, such as biological oscillators. Here, we combine these two fields of physics and reveal the topological way to control synchronization. |
Kazuki Sone ; Yuto Ashida ; Takahiro Sagawa; |
| 476 | Synchronization in The Quaternionic Kuramoto Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose an $N$ oscillators Kuramoto model with quaternions $mathbb{H}$. |
Ting-Yang Hsiao ; Yun-Feng Lo ; Winnie Wang; |
| 477 | Parametric Oscillator Networks Naturally Implement The Lagrange Multiplier Primal-Dual Algorithm for Combinatorial Optimization Problems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While prior literature often derives the dynamics of such systems, it hasn’t explained why exactly the dynamics perform optimization so well. We present a previously unrecognized precise mathematical equivalence between parametric oscillator network dynamics and the primal-dual method of Lagrange multipliers that (1) lucidly explains how coupled oscillator solvers implement the correct optimization constraints and find high-quality solutions, (2) provides precise mathematical meaning to each physical component, (3) and enables theoretically-supported design of systems that implement more sophisticated optimization algorithms; we give one such design example. |
Sri Krishna Vadlamani ; Tianyao Patrick Xiao ; Eli Yablonovitch; |
| 478 | Learning of Networked Spreading Models from Noisy and Incomplete Data Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Some of the remaining challenges include model selection under the scenarios of unknown network structure, noisy data, missing observations in time, as well as an efficient incorporation of prior information to minimize the number of samples required for an accurate learning. We introduce a universal learning method based on scalable dynamic message-passing technique that addresses these challenges often encountered in real data. |
Andrey Lokhov ; Mateusz Wilinski; |
| 479 | Oral: On-chip Spike Pattern Classification for Neuromorphic Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present on-chip learning results for the adaptive STDP rule. |
Ashish Gautam ; Takashi Kohno; |
| 480 | Machine Tells You How Many Variables Are at Least Needed to Describe Space-time Chaos You See Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The Lyapunov exponents and the associated Lyapunov vectors serve as central quantities to characterize various aspects of spatiotemporal chaos, such as the instability, the fractal dimension, and even the inertial manifold dimension, which indicates the smallest possible number of variables needed to describe the trajectory. Nevertheless, such Lyapunov analysis has remained an immense challenge for large experimental systems, even after Pathak et al. (2017) numerically demonstrated that a machine learning technique, specifically the reservoir computing, may be used to obtain the Lyapunov spectrum from space-time data. |
Taro Shimizu ; Daiki Nishiguchi ; Kazumasa Takeuchi; |
| 481 | Associative Memory for Complex Dynamical Attractors in Reservoir Computing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The work provides foundational insights into developing models of long-term memories for complex dynamical patterns. |
Ling-Wei Kong ; Gene Brewer ; Ying-Cheng Lai; |
| 482 | Diffusion RNN: Extracting Low-Dimensional Structures in Data As Quasi-stable Manifolds Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce Diffusion RNN (Recurrent Neural Network), a neural-dynamical model that extracts hierarchies of low-dimensional manifolds from observed data. |
Toni Liu ; Jason Kim; |
| 483 | Energy-based Sequential Memory Networks at The Adiabatic Limit Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a new neural memory model featuring a dynamic energy surface. |
Arjun Karuvally ; Terrence Sejnowski ; Hava Siegelmann; |
| 484 | Generalized Time-reversal Symmetry and Effective Theories for Nonequilibrium Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will describe an analogous effective theory framework that applies to the classical stochastic dynamics of nonequilibrium systems. |
Jack Farrell ; Xiaoyang Huang ; Aaron Friedman ; Isabella Zane ; Paolo Glorioso ; Andrew Lucas; |
| 485 | Effective Field Theory Approach to Odd Elasticity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This approach offers an alternative pathway for constructing phenomenological models for driven and active matter. In this work, we apply our EFT formalism to problems in active solids—solids with active, non-conservative microscopic interactions that enable the material to perform work on its environment through quasi-static cycles of deformations. |
Isabella Zane ; Jack Farrell ; Xiaoyang Huang ; Aaron Friedman ; Andrew Lucas; |
| 486 | Optimal Design of Odd Elastic Metamaterials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Non-reciprocal interactions in active solids yield elastic moduli forbidden in equilibrium. These odd moduli offer a bottom-up approach to designing autonomous materials that spontaneously crawl, roll or swim. |
Jack Binysh ; Guido Baardink ; Jonas Veenstra ; Anton Souslov ; Corentin Coulais; |
| 487 | Non-reciprocity Permits Novel Dynamics in Living and Active Topological Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will introduce stochastic networks in molecular configuration space that model different systems from a circadian clock to ring attractors. |
Evelyn Tang; |
| 488 | Tuning Non-reciprocal Pattern Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we demonstrate the potential of multiple states in non-reciprocity active metamaterials, both theoretically and experimentally. |
Xiaofei Guo ; Jonas Veenstra ; Corentin Coulais; |
| 489 | Lorentz Reciprocal Theorem in Fluids with Odd Viscosity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show that the theorem can be generalized to fluids with odd viscosity by choosing an auxiliary problem with the opposite sign of the odd viscosity [1]. |
Yuto Hosaka ; Ramin Golestanian ; Andrej Vilfan; |
| 490 | Non-reciprocal Stochastic Topological Networks Show New Properties As Compared to Quantum Counterparts Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: More broadly, this work characterizes unique physical properties that emerge from identical networks described by Laplacian and adjacency matrices respectively. |
Ziyin Xiong ; Aleksandra Nelson ; Evelyn Tang; |
| 491 | Active Boltzmann Equation for Self-propelled Particles with Non-reciprocal Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have introduced the methods for Vicsek-type active particles with anti-alignment that allows for an asymptotically exact analytical solution. |
Horst-Holger Boltz ; Jakob Mihatsch ; Rüdiger Kürsten ; Thomas Ihle; |
| 492 | Multicomponent Active Diffusion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we present a dynamical framework for determining the stability of multicomponent active systems. |
Yu-Jen Chiu ; Ahmad Omar ; Daniel Evans; |
| 493 | Odd Diffusivity and Odd Mobility in A System with Equilibrium Structure Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we consider a system of interacting Brownian particles evolving under the influence of forces that have components transverse to energy gradients [3]. |
Grzegorz Szamel ; Federico Ghimenti ; Ludovic Berthier ; Frederic van Wijland; |
| 494 | Space-time Symmetry and Non-reciprocal Transport in Dynamic Mechanical Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While parametric resonance of individual oscillators is well understood, identifying the conditions for parametric resonance in systems of coupled oscillators remains challenging. In this talk, we will identify and use the non-Hermitian internal symmetries arising from the real-valued and symplectic nature of classical mechanics to determine these parametric resonance conditions. |
Abhijeet Melkani ; Jayson Paulose; |
| 495 | Molecular Modelling of Odd Viscoelastic Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will describe and analyze the first known microscopic model that produces an odd viscoelastic fluid. |
Pawel Matus ; Piotr Surowka ; Ruben Lier; |
| 496 | Non-reciprocal Alignment Can Induce Asymmetric Clustering in Active Repulsive Mixtures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a full non-equilibrium phase diagram in the parameter space of inter-species coupling strengths and compare with particle-based simulations, highlighting the impact of non-reciprocity on various scales. |
Kim Kreienkamp ; Sabine H. L. Klapp; |
| 497 | Cooperative Transport of Emulsions in Porous Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the transport of emulsions in a micromodel of porous medium using microfluidics and optical imaging. |
Shima Parsa; |
| 498 | Active Matter Transport in Porous Mediums Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will show how the worm employs the different strokes to move through the medium, which changes character with increasing overburden pressure. |
Arshad Kudrolli; |
| 499 | Foam Transport in Porous Media Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Foams are essential in a variety of geophysical systems such as enhanced oil recovery, environmental remediation, to subsurface carbon dioxide sequestration. Thus, there is a need … |
Sibani Lisa Biswal ; Yiwei Wang; |
| 500 | Phoretic Delivery of Colloids to Biofilms in Complex Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present an effective approach to enhance nanoparticle penetration into biofilms formed in complex environments. |
Zehao Chen ; Amir Pahlavan; |
| 501 | Barriers, Chutes and Long-range Transport of Active Tracers in Vortex Flows Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present experiments on the effects of imposed, two-dimensional, laminar flows on the motion of self-propelled tracers. |
Thomas Solomon ; Nghia Le; |
| 502 | The Dynamics of Swimmers in Vortex-dominated Flows: The Role of Rotational Noise Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use dynamical systems techniques to study the transport of swimming microorganisms, such as the marine algae tetraselmis, in vortex-dominated, two-dimensional flows. |
Kevin Mitchell ; Taylor Whitney ; Thomas Solomon; |
| 503 | Life of Cyanobacteria in Turbulent Lakes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A numerical model based on non-linear population dynamics describes the measured size distribution. |
Yuri Sinzato ; Robert Uittenbogaard ; Petra Visser ; Jef Huisman ; Maziyar Jalaal; |
| 504 | Microbe-fluid-sediment Interactions in Aquatic and Terrestrial Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will discuss how I use flume experiments to study sediment transport, microfluidic experiments to study soil carbon dynamics, and meso-scale microbial experiments to study bacterial spreading in soil. |
Judy Yang; |
| 505 | Aerobiology with Acoustic Levitation Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Airborne microbes critically impact our everyday lives, e.g., rainfall, disease spread, land fertilization, and food production. Often these microbes hitchhike on particulates – … |
Derrick Rodriguez ; Ranjiangshang Ran ; Schuyler Arn ; Keiran Stevenson ; Minsu Kim ; Josef Dufek ; Joshua Mendez Harper ; Justin Burton; |
| 506 | Submerged Cohesive Granular Collapse: Influence of Packing Density Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore the submerged collapse of cohesive granular columns, as a function of packing density and cohesive force strength, via grain-resolving direct numerical simulations. |
Eckart Meiburg ; Rui Zhu; |
| 507 | Cephalopod Skin Patterns As Windows Into Brain Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe our recent work revealing the space of camouflage patterns and dynamics of pattern matching. |
Sam Reiter; |
| 508 | Characterizing The Dynamics of Syllable Emergence in The Juvenile Songbird Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To characterize the dynamics of emergence, the acoustic structure of songs is usually classified using manual labeling and quantified by computing scalar acoustic measures such as pitch, amplitude and spectral entropy. To go beyond such human-defined features, we use low-dimensional latent representations that can be learned from the syllables’ spectrograms to analyze the vocal repertoire of songbirds at different developmental points. |
Michael Pasek ; Leila Pascual ; Samuel Sober ; Ilya Nemenman; |
| 509 | A Novel High Throughput Experimental Assay for Studying Distance Estimation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a novel experimental assay that leverages a simply engineered rig and machine learning tools to provide a high throughput means of probing the neuronal underpinnings of distance estimation in insects. |
Elizabeth Wu ; Joseph Shomar ; Damon Clark; |
| 510 | Robust Gait Stability Analyses Using Dynamical Machine Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show applications of this method from fly, mouse, and human gait dynamics. |
Michael Hess ; Gordon Berman ; Shinyoung Kang; |
| 511 | Phase Oscillator Model of Inter-limb Coordination in Free-running Mouse Locomotion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This linearized Kuramoto description outputs not only traditional gait descriptors such as phase offset and speed, but also novel measures such as inter-limb coupling and underlying noise structures. Using these model parameters, we generate a description and comparison of inter-limb dynamics at various locomotion speeds and turn angles, and investigate the source of naturally occurring variations in locomotion. |
Haolin Liu ; Chenyi Fei ; Mikhail Kislin ; Jorn Dunkel ; Samuel Wang ; Joshua Shaevitz; |
| 512 | Oral: Hydrodynamic Study on The Water-hopping Behavior of Mudskipper Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study aims to explore the hydrodynamics of water-hopping in mudskippers through experimental setups and theoretical analysis. |
Daehyun Choi ; Kai Yung ; Saad Bhamla; |
| 513 | Preventing Ankle Twists: The Role of The Human Foot Arch in Enhancing Lateral Dynamic Stability Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show that modern humans possess an optimized foot arch height, which provides enhanced lateral dynamic stability when compared to individuals with either flat or high-arch feet. To quantify this lateral stability, we introduce a novel dimensionless stability indicator for single-legged landings, utilizing a nonlinear multi-Degree-of-Freedom mathematical model and an energy-based approach. |
Yue Guan; |
| 514 | The Effects of Surface Feature Geometry on The Propulsive Locomotion of Tree-climbing Snakes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study investigates the force output over the body of the snakes through the combination of 3D-kinematic tracking data as well as time-resolved force data. |
Michelle Lee ; Calvin Riiska ; Joseph Mendelson III ; Jennifer Rieser; |
| 515 | Climbing Without Feet: Effect of Surface-feature Size on The Physics of Vertical Snake Locomotion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we created a simplified model of a large-diameter tree consisting of a flat, smooth, vertical surface with force-sensitive pegs acting as surface features. |
Calvin Riiska ; Michelle Lee ; Joseph Mendelson III ; Jennifer Rieser; |
| 516 | Unifying Framework of Vortex Interactions from Air to Water and in Between Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore how organisms from jellyfish to fruit flies harness vortex interactions to boost locomotion. |
Pankaj Rohilla ; Johnathan O’Neil ; Victor Ortega-Jimenez ; Daehyun Choi ; Saad Bhamla; |
| 517 | Moving on Snowflakes and Melting Ice: Jumping, Glandular-landing and Meniscus-climbing Abilities of Snow Springtails Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We found that snow springtails are extraordinarily fast when jumping on snow. |
Richard Viveiros ; Victor M. Ortega Jimenez; |
| 518 | Deciphering Multi-scale Interaction Networks Driving Microbial Community Dynamics and Functions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides a foundation for exploring and exploiting the interaction networks driving microbial communities for a wide range of potential applications in precision medicine, agriculture and bioprocessing. |
Ophelia Venturelli; |
| 519 | Visualizing Bacterial Dynamics in Transparent Soil Mimics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Traditional methods of studying bacterial behavior in soils are inaccessible due to the opacity of natural soil matrices. To address this challenge, we create a transparent porous medium that emulates the structural heterogeneity found in natural soils. |
Ahmed Al Harraq ; Joshua Shaevitz ; Sujit Datta; |
| 520 | Interplay of Spatiotemporal Dynamics and Population Dynamics of Native and Engineered Bacteria in The Gut Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent studies indicate a key role for the gut microbiome in CRC. As part of an interdisciplinary team, we seek to use genetically modified gut bacteria to detect early CRC and possibly influence its progression. |
Alberto Alonso ; Moumita Das; |
| 521 | Bistability in Dynamics of Worm-microbe Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We observe a bistable distributions of population sizes across individual hosts. |
Satya Spandana Boddu ; K. Michael Martini ; Ilya Nemenman ; Nic Vega; |
| 522 | Diffusible Public Goods in Microbial Communities: Understanding Spatial Dynamics and Implications for Antibiotic Resistance Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: With this perspective in hand, we study the outcome of diffusible public goods games in the context of a spatially structured resistant-susceptible microbial community exposed to an antibiotic gradient where the resistant strategy produces and secretes a diffusible public good capable of protecting the susceptible strategy. |
Raymond Copeland ; Miles Wetherington; |
| 523 | Flower Petal Patterns Formed By Dense Colony of Cross-feeding Bacteria Growing on Hard Agar Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Contrary to expectations formulated based on batch culture measurements, we observed the emergence of a flower petal pattern formed by the two strains in the colony after initial inoculation as a uniform mixture. |
Harish Kannan ; Kinshuk Sahu ; Paul Sun ; Zhongge Zhang ; Bo Li ; Terence Hwa; |
| 524 | Controlling Species Coexistence Through Temporal Niche Engineering Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop and computationally test a general strategy to engineer a set of resources that allows a given set of species to stably coexist. |
Sergei Maslov ; Akshit Goyal ; Zihan Wang; |
| 525 | Death And Chemotaxis: Dynamics of Phage-Bacteria Interactions in Crowded Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Furthermore, phage-bacteria interactions are typically studied at limited timepoints due to the experimental challenges of real-time analysis, further limiting understanding of how they influence microbiomes in practice. Here, we address this gap in knowledge using direct visualization of phage-bacteria interactions in transparent crowded matrices composed of packed hydrogel microparticles. |
Victoria Muir ; Sujit Datta ; Alejandro Martinez-Calvo ; Ned Wingreen; |
| 526 | The Spread of Antibiotic Resistance in Multi-colony Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate how intra-colony interactions shape inter-colony dynamics, and vice versa, in communities of E. faecalis, an opportunistic pathogen. |
Jacob Moran ; Kevin Wood; |
| 527 | New Sector Morphologies Emerge from Anisotropic Colony Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we use a simple model to analyze the influence of anisotropy on bacterial range expansion, with specific focus on sector morphology. |
Daniel Swartz ; Hyunseok Lee ; Mehran Kardar ; Kirill Korolev; |
| 528 | Range Expansion and Localization in Patchy Landscapes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Coupling microfluidics experiments of bacterial colonization dynamics in patchy landscapes with a simple lattice model, this work aims to connect key processes at play in planktonic-to-sessile transitions to understand observed patterns in metapopulation distribution including localization events. |
Miles Wetherington ; Peter Yunker; |
| 529 | Cooperative Antibiotic Resistance in Spatially Structured Bacterial Colonies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this project, we investigated how antibiotic exposure affects the spatial organization of a bacterial community in which antibiotic resistance is a social trait. |
Marlis Denk-Lobnig ; Kevin Wood; |
| 530 | Single-cell Morphology Dictates Bacterial Growth Dynamics Under 3D Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides an example of how the alteration in the physical of the microenvironment can dictate the microbiome composition in 3D disordered materials. |
Tapomoy Bhattacharjee ; M Sreepadmanabh ; Meenakshi Ganesh ; Pratibha Sanjenbam ; Christina Kurzthaler ; Deepa Agashe; |
| 531 | Revisiting Resonance in Flapping Flight: Supra-resonant Oscillations in Moths, Bees, and Robophysical Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: And what are the different implications for periodically forced and self-excited flapping flight especially when both types of forcing are present? Here we show that synchronous hawkmoths and asynchronous bumblebees are both supra-resonant, operating above their kinematic resonance peak. |
Simon Sponberg ; Ethan Wold ; Ellen Liu ; Jeffrey Gau ; James Lynch ; Nick Gravish; |
| 532 | Directional Take-off and Aerial Control of Ultrafast Jumps in Springtails and Robots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We analyzed the takeoff kinematics across several species of springtails leaping off rigid and compliant substrates. |
Jacob Harrison ; Adrian Smith ; Hungtang Ko ; Baekgyeom Kim ; Jesung Koh ; Saad Bhamla; |
| 533 | Creating A Robophysical Model to Study How Malaria Infiltrates Human Skin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, based on recent biological observations, we created a robophysical model that mimics the movement of sporozoites along collagen fibers. |
Kyungmo Choi ; Shruthika Kandukuri ; Yaqing Wang ; Yun Chen ; Chen Li; |
| 534 | Fiber-Robot with Adjustable Electrodes for Long Term Neural Recording Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present, in collaboration with Virginia Tech, a prototype of a novel fiber-robot probe, with individually controllable electrode arms – capable of moving through gels with mouse brain modulus, which will be able to detect and position the arms in the best location for neural sensing. |
Jacob Pelster ; Itai Cohen ; Xiaoting Jia ; Yujing Zhang ; Alexander Parrott ; Qingkun Liu ; Hengji Huang ; Jongwoong Kim; |
| 535 | Towards A Computational Toolbox for Resolving The Multiscale Dynamics of Animal and Robot Behavior Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The complexity of animals’ and robots’ coupled, nonlinear hybrid (contact-making and -breaking) dynamics can be mitigated by postulating that agile behaviors arise from composition of favorable postural subspaces within which constituent tasks are encoded as "templates" (low degree of freedom dynamical abstractions) and down toward which the high degree of freedom body and limbs are "anchored" (quickly controlled to converge). To take the next step towards discovery of the template representations that enable agile animal locomotion, we developed a computational pipeline that extracts such low dimensional attracting invariant postural submanifolds from high dimensional trajectory data. |
Benjamin McInroe ; Daniel Koditschek ; Robert Full ; Yuliy Baryshnikov; |
| 536 | Drag Forces on Objects Moving on Elastically Deformable Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To develop a resistive force theory (RFT) type model of the dynamics of a wheeled vehicle locomoting on a deformable spandex membrane (discussed in Li et al., PNAS, 2022), we investigate drag forces on a wheel moving at constant speed across the surface. |
Hussain Gynai ; James Lewis ; Shengkai Li ; Daniel Goldman; |
| 537 | Finding Tradeoffs in Muscle Types Through A Robophysical Model of The Hill Muscle Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, using feedback control and a DC motor as our actuator, we create a robophysical model of the Hill muscle. |
Jake McGrath ; José Alvarado; |
| 538 | Lightweight Autonomous Crawling Robot Utilizing Vacuum-Driven Self-sensing Origami Actuators for 3D Multi-Terrain Exploration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This research presents a novel lightweight, autonomous crawling robot, equipped with trio parallel 3D-printed Kresling origami actuators. |
Jiaqi Wang ; Xiaohao Xu ; Jonathan Mi ; Wenzhe Tong ; Xiaonan Huang; |
| 539 | Decoding Frequencies Generated During Spider Vibration Sensing Through Robophysical Modeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we developed a robophysical model of the spider-web-prey system. |
Eugene Lin ; Yishun Zhou ; Luke Moon ; Andrew Gordus ; Chen Li; |
| 540 | Understanding The Buckling Instability in Jumping Nematode and Inspired Soft Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we designed a soft jumping model by drawing inspiration from nematode leaping using buckling, which showed similar jumping behavior and performance. |
Sunny Kumar ; Ishant Tiwari ; Victor M. Ortega Jimenez ; Adler Dillman ; Saad Bhamla; |
| 541 | Nonlinear, Muscle-like Actuation Reduces Energy Consumption— Does It Also Simplify Control? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Seminal work by Hill demonstrated that muscle is inherently nonlinear, with a hyperbolic force-velocity relation. |
José Alvarado ; Jake McGrath ; Brian Kent; |
| 542 | Nonlinear Dynamics of Sound Detection in The Auditory System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Furthermore, its highly nonlinear response has characteristics that are well captured by equations based on the Hopf bifurcation. The study of auditory detection therefore poses a problem at the intersection of nonlinear dynamics with out-of-equilibrium physics. |
Dzmitry Vaido ; Martín Toderi ; Dolores Bozovic; |
| 543 | A Mechanical Origin of Cooperative Transport Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In my talk, I will present the “transporton”, a new kind of self-propelled particle whose mechanical design gives rise to a novel dynamical response: when subjected to an external force, a transporton aligns and propagates in a direction opposite to the force. |
Matan Yah Ben Zion; |
| 544 | Dissect The Motility Mechanism and Regulation of The C-terminal Kinesin KlpA Using Single-molecule Fluorescence Microscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our previous work showed that while all other C-terminal kinesins exclusively exhibit directional preference for the microtubule minus end, KlpA uniquely exhibit directional preference for the microtubule plus end. In this talk, we will discuss our effort toward understanding the mechanisms underlying KlpA motility and its regulation. |
Weihong Qiu ; Akasit Visootsat ; Yuan Gao ; Andrew Popchock; |
| 545 | Assessing Mechanical Properties of A Utrophin Fragment with Two Operational Modes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study mechanical properties of a utrophin fragment encoding the N terminus through spectrin repeat 3 (UtrN-R3) using atomic force microscopy (AFM). |
Cailong Hua ; Murti Salapaka; |
| 546 | Temperature Profiles of Beta-amyloid and Tau Protein Using Raman Spectroscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study demonstrates a label-free and non-destructive technique to investigate amyloid fibril formation and study their secondary and tertiary structure as a function of temperature. |
Yin-Ting Yeh ; Thuc Mai ; Angela Hight Walker; |
| 547 | Inter-domain Signaling: Clues and Questions from The Photoactive Yellow Protein Family of Photoreceptors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Two widely occurring evolutionary processes in Bacteria and Archaea can potentially provide insights into this question: (1) the two proteins involved in some cases are fused into one larger multi-domain protein; and (2) the genes encoding two proteins involved is some cases are encoded adjacent on the DNA in an operon. We cataloged these two processes for the PYP family of photoreceptors and used them to derive clues regarding inter-domain signaling mechanisms. |
Wouter Hoff ; Gunnar Hoogerwerf ; Rosalie Dohmen ; Catalina Bradley ; Amber Dohmen ; Saylor Hampton ; Clarice Huffman ; Scout Powell ; Sarah Teeman; |
| 548 | Evolutionary Selection of Proteins with Two Folds Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we hypothesize that coevolutionary signatures are being missed. |
Joseph Schafer ; Lauren Porter; |
| 549 | Structural Mechanism of TCR-pMHC Catch Bonding Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have developed a mathematical framework of protein-ligand binding under force, showing how catch bonding is induced by singularities in the “flow field” that describes force-induced molecular deformations. |
Casey Barkan; |
| 550 | Functional Clustering of Proteins to Map Out The Protein Shape Space Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a method for protein function classification and prediction of functional sites. |
Ella Carlander ; Uchenna Nwaege ; Gian Marco Visani ; Michael Pun ; Armita Nourmohammad; |
| 551 | Understanding and Design of Beta-sheet Forming Antimicrobial Peptides Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will report on our work in devising a workflow for the active learning design of beta-sheet-forming AMPs. |
Rachael Mansbach ; Mohammadreza Niknam Hamidabad ; Natalya Watson ; Lindsay Wright ; Samuel Renaud; |
| 552 | A Rapid Transition in The Unfolding of Ubiquitin at High SDS Concentrations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Understanding the intricacies of this interaction is crucial for unraveling the dynamics of protein-surfactant complexes. This study focuses on ubiquitin (Ubi) as a model protein and employs small-angle X-ray Scattering (SAXS) and molecular dynamics (MD) simulations to investigate its behavior in the presence of SDS. |
Hrachya Ishkhanyan ; Armen Poghosyan ; Jan Pedersen ; Daniel Otzen; |
| 553 | Designing Protein Stabilizers: Small Molecule Effects on Protein Folding Are Driven By Direct Interactions and Solvent Rearrangement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To establish a molecular picture, we have utilized molecular dynamics simulations to explore the effects of various excipient solutions on miniprotein folding. |
Jonathan Zajac ; Praveen Muralikrishnan ; Caryn Heldt ; Sarah Perry ; Sapna Sarupria; |
| 554 | Effects of Lipids During Insertion Process of PH Low Insertion Peptide Into Membrane Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk aims to focus on lipid effects to the free energy cost for insertion of pH Low Insertion Peptide into membrane. |
Ganga Sharma; |
| 555 | Connecting Relevant Information to Coarse-graining in Biological Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For example, we cannot see every feature of the light field that reaches our eyes; temporal resolution is limited by transmission noise and delays, and spatial resolution is limited by the finite number of photoreceptors and output cells in the retina. Classical efficient coding theory describes how sensory systems can maximize information transmission given such capacity constraints, but it treats all input features equally. |
Stephanie Palmer; |
| 556 | Trading Information Among Multiple Variables Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The amount of relevant information that can be extracted is limited by the precision or information capacity of the mechanisms that respond to changing concentrations. We have explored this tradeoff in the context of early events in the fruit fly embryo [1] and shown that there are universal features to this tradeoff in limits that are relevant to the embryo [2]. |
Marianne Bauer ; William Bialek; |
| 557 | Coarse-graining Retinal Responses to Reveal Predictive Information Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, it is not well understood how correlations between neurons enable prediction in large subpopulations (greater than ten) or when the visual stimulus is complex. In this work, we address these challenges together by searching for maximally-predictive collective variables in large subsets of 93 salamander retinal ganglion cells under stimulation with natural movies. |
Adam Kline ; Aleksandra Walczak ; Thierry Mora ; Maciej Koch-Janusz ; Stephanie Palmer; |
| 558 | Quantifying Information Flow in Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study information flow in MAPK pathway, one of key signalling pathways in eukaryotes. |
Mirna Elizabeta Kramar ; Lauritz Hahn ; Aleksandra Walczak ; Thierry Mora ; Mathieu Coppey; |
| 559 | Coordination Between Sub-populations of Interneuron in The Spinal Cord Revealed By Information Theory Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use information theory to predict how subpopulations of spinal inhibitory and excitatory interneurons may coordinate their responses to their synaptic inputs to achieve maximal information transmission. |
Weiheng Qin ; Candida Tufo ; Ying Zhang ; Francisco Alvarez ; Martyn Goulding ; Eiman Azim ; Graziana Gatto ; Tatyana Sharpee; |
| 560 | Estimating Mutual Information with The Deep Variational Symmetric Information Bottleneck Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, such a reduction can destroy correlations between the variables. We resolve this problem using the Deep Variational Symmetric Information Bottleneck (DVSIB), which simultaneously compresses the variables X and Y into two corresponding lower dimensional latent variables Z X and Z Y, while maximizing the information between the latent variables. |
Eslam Abdelaleem ; K. Michael Martini ; Ilya Nemenman; |
| 561 | The Information Bottleneck Learns Spectral Properties of Dynamical Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we investigate model reduction for dynamical systems using the information bottleneck framework. |
Matthew Schmitt ; Maciej Koch-Janusz ; Michel Fruchart ; Daniel Seara ; Vincenzo Vitelli; |
| 562 | Obtaining Machine Learned Surrogate Underwater Acoustics Models to Enable Model Reduction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose methods for obtaining machine learned (ML) surrogates of the model to which AD can be easily applied. |
Jay Spendlove ; Mark Transtrum ; Tracianne Neilsen; |
| 563 | Extending The Manifold Boundary Approximation Method to Reduce Large-scale, Multi-parameter Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I present a computationally efficient generalization of MBAM, applicable to models with many more parameters. |
Mark Transtrum; |
| 564 | Information Theoretic Characterization of Critical Phenomena in The Ising Model and Flocking Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we characterize aspects of the informational architecture of the Ising model on the square lattice using multiple measures, including configurational entropy, configurational complexity, and transfer entropy. |
Sean Kelty ; Gourab Ghoshal ; Damian Sowinski; |
| 565 | Random-Energy Secret Sharing Via Extreme Synergy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work offers a further example of information theory as a unifying concept, connecting problems in statistical physics to those in computation. |
Vudtiwat Ngampruetikorn ; David Schwab; |
| 566 | A Fourier Tour of Protein Function Prediction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discuss how WH transform allows us to view protein functions as a multilinear polynomial and in terms of high-order sparse nonlinear interactions. |
Amirali Aghazadeh; |
| 567 | Odd Mechanics of Active Slender Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We describe examples for spheroids, membranes tubes and helicoids, discussing the relevance and predictions for left-right symmetry breaking in morphogenesis. |
Sami Al-Izzi ; Jack Binysh ; Gareth Alexander; |
| 568 | Confinement-induced Phase Transitions of Living Chiral Crystal Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we explore the influence of boundary interactions on the structure and dynamics of LCC. |
Yuchao Chen ; Shreyas Gokhale ; Hamza Coban ; Vicki Mu ; Nikta Fakhri; |
| 569 | Spontaneous Self-excited Odd Elastic Waves in Living Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we show how to detect odd elastic waves by measuring appropriate current correlation functions. |
Sang Hyun Choi ; Zhi-Feng Huang ; Nigel Goldenfeld; |
| 570 | Chiral Matters Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss the physics of out-of-equilibrium solids and fluids built out of mechanically spinning components. |
William Irvine; |
| 571 | Nonreciprocity in Active Microbial Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Intriguingly, the emerging concept of nonreciprocity offers fresh angles to untangle these complexities. In this presentation, I will summarize our recent experimental endeavors to understand nonreciprocity and its biological relevance. |
Askin Kocabas ; Baha Altın ; Alp Ünlü; |
| 572 | Microscopic Nonreciprocity Drives Emergent Dynamic Phase of Living Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Moreover, extended observations over several hours indicate a transition from this dynamic state to a static crystalline phase. To elucidate these phenomena, we introduce a coarse-grained theoretical framework that accounts for both the emergence of the dynamic phase through imbalanced hydrodynamic force interactions and the exceptional phase transition driven by variations in embryo number densities. |
Hyunseok Lee ; Junang Li ; Shreyas Gokhale ; Chenyi Fei ; Alasdair Hastewell ; Chih-Wei Joshua Liu ; Lisa Lin ; Yuchao Chen ; Jorn Dunkel ; Nikta Fakhri; |
| 573 | Spontaneous Demixing of Binary Colloidal Flocks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Combining evidence from synthetic active fluids assembled from self-propelled colloidal particles along with theoretical predictions at the continuum scale, we demonstrate the spontaneous demixing of binary polar liquids within circular confinement. |
Samadarshi Maity ; Alexandre Morin; |
| 574 | Non-Reciprocal Landau-Ginzburg Theories Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In critical phenomena at equilibrium, the study of the emergent conformal symmetry at a phase transition provides a way to systematically classify critical behavior. |
Gabriel Weiderpass ; Savdeep Sethi; |
| 575 | Statistical Mechanics of The Non-reciprocal Ising Model Near Zero Temperature Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the kinetic Ising model with non-reciprocal interactions between spins, the maximum entropy distribution of binary variables conditioned on a past state with constraints on means and lagged correlations. |
Cheyne Weis ; Peter Littlewood; |
| 576 | Emergence of Hidden Nonreciprocity As A Stabilizing Effective Potential in Active Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we identify a special class of systems evolving on a potential and under nonreciprocal interactions. |
Matthew Du ; Suriyanarayanan Vaikuntanathan; |
| 577 | The Three-Body Problem: Non-reciprocity and Multibody Interaction in Acoustically Levitated Granular Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we highlight the inherent multibody and non-reciprocal nature of acoustic interactions, even in systems comprising as few as three particles. |
Brady Wu ; Qinghao Mao ; Bryan VanSaders ; Heinrich Jaeger; |
| 578 | Time-modulated Chiral Solids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using an external field, we drive magnetic colloids to rotate with a rotational frequency that is modulated in time, generating non-trivial structure. |
Yehuda Ganan ; Ephraim Bililign ; Alexis Poncet ; Denis Bartolo ; William Irvine; |
| 579 | Dynamics of Topological Defects in The Presence of Non-reciprocal Interactions: Twisting, Stabilisation and Enhanced Annihilation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce an extension of the celebrated 2D XY model with non-reciprocal couplings, where short-range spin-spin interactions are weighted by a smooth anisotropic kernel. |
Demian Levis ; Ylann Rouzaire ; Ignacio Pagonabarraga; |
| 580 | Global and Local Approaches to Detect Subtle Behavioural Changes in Large-scale Behavioural Screens Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose multiple robust methods to mine detailed information from behavioural screens: – A generative method to regularize inference of larva shape across the entire screen. |
jean-baptiste masson ; alexandre blanc ; françois Laurent ; christian vestergaard ; tihana jovanic ; chloe barre; |
| 581 | Constructing Motion Spaces of Ant Mandibles from MicroCT Scans Using Vector Embeddings Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Taking ants as a motivating example, we set out to characterize the range of three-dimensional kinematics of ant mandibles across several ant families and among several Hymenopteran clades for a broader phylogenetic context. |
Henry Cerbone ; Julian Katzke ; Evan Economo; |
| 582 | Long Timescale Structure and Scale Invariance in Animal Behavior Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose an analysis scheme that deals with the challenges of non-independence of samples and individual differences to extract long-ranged correlations in behavior trajectories. |
Abir George ; Grace McKenzie-Smith ; Scott Wolf ; Joshua Shaevitz ; William Bialek; |
| 583 | Controlling Noisy Herds Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This well-known collective behavior falters in small groups (N<5), where sheep unpredictably oscillate between fleeing and clustering. In this talk, we will discuss the physics of controlling such small N, noisy collectives, using the interaction between sheep and shepherd dogs as a case study. |
Tuhin Chakrabortty ; Saad Bhamla; |
| 584 | Environmental Adaptations in Fire Ant Mound Construction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesize that fire ants’ success is linked to above- and below-ground architectural adaptations across environmental conditions. |
Zachariah Germain ; Thomas Bochynek ; Zhuo Chen ; Emmaline Arter ; Jennifer Rieser; |
| 585 | Cradle-to-grave Continuous Monitoring of Drosophila Melanogaster to Quantify Behavioral Correlates of Lifespan and Healthspan Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have designed a setup for continuous behavioral monitoring of the fruit fly Drosophila melanogaster over weeks and months, and have successfully recorded multiple animal lifespans of greater than 4 weeks. |
Grace McKenzie-Smith ; Scott Wolf ; Coleen Murphy ; Joshua Shaevitz; |
| 586 | Coarse-graining Non-stationary Dynamics: Linking Early to Late Phases of Zebrafish Contests Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we adopt a transfer operator approach to identify coarse-grained modes of non-stationary dynamics in the pair fighting behavior of zebrafish. |
Akira Kawano ; Greg Stephens; |
| 587 | A Physical Theory for Social Behavior Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine data-driven techniques with analytical tools from statistical physics to illustrate how to construct continuum models of social behavior. |
Daniel Seara ; Michel Fruchart ; Jonathan Colen ; Yael Avni ; David Martin ; Vincenzo Vitelli; |
| 588 | Dynamics, Statistics, and Task Allocation of Foraging Ants Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: It is well studied from an entomology viewpoint but there is currently a lack of mathematical synthesis of this phenomenon. We address this by constructing an ant foraging model that incorporates simple behavioral rules within three task groups of the ant colony during foraging (i.e., foragers, transporters, and followers), pheromone trails, and memory effects. |
Ee Hou Yong ; Nuoya Zhang; |
| 589 | Uncovering Principles of Long Timescale Sensory Evoked Navigation in Larval Zebrafish Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By concatenating the fish’s tail pose across bouts over time, we constructed maximally predictive sequences and investigated the time evolution of behavior through a high-fidelity Markovian model. |
Gautam Sridhar ; Antonio Carlos Costa ; Massimo Vergassola ; Claire Wyart; |
| 590 | How Do Biofilms Defend Public Goods? Mechanisms of Protection Against Planktonic Invasion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using the model biofilm forming species Vibrio cholerae — the causative agent of the pandemic disease cholera — we combine confocal microscopy that can resolve biofilms containing hundreds of cells at single-cell resolution with digital in-line holography, a technique that can reconstruct three-dimensional trajectories of cells swimming at speeds in excess of 100 microns per second. |
Merrill Asp ; Jing Yan ; Alexis Moreau ; Jung-Shen Benny Tai; |
| 591 | Comparative Studies of Nematically Aligned Bacterial Domains in Biofilms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In particular, we observed large scale plates of nematically aligned bacteria dubbed “shields.” In this work, we are interested in exploring the generality of these structures across several P. aeruginosa mutant strains and S. aureus, as well as characterizing the nematic order parameter of shield structures across length scales where present. |
Hailey Currie ; Vernita Gordon ; Marilyn Wells; |
| 592 | Active PH Regulation Facilitates Biofilm Development in Minimally Buffered Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Because such pH stress is commonly masked in buffered laboratory media, it remains unclear how biofilms cope with minimally buffered natural environments. Here, we report Bacillus subtilis biofilms overcome this intrinsic metabolic challenge through an active pH regulation mechanism. |
Arthur Prindle; |
| 593 | Morphodynamics of Growing Bacterial Communities in Polymeric Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that, when the polymer is sufficiently concentrated, the cells grow in striking “cable-like” morphologies—in stark contrast to the compact morphologies that arise in the conventionally-studied polymer-free case. |
Sebastian Gonzalez La Corte ; Sujit Datta ; Ned Wingreen; |
| 594 | The Effects of Substrates on Biofilm Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Several experiments have also observed biofilms expand at rates that depend on substrate stiffness, but the exact mechanisms behind this collective behavior are not well understood. We present an agent-based model to address these observations and suggest a possible mechanism for biofilm expansion on substrates characterized by their stiffness, where the individual’s tasks are coupled to nutrient availability and substrate properties. |
Sounok Ghosh ; J. M. Schwarz ; Alison Patteson ; Antun Skanata; |
| 595 | Creating Multi-antibiofilm Therapeutics with Cellulase Based Carbon Dots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we explore the potential of cellulase based carbon dots as a potential therapeutic. |
Gordon Christopher ; Vikram Sawant ; Dimitri Pappas ; Hamed Dari-Sarraf; |
| 596 | Incorporation of Collagen Into Bacterial Biofilms Impedes Phagocytosis By Neutrophils Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use two biofilm-forming human pathogens, Pseudomonas aeruginosa and Staphylococcus aureus, to study the role of incorporated collagen in the immune clearance of biofilms by human neutrophils. |
Xuening Zhou ; Vernita Gordon ; Marilyn Wells ; Hailey Currie; |
| 597 | Climate Change and Crops: How High-performance Modeling of Bacterial-fungi Communities Can Improve Food Security and Biofuel Production in An Ever-changing Climate Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop hybrid continuum-discrete models for physics and biology informed modelling of the complex interactions between microbes and their shared environment. |
Connah Johnson; |
| 598 | Rapid Antibiotic Susceptiblity Test Using White-light Interferometry Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Now we take advantage of the coffee ring effect to develop a novel method of relative cell counting using volume from white light interferometry as a proxy for number of cells. |
Adam Krueger ; Peter Yunker ; Bikash Bogati ; David Weiss; |
| 599 | Using Gnotobiotic Living Food to Study Gut Bacterial Stability in Zebrafish Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Community composition is known to fluctuate strongly, but the factors that set the relevant timescales remain minimally studied due to the difficulty of generating controllable experimental systems, especially in which the role of food ingestion can be separated from the role of microbial input. To address this, we have developed a protocol to eliminate the innate bacteria in the micro-animal rotifers and use them as a nutrient source for zebrafish larvae, a model vertebrate organism. |
Susana Marquez ; Peter Bouchard ; Jonah Sokoloff ; Matthew Bucher ; Carrie McCurdy ; Raghuveer Parthasarathy; |
| 600 | Predicting Metabolic Response to Dietary Intervention Using Deep Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Deep learning methods dedicated to such tasks are still lacking. Here we develop a new method McMLP (Metabolic response predictor using coupled Multilayer Perceptrons) to fill in this gap. |
Tong Wang ; Hannah Holscher ; Sergei Maslov ; Frank Hu ; Scott Weiss ; Yang-Yu Liu; |
| 601 | Uncovering Molecular Mechanisms of Legionnaires’ Disease: Coarse-Grained Martini Simulations of T4SS Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To develop simulations of relevant duration, we built a coarse-grained model using the Martini force field for molecular dynamics in GROMACS. |
Cayson Hamilton ; Gus Hart; |
| 602 | Co-aging Complex Systems: Featuring Infected Worms, Competing Trees and Chess Battles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, hazard curves with peculiar ups and downs have been observed in nature in seeming contradiction with theory. Here we introduce the concept of "co-aging", where the demographics of multiple cohorts are intertwined and show that co-aging dynamics can account for these peculiar bumps empirically observed in mortality curves. |
Cagatay Eskin ; Dervis Vural; |
| 603 | Theoretical Modeling of Sporulation Patterns in Bacillus Subtilis Biofilms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Specifically, the lab strain forms biofilms with mostly matrix-producing cells, whereas the wild strain has matrix-producing cells at the edge of the biofilm and spores in the center. We hypothesize that sporulation in wild isolates occurs via a temporal program, and we develop a model to test whether this hypothesis explains the biofilm structure. |
Meiyi Yao ; Joshua Jones ; Joseph Larkin ; Andrew Mugler; |
| 604 | Condensates in Chromatin Organization and Cancer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce VECTOR (ViscoElastic Chromatin Tethering and ORganization), which uses light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. |
Amy Strom; |
| 605 | Imaging Transcription Condensates in Three Dimensional Genomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report that endogenous YAP forms sub-micron scale condensates in response to Hippo pathway regulation and actin cytoskeletal tension. |
Danfeng Cai; |
| 606 | The Ripening Dynamics of Nuclear Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we show that condensate surface tension and the interplay with chromatin mechanics govern condensate growth in the nucleus. |
Tafadzwa Chigumira ; Deb Banerjee ; Rachel Lackner ; Josiah Kratz ; David Chenoweth ; Shiladitya Banerjee; |
| 607 | Condensate-mediated Chromatin Organization Through Elastocapillary Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we propose a novel computational model for the complex elastocapillary interactions between condensates and fiber networks, augmented experimentally by a set of light-inducible proteinaceous condensates with a wide range of binding affinities to chromatin. |
Hongbo Zhao ; Amy Strom ; Jorine Eeftens ; Natalia Orlovsky ; Mikko Haataja ; Cliff Brangwynne ; Andrej Kosmrlj; |
| 608 | Transcription Factor Clusters As Information Transfer Agents Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present evidence that the nuclear concentration gradient of Bicoid, a central transcription factor driving the anterior-posterior patterning genes during early fly development, is accurately reflected by the sub-nuclear clusters. |
Rahul Munshi ; Sergey Ryabichko ; Michal Levo ; Eric Wieschaus ; Thomas Gregor; |
| 609 | Genomic Clustered Pattern of Transcription Factor Binding Reflects Phase-separated Transcriptional Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we systematically analyzed 528 DNA sequence motifs across the human genome and 6,650 TF binding profiles across different cell types to identify the molecular features contributing to the formation of transcriptional condensates. |
Chongzhi Zang ; Zhenjia Wang ; Shengyuan Wang; |
| 610 | The Transcription Factor TEAD1 Forms Repressive Biomolecular Condensates in Renal Cell Carcinomas Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have found that in certain patient-derived RCC cell lines with high levels of YAP1 and TEAD1 expression, TEAD1 forms atypical large nuclear foci, distinct from normal kidney cells and other subtypes of RCC. |
Jindayi Liang ; Danfeng Cai ; Justin Demmerle; |
| 611 | Chromatin Heterogeneity Modulates Nuclear Phase Behavior and Condensates Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we employ an optogenetic oligomerization system to investigate the role of the chromatin network in the phase separation dynamics within living cell nuclei. |
Jing Xia ; Cliff Brangwynne; |
| 612 | Spatial Organization of Regulatory Chromatin At Transcription Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Many biomolecular condensates associate with specific chromatin loci in the cell nucleus. Transcription condensates in mouse embryonic stem cells are thought to form at … |
Jan-Hendrik Spille ; Ganesh Pandey ; Jonah Galeota-Sprung ; Filmon Medhanie ; Alisha Budhathoki; |
| 613 | Mechanisms of Sensitive and Selective Nucleation of Chromatin-associated Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the biophysical mechanisms by which such spatial control is achieved remain poorly understood. To address this question, we present an experimentally motivated coarse-grained model of a class of transcriptional condensates that are believed to play a role in initiating DNA transcription. |
Yury Polyachenko ; Hans-Frederick Watanabe ; William Jacobs; |
| 614 | Role of Electrostatics and Phase Separation in Regulation of Gene Expression in Escherichia Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we explore the role of nucleoprotein phase separation on the dynamics of mRNA translation by the ribosomal machinery. |
Vishal Sankar Sivasankar ; Gesse Roure ; Roseanna Zia; |
| 615 | Functional Block Copolymer Gyroidal Hybrid Nanomaterials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk will discuss block copolymer self-assembly directed hybrid materials with double and single gyroid morphologies. |
Ulrich Wiesner; |
| 616 | Stabilizing Gyroid Structures By Blending or Asymmetry of High-χ Oligomers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work provides molecular-level insights into how blending and asymmetry of shape-filling molecular architectures enables network phase formation with extremely small feature sizes over a wide composition and volume fraction ranges. |
J. Ilja Siepmann ; Daoyuan Li ; Caini Zheng ; Mahesh Mahanthappa ; Timothy Lodge ; Zhengyuan Shen; |
| 617 | Gyroid Materials: Triply Periodic Minimal Surfaces, Skeletal Graphs, Mesoatoms and Crystallographic Defects Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Triply periodic minimal surfaces (TPMS) have zero mean curvature and their associated constant mean curvature families are all quite good structural models for many … |
Edwin Thomas; |
| 618 | Conformational and Topological Correlations in The Gyroid Morphology Formed By Non-frustrated Triblock Copolymers with Homopolymers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate whether the stability of the gyroid phase can be improved by relieving the packing frustration using homopolymers. |
Natalie Buchanan ; Krysia Browka ; Lianna Johnson ; Hillary Le ; Poornima Padmanabhan; |
| 619 | Metastable Network Phases from Controlled Self-Assembly of High-χ Block Copolymers for Biomimetic Materials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, this work aims to suggest a facile method for acquiring network phases from self-assembly. |
Rong-Ming Ho; |
| 620 | How Does Your Gyroid Grow? A Mesoatomic Perspective on Supramolecular, Soft Matter Network Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I describe a proposed framework for understanding the structure of supramolecular network crystals formed in soft matter in terms of mesoatomic building blocks, collective groupings of amphiphilic molecules that play a role analogous to atomic or molecular subunits of hard matter crystals. |
Gregory Grason; |
| 621 | Programmable Self-Assembly of Nanoplates Into Bicontinuous Nanostructures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, we demonstrate coarse-grained Monte Carlo simulations showing self-assembly of hexagonal/triangular nanoplates via complementary interactions into facetted, sponge-like "bicontinuous polyhedra" whose flat walls partition space into a pair of mutually interpenetrating labyrinths. |
Tomonari Dotera ; Hideaki Tanaka ; Stephen Hyde; |
| 622 | "Inverting" Caspar-Klug Design Rules for Programmable Assembly of Size-controlled Minimal-surface Assemblies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply-periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. |
Christian Santangelo ; Carlos Duque ; Douglas Hall ; Botond Tyukodi ; Michael Hagan ; Gregory Grason; |
| 623 | A Multiscale Molecular Simulation Approach to Designing DNA Decorated Colloids for Double Gyroid Self-Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Gyroidal sructures are of interest for different applications, which has fueled interest in developing different types of building blocks to achieve them. Inspired by previous modeling studies, in this simulation work we focus on developing colloidal particles as building blocks and take advantage of hybridizing DNA strands grafted to nanoparticle surfaces to design effective interactions that lead to the self-assembly of the double gyroid phase. |
Luis Nieves Rosado ; Fernando Escobedo; |
| 624 | Oral: Role of Interaction Range on The Microstructure and Dynamics of Attractive Colloidal Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using molecular simulations, we explored the effect that the range of attractions has on the microstructure and dynamics of both weakly and strongly attractive colloidal systems. |
Deepak Mangal ; Safa Jamali; |
| 625 | Theoretical Results for The Gyroid Wire System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discuss the classical and non-commutative geometry of wire systems which are the complements of triply periodic surfaces. |
Birgit Kaufmann ; Ralph Kaufmann ; Sergei Khlebnikov; |
| 626 | Disconnectivity Graphs of Spin Glass Systems on Snub Archimedean ($3^2$, 4, 3, 4 ) Lattices Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use augmented disconnectivity graphs to visualize and analyze the energy landscapes of small spin systems confined to Snub Archimedean lattices of type ($3^2$,4,3,4). |
Anil Katwal ; Katja Biswas; |
| 627 | Locomotion of Flagellated Bacteria: The Influence of Complex Fluids and The Role of Multiflagellarit Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I discuss two recent experimental works in my group on the fascinating swimming behaviors of a prominent example of flagellated bacteria, Escherichia coli. |
Xiang Cheng; |
| 628 | Self-Regulation of Minimal Contractile Active Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we perform fluorescence microscopy assays on a minimal system of stabilized filaments and molecular motors. |
Daisy Achiriloaie ; Claire Benjamin ; K. Alice Lindsay ; Jennifer Ross ; Janet Sheung; |
| 629 | Analysis of Elastic Strains Reveals Shape Selection Pathways in Active Gels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Future work will reveal how the in-plane strain distribution determines the final 3D buckled shapes. |
Subhaya Bose ; Sakshi Choudhary ; Shachar Gat ; Gefen Livne ; Dina Aranovich ; Anne Bernheim-Groswasser ; Kinjal Dasbiswas; |
| 630 | Heterogenous Population of Kinesin-Streptavidin Complex Revealed By Mass Photometry Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we employ mass photometry, a label-free single-molecule technique, to determine the mass of individual kinesin-streptavidin complexes in solution. |
Nathaniel Brown ; Jing Xu ; Yeonee Seol ; Keir Neuman; |
| 631 | Organization of Cytoskeletal Networks Creates Non-Equilibrium Energy Gradients Through Space and Time Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To gain insight into the energetic cost of structure formation, we investigate the assembly of an ordered aster from a disordered, uniform mixture of microtubules and kinesin motors. |
Ana Duarte ; Heun Jin Lee ; Rachel Banks ; Soichi Hirokawa ; Bibi Najma ; Vahe Galstyan ; Catherine Ji ; Victor Gomez ; Mohammadamin Tajik ; Minakshi Ashok ; Henk Postma ; Matt Thomson ; Rob Phillips; |
| 632 | Activity-driven Phase Transition Causes Coherent Flows of Chromatin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. |
Iraj Eshghi ; Alexandra Zidovska ; Alexander Grosberg; |
| 633 | Microtubule-based Unidirectional Pumping in Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use two and three-dimensional discrete and coarse-grained biophysical models to study unidirectional streaming through tube-like connectors between cells, such as ring canals in Drosophila egg chambers. |
Ebrahim Kolahdouz ; David Stein ; Stanislav Shvartsman ; Michael Shelley; |
| 634 | Controlling An Elastic Network’s Structure, Mechanics and Dynamics with An Active Fluid Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate the behavior of actin networks whose assembly is driven by turbulent-like flows generated by extensile microtubule-kinesin active fluids. |
Sattvic Ray ; John Berezney ; Itamar Kolvin ; Zvonimir Dogic; |
| 635 | Shape Change and Orientational Order in Contractile Active Gels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Biological active gels comprising cytoskeletal filaments and molecular motors can show complex shape changes driven by mechanical forces. Here, we consider a general theoretical model for the feedback between active forces (generated by molecular motors such as myosin) and orientational order of fibers (such as actin bundles). |
Arnab Roy ; Kinjal Dasbiswas; |
| 636 | Dynamics of Passive and Active Microtubules in Entangled Actin Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: They escape their effective cage by passive diffusion along their long axis. We study these escape dynamics by visualizing 3D trajectories of individual microtubules confined in a network of semiflexible actin filaments. |
Isabel Ruffin ; Zvonimir Dogic; |
| 637 | Form Follows Function – Morphodynamics in Single-celled Algae Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study shows how topologically complex metamaterials are applied in critical life-sustaining processes in nature and that simple dynamical rules can account for complex material transport in a crowded intracellular environment. |
Nico Schramma ; Gloria Canales ; Maziyar Jalaal; |
| 638 | Pattern Formation in Active Droplets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We report active analogs of the viscous fingering and Rayleigh-Plateau instabilities in passive liquids: activity competes against surface tension to destabilize the interface. |
Bennett Sessa ; Guillaume Duclos; |
| 639 | Geometric Computation of Finite, Disordered Mineral Lattices Through Topologically Complex Active Confinements Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This wrapping restricts transport of mineral precursors through microtubule networks along the surface of the existing geometry, thus coupling shape and material transport. The continuous extension of this wrapping around growing tips makes growth of actin filament based membranous projections possible. |
Pranav Vyas ; Charlotte Brannon ; Laurent Formery ; Christopher Lowe ; Manu Prakash ; Manu Prakash; |
| 640 | Learning The Shape of The Immune and Protein Universe Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will introduce physically motivated machine learning approaches to learn representations of protein micro-environments in general, and of immune receptors, in particular. |
Armita Nourmohammad ; Michael Pun ; Gian Marco Visani ; Andrew Ivanov ; Quinn Bellamy ; Zachary Montague ; Colin LaMont ; Philip Bradley ; Jakub Otwinowski ; Arman Angaji; |
| 641 | Learning Evolutionary Parameters from B-cell Lineage Trees Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite its significance, current methods face limitations: they often do not extend beyond neutrality, and there is a lack of reliable summary statistics for discerning non-neutral evolutionary processes. To address this issue, we construct mathematical models that capture the dynamics of proliferating cell populations undergoing non-neutral mutations, and, informed by these models we develop an expectation maximisation inference scheme to learn the parameters of selection from data. |
Antoine Aragon ; Aleksandra Walczak ; Thierry Mora ; Amaury Lambert; |
| 642 | Biophysical Modeling for Accurate and Efficient Predictions of T Cell-antigen Specificity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we describe insights derived from our random energy models focused on mapping the TCR-antigen contact interface. |
Jason George; |
| 643 | How Different Are Self and Nonself? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In contrast to other examples, we show that the distributions of self and nonself peptides are nearly identical but strongly inhomogeneous. |
Benjamin Greenbaum ; Andreas Mayer ; Christopher Joel Russo ; Quentin Marcou ; William Bialek; |
| 644 | Signatures of Functional Immune Responses to Acute and Chronic COVID-19 Infections Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To describe those differences, we focus on the adaptive immune response to COVID-19. |
Rhea Grover ; Zachary Montague ; Assya Trofimov ; Andrew Baumgartner ; Jennifer Hadlock ; Armita Nourmohammad; |
| 645 | Optimizing Multi-Dose Vaccination Protocols for Enhanced Viral Infection Defense Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we present a computational model for antibody generation in response to multi-dose vaccination regimens, employing a stochastic simulation that encompasses the dynamics within both germinal and extra-germinal centers. |
Saeed Mahdisoltani ; Sam Melton ; Mehran Kardar ; Arup Chakraborty; |
| 646 | Real-time Immune Recognition in A Primary Acute Infection Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show that B-cells can efficiently recognise antigens by a kinetic proofreading mechanism that is tuned to the complexity of the immune repertoire. |
Roberto Morán-Tovar ; Michael Lässig; |
| 647 | Dynamic Role of T Follicular Helper Cells in Shaping B Cell Affinity Maturation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How does this dynamic behavior of TFH cells influence B cell affinity maturation? To address this question, we developed a population dynamics model which explicitly incorporates TFH cell properties and proliferation. |
Andrew Pyo ; Julia Merkenschlager ; Ned Wingreen; |
| 648 | Computational HLA Typing from Repertoires Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we analyze the TCR alpha and beta repertoires of large cohorts of HLA-typed donors to systematically infer such associations, by looking for overrepresentation of TCRs in individuals with a common allele. We describe the sequence features of these HLA-associated TCRs. |
Maria Ruiz Ortega ; Thierry Mora ; Aleksandra Walczak ; Mikhail Pogorelyy ; Anastasia Minervina ; Paul Thomas; |
| 649 | Computational Detection of Antigen-specific B-cell Receptors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, a fundamental question remains: to what extent can we accurately identify antigen-specific sequences within the extensive BCR repertoire, since only a minor fraction of these receptors actively participate in any given infection? To address this challenge, we present a computational method grounded on sequence similarity, aimed at identifying statistically significant responsive BCRs. |
Maria Francesca Abbate ; Aleksandra Walczak ; Thierry Mora ; Melody Shahsavarian; |
| 650 | Binding Affinity Landscapes of Broadly Neutralising Antibodies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explored the landscapes of two key bnAbs, CR9114 and CR6261, by measuring the binding affinity over 100,000 antibody variants against a panel of antigens. |
Thomas Dupic ; Angela Phillips ; Alief Moulana ; Michael Desai ; Katherine Lawrence ; Thierry Mora ; Aleksandra Walczak; |
| 651 | T Cells Function and Similarity- Predictions from Statistical and Network Analysis of The Immune Repertoire Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present a novel approach to study the connection between sequence similarity and functional similarity, based on data of reactive T cells from mice and patients. |
Yuval Elhanati ; Benjamin Greenbaum ; Andreas Mayer; |
| 652 | Immune Control of The Gut Microbiota Via Avoidance and Tolerance Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a generalized consumer-resource model coupled with a model for the tolerogenic and humoral immune responses, we investigate how host-supplied nutrients impact the composition of commensal microbes in the gut, and how in turn the microbial ecology can confer a metabolic benefit to the host. |
Obinna Ukogu ; Armita Nourmohammad; |
| 653 | Dynamic Energy Allocation Model for Microbial Growth Control and Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To quantitatively understand how unicellular organisms utilize their resources in response to changes in their environment, we introduce a theory of dynamic energy allocation which describes microbial growth dynamics based on partitioning of metabolizable energy into key physiological functions: growth, division, cell shape regulation, energy storage, and loss through dissipation. |
Arianna Cylke ; Diana Serbanescu ; Shiladitya Banerjee; |
| 654 | Interplay Between Metabolism, Growth Rate, and Physical Properties of The Cytoplasm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The relationships between the physical properties of the cytoplasm and metabolism, growth rate, and cell cycle progression remain unexplored. Here, we study these relationships in response to nutritional changes in the fission yeast Schizosaccharomyces pombe. |
Arthur Molines ; Fred Chang; |
| 655 | The Physiological Origin of Bacterial Growth Rate Variations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Glucose, for example, is not always a "good" carbon source promoting fast growth. Utilizing biochemical assays and mass-spec methods, we show that this variation is not due to differences in the overall ability of strains to promote protein synthesis and biomass accumulation. |
Jonas Cremer ; Richa Sharma ; Griffin Chure; |
| 656 | Biomass Transfer and Autocatalytic Waiting Time on Growing Reaction Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, I analyzed biomass transfer process on scalable reaction networks [1]. |
Wei-Hsiang Lin; |
| 657 | Resource Optimization in Protein Synthesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Consequently, there is a compelling argument for a more pronounced selection pressure aimed at optimizing ribosome utilization over translation efficiency. Our research presents strong evidence of this optimization, particularly in the context of highly expressed transcripts that place a substantial demand on cellular resources. |
Ajeet Sharma; |
| 658 | Nutrient Transport Shapes Antibiotic Efficacy in Structured Bacterial Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we develop an experimentally tractable system to investigate the synergistic effects of nutrient (glucose) and antibiotic (fosfomycin) gradients on structured bacterial ( E. coli) populations in real-time with confocal microscopy. |
Anna Hancock ; Arabella Dill-Macky ; Jenna Ott ; Catherine Day ; Mohamed Donia ; Sujit Datta; |
| 659 | Motility Turns Sour: Glucose Fermentation By Dense Suspensions of Escherichia Coli Results in Metabolic Shutdown and Prevents Swimming Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the motility of dense suspensions of Escherichia coli supplied with abundant sugar in anaerobic conditions. |
Lucas Le Nagard ; Jana Schwarz-Linek ; Ekaterina Krasnopeeva ; Carine Douarche ; Jochen Arlt ; Angela Dawson ; Vincent Martinez ; Wilson Poon ; Teuta Pilizota; |
| 660 | Does Hyperosmotic Stress Reduce Bacterial Growth Rate By Decreasing Enzymatic Velocity? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present evidence that, unlike changes in the nutrient environment, osmotic stress does not significantly affect the ribosomal content, and instead leads to a reduction in the rate of enzymatic activity. |
Mark Zurbruegg ; Hiroyuki Okano ; Zhongge Zhang ; Keiran Stevenson ; Matt Scott ; Terence Hwa ; Teuta Pilizota; |
| 661 | Determining Limiting Processes of Bacteriophage Growth By Varying Ribosome Content of Bacterial Hosts Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A delay differential model has been applied to predict the relationships between ribosome-dependant and independent variables for one to dominate phage growth over the other. |
Eric Chapman ; Aidan Brown ; Teuta Pilizota; |
| 662 | Modeling Selection Mechanisms for for Quality Control of Mitochondrial DNA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use theoretical methods to compare experimental data, including generational mutation levels from fruit flies, to predictions from proposed quality control mechanisms. |
Eshan Merali ; Aidan Brown ; Thomas Hurd; |
| 663 | Design Principles of Cdr2 Node Patterns in Fission Yeast Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combined experimental and modeling approaches to investigate pattern formation by the Pom1-Cdr2 system. |
Shuhan Geng ; Hannah Opalko ; Aaron Hall ; Dimitrios Vavylonis ; James Moseley; |
| 664 | The Three-dimensional Architecture of The Human Genome: Understanding The Physical Mechanisms Controlling Gene Expression Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. This model was generalized by utilizing a neural network to infer these chromatin types using epigenetic marks present at a locus, as assayed by ChIP-Seq. |
Jose Onuchic; |
| 665 | Machine Learning-based Parametrization of A Chromatin Polymer Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop an approach to train the GNN using exclusively simulated data from the polymer model, avoiding the need for large quantities of experimental data. |
Eric Schultz ; Soren Kyhl ; Rebecca Willett ; Juan De Pablo; |
| 666 | From Effective Interactions Extracted Using Hi-C Data to Chromosome Structures in Conventional and Inverted Nuclei Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Such an unusual organization of chromosomes is found in the inverted nuclei of photoreceptor rods in nocturnal mammals. The proposed method without free parameters and its applications show that compartment formation in conventional and inverted nuclei is best explained by the inequality between the effective interaction energies, with heterochromatin attraction being the dominant driving force. |
Sucheol Shin ; Guang Shi ; Devarajan Thirumalai; |
| 667 | Illuminating The Link Between Nuclear Geometry and Chromatin Structure Dynamics Through 4D Nucleus Modeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a mesoscale liquid model of the nucleus called MELON-4D, which describes the state of the nucleus as a mixture of incompressible multiphase liquid-like chromatin types. |
Rabia Laghmach ; Michele Di Pierro ; Davit Potoyan; |
| 668 | Data-Driven Simulation of Chromatin Structure and The Epigenetic Code Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a chromosome scale model to study the relationship between one-dimensional epigenetic sequences and three-dimensional chromatin structure. |
Soren Kyhl ; Juan De Pablo; |
| 669 | A Wave Pinning Model for Spread of Chromosomal Inactivation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we formulated a wave pinning model that elucidates chromosomal inactivation through a bistable reaction-diffusion system. |
Shibashis Paul ; Tian Hong; |
| 670 | Activity-driven Chromatin Organization During Interphase: Compaction, Segregation, and Overlap Suppression Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work provides a theoretical basis for the compact organization of interphase chromatin explaining the physical reason for segregation of TADs and suppression of chromatin entanglements which contribute to efficient gene regulation. |
Brian Chan ; Michael Rubinstein; |
| 671 | Cohesin Distribution Encodes Chromatin 3D Organization Via Conserved-current Loop Extrusion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To extend the LEF model across the tree of life, we propose the conserved-current loop extrusion (CCLE) model that interprets loop-extruding cohesin as a nearly-conserved probability current. |
Tianyu Yuan ; Hao Yan ; Kevin Li ; Ivan Surovtsev ; Megan King ; Simon Mochrie; |
| 672 | Loop Extrusion with Dynamic Barriers Explains Genome Folding for Long-lived Cohesin Mutants Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While existing polymer physics models successfully reproduce certain features of contact maps, they do not account for recent observations of CTCF binding dynamics. Motivated by these findings, we propose a model where boundary elements dynamically switch between bound and unbound states, with rates parametrized from recent biophysical data. |
Hadi Rahmaninejad ; Maxime Tortora ; Geoffrey Fudenberg; |
| 673 | Polymer Loop Extrusion with Motor-motor Bypassing Can Explain Mitotic Chromosome Elasticity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We performed polymer simulations to investigate the chromosomal mechanical properties that emerge from loop extrusion. |
Edward Banigan ; John Marko ; Leonid Mirny; |
| 674 | Phage and Bacteria: Competition and Coexistence Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe a mathematical model demonstrating that phage coexistence is a natural outcome of chaotic dynamics arising from competition among multiple phage and their bacterial hosts. |
Ofer Kimchi; |
| 675 | Illuminating Cellular Individuality Through Bacteriophage Infection Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this effort, the process bacteriophage infection again provides us with an ideal opportunity. |
Ido Golding; |
| 676 | Prophages Exploit Bacterial Communication to Modulate Antiviral Defence Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Bacteria possess a diverse array of defences that protect them from their viral predators, known as phages. While these defences provide a selective advantage in the presence of … |
Karen Maxwell; |
| 677 | The Art of Being Sloppy: Stochasticity As An Evolutionary Trait in Phage Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Surprisingly, in contrast to model expectations and previous similar experiments that predict a decrease in adsorption rate, our evolved lines fail to show any significant or consistent change in life history parameters bringing into questions both the assumptions underneath current models and the experimental methods we use to assess phage-bacteria interactions. |
Diana Fusco; |
| 678 | Biophysics of Phage-bacteria Evolutionary Interactions in Context of Patient Therapy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk presents our method for high-throughput quantification of phage adsorption to host cells, to test hypotheses concerning evolved changes in phage-bacteria interactions. |
Paul Turner; |
| 679 | Breaking Symmetry in Self-assembled, Triply-periodic, Supramolecular Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We turn to a recently-developed, pseudo-mechanical model of BCP network deformations, "liquid network theory," which is able to capture key elements of network response, including non-affinity, strut length variations, and mass transport. Using comparisons with molecular theory and experiments, we show how this relatively simple construction captures the complex, coordinated motion of macromolecules under different deformation protocols. |
Michael Dimitriyev ; Xueyan Feng ; Edwin Thomas ; Gregory Grason; |
| 680 | The Effect of Orientation in Double-Gyroid Thin Films Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To better understand the effect of thin-film confinement on the DG phase, we use self-consistent field theory to compute the equilibrium morphology and energetics of DG thin films confined between non-preferential walls. |
Benjamin Magruder ; David Morse ; Christopher Ellison ; Kevin Dorfman; |
| 681 | Shine on You Crazy Gyroid: Lessons from Birds, Butterflies and Beetles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using synchrotron Small Angle X-ray Scattering (SAXS), we have unambiguously elucidated the nanoscale organization of biophotonic nanostructures across hundreds of species and discovered the enigmatic single network gyroid photonic crystals within wing scales of butterflies 1, beetles 2 and more recently in the feather barbs of some birds 3. |
Vinodkumar Saranathan ; Eric Dufresne ; Richard Prum; |
| 682 | Molecular Dynamics Simulation of Guerbet Glycolipid Self-assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Overall, this work provides an atomistic perspective of glycolipid self-assembly, shedding light on the packing mechanism in amphiphiles. |
Caini Zheng ; Soumi Das ; Michelle Calabrese ; Theresa Reineke ; Mahesh Mahanthappa ; Timothy Lodge ; J. Ilja Siepmann; |
| 683 | Łucja Kowalewska (Gyroid Focus Session)Gyroid- and Diamond-Type Membrane Configurations of Plants – Where Geometry Defines The Biological Function Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In my talk, I will present how we recognize and annotate cubic assemblies using our SPIRE software tool, which enables the identification of bicontinuous membrane structures from TEM sections through interactive matching by comparison to mathematical “nodal surface” models. |
Łucja Kowalewska; |
| 684 | Reformulation of Elasticity Theory for Lipid Membranes, with Implications for Gyroid Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we suggest a mathematical reformulation of the theory, which writes the free energy as the sum of squares of two modes. |
Jonathan Selinger; |
| 685 | Predicting Surfactant Phase Behavior from Molecularly Informed Field Theories Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The resulting molecularly-informed field theory can then be simulated with the mean-field approximation to efficiently determine the stable surfactant mesophases. In this project, we will demonstrate how we apply this multiscale methodology to predict surfactant solution phase behavior for several, well-studied surfactants de novo and obtain qualitative agreement with experimentally observed phase behavior. |
David Zhao ; Steven Arturo ; M. Scott Shell ; Glenn Fredrickson; |
| 686 | Analysis of Stability of Cylindrical Multicomponent Vesicles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we inspect the linear stability of a cylindrical vesicle with multiple phospholipids on the surface undergoing phase separation and diffusion. |
Anirudh Venkatesh ; Aman Bhargava ; Vivek Narsimhan; |
| 687 | Bacterial Vesicle Production Scales with Outer Membrane to Cell Wall Crosslink Density Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we examine how vesicle production scales with the number of crosslinkers tethering the outer membrane to the cell wall. |
Brian Weaver ; Fengjie Zhao ; Christoph Haselwandter ; James Boedicker; |
| 688 | Network Statistics of The Whole-Brain Connectome of Drosophila Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: With the completion of the Flywire project, we now have access to the connectome of a complete adult Drosophila brain, containing 130,000 neurons and millions of connections. Here, we present a statistical summary and data products of the Flywire connectome, delving into its network properties and topological features. |
Albert Lin ; Runzhe Yang ; Sven Dorkenwald ; Arie Matsliah ; Amy Sterling ; Philipp Schlegel ; Szi-chieh Yu ; Claire McKellar ; Marta Costa ; Katharina Eichler ; Alexander Bates ; Nils Eckstein ; Jan Funke ; Gregory Jefferis ; Mala Murthy; |
| 689 | Modulation of Brain Waves Via Auditory Stimuli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For this purpose, we used the electroencephalogram (EEG) device from BIOPAC with three different recording channels. |
Maximus London-Kolb ; Sorinel Oprisan; |
| 690 | A Convolutional Neural Network for Seizure Prediction Using Synthetic and Electrocorticographic Intracranial Data Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine intracranial electrocorticographic recordings possessing high temporal resolution from a patient database with synthetically created data to train a convolutional neural network. |
Louis Nemzer; |
| 691 | Comparative Analysis of Embolism Dynamics in Biomimetic Models and Adiantum Leaves Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study reveals that the intermittent, or jerky, propagation patterns observed in Adiantum leaves can be replicated in biomimetic veins through the incorporation of constrictions that simulate membrane pits found in natural leaves. |
Ludovic Keiser ; Benjamin Dollet ; Philippe Marmottant; |
| 692 | Air Invasion in A Transpiring Biomimetic Leaf-on-chip Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: During this presentation, I will demonstrate the propagation of embolism within a more complex biomimetic network that emulates diverse leaf venation patterns. |
François-Xavier Gauci ; XAVIER NOBLIN ; Ludovic Keiser ; Céline Cohen ; Philippe Marmottant ; Benjamin Dollet; |
| 693 | Mechanical Memory in Plants: Insights from Mimosa Pudica Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We perform a behavioral assay on Mimosa pudica plants using a controllable electrical stimulation setup to investigate how the plants’ leaf-folding response varies with stimulation intensity and frequency. |
Chantal Nguyen ; Patricia Mendoza-Anselmi ; Orit Peleg; |
| 694 | Unveiling Decentralized Feedback Mechanisms in Sea Star Locomotion Using Deep Reinforcement Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a decentralized control framework where individual tube feet have local autonomy over their actuation, via peripheral sensori-motor feedback loops. |
Sina Heydari ; Josh Merel ; Matthew McHenry ; Eva Kanso; |
| 695 | Selective Social Interactions and Speed-induced Leadership in Schooling Fish Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce a force map technique suitable for the analysis of velocity alignment interaction. |
Andreu Puy ; Palina Bartashevich ; Elisabet Gimeno ; Jordi Torrents ; M. Carmen Miguel ; Romualdo Pastor-Satorras ; Pawel Romanczuk; |
| 696 | Inoculum-dependent Instability of A Biofilm Pellicle Is Rescued By Non-biofilm Formers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Although genetic factors that drive pellicle formation, such as extracellular matrices and fimbriae, have been extensively investigated, no clear understanding of the spatio-temporal dynamics has been achieved. In this work, combining experimental and computational approaches, we studied the physical principle of bacterial colonization at an air-liquid interface and its ecological and evolutionary implications. |
Yuya Karita ; Gisela Rodríguez-Sánchez ; Elisa Brambilla ; J. Carlos Hernandez-Beltran ; Michael Schwarz ; Paul Rainey; |
| 697 | Modulating The Living Cell Dynamics By Surface Functionalization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work aims at elucidating the relation between adhesion and collective migration, while also providing a useful platform to tune cell migration. |
Prasoon Awasthi ; Kirsten Endresen ; Aniruddh Murali ; Francesca Serra; |
| 698 | Balancing Reaction-diffusion Network for Cell Polarization Pattern with Stability and Asymmetry Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Interestingly, the combination of two of those unbalanced modifications can stabilize the polarized pattern. To test if this fundamental rule governs the network programming in the real system, we conduct an elaborate literature search to reconstruct the cell polarization network in the nematode Caenorhabditis elegans zygote, where a 4-node network with full mutual inhibitions between anterior and posterior is modified by a mutual activation in the anterior and an additional mutual inhibition between the anterior and the posterior, constituting a 5-node network. |
Yixuan Chen ; Guoye Guan ; Lei-Han Tang ; Chao Tang; |
| 699 | Long-Range Repulsion Between Chromosomes in Mammalian Oocyte Spindles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work highlights the surprising relevance of materials physics in understanding the structure, dynamics, and mechanics of cellular structures, and presents a novel and potentially generic mode of chromosome self-organization in large spindles. |
Colm Kelleher ; Daniel Needleman; |
| 700 | The Flow Patterns of Ink Released By Cuttlefish Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we observe live cuttlefish inking and mimic the process with a table-top. |
Yu Ting Lin ; I Hsuan Chen ; Patricia Yang; |
| 701 | Malignant Brain Tumors Behave in Vivo As Liquid Crystals: Quasi Long-range Nematic Order and Topological Defects Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work will define the role of liquid crystal organization as novel physical structures in GBM, eventually leading to the development of therapeutic strategies targeting the structure underlying brain tumor organization, namely, the liquid crystalline order. |
Pedro Lowenstein ; Anna Argento ; Maria Luisa Varela ; Marta Edwards ; Carles Blanch-Mercader; |
| 702 | Modeling Cell Division-Induced Motion in Cell Aggregates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop a novel deformable particle model for cell division, which includes cell-cell adhesion and energy costs for changes in cell area and perimeter in two dimensions (2D). |
Emmanuel Mintah ; Mark D Shattuck ; Corey O’Hern; |
| 703 | Curious Run-and-Tumble Behavior in Multicellular Organisms on The Water’s Surface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our findings extend the concept of "run-and-tumble" to macroscopic organisms, offering insights into its evolutionary advantages. This research has implications for the development of search robots mimicking this efficient movement strategy and suggests a unifying principle behind "run-and-tumble" motion across different length scales. |
Ishant Tiwari ; Nithil Nagappan ; Jacob Harrison ; Saad Bhamla; |
| 704 | Spatio-temporal Dynamics of Nutrient Exchanges in Microbial Active Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Even in their simplest arrangement in a localized illuminated domain, we find a complex dynamics involving nutrient exchanges, enhanced algal diffusivity due to the bacteria, and a stochastic version of “flux expulsion”. |
Praneet Prakash ; Raymond Goldstein; |
| 705 | Understanding The Collective Chemotactic Behavior of Malignant Lymphocyte Clusters Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This distinct collective behavior is not well understood and is linked to the increased metastatic potential of lymphocyte clusters over that of individual cells. To understand these cluster dynamics, we develop an agent-based model that incorporates contact inhibition, adhesive interactions, and gradient sensing capabilities. |
Monika Sanoria ; Ajay Gopinathan ; Nir Gov; |
| 706 | Universal Distribution of Cell Shapes in Active Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use agent-based modeling of cells as deformable particles, to explore the distribution of cell shapes in active-driven systems. |
Mark D Shattuck ; Corey O’Hern ; Andrew Ton; |
| 707 | Chaos of Cardiac Tissue Under Periodic Stimuli and Fibrillation: Experiments and Control Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study aims to both quantify and qualify the chaotic nature of cardiac tissue from the system’s arrhythmic electrical response to fast periodic forcing. |
Mikael Toye ; Conner Herndon ; Molly Halprin ; Eva Greiner ; Carolyn Martsberger ; Flavio Fenton; |
| 708 | Surface Chemistry Influence on Orientations, Contact Area, and Deformation of Adhering E. Coli Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Motivated by the significant role of cell adhesion in biofilm formation, we investigated the impact of surface chemistry starting at the single-cell level. |
Zhou Xu ; Wuqi Niu ; Sloan Siegrist ; Mark Tuominen ; Maria Santore; |
| 709 | Flying Fish Taxiing on The Water’s Surface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we investigate the tail-slapping frequency of flying fish experimentally and theoretically. |
Hao-Ping Wang ; Yun-Jhe Li ; Patricia Yang; |
| 710 | Chemical Gradients Coupled to Self-generated Flow Exhibit Large-scale Pattern Formation in Active Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate the mechano-chemical coupling between spatial distributions of energy sources and self-organized flows. |
Alana Hartsell-White ; Isabel Ruffin ; John Berezney ; Seth Fraden ; Zvonimir Dogic; |
| 711 | Principles of Cellular Behavior: Integrating Cellular Structure, Dynamics, and Decision Making Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Although it may be easy to think of cells as the simple building blocks of more complex organisms such as animals, single cells are capable of remarkably sophisticated behaviors … |
Ben Larson; |
| 712 | Three Ways to Control Dynamical Systems Robustly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I review three classes of strategies for controlling dynamical systems robustly: feedforward, feedback, and worst case. |
John Bechhoefer; |
| 713 | Controlling The Nonlinear Configuration Space of Mechanical and Dynamical Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, knowledge of these maps is made difficult due to the nonlinearities in both the interactions and the functions. In this talk, I will discuss several strategies for how to obtain these maps to wield control over the nonlinear configuration space. |
Jason Kim; |
| 714 | Bounds on Information Transfer for Stabilization of Insect Flight Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Many insects are passively unstable in flight, requiring active control to remain stable. In the fly, an organ called the haltere measures angular velocities and provides fast … |
Nick Weaver ; Benjamin Machta ; Henry Mattingly ; Bradley Dickerson; |
| 715 | Nonlinear Effects of Electrical Stimulation Strength on Tissue-scale Collective Migration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Thus, approaches to formally control the many cells within a tissue as a group are quite valuable, necessitating new control frameworks suitable for large-scale agent-based systems. We have been developing a unique approach to do this in living tissues that harnesses a natural process called electrotaxis—directed cell migration to ionic currents/DC electric fields. |
Jeremy Yodh ; Yubin Lin ; Daniel Cohen; |
| 716 | Nonequilibrium Free Energy Calculations from Time-reversed Path Ensembles Through Stochastic Optimal Control Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our work, we build from Jarzynski’s observed connection between time-reversed driven trajectory ensembles and statistically optimal nonequilibrium averages [C. Jarzynski, Phys. |
Jorge Rosa-Raíces ; David Limmer; |
| 717 | Curiosity-driven Discovery of Novel Non-equilibrium Behaviors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine active and unsupervised learning for automated exploration of novel behaviors in non-equilibrium systems with unknown order parameters. |
Martin Falk ; Arvind Murugan ; William Gilpin ; Finn Roach; |
| 718 | Chemomechanical Sensing and Feedback in Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In my talk, I distinguish between exogenous and endogenous control of active materials and discuss the role each has in developing self-regulating materials. |
Michael Norton ; Piyush Grover; |
| 719 | Spatiotemporal Control of 2D Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we examine how spatiotemporal patterns of activity affect the dynamical organization of a model two-dimensional active nematic. |
John Berezney ; Katsu Nishiyama ; Michael Norton ; Zvonimir Dogic ; Seth Fraden; |
| 720 | Optimal Boundary Control of A Model Thin-Film Fiber Coating Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we consider control of a fluid film on a solid vertical fiber, where the fiber radius is larger than the film thickness. |
Shiba Biswal; |
| 721 | Network Control of Jammed Materials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In general, this work demonstrates that network control theory is a promising mathematical framework for predicting and designing yield behavior in disordered media. |
Erin Teich ; Jason Kim ; Dani Bassett; |
| 722 | Predicting Gene Level Sensitivity to JAK-STAT Signaling Perturbation Using A Mechanistic-to-machine Learning Framework Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed a computational framework to make global cytokine-induced gene predictions from STAT phosphorylation dynamics, modeling macrophage responses to IL-6 and IL-10, which signal through common STATs, but with distinct temporal dynamics and contrasting functions. |
Rachel Gottschalk; |
| 723 | Constraints on Pathogen Evolution from Order-dependent Immunity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we propose a model of pathogen evolution which incorporates OAS into assumptions about immune memory creation and cross-protection. |
Lauren McGough ; Sarah Cobey; |
| 724 | Bacterial Modulation of Intestinal Motility Through Macrophage Redistribution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The connection between bacterial components and host mechanical response, however, has remained unclear. Through live imaging, we show that macrophages provide this link. |
Raghuveer Parthasarathy ; Julia Ngo ; Piyush Amitabh ; Jonah Sokoloff ; Karen Guillemin; |
| 725 | Deciphering Spatial Patterns of Immune Response in Fruit Fly Larvae Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work highlights the role of physical processes in driving immune variability. |
Brandon Schlomann ; Ting-Wei Pai ; Jazmin Sandhu ; Thomas Graham ; Hernan Garcia; |
| 726 | Mapping in Toto Immune Cell Dynamics During Viral Infection in Zebrafish Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite the large number and diversity, the interactions of these viruses with our immune system remains to be well characterized, particularly in the context of infection. To map the dynamics of various immune cells upon viral infection in toto, we employ larval zebrafish as a model system given its transparency, small size, and genetic tractability. |
Deepika Sundarraman ; Talon Chandler ; Shalin Mehta ; Keir Balla; |
| 727 | Role of An IL-15-driven Feedback Loop in Antigen-independent Cytotoxic T Cell Response Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: IL-15 signaling can also induce a cytotoxic T cell response involving the production of granzymes as well as secretion of interferon (IFN)-γ by memory T cells. Here, we present a mathematical model of a cellular circuit involving memory T cells and myeloid cells (such as monocytes) that incorporates IL-15 and IFN-γ-mediated signaling, and show that the circuit can exhibit bistable behavior, including a state characterized by high memory T cell count, activation, and cytotoxicity. |
Shubham Tripathi ; Can Liu ; William Lau ; Rachel Sparks ; John Tsang; |
| 728 | Size of Inflammasome As A Regulatory Motif in Caspase-1 Activation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our study, we employ stochastic simulation models to explore the regulatory role of the number of activation sites for caspase-1. |
Kevin Yang ; Roya Zandi ; John Barton; |
| 729 | Interacting Gaussian Curvatures and Their Role in Connecting Inflammation and Cardiovascular Disease Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we investigated the role of LL37, a host defense peptide upregulated in skin inflammation, in promoting Low-Density Lipoprotein (LDL) uptake and lipid accumulation in macrophages and endothelial cells. |
Jaime de Anda ; Haleh Alimohamadi ; Wei-Chia Luo ; Yoshiyuki Nakamura ; Richard Gallo ; Gerard Wong; |
| 730 | Spatial Modes of Inflammatory Signaling in Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use some of these tools to characterize spatial patterns of inflammatory gene expression in the tailfin of the zebrafish, via quantitative snapshots. I will discuss the avenues that this opens for investigating collective control of inflammatory responses. |
Elizabeth Jerison; |
| 731 | Infiltration of Tumor Spheroids By Activated Immune Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a computational model incorporating immune cells with active, persistent movement and a proliferation rate that depends on the presence of cancer cells, and show that the model able to reproduce semi-quantitatively the experimentally measured infiltration profile. |
Mrinmoy Mukherjee ; Oleksandr Chepizhko ; Maria Lionetti ; Stefano Zapperi ; Caterina La Porta ; Herbert Levine; |
| 732 | Microscopic Spatial Organization of Immune Cells and Stochastic Fluctuations Regulate Patient Response to Immune Checkpoint Inhibitor Drugs in Melanoma Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Utilizing publicly available imaging mass cytometry (IMC) data of melanomas of patients who later underwent ICI therapy, we use densities and pair correlations to extract spatial relationships between cells of interest and formulate hypotheses about their mechanistic relationships. |
Giuseppe Giuliani ; Ciriyam Jayaprakash ; Jayajit Das ; William Stewart; |
| 733 | Collective Behaviors of Bacteria in Flow: Divergent Roles for Transport and Microcolony Morphology Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed a microfluidic system to study flow effects on colonization of two endocarditis-inducing pathogens: Staphylococcus aureus MRSA and Enterococcus faecalis. |
Kelsey Hallinen ; Zemer Gitai; |
| 734 | Mechanical Properties of Staphylococcus Aureus and Pseudomonas Aeruginosa Dual-species Biofilms Grown in Chronic Wound Based Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesize that collagen, a primary component in wound extracellular matrix, mediates between S. aureus and P. aeruginosa allowing formation of more robust polymicrobial biofilms. |
Gordon Christopher ; Bikash Bhattarai ; Kendra Rumbaugh; |
| 735 | Biophysical Constraints on Vertical Biofilm Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using interferometry and confocal imaging techniques, we investigate how different factors such as cell death and viscous relaxation affect biofilm heights. |
Maryam Sadat Hejri Bidgoli ; Peter Yunker ; Pablo Bravo; |
| 736 | Liquid Channels Within B. Subtilis Biofilms Allow The Escape of Trapped Clones and Population Rescue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We employ an experimental procedure that enables a rapid switch of the chemical environment with minimal physical manipulation of the community to investigate the fate of trapped clones carrying a selective advantage in wrinkly B. subtilis biofilms. We find that these clones are able to use the channels underneath the wrinkles to traverse long distances and take over the expansion front. |
Nikhil Krishnan ; Joseph Knight ; Abhirup Mookherjee ; Luis Ruiz Pestana ; Diana Fusco; |
| 737 | Effective Bacterial Aggregation Is Achieved By Partial Disassembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we study a system of suspended bacteria expressing blue-light-sensitive adhesive proteins on their membranes. |
Rachel Los ; Timon Idema ; Juan Jose Quispe Haro ; Seraphine Wegner; |
| 738 | Physics of Phenotypic Segregation in A Developing Biofilm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using fluorescent biosensors and reporters, we reveal that a growing Vibrio cholerae biofilm exhibits high levels of heterogeneity in the intracellular cyclic diguanylate (c-di-GMP) concentration and expression of biofilm matrix genes. |
Jung-Shen Benny Tai ; Japinder Nijjer ; Kee Myoung Nam ; Christopher Waters ; Jing Yan; |
| 739 | Determining Biophysical Mechanisms of Phenotypic Segregation in Bacterial Biofilms with Agent-based Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we discuss the consequences of spatiotemporal heterogeneity in intracellular signaling on the architecture of biofilms formed by the model species Vibrio cholerae. |
Kee Myoung Nam ; Jung-Shen Benny Tai ; Japinder Nijjer ; Jing Yan; |
| 740 | Cellular Surfaces As Regulators of Biomolecular Condensation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I discovered that Whi3 condensates are attached to endomembranes in cells. |
Wilton Snead ; Amy Gladfelter; |
| 741 | Polymer Collapse Facilitates Protein Phase-separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use approaches from statistical physics to explore a model where proteins with a propensity to phase-separate in 3D modulate the collapse transition of a long polymer. |
Mason Rouches ; Benjamin Machta; |
| 742 | Molecular Transport Across Phase Boundaries Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use a combination of quantitative (live) imaging techniques and theory to quantify the transport of molecules across the condensate-bulk interface in PGL-3 and FUS model condensates and compare to several theoretical models. |
Lars Hubatsch ; Anatol Fritsch ; Marta Mestroni ; Koichiro Takenaka ; Christoph Weber ; Frank Jülicher ; Anthony Hyman ; Patrick McCall; |
| 743 | Exchange Dynamics of Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Motivated by recent experimental evidence that condensates of a single type of biomolecule can consist of multiple species with drastically different mobilities, we theoretically derive diffusion-reaction equations to model a two-species system, where the two species represent molecules of different mobilities within the condensate. |
Ross Kliegman ; Yaojun Zhang; |
| 744 | Non-linear Partitioning of Client Proteins to The Bulk and Interface of Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we quantify bulk and interfacial partitioning of tubulin to FUS-polyU droplets using light microscopy. We find that classical partitioning coefficients are insufficient to characterize these phenomena. |
Teagan Bate ; Kathryn Rosowski ; Eric Dufresne; |
| 745 | Lightning The Interface: The Electrochemical Features of Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce how an associative transition of biomacromolecules can result in a segregative transition of ions, forming an electric potential gradient between the dilute and the dense phases, which corresponds to an interfacial electric double layer. |
Yifan Dai ; Richard Zare ; Lingchong You ; Ashutosh Chilkoti; |
| 746 | Nucleation Pathways of Multicomponent Biomolecular Condensates: A Cautionary Tale of The Classical Nucleation Theory Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, a quantitative description of the nucleation landscape must also account for both the multicomponent nature of bimolecular condensates and the crowded intracellular environment. Here, we address this question by combining theory, molecular simulation, and continuum-scale numerical methods. |
Qiwei Yu ; Yury Polyachenko ; Ned Wingreen ; Mikko Haataja ; William Jacobs ; Andrej Kosmrlj; |
| 747 | Merging-limited Coarsening of Nanoscale Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we observe that coacervate droplets of small sizes (ranging from tens to hundreds of nanometers) remain stable over hours with significantly slower coarsening rates than predicted by classic theories. |
Yaojun Zhang ; Feipeng Chen ; Ho Cheung Shum; |
| 748 | Capillary Forces from Biomolecular Condensates on Microtubules Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, using atomic force microscopy, we directly measure the attractive capillary interactions on TPX2-coated microtubule surfaces. We find that the capillary interactions are significant and can therefore underly the functional role of TPX2 in microtubule nucleation and organization. |
J. Pedro de Souza ; Bernardo Gouveia ; Sabine Petry ; Howard Stone; |
| 749 | Phase Behavior of Mixtures of Intrinsic Disordered Proteins and Rod-like Colloidal Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Notably, at intermediate fd concentration, the fd and the IDPs form well-mixed condensates in which the fd are highly concentrated ( i.e., compared to the background liquid phase). We will describe the experiments and offer some analysis of the phase behavior of these mixtures and the microscopic structure of the condensates. |
Yihao Chen ; Mikael Garabedian ; Mathew Good ; Arjun Yodh; |
| 750 | Predicting Morphology of Biomolecular Condensates from Protein Interaction Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work shows how a low-concentration protein species might function as a biological switch for regulating condensate morphologies. |
Tianhao Li ; William Jacobs; |
| 751 | Size, Shape, and Fluctuations of Condensates in Non-equilibrium Liquid-liquid Phase Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Equilibrium phase separation, in the absence of chemical reactions, leads at long times, to a condensate of system size due to the interfacial tension of smaller-sized domains. In … |
Amit Kumar ; Dan Deviri ; Samuel Safran; |
| 752 | Designing The Morphology of Phase-Separated DNA Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate how to design the morphology of multiphase condensates that form in solutions of DNA nanostars. |
Sihan Liu ; Andrej Kosmrlj; |
| 753 | The Physical Basis of Using MRI for Detecting Cancer and Pre-cancer Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, we will start by reviewing the history of the development of the spin-echo NMR technique for cancer detection. |
Donald Chang; |
| 754 | Magnetic Resonance Elastography: Combining Magnetic Resonance and Acoustics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Like most other advances in medical imaging technology, MRE was developed through convergence science: bringing the disciplines of physics, mathematics, and engineering together with biological science. The presentation will discuss challenges and opportunities where convergence science promises to further advance MRE and its applications. |
Richard Ehman; |
| 755 | The Endless Capabilities of Magnetic Resonance, from Zero to High Fields Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Magnetic resonance techniques (NMR, MRI, EPR) continue to play ever expanding roles in biomedical research and modern medicine. NMR and MRI detect the angular momentum (“spin”) of … |
Michael Garwood; |
| 756 | Time Reveals Length Scale: Human Tissue Microstructure Characterization By Time-dependent Diffusion MR Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk will discuss: 1) how tissue microstructures at the length scale of micrometer can be specifically characterized by time-dependent diffusion MRI; 2) how the time-dependent diffusion MRI became feasibility in today’s MRI system; and 3) how MRI-based tissue microstructure imaging is defining the future of precision medicine. |
Ante Zhu; |
| 757 | Quantitative MRI and The Aging Brain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The goals of our work are twofold: to improve the capacity of MR to evaluate tissue pathology, and to develop methods for application to inverse problems more generally. |
Richard Spencer; |
| 758 | Dynamics of Representational Learning in Brain and Artificial Neural Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we will discuss the commonalities and differences between learning dynamics of realistic neural networks and artificial neural networks in the context of representational learning by using two examples from the mammalian olfactory system: 1) representational drift in piriform cortex; 2) alignment of neural representations from two sides of the brain. |
Yuhai Tu ; Guillermo Barrios Morales ; Miguel Muñoz ; Bo Liu ; Venketash Murthy ; Shanshan Qin; |
| 759 | What Does A Neuron Do? A New Model for Neuroscience and AI Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present an alternative viewpoint, casting neurons as feedback controllers in closed loops comprising fellow neurons and the external environment. |
Dmitri Chklovskii; |
| 760 | A Statistical Theory of Inferring Population Geometry from Large-Scale Neural Recordings Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: As we add more neurons, are we recording enough trials in order to infer the population geometry of neural activity? We derive new theories, based on random matrices and free probability, to answer this question, comparing the predictions made in two distinct regimes: an extensive limit where the dimensionality of data is proportional to the number of recorded neurons and trials, and an intensive limit where the dimensionality is finite. |
Itamar Landau; |
| 761 | Hyperbolic Geometry and Information Acquisition in Biological Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe how the use of hyperbolic geometry can be helpful for visualizing and analyzing information acquisition and learning process from across biology, from viruses, to plants and animals, including the brain. |
Tatyana Sharpee; |
| 762 | Signatures of Abstraction Learning in Primates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How are these models represented in the dynamics of brain activity? We approach this question through the exploration of schema formation in nonhuman primates. |
Adrienne Fairhall; |
| 763 | Glass-like Relaxation Dynamics During The Disorder-order Transition of Viral Nucleocapsids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By using time-resolved small-angle X-ray scattering with synchrotron source, we investigated the relaxation dynamics of CCMV-based nucleoprotein complexes with various RNA. |
Guillaume Tresset; |
| 764 | The Role of Elastic Energy in The Formation of Highly Symmetric Viral Shells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we introduce a coarse-grained model that enables us to explore the assembly pathway while taking into account the elastic energy involved in the growth of the viral shell. |
Siyu Li ; Kalouna Kra ; Stephane Bressanelli ; Guillaume Tresset ; Roya Zandi; |
| 765 | New Viral Protein Cage Structures Observed from In-vitro Co-assembly Experiments of Oligonucleotides and Brome Mosaic Virus Coat Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While the reason for non-specific encapsulation in vitro is relatively well understood, how does a virus avoid production of virus-like particles that encapsulate many of the smaller, non-viral, transient RNAs and other polyions occurring in the cytoplasm, is still a puzzle. In attempting to answer this long-standing question we have studied the nature of chimeras which assemble out of small ssDNA oligonucleotides and viral coat protein. |
Irina Tsvetkova ; Bogdan Dragnea; |
| 766 | Liquid-Liquid Phase Separation Enhances The Self-Assembly of Viral Capsids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use rate equations and a coarse-grained computational model to study the effect of attractive compartments formed by LLPS on capsid assembly thermodynamics and kinetics. |
Naren Sundararajan ; Anthony Trubiano ; Michael Hagan; |
| 767 | The Role of Electrostatic Interactions in The Formation of Bacteriophage MS2 Capsid Protein Shells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To further understand how non-specific interactions such as electrostatic forces drive capsid formation, we study the assembly of bacteriophage MS2 coat-proteins around MS2 RNA and wild-type bacteriophage MS2 at varying ionic strengths. |
LaNell Williams ; Kellianne Kornick ; Amelia Paine ; Rees Garmann ; Vinothan Manoharan; |
| 768 | Oral: Multiple Nanoparticle Encapsulation in Virus-like Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, I will present details of the synthesis of virus-like particles (VLPs) encapsulating multiple metal nanoparticles (NPs). |
Ayesha Amjad; |
| 769 | Impact of Membrane Thinning and Curvature in SARS-CoV-2 Membrane Protein Aggregation and Viral Budding Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides a better understanding of how the dynamics and interactions of M protein leads to viral assembly and budding, which may provide insights into alternative methods for preventing viral replication. |
Joseph McTiernan ; Yuanzhong Zhang ; Siyu Li ; Umar Mohideen ; Thomas Kuhlman ; Roya Zandi ; Michael Colvin ; Ajay Gopinathan; |
| 770 | How Cells Wrap Around Coronavirus-like Particles Using Extracellular Filamentous Protein Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study identifies new evolutionary pressures for viruses given the cellular microenvironment that includes filamentous ECCs. |
Sarthak Gupta ; Christian Santangelo ; Alison Patteson ; J. M. Schwarz; |
| 771 | Modeling and Characterization of Virus-mediated Cell Fusion Assays Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that the alpha variant has a syncytia formation rate higher than other variants. |
Hana Dobrovolny ; Ava Amidei ; Gabriel McCarthy; |
| 772 | Competitive Binding of Cleavage Factors Facilitates The Translocation of An Intact HIV-1 Capsid Through The Nuclear Pore Complex Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How the HIV-1 capsid of diameter ~60 nm overcomes the steric barriers created by a dense arrangement of NPC proteins within the nuclear pore which is barely larger than the capsid is still an open question. Here, we address this question with an analytical model that accounts for the capsid geometry and its interactions with the NPC proteins. |
Bhavya Mishra ; Roya Zandi ; Ajay Gopinathan; |
| 773 | Mechanisms of Budding of Virus Particles Through A Spherical Vesicle Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study combines analytical and numerical methods, along with a coarse-grained model and molecular dynamics simulations, to examine budding dynamics in relation to membrane curvature. |
Shuyang Zhang ; Siyu Li ; Ajay Gopinathan ; Paul Van der Schoot ; Roya Zandi; |
| 774 | Elasticity Theory on Curved Surfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In a recent study, using effective defect interaction models, we developed a unified elasticity theory that successfully addressed the limitations of the linear theory. |
Yankang Liu ; Yinan Dong ; Siyu Li ; Alex Travesset ; Roya Zandi; |
| 775 | The Protein Hourglass: First Passage Time Distributions for Protein Thresholds Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our study, we derive the exact probability distribution of threshold crossing times for protein levels in both Laplace and time domains, along with their associated statistical moments: mean, variance, and skewness. |
Krishna Rijal ; Dibyendu Das ; Ashok Prasad ; Abhyudai Singh; |
| 776 | Micro and Macroscopic Stress-strain Relations in Disordered Tessellated Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we discover one simple “hidden” correlation between the microscopic, cellwise stress and strain in planar tessellated networks. |
Hao Lin ; Ran Li ; Seyedsajad Moazzeni ; Liping Liu; |
| 777 | Micromechanical Model of Effects of Matrix Viscoelasticity on Cell Contractility in Collagenous Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The model accurately predicts the rate-dependent load-unload response of an untreated tissue and displays hysteresis during the load-unload. |
Kalyn Younger ; William Cortes ; Daniel Reich ; Thao (Vicky) Nguyen; |
| 778 | Mechanically-driven Closure of Extreme Membrane Wounds in A Single Cell Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work highlights how single cells can act as mechanical systems to enable large-scale cell functions. |
Kevin Zhang ; Ambika Nadkarni ; Martín Koch ; Wallace Marshall ; Sindy Tang; |
| 779 | The Role of Cytoskeletal Mechanics in Conferring Wound Resilience in The Giant Single-celled Ciliate Stentor Coeruleus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that the wounding regime depends on the dimensionless parameter D*, which is the cell diameter relative to the constriction width. |
Rajorshi Paul ; Ambika Nadkarni ; Kevin Zhang ; Moumita Das ; Wallace Marshall ; Sindy Tang; |
| 780 | The Mechanics of Tumor Spheroids Revealed By A 3D Microfluidic Rheometer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we will present the development of a microfluidic rheometer that can characterize the stiffness of the tumor spheroid alongside their invasiveness into a 3D ECM. |
Young Joon Suh ; Mrinal Pandey ; Brian Cheung ; Alan Li ; Jeffrey Segall ; Mingming Wu; |
| 781 | Intrinsic Curvature in The Extracellular Matrix of A Simple Multicellular Organism Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We report the first quantitative study of the sheet-like ECM in simple multicellular eukaryotes, using mechanical shear to break up the spheroidal alga Volvox carteri into smaller sections, which are found to curl spontaneously into a variety of forms, some resembling seed pods of plants, others exhibiting bistability. |
Jane Chui ; Marco Vona ; Raymond Goldstein; |
| 782 | Controlling Cell Position in Heterotypic Spheroids: An Experimental and Computational Demonstration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use spheroid tumor models and complementary computational models to predict and control spatial organization in aggregates composed of multiple cell types. |
Laura Kaufman; |
| 783 | Physical Cues of The Extracellular Matrix Directs Invasion Phenotypes of Tumor Spheroids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use spheroids embedded in type 1 collagen gels as our tumor model to create a more physiologically relevant model for how tumors react to their environment. |
Austin Naylor ; Wouter-Jan Rappel ; Bo Sun; |
| 784 | Are Tumors Intelligent? – A Learning-based Approach to Tumor Invasion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Tumor spheroids embedded in fiber networks are an important in-vitro experimental setup for studying cancer systems. We develop a three-dimensional computational model to capture the dynamics of such embedded systems. |
Shabeeb Ameen ; Tao Zhang ; J. M. Schwarz; |
| 785 | Forces Controlling Motion of Topological Defects in Epithelial Cell Layers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we studied motion of cells and topological defects in monolayers of MDCK cells with and without perturbations of actomyosin contraction. |
Jun Zhang ; Molly McCord ; Jacob Notbohm; |
| 786 | Strain and Strain Rate Biochemical Feedback on The Mechanics of Epithelial Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we focus on the emergence of spatiotemporal density waves ubiquitously observed in the collective migration of expanding tissue monolayers and in their rheological response to external forces. |
Toshi Parmar ; M Cristina Marchetti; |
| 787 | Stress-shape Misalignment in Confluent Cell Layers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study investigates the relationship between cell shape and cell-generated stresses in confluent cell layers. |
Mehrana R. Nejad ; Liam Ruske ; Molly McCord ; Jun Zhang ; Guanming Zhang ; Julia Mary Yeomans ; Jacob Notbohm; |
| 788 | Mechanical Regulation of Neurite Polarization and Growth: A Computational Study Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Based on spring network calculations we predict an optimal shape for GC pulling force on the neurite shaft. |
Assaf Zemel ; Kristian Franze ; Maximilian Jakobs; |
| 789 | From Entangled Living Polymerlike Worms to Soft Robotic Chains Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This blob can respond to external stimuli such as light, to move or change shape. We will illustrate how these living worms provide a fascinating experimental platform for investigating the physics of active, polymer-like entities. |
Antoine Deblais; |
| 790 | Tangling Induced Phase Separation in Active Polymers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce an active polymer model, where each active polymer exhibits unique head dynamics that enable self-propulsion and entanglement. |
Prathyusha K R ; Harry Tuazon ; Saad Bhamla; |
| 791 | Light-driven Transformations in Entangled Active Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: From the active matter perspective, these tangled worm blobs represent a remarkable material that can autonomously self-assemble, shape-shift, and exhibit other emergent collective functions. Here, we investigate the response of these worm blobs to light exposure. |
Nitesh Arora ; Harry Tuazon ; Saad Bhamla; |
| 792 | Entangling and Localization of Active Filaments in Square Wells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will present a study of the dynamics of Lumbriculus variegatus (or California blackworm) under quasi 2D square confinement as a model of active filaments that can entangle as a function of their number density. |
Sohum Kapadia ; Animesh Biswas ; Arshad Kudrolli; |
| 793 | Active Hierarchical Self-assembly of Liquid Crystalline Filamentous Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study the phase separation of a mesogenic liquid crystal from an isotropic fluid as a model system for liquid-liquid crystal phase separation. |
Christopher Browne ; Yuma Morimitsu ; Zhe Liu ; Chinedum Osuji; |
| 794 | Topology Governs The Presence and Timescale of Anomalous DNA Transport Across Cytoskeletal Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the cytoskeleton, motor proteins (such as kinesin) consume energy from their environment to push and pull on the network’s polymers, instigating various forms of flow and contraction that make the transport dynamics across the composite challenging to understand. Here, we investigate the effect of DNA topology on its transport within reconstituted cytoskeletal networks of microtubules and kinesin. |
Dylan McCuskey ; Daisy Achiriloaie ; Jemma Kushen ; Isaac Blacklow ; Jennifer Ross ; Rae Robertson-Anderson ; Janet Sheung; |
| 795 | How to Efficiently Extract A Filament from A Topological Tangle: Part 1 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How does the entanglement between individual filaments affect their untangling behavior? We explore this question by considering the extraction of a single soft fiber from a tangled ball of similar fibers hanging in gravity. |
Ishant Tiwari ; Vishal Patil ; Sutikshan Bansal ; Jorn Dunkel ; Saad Bhamla; |
| 796 | How to Efficiently Extract A Filament from A Topological Tangle (Part 2) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In particular, the question of how to extract a single filament from a tangle represents a fundamental problem of tangle control. Here, we theoretically explore filament oscillation as a dynamical protocol for solving this extraction problem. |
Vishal Patil ; Ishant Tiwari ; Sutikshan Bansal ; Jorn Dunkel ; Saad Bhamla; |
| 797 | Actively Entangling Filaments for Passive Adaption in Soft Robotic Grippers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate a soft robotic gripper made of an array of slender, hollow, elastomeric filaments that are reversibly and pneumatically actuated to take a highly curved state, enabling entanglement on demand for grasping. |
Kaitlyn Becker ; Yeonsu Jung ; L Mahadevan ; Robert Wood ; james weaver ; Daniel Baum ; Clark Teeple; |
| 798 | Helical Fungi Under Physical Constraints Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We here focus on the oscillatory shapes adopted by the filaments (hyphae) of the fungus Candida albicans in different conditions of physical constraints such as z-confinement. |
Catherine Villard ; Igor Kulic ; Elodie Couttenier; |
| 799 | Growth of Physarum Polycephalum Under Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The slime mold Physarum polycephalum is a unicellular organism that can grow its network-like body to adapt to its environment and solve mazes. Due to its simple geometry and fascinating abilities, fluid dynamicists used it as a model organism to investigate morphogenesis, network theory, and physically encoded memory. |
Shankar Kharal ; Tori McDermott ; Jean-Francois Louf; |
| 800 | Digital Reconstruction and Analysis of The Growing and Branching Mycelial Network of The Model Filamentous Fungus Podospora Anserina Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we characterize the hyphal network expansion and the structure of the model filamentous fungus Podospora anserina under controlled culture conditions. |
Thibault Chassereau ; Éric Herbert ; Florence Chapeland-Leclerc; |
| 801 | Prediction and Experimental Evidence of Different Growth Phases of The Podospora Anserina Hyphal Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose in this work to discuss the advantages of each branching type using a new observable for the network growth, allowing us to compare growth configurations. |
Éric Herbert ; Florence Leclerc ; Pascal David ; Clara Ledoux; |
| 802 | Task-level Dynamics of Rice Root Gravitropism Revealed By Frequency Response Analysis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To elucidate mechanisms and algorithms underlying gravitropism during root growth, we employ the “system identification” framework: we apply sinusoidal periodic orientational forcing and monitor how rice roots ( O. sativa) generate corrective feedback to attempt to grow downward (in the direction of gravity). |
Madison Hales ; Yu Yang ; Aradhya Rajanala ; Christopher Pierce ; Mingyuan Zhu ; Philip Benfey ; Noah Cowan ; Daniel Goldman ; Daniel Goldman; |
| 803 | Plant Hydraulic Redistribution Visualization in A Transparent Hydrogel-Based Soil Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, we introduce a novel approach using transparent hydrogel-based soil to visualize HR in soy plants in a controlled environment within a growth chamber, allowing for visualization and quantifying of HR under various environmental conditions. |
Tori Phillips ; JEAN-FRANÇOIS LOUF; |
| 804 | Modeling Growth and Anchoring of Plant Root-inspired Structures in Dry Granular Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The robophysical model reveals that incorporation of hairs increases pull-out forces more than twice. |
Deniz Kerimoglu ; Elliot Hawkes ; Nicholas Naclerio ; Daniel Goldman ; Aradhya Rajanala; |
| 805 | Robust Posture Control By Plants in Dynamic Gravity Field Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the absence of rotation, we identify a universal planar shape towards which all shoots eventually converge. |
Hadrien Oliveri ; Derek Moulton ; Heather Harrington ; Alain Goriely; |
| 806 | Aerodynamics of Seeds and Leaves Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: In contrast to seeds, which are aerodynamically optimized to settle slowly and travel far (Cummins et al., Nature 2018), evolutionary thinking suggests that leaves must fall to … |
Kaare Hartvig Jensen ; Matthew Biviano; |
| 807 | Discovery of A New Active Matter Process That Controls Plant-atmosphere Coupling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, I will describe experiments with a new fluorescent nanoreporter of chemical potential of water that has allowed us to interrogate the constitutive properties relative to water transfer of the leaf mesophyll, the tissue that carries water from the xylem vessels to the sites of evaporation beneath the stomates. |
Sabyasachi Sen ; Piyush Jain ; Fulton Rockwell ; Robert Twohey III ; Matthew Runyon ; Anthony Studer ; Noel Michele Holbrook ; Abraham Stroock; |
| 808 | Sum Frequency Generation Vibrational Spectroscopy and Imaging of Crystalline Cellulose Microfibrils in Plant Cell Walls Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, CMF orientation and directionality were determined using SFG spectroscopy with theoretical calculations, employing the polarizability and dipole derivative tensors obtained from density functional theory (DFT) calculations. |
Juseok Choi ; Mohamadamin Makarem ; Chonghan Lee ; Jongcheol Lee ; Sarah Kiemle ; Albert Kwansa ; Yaroslava Yingling ; Daniel Cosgrove ; Seong Kim; |
| 809 | Multimodal Characterization of Systems-Level Robustness in The Cellular Organelle Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here I aim to address the systems-level role organelle interactions have in regulating organelle composition and metabolic flows. |
Aline Arra ; Shankar Mukherji; |
| 810 | Optimality in Organelle Number and Size Control Under A Limiting Pool of Resources Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that the solutions to the constrained optimization fall into two regimes separated by a critical point, suggesting that cells face an unexpectedly sharp tradeoff between organelle number and size in resource-limited contexts. |
Shankar Mukherji ; Shixing Wang ; Peyman Fahimi ; Ronan Hanley ; Fang Yu; |
| 811 | The Coordination of Global Macromolecular Synthesis and Organelle Biogenesis During Cellular Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite remarkable progress in our molecular understanding of how the cell can change the rate of global protein and lipid synthesis, it is still unclear how organelles react, both alone and in concert with the other organelles in the cell, upon perturbations to these global material fluxes. Here, we tuned the rates of global protein, lipid, and nucleic acid synthesis in the model organism Saccharomyces cerevisiae and used hyperspectral confocal microscopy to monitor the effects of these perturbations on the systems-level organelle architecture of individual cells. |
Shankar Mukherji ; Anangkumark Singh; |
| 812 | Tight Control Over Cytoplasmic and Membrane Protein Densities Defines Regulation of Cell Geometry in Escherichia Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present a simple theory of cellular resource allocation that quantitatively predicts how rod-shaped bacterial cells control their surface-area-to-volume across a broad range of growth conditions. |
Griffin Chure ; Roshali De Silva ; Richa Sharma ; Michael Lanz ; Jonas Cremer; |
| 813 | Cell Division and Motility Enable Hexatic Order in Biological Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we study the effect of cell division and apoptosis on global hexatic order within the framework of the self-propelled Voronoi model of tissue. |
Yiwen Tang ; Dapeng(Max) Bi ; Mark Bowick ; Siyuan Chen; |
| 814 | Amphiphilic Nanoparticles Induce Membrane Capacitance and Tension Reductions in Planar Lipid Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Herein, we utilize the planar lipid bilayer, which allows for subsequent electrophysiological characterization. |
Farzin Masshali ; Colin Basham ; Paulo Henrique Jacob Silva ; Xufeng Xu ; Camila Servidio2 ; Francesco Stellacci ; Stephen Sarles; |
| 815 | Limits on Cellular Size Precision Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Experiments have shown that unicellular organisms’ division size typically varies by about 10%-20% in a constant environment. To understand what sets this level of precision, we model stochastic growth dynamics and use a first-passage formalism wherein the cell decides to stop growing based on a noisy estimate of its own size. |
Daniel McCusker ; David Lubensky; |
| 816 | MreB Mechanically Couples The Cytoplasmic Membrane to The Cell Wall in Escherichia Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: GFP labeling of MreB confirmed that relocation of MreB to the cell poles was key to such phenotypical differences. Based on these data, we propose a physical model in which MreB, together with the other components of the cell-wall synthesis machinery, serves as the major linkage between the cytoplasmic membrane and the cell wall. |
Jiawei Sun ; Kerwyn Huang; |
| 817 | Directly Measuring Turgor Pressure in Bacterial Cells: Effects of Osmolality of Growth and Nutrient Conditions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Directly measuring turgor has been an experimental challenge, and a rapid, precise method has been lacking. We here present an experimental method based on force spectroscopy using an atomic force microscope to quantify turgor and its variations at the single cell level in vivo. |
renata garces ; Octavio Albarran ; Harold Erickson ; Nikhil Malvankar ; Giacomo Po ; Jeff Eldredge ; Christoph Schmidt; |
| 818 | Modeling The Peptidoglycan Layer of Gram-negative Bacteria As An Anisotropic, Elastic Network Composed of Two Types of Nonlinear Springs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a quantitative physical model of the bacterial cell wall, based on molecular details, that predicts the mesoscopic mechanical response of the cell wall for the Gram-negative bacterium Escherichia coli. |
Xiaoxuan Jian ; Octavio Albarran ; renata garces ; Giacomo Po ; Jeff Eldredge ; Christoph Schmidt; |
| 819 | Structure, Dynamics, and Transport in Mitochondrial Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate that increased mitochondrial motion and junction flexibility inhibit the onset of a percolation transition in network connectivity. |
Keaton Holt ; Elena Koslover; |
| 820 | Finding The Last Bits of Positional Information Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The result is that this precision, while higher than expected, is not quite enough to specify the identity of each cell uniquely. We make this “information gap” precise, in bits. |
Milos Nikolic ; Lauren McGough ; Helena Casademunt ; Mariela Petkova ; Thomas Gregor ; William Bialek; |
| 821 | Osmotic Regulation of Nuclear Size in Yeast Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we developed a quantitative model for nuclear size control based upon colloid osmotic pressure and tested key predictions in the fission yeast Schizosaccharomyces pombe. |
Joël Lemière ; Fred Chang; |
| 822 | Computational Approaches to Dissect The Multi-scale Chromatin Landscape and Gene Regulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will present several computational methods my group developed for in-depth analysis of high- throughput omics data, to better infer biologically meaningful information and better account for intrinsic biases from the complicated experimental data. |
Chongzhi Zang; |
| 823 | Geometric Properties of Deinococcus Radiodurans Cells and Nucleoids Reflect Effects of Radiation Exposure or The Deletion of Key Genome-associated Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a high-throughput approach to quantifying the geometric properties of cells and nucleoids, using confocal microscopy, digital reconstructions of bacterial cells, and machine learning. |
Vernita Gordon ; Antonio Cordova ; Brandon Niese ; Philip Sweet ; Lydia Contreras; |
| 824 | Design Principles of 3D Epigenetic Memory Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: But in the simplest models of this mechanism, there is a basic instability—if mark spreading is strong enough to restore a partially erased pattern, marks also spread uncontrollably to the rest of the genome. We developed a simple model coupling the dynamics of marks with the phase separation of chromatin, which reveals that emergent 3D genome organization can stabilize an epigenetic memory, as long as (1) there is a large density difference between chromatin compartments, (2) modifying “reader-writer” enzymes spread marks in 3D, and critically, (3) these enzymes are limited in abundance relative to their substrates. |
Jeremy Owen ; Dino Osmanovic ; Leonid Mirny; |
| 825 | Landscapes of Genomic Architecture Across Evolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will demonstrate how the architecture of interphase chromosomes is encoded in the one-dimensional sequence of epigenetic markings much as three-dimensional protein structures are determined by their one-dimensional sequence of amino acids. |
Michele Di Pierro; |
| 826 | Model of Euchromatin Clustering Resulting from Local Nucleosome Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop a physical model that explains the heterogeneous architecture of euchromatin in vivo. |
Joseph Wakim ; Andrew Spakowitz; |
| 827 | Chromatin Configurational Dynamics in Live Cells Reveals Insights Into Gene Localization Within Nucleus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present data from ten different loci spaced more-or-less regularly across Chr II (4.5 Mb) of Schizosachromyces pombe, which reveal gene-specific tendencies to localize to particular nuclear regions, demonstrating that the territory concept applies not only to entire chromosomes, but also to chromatin regions within chromosomes. |
Andrew Rodriguez ; Ivan Surovtsev ; Megan King ; Simon Mochrie; |
| 828 | Distinct Material States of Interphase Chromatin in Normal and Cancer Cells Revealed By CRISPR Live-cell Imaging Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we measured the viscoelasticity of chromatin by tracking genomic locus dynamics and calculating dynamic (complex) modulus. |
Yu-Chieh Chung ; Li-Chun Tu; |
| 829 | Polymer Model Predicts Epigenetic Memory and Heterogenous Dynamics of Constitutive Heterochromatin Domains Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study proposes a simplified model incorporating intrinsic HP1a interactions and their affinity towards methylation markers. |
Ramin Basir ; Vinayak Vinayak ; Vivek Shenoy; |
| 830 | Force Spectroscopy on Tetranucleosomes Using DNA Origami Nanocalipers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use hinge-like DNA origami nanocalipers with tunable mechanical properties to perform force spectroscopy experiment on tetranucleosomes. |
Kalven Bonin ; Yuchen Wang ; Ralf Bundschuh ; Carlos Castro ; Michael Poirier; |
| 831 | Effects of Chromatin Phase Separation on The Morphology of Eukaryotic Cell Nucleus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using coarse-grained random tri-block copolymers and an elastic-shell model that can capture conventional chromatin organization while maintaining the mechanical deformability of the cell nucleus, we focus on how chromatin (micro)phase separation can affect nuclear morphology. |
Aykut Erbas ; A Goktug Attar ; Edward Banigan ; Jaroslaw Paturej; |
| 832 | Unravelling The Mechanism of HP1 Eviction from Methylated Histone H3: A DFT Study Suggests A Complex Salt Bridge As The Spurring Interaction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we constructed a representative molecular system of the HP1-H3 K9me 3S10 phos complex, comprised of the aromatic cage of HP1 (Y24, W45 and Y48) and the R8K9 me3S10 tripeptide by reproducing Cartesian Coordinates from the crystal structure with the PDB code 1KNE. |
Georgios Papamokos ; Efthimios Kaxiras; |
| 833 | Learning Mechanisms of Rare Events from Short-trajectory Data Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, calculating such statistics for more complex processes with rugged landscapes and/or multiple pathways requires more general numerical methods. In this lecture, I will describe my group’s recent efforts to develop both linear (Galerkin) and nonlinear (neural-network) methods for estimating transition-path statistics by combining information from many short molecular dynamics trajectories. |
Aaron Dinner; |
| 834 | Target Structural Based De Novo Drug Generation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed DeepLigBuilder that can directly design 3D molecules inside the target binding pocket, by combining a novel 3D deep generative network for drug-like molecules and an optimization module that performs Monte Carlo Tree Search. |
Luhua Lai; |
| 835 | Bayesian Hi-C Metainference of Chromatin Structure Via Molecular Dynamics Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce the Hi-C metainference method to infer the heterogeneous structure ensemble from the Hi-C data with the prior distribution constructed from molecular dynamics simulations and Markov state modeling. |
Shoji Takada; |
| 836 | Graph Deep Learning Locates Magnesium Ions in RNA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce a machine-learning method, originally designed for computer vision, to predict Mg2+ binding sites in RNA by considering geometric and electrostatic RNA features. |
Shi-Jie Chen; |
| 837 | Spectroscopic Insights Into The Nano-bio Interface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will provide an overview of the nano-bio interface from the standpoint of nanotoxicity. |
Ramakrishna Podila; |
| 838 | Real-Time Detection and Analysis of Biomolecular Interactions in Crowded Environment Using Nanopipette Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will introduce a low-cost, and label-free based detection technique, for real-time detection and analysis of biomolecular interactions in a crowded environment. |
Santosh Khatri ; Jin He; |
| 839 | Control of Biomechanical Properties By Cell Encapsulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, THP-1 cells, a human leukemia monocytic cell line, were encapsulated with chemically modified charged silks, ionomers, through electrostatic layer-by-layer deposition. We will present findings on cell viability and functionality, as well as the cytocompatibility of the silk material in these systems. |
Udathari Kumarasinghe ; Cristian Staii ; David Kaplan ; Ying Chen; |
| 840 | Biophysical Parameters of Bacteriophage Adsorption to Host Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose an updated model of the biophysics of phage adsorption. |
Jyot Antani ; Timothy Ward ; Isabella Graf ; Thierry Emonet ; Paul Turner; |
| 841 | Solubilization of Hydrophobic Astaxanthin in Water By Physical Association with Phytoglycogen Nanoparticles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the present study, we demonstrate that PG can be used as an effective solubilizing agent for the hydrophobic carotenoid astaxanthin (AXT), which has reported health benefits. |
Nicholas van Heijst ; John Dutcher; |
| 842 | Single Particle Tracking to Probe Small Molecule Ligand-receptor Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, the effect of nanoparticle design on promoting successful targeting events was measured by analyzing the dynamics of small molecule ligand-receptor interactions. |
Jessica Chiu; |
| 843 | Immune Stealth VP28-conjugated Heparin Nanocomplex Development for Reducing Self-aggregation Risk of Heparin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, self-aggregation induced life-threatening complications. We proposed that the conjugation of heparin to immuno-stealth biomolecules may overcome these obstacles. |
Chia-Ching Chang ; Hussein Hussein ; Chia-Yu Chang ; Chih-Yu Yang ; Yu-Chaun Liang ; Lik Voon Kiew; |
| 844 | Age and Temperature Effects on Collagen Structure, Stability and Mechanics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How these chemical modifications affect the interplay between structure, stability and mechanics of individual collagen proteins is not known. In this study, we combine biochemical approaches with atomic force microscopy (AFM) imaging, to investigate how these properties of collagen are affected by AGEs. |
Nancy Forde ; Daniel Sloseris ; Alaa Al-Shaer; |
| 845 | Rheological Tunability of Fibers Networks with Embedded Magnetic Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Experimental difficulties arise from stress response measurement precision, contrasting agents’ noise, the spatial dispersion of magnetic particles and dynamic measurement of rheological quantities. To address this, we present a minimalistic numerical model to study the effects of external magnetic fields on the mechanical response of nonlinear fiber networks with embedded magnetic particles. |
Anupama Gannavarapu ; Lucas Cunha ; Frederick MacKintosh; |
| 846 | Design of Double Network Gels Using Molecular Dynamics Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In order to predict properties of DNs, we designed a series of rheological tests performed on in-silico self-assembled colloidal gels. |
Mauro Mugnai ; Emanuela Del Gado; |
| 847 | Viscoelastic Materials Are Most Energy Efficient When Loaded and Unloaded at Equal Rates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that mechanical efficiency is highest at symmetric rates and significantly decreases with a larger degree of asymmetry. |
Lucien Tsai ; Paco Navarro ; Elizabeth Mendoza ; Emanuel Azizi ; Mark Ilton; |
| 848 | Growth Dynamics of Yeast in 3D Granular Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These present dramatically different mechanical regimes from what can be realized using conventional culture methods. Our present study focuses on bridging this gap by investigating yeast growth dynamics in 3D porous, granular environments. |
Ashitha Arun ; M Sreepadmanabh ; Sunil Laxman ; Tapomoy Bhattacharjee; |
| 849 | Transition Metal Doped ZnO Ferromagnetic Nanoparticles for Cancer Cure Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study presents the synthesis, characterization, and potential applications of these nanoparticles in the context of cancer cure. |
Aurangzeb Khan; |
| 850 | In Vivo Protein Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Protein dynamics in cells is subject to both physical and evolutionary constraints. I will discuss a series of experiments and simulations to highlight how protein dynamics is modulated in its native cytoplasmic environment, and how it differs from similar dynamics in aqueous solution. |
Martin Gruebele; |
| 851 | Graph Neural Networks As Protein-Protein Interface Scoring Functions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose that the lower performance of GNN-based scoring functions stems from the imbalance in the quality of the computational models within the training set. |
Naomi Brandt ; Jake Sumner ; Alex Grigas ; Corey O’Hern; |
| 852 | Probing Dynamics of Transferrin and Their Interaction with Metal Ions Using High Sensitivity Dielectric Spectroscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Transferrin performs its functions by binding two ferric-ions and an anion, while doing so, the conformation of transferrin would change. To probe the conformational dynamics of transferrin and its interaction with ferric-ion in aqueous solutions at molecular level, we have employed a highly sensitive dielectric megahertz-to-terahertz frequency-domain spectroscopy. |
Jiarong Cui ; Nathan Peters ; Vinh Nguyen; |
| 853 | Modeling Flexible Docking of Protein Monomers Using Rigid-body Docking Along Minimal Energy Paths Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will perform rigid-body docking and model scoring for successive conformations along the minimal energy path, which will allow us to assess the magnitude of the root-mean-square deviations in atomic coordinates beyond which it is difficult to predict protein-protein interfaces using the unbound structures. |
Devon Finlay ; Grace Meng ; Alex Grigas ; Corey O’Hern; |
| 854 | Oral: How to "see" Proton Transfer During Protein Function Using Signature Vibrational Modes? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We report how to use an integrated approach, combining Fourier transform infrared spectroscopy, histidine specific isotope-editing, site-specific mutation, and density-functional-theory based computational study to develop a general method for probing the three protonation states of histidine. |
Aihua Xie ; Rosalie Dohmen ; Wouter Hoff ; Salma Priya ; Sarah Teeman; |
| 855 | Protein Cores Explore A Glassy Energy Landscape Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Since the energy minimum for protein cores should correspond to the maximum density, here we develop a purely geometric model of proteins to generate collapsed proteins that are resistant to further compression. |
Alex Grigas ; Jack Logan ; Mark D Shattuck ; Corey O’Hern; |
| 856 | Rotational Effects on Free Energy Landscapes of Diffusing Molecules in Coarse-Grained Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate that the free energy landscape of a diffusing molecule can be distorted by the coupling of internal fluctuations with centrifugal forces. |
Jesse Hall ; Marina Guenza; |
| 857 | Functionalization for Graphene-based Field Effect Transistor Biosensors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a combined method of electrical and optical techniques, which utilizes absorption properties of the proteins, biochemical functionalization, and optoelectronic properties of graphene field effect transistors to produce a high electrical response when light is illuminated on the surface of the biosensor-bioanalyte system. |
Leslie Howe ; Tharindu Rajapaksha ; Kalani Ellepola ; Ellee Pyle ; Zachary Aycock ; Vinh Nguyen; |
| 858 | The Minimum and Optimal Restraints in FRET-assisted Protein Structural Modeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that it is possible to induce conformational changes using only a small fraction of restraints, N r/N, where N is the number of amino acids. |
Zhuoyi Liu ; Alex Grigas ; Jake Sumner ; Edward Knab ; Caitlin Davis ; Corey O’Hern; |
| 859 | Investigation of GapR Protein-mediated DNA Softening and Supercoiling Using Magnetic Tweezers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the binding and deformation properties of GapR remain incompletely characterized. Here, we use single-molecule magnetic tweezers to study the binding of GapR to DNA, and its effect on DNA stiffness and twisting. |
Xinjue Wei ; John Marko ; Ryo kawamura ; Monica Guo; |
| 860 | Molecular Docking and Dynamics of Flexible Heteroarotinoids As Potential Inhibitors Against SARS-CoV-2 Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study utilizes an in-silico molecular docking approach to screen 26 anti-cancer compounds known as flexible heteroarotinoids against all 24 SARS-CoV-2 proteins. |
Sujan Timsina; |
| 861 | Assessing The Current State of Computational Models for Protein-protein Interfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Thus, PPI scoring algorithms have been designed to classify computational models as high- or low-quality without direct knowledge of the experimentally determined structures. To assess PPI scoring algorithms, we scored models of heterodimeric proteins generated with a rigid-body docking algorithm (ZDOCK) and compared these scores to a measure of structural similarity (i.e. DockQ score) to the associated heterodimeric x-ray crystal structures. |
Jacob Sumner ; Grace Meng ; Naomi Brandt ; Andrés Córdoba ; Alex Grigas ; Lynne Regan ; Corey O’Hern; |
| 862 | Topological Defects in Cell Monolayers Controlled By Topography Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesize that the density difference is mainly not driven by collective cell migration, but by a different rate of cell division in the defects’ proximity, and we test the hypothesis by suppressing cell migration using high ridges. |
Francesca Serra ; Kirsten Endresen ; Aniruddh Murali ; Prasoon Awasthi ; Kurmanbek Kaiyrbekov ; Brian Camley; |
| 863 | Statistical Correlations of Topological Defects in A Model Monolayer Confluent Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To bridge this research gap, we employ the AVM to investigate the statistical correlations between lattice defects (cell shapes deviating from hexagons) and orientational defects. |
Jiusi Zhang ; Rui Zhang ; Chung Wing Chan; |
| 864 | Coupling 3D Reaction-diffusion and Active Matter to Investigate Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This project aims at unraveling the physical mechanisms by which pattern formation coupled with active matter can lead to robust morphogenesis. |
Amelie Chardac ; Guillaume Duclos; |
| 865 | Boundary Geometry Drives Three-dimensional Defect Transitions in A Polar Fluid Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides insights into luminogenesis and embryonic viability, while paving the way for defect control by geometry manipulation in more general settings. |
Pamela Guruciaga ; Takafumi Ichikawa ; Takashi Hiiragi ; Anna Erzberger; |
| 866 | Chaotic Control of Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, I will introduce experiments that demonstrate how geometrical confinement can influence the braiding dynamics of the topological defects. |
Linda Hirst ; Kevin Mitchell ; Fereshteh Memarian ; Derek Hammar ; Md Mainul Hasan Sabbir; |
| 867 | Self-organized Dynamics of Viscous Drops with Surface Nematic Activity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we study morphological dynamics in a freely-suspended viscous drop with surface nematic activity that drives the system out of equilibrium. |
Mohammadhossein Firouznia ; David Saintillan; |
| 868 | Acoustically Powered Active Liquid Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we report the discovery of a fully synthetic active nematic system comprised of a lyotropic chromonic liquid crystal externally energized by ultrasonic waves. |
Andrey Sokolov ; Alexey Snezhko ; Jaideep Katuri; |
| 869 | Probing Active Nematics with In-situ Microfabricated Elastic Inclusions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work introduces a novel microfabrication method for the in-situ polymerization of hydrogel structures within a tubulin/kinesin active nematic gel. |
Jordi Ignés-Mullol ; Pau Guillamat ; Francesc Sagues ; Ignasi Vélez-Cerón; |
| 870 | Controlling Active Nematic Topological Chaos Through Defect Pinning on Sharp Boundary Features Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In particular, we investigate the effects of varying bulk topological charge via pinning defects on boundary features. |
Brandon Klein ; Kevin Mitchell ; Linda Hirst ; Daniel Beller; |
| 871 | Coarsening of Topological Defects in 2D Polar Active Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I’ll describe how topological defects in 2D polar active materials coarsen and form dynamic patterns. |
Sumantra Sarkar ; Soumyadeep Mondal; |
| 872 | Spatiotemporal Control of Active Topological Defects Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present an additive design framework to use elementary activity patterns, as active topological tweezers, to create, move and braid individual defects. |
Suraj Shankar ; Luca Scharrer ; Mark Bowick ; M Cristina Marchetti; |
| 873 | Periodic Orbits, Pair Nucleation, and Unbinding of Active Nematic Defects on Cones Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By combining analytical arguments derived from the Born-Oppenheimer approximation with numerical simulations, we investigate the simultaneous impact of confinement together with curvature singularity by characterizing the dynamics of an active nematic on a cone. |
Farzan Vafa ; David Nelson ; Amin Doostmohammadi; |
| 874 | Modeling Microtubule Turnover Dynamics in Neurons Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: In neurons, microtubule filaments are believed to be stable and to have specific orientations. This is crucial, since other key proteins get transported along these polarized … |
Veronica Ciocanel; |
| 875 | Can Microtubule Diffusiophoresis Be Present During Spindle Formation? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we demonstrate migration of MTs in assembly buffer under MgCl 2 gradients and quantify the diffusiophoretic behavior by comparison with multi-ion diffusiophoresis and diffusioosmosis models. |
Suin Shim ; Bernardo Gouveia ; Beatrice Ramm ; Sabine Petry ; Howard Stone; |
| 876 | Slow Axonal Transport and Radial Diffusion of Neurofilaments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we investigate the physics of radial diffusive search for randomly distributed microtubules across the axon to determine how the average binding rate depends on the density of microtubules, their sizes and the size of the NFs. |
Rawan Nowier ; Nilaj Chakrabarty ; Peter Jung; |
| 877 | Geometry Controls Diffusive Target Encounter and Escape in Endoplasmic Reticulum Tubules Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explored how local ER tube geometry affects diffusive target search. |
Junyeong Kim ; Aidan Brown; |
| 878 | Tunneling Calcium Ions Through The Endoplasmic Reticulum Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Overall, our work highlights the importance of the ER network architecture in supporting the efficient delivery of calcium throughout the cell. |
Elena Koslover ; Cecile Crapart ; Zubenelgenubi Scott ; Laura Westrate ; Edward Avezov; |
| 879 | Understanding Kinesin and Dynein Mechanochemistry Underlying Bidirectional Transport Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Bidirectional cargo transport in neurons involves competing activity of kinesin and dynein motors attached to a shared cargo, but the mechanisms by which these antagonistic motors coordinate and compete are not well understood. We are investigating these motor coordination mechanisms using reconstituted pairs of kinesin family and dynein-dynactin-BicD2 (DDB) complexes, which are visualized by total internal reflection fluorescence microscopy. |
William Hancock; |
| 880 | Investigating Organelle Dynamics in Saccharomyces Cerevisiae Using Advanced Imaging and Deep Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present our efforts at bringing high precision spatiotemporal fluorescence imaging to the scale of systems-level organelle dynamics in the model organism Saccharomyces cerevisiae. |
Shixing Wang ; Shankar Mukherji; |
| 881 | Clustering and Spatial Distribution of Mitochondria in Dendritic Trees Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by experimental measurements of mitochondrial transport and localization in Drosophila visual system neurons, we introduce a mass-aggregation model to describe the spatial distribution of mitochondrial clusters within dendritic arbors. |
Mario Hidalgo-Soria ; Elena Koslover; |
| 882 | The Impact of Endoplasmic Reticulum Morphology on IRE1 Protein Clustering Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We quantitatively modeled IRE1 protein cluster dynamics on a tube surface as a lattice gas using a kinetic Monte Carlo algorithm. |
Aidan Brown ; Liam Kischuck; |
| 883 | Macromolecular Interactions and Geometrical Confinement Determine The 3D Diffusion of Ribosome-sized Particles in Live Escherichia Coli Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The bacterial cytoplasm is a heterogenous dynamic environment, with many physical factors that impact biological function. In this work, we present a physics-based whole-cell model of Escherichia coli that represents confinement, macromolecular crowding, size polydispersity, electrostatic intermolecular interactions, and the presence of the nucleoid at the center of the cell to parse the impacts of each of these attributes on macromolecular motion and localization. |
Alp Sunol ; Diana Valverde Mendez ; Jennifer Hofmann ; Benjamin Bratton ; Joseph Sheehan ; Liam Holt ; Zemer Gitai ; Joshua Shaevitz ; Roseanna Zia; |
| 884 | Doppler Spectroscopy of Intracellular Dynamics in Esophageal Cancer Biopsies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Near infrared optical coherence tomography, combined with digital holography coherence-gated read-out, provides rich speckle dynamics from light scattered inside the living tissue. This novel technique, called biodynamic imaging (BDI), uses fluctuation spectroscopy to extract the Doppler spectra associated with active transport of organelles, membranes and cell movements. |
David Nolte ; John Turek ; Shadia Jalal ; Dawith Lim; |
| 885 | Molecular Origin of Aging in Biomolecular Condensate Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We reveal the Maxwell fluidic nature of the biomolecular condensates, which was not captured in the previous simulations studies. This comprehensive study sheds light on the aging of the biomolecular condensates and how the rheological nature changes over time. |
Subhadip Biswas ; Davit Potoyan; |
| 886 | PTM-Psi: A Python Package to Facilitate The Computational Investigation of Post-Translational Modification on Protein Structures and Their Impacts on Dynamics and Functions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite the central role of PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains difficult to interpret PTMs in terms of protein dynamics and function because there are many combinatorially enormous methods to modify the amino acids in response to changes in proteins’ environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein’s properties, dynamics, and interactions with its binding partners from an inferred or experimentally determined protein structure. |
Margaret Cheung ; Daniel Rodriguez ; Hoshin Kim ; Natalie Sadler ; Xiaolu Li ; Pavlo Bohutskyi ; Marat Valiev ; Weijun Qian; |
| 887 | Experiment and Simulations Reveal Residue Details for How Target Binding Tunes Calmodulin’s Calcium Binding Properties Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This reciprocal effect between Ca 2+, CaM, and CaMKII has been shown by many research groups; however, the basic mechanism underlying such complex process is still not well understood. In this work, we used the experimental and non-equilibrium coarse-grained molecular dynamics simulations to study the dynamics of CaM and its interactions with a family of three peptides (wildtype, 1-residue mutation, and 3-residue mutation) from the CaM-binding domain of CaMKII. |
Jules Berlin Nde Kengne ; Pengzhi Zhang ; Neal Waxham ; Margaret Cheung; |
| 888 | Modeling The Global Dynamics of The Tropomyosin-Actin Molecular Switch That Governs Cardiac Cell Contraction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this project, we utilize Elastic Network Modelling to construct a coarse-grain representation of thin filament dynamics and characterize possible actin-myosin coupling events. |
Harshita Pajarla ; Stuart Campbell; |
| 889 | Molecular Mechanisms of Thermal Sensing By TRP Ion Channels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work employs molecular simulations, multi-ensemble contact analysis, graph theory, and machine learning techniques to reveal the temperature-sensitive residue-residue interactions driving allostery in TRPV3. |
Davit Potoyan; |
| 890 | Insights Into Alzheimer’s Risk Factors Through Waste Protein Transport Modeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the aggregation and clearance mechanisms of Aβ in the interstitial spaces of the brain through the development of a numerical model. |
Lily Watkins ; Saikat Mukherjee ; Jeff Tithof; |
| 891 | Understanding The Physical Processes Behind DNA-DNA Proximity Ligation Assays Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the inner workings of DNA-DNA proximity ligation assays by means of numerical experiments and theoretical modeling. |
Bernardo Zubillaga Herrera ; Amit Das ; Linden Burack ; Ailun Wang ; Michele Di Pierro; |
| 892 | Simulation-based Inference for Non-parametric Statistical Comparison of Biomolecule Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study introduces a two-step statistical approach for comparing biomolecular dynamics across varied experiments without needing to pre-define a specific model for the observed random walks. |
jean-baptiste masson ; hippolyte verdier ; christian vestergaard ; françois Laurent ; christian Specht ; alhassan cassé; |
| 893 | Statistical Physics of Biological Aging Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Specifically, we define a biophysical model predicting the time evolution of DNA methylation patterns during ageing based on a wave localization mechanism of tilted competition between antagonistic chromatin modifiers. |
Steffen Rulands ; Aida Hashtroud ; Matteo Ciarchi; |
| 894 | Thermodynamics of Morphological Transitions in Growing Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This challenge stems from the fact that, at these scales, membrane growth reflects a delicate interplay of material exchange, bending deformation, apparent variation in material properties, and, crucially, in-plane viscous flow that often cannot be neglected. To address this challenge, we consider the nonequilibrium growth dynamics of a minimal model of fluid membranes, in which sufficiently large driving forces produce a striking morphological transition marked by out-of-plane buckling, in-plane flow, and dramatic changes in the growth rate. |
Jordan Shivers ; Michael Nguyen ; Aaron Dinner ; Suriyanarayanan Vaikuntanathan; |
| 895 | Deciphering The Interface Laws of Turing Foams Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our theory offers a new ansatz to find principles of macroscopic self-organization in mass-conserving systems far from equilibrium. |
Henrik Weyer ; Tobias Roth ; Erwin Frey; |
| 896 | Unraveling The Structure of Cofilin Oligomers: Insights Into Actomyosin Network Regulation Through Coarse-Grained Molecular Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we conducted an exploration of potential cofilin dimer structures using molecular dynamics simulations performed on human cofilin 1 (PDB ID: 4BEX). |
Chengxuan Li ; Tingyi Wei ; Min-Yeh Tsai ; Margaret Cheung; |
| 897 | Microscopic Origins of The Viscosity of RNA-peptides Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we investigate the microscopic origin of flow activation energy in bio-condensates by using coarse-grained simulations of peptide and nucleic acid mixtures. |
Sean Yang ; Davit Potoyan; |
| 898 | Probing The Anisotropic Bendability of Double-stranded DNA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we utilize a single-molecule DNA looping assay to probe the local asymmetric bendability of DNA, both with and without a base pair mismatch. |
Harold Kim ; Michael Ryan; |
| 899 | The Surprising Ways in Which Macromolecular Crowders Affect DNA Structure and Topology Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using single molecule approaches, we show that macromolecular crowders, such as PEG and Dextran, which are often used in medical/pharma applications, (1) stabilize the right-handed structure of DNA against unwinding, (2) favor the parallel (solenoidal) vs. anti-parallel conformation of commonly sized protein-mediated DNA loops and (3) decrease the persistence length of DNA facilitating compaction. |
Laura Finzi ; David Dunlap ; Jin Qian ; Zachary Montgomery ; Andrew Spakowitz; |
| 900 | Controlling Gene Expression Timing Through Gene Regulatory Architecture Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this project, we systematically investigate how the response time of genes in auto-regulatory networks is controlled by the molecular details of the network. |
MD ZULFIKAR ALI ; Robert Brewster; |
| 901 | Maximum Entropy Models for Patterns of Gene Expression Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use the available data to write models for the number of copies of mRNAs and then study the statistical properties of the resulting distribution. |
Camilla Sarra ; William Bialek; |
| 902 | Supercoiling-mediated Feedback Rapidly Couples and Tunes Transcription in Mammalian Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesized that mechanical sources of gene regulation may be a powerful force driving expression changes at the kilobase scale that we could harness through design. |
Christopher Johnstone ; Kate Galloway; |
| 903 | Regulation of Chromatin Transcription Via DNA Supercoiling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our model recapitulates the experimentally observed weaker torsional response of chromatin compared to bare DNA, and proposes structural transitions of nucleosomes into chirally distinct states as the driver of the contrasting torsional mechanics. |
Sumitabha Brahmachari ; Shubham Tripathi ; Jose Onuchic ; Herbert Levine; |
| 904 | Stochastic Nucleosome Disassembly Mediated By Remodelers and Histone Fragmentation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. |
Xiangting Li ; Tom Chou; |
| 905 | AMPK Regulates Chromatin Dynamics and Structure Through LaminA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Silencing SUN2 showed no contribution to AMPK regulation, but silencing LaminA did. |
Fadil Iqbal; |
| 906 | Modeling The Origin of Long-Range Correlation of DNA Methylation in Chromosomal DNA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our study, we introduce a dynamic model that captures the transport behavior of methyltransferases. |
Ariana Tse ; Andrew Spakowitz; |
| 907 | Quantum Biology: Magnetic Fields, Reactive Oxygen Species, and Stem Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In planarians, we have shown that at the wound site there are concentration-dependent effects of ROS accumulation on the amount of regenerative tissue produced. |
Wendy Beane; |
| 908 | Probing The Optimality of The Radical Pair Quantum Compass Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Nevertheless, such studies were limited by their use of simplified models, which overlook complex inter-radical interactions and hyperfine couplings present in biological settings. We aim to address this gap by probing the quantum fisher information in spin models of realistic complexity. |
Farhan Chowdhury ; Luke Smith ; Jonas Glatthard ; Daniel Kattnig; |
| 909 | Entanglement and Coherence in Pure and Doped Posner Molecules Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have modelled the spin dynamics of entangled phosphorus nuclei in pure and doped calcium phosphate molecules. |
Francesco Petruccione ; Betony Adams ; Ilya Sinayskiy; |
| 910 | Li Isotopes Differentiation in Neuronal Activity – Evidence for Novel Quantum Effects in Neuroscience Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our work, we studied the role of the two stable isotopes of lithium (Li) to elicit a Li isotope differentiation in neuronal activity. |
Khadijeh Esmaeilpour ; Irina Bukhteeva ; James Livingstone ; Michael Beazely ; Evgeny Pavlov ; Brian Kendall ; John Mielke ; Michel Gingras ; Zoya Leonenko; |
| 911 | A Resonantly Enhanced Relaxation Rate in The Fenna-Matthews-Olson Complex Produces A Resonantly Suppressed Dephasing Rate Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discovered resonant behavior based on a dimer model submerged in a bosonic bath with a pronounced vibrational mode. |
Jiahao Chen ; Elyana Crowder ; lance lampert ; Xiang Lian ; Shantanu Chaudhary ; Dragomir Davidovic; |
| 912 | Heteropolymer Modelling and Design Incorporating Quantum Chemistry with RosettaQM Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This presentation will explore the many applications of quantum chemistry calculations for heteropolymer design, docking, and structure prediction. |
Vikram Mulligan ; Bargeen Turzo ; P Douglas Renfrew ; Christopher Jurich ; Benjamin Brown; |
| 913 | X-ray Standing-Wave X-ray Fluorescence Study of The Interaction of An Anti-microbial Peptide with A Supported Phospholipid Bilayer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have used standing wave x-ray fluorescence (SWXF) to measure the configuration of the anti-microbial peptide indolicidin within a solid supported phospholipid bilayer. |
Gobind Basnet ; Jonathan Maloney ; Elizabeth Gaillard ; Laurence Lurio; |
| 914 | Applying Radio Frequency Analysis Techniques to Characterize DNA Both Experimentally Via Dielectric Response and Computationally Via Molecular Dynamics Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed a novel technique to probe biomolecular solutions using electromagnetic waves in the radio frequency (RF) spectrum (10 MHz – 40 GHz) to rapidly characterize electrophysical properties such as the dielectric permittivity spectrum. |
Elisa Rheaume ; Alec Cook ; Ryan Westafer ; James Dee ; Harold Kim ; JC Gumbart; |
| 915 | Expansion Microscopy Through Mechanical Force Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To overcome the fragmentation and time issues, we use a highly stretchable hydrogel and a mechanical stretcher device to achieve near 20X linear expansion faster. |
Vignesh Venkataramani ; Zhanda Chen ; Cole Reinholt ; Lydia Kisley; |
| 916 | All-Electronic Extracellular PH Control Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have developed an electrical approach utilizing graphene transistor-based pH sensors, to accurately characterize pH within cellular systems. |
Xiaoyu Zhang ; Xin Zhang ; Xiao Fan ; Huilu Bao ; Jinglei Ping; |
| 917 | Collective Self-caging of Active Filaments in Virtual Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study unveils an intriguing aspect of photosensitivity: the formation of intricate super-filamentous aggregates with collective mechanical capabilities at boundaries of illuminated regions. We investigate the influence of light pattern, especially boundary curvature, on this aggregation process using an agent-based model for active, flexible filaments. |
Leila Abbaspour; |
| 918 | Magnetically Controllable Bacterial Turbulence Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we show that the active turbulence of swimming bacteria can be driven into a nematic-aligned state over long distances by doping magnetic nanoparticles and applying a uniform magnetic field. |
Kazusa Beppu ; Jaakko Timonen; |
| 919 | The Momentum Transfer During Take-off in Birds Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we recorded high-speed videos of birds at the zoo and derived a theoretical model across body size. |
Guan-Yu Chen ; Zhi-Yong Wu ; Shan-Hung Chen ; Yi-Hsuan Chen ; Patricia Yang; |
| 920 | Defect Interactions and Dynamics Control Ordering in Self-propelled Rod Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: When nutrients are prevalent they spread out into a thin layer of densely packed cells on the surface of a gel, forming an active nematic liquid crystal. In order to understand the detailed effects of tuning reversal rate and speed on this material we developed an agent-based simulation for M. xanthus as a system of self-propelled flexible rods. |
Katherine Copenhagen ; Matthew Black ; Joshua Shaevitz; |
| 921 | From Chaos to Order: Boundary-driven Flow Transitions in Microtubule-kinesin Active Fluid Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the role of a moving boundary on the flow kinematics of active fluids. |
Joshua Dickie ; Tianxing Weng ; Yen-Chen (Anderson) Chen ; Yutian He ; Saloni Saxena ; Robert Pelcovits ; Thomas Powers ; Kun-Ta Wu; |
| 922 | Asymmetry in Active-Passive Phase Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study how activity influences the morphology of microphase separation. |
Paarth Gulati ; Fernando Caballero ; Liang Zhao ; Itamar Kolvin ; Zvonimir Dogic ; M Cristina Marchetti; |
| 923 | Arrested Development of Active Matter in Liquid Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will discuss analytical and numerical insights into swimming through model liquid-crystalline fluids, including the observation of an arrested steady state with connections to the nonlinear pendulum equation and associated Jacobi elliptic function solutions. |
Jingyi Li ; Laurel Ohm ; Saverio Spagnolie; |
| 924 | Control of Active Nematics Via Viscoelastic Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will consider the dynamics of an active nematic confined in a channel made of viscoelastic material. |
Francesco Mori ; Saraswat Bhattacharyya ; Julia Yeomans ; Sumesh Thampi; |
| 925 | Cells Around The Corner Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Anisotropically shaped cells exhibit a tendency to self-align, giving rise to domains of nematic ordering while experiencing splay and bend, and forming topological defects akin to those observed in 2D nematic liquid crystals. To elucidate the physical properties of this unique liquid crystal, the research explores the behavior of monolayers of cells in proximity to corners and sharp edges. |
Aniruddh Murali ; Kirsten Endresen ; Prasoon Awasthi ; Francesca Serra; |
| 926 | Emergent Metric-like States of Active Particles with Metric-free Polar Alignment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study a model of self-propelled particles interacting with their k-nearest neighbors via polar alignment. |
Pawel Romanczuk ; Yinong Zhao ; Cristian Huepe; |
| 927 | In Silico Conformational Dynamics and Mechanics of Soft Vesicle Enclosing Self-Propelled Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study offers a simple computational model that helps us understand the intricate dynamics of vesicles laden with active particles. |
Haosheng Wen ; Sunil Kumar P B ; Mohamed Laradji; |
| 928 | Extracting Active Fluctuating Forces from Fluctuating Motions of An Active Particle in A Viscoelastic Medium in A Quadratic Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study uses two different wavelength lasers to create an optical trap and to serve as a tracking beam. |
Simin Xia ; Chong Shen ; Johanna Harding ; H Daniel Ou-Yang; |
| 929 | Spatial Pattern Formation with Multi-scale Ordering in Living Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we discovered that dense bacterial living matter can spontaneously develop large-scale regular spatial patterns with multiscale order. |
Haoran Xu ; Yilin Wu; |
| 930 | Asymmetric Deformation and Disintegration of An Active Interface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We combine conventional equilibrium liquid-liquid phase separation with a microtubule-based active fluid. |
Liang Zhao ; Paarth Gulati ; Itamar Kolvin ; Fernando Caballero ; M Cristina Marchetti ; Zvonimir Dogic; |
| 931 | Design Principles for Fast and Efficient Self-assembly Processes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss how the time efficiency and other dynamical properties of reversible self-assembly depend on the morphology (shape) of the building blocks for systems in which the binding energy between the constituents is large. |
Erwin Frey ; Florian Gartner; |
| 932 | Asymptotic Designability of Self-Assembled Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce the concept of Asymptotic Designability, which allows us to quickly identify which structures are thermodynamically stable at high yield, and to determine the degree of control over the relative yields within a group of designable structures. |
Maximilian Huebl ; Carl Goodrich; |
| 933 | Escaping Kinetic Traps Using Non-reciprocal Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce a mechanism that leverages non-reciprocal interactions among system components, disrupting the conventional action-reaction symmetry and introducing non-equilibrium effects. |
Saeed Osat ; Jakob Metson ; Mehran Kardar ; Ramin Golestanian; |
| 934 | Dynamical Phase Transition in Programmable Multicomponent Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use a lattice model to study the seeded growth of prototypical multicomponent crystals, where different unit cell designs can be encoded through directional interactions. |
Fan Chen ; William Jacobs; |
| 935 | Understanding The Mechanisms of Crystallization and Reconfiguration of Anisotropic Nanoparticle Superlattices Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To explain observations from LCTEM experiments, we develop a computational model that reproduces the experimental phase behavior and show that variable charge screening by the solvent drives the assembly of the nanocubes into different phases. |
Tim Moore ; Tobias Dwyer ; Yaxu Zhong ; Jun Chen ; Xingchen Ye ; Sharon Glotzer; |
| 936 | Elasticity-Mediated Assembly and Transitions of Colloids in An 2D Fluid Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we demonstrate three classes of domain configurations, controlled by the availability of membrane bending, which is manipulated osmotically. |
Maria Santore ; Weiyue Xin ; Gregory Grason; |
| 937 | Multi-objective Optimization for Targeted Self-assembly Among Competing Polymorphs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a machine-learning guided approach to explore pair potentials that maximizes both the thermodynamic stability and kinetic accessibility of the honeycomb polymorph. |
Sambarta Chatterjee ; William Jacobs; |
| 938 | Programmable Nanomagnets for Microscopic Self-Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Once released, we drive particles to explore their configuration space by a rotating magnetic field, generating chaotic flows that mix particles and drive assembly at the air-water interface. |
Melody Lim ; Zexi Liang ; Conrad Smart ; Chrisy Xiyu Du ; Michael Brenner ; Paul McEuen ; Itai Cohen; |
| 939 | Proofreading Mechanism for Robust Self-assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce an explicit proofreading scheme for the assembly of colloidal structures. |
Qian-Ze Zhu ; Ella King ; Chrisy Xiyu Du ; Michael Brenner; |
| 940 | Theory of Nonequilibrium Symmetry-Breaking Coexistence and Active Crystallization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The breaking of detailed balance, and the resulting absence of Boltzmann statistics, motivates the need for a symmetry-breaking coexistence theory that is independent of the underlying distribution of microstates. Here, we develop such a theory, relying only on mechanics, balance laws, and system symmetries. |
Daniel Evans ; Ahmad Omar; |
| 941 | A Binary System to Investigate Photothermally Driven Self-assembly of Colloidal Particles and Nanocomposites Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Interestingly, we find a transition from 2D monolayers to 3D clusters as the assembled particle size gets smaller than 1 μm. |
Nabila Tanjeem ; Jose Lopez-Ceja ; Shirlaine Juliano ; Vanessa Flores ; Stephen Smith ; Gargi Mansingh; |
| 942 | Effect of Calamitic Ligands on Quantum Dot Size and Packing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate the use of calamitic ligands in quantum dot (QD) dispersion and assembly. |
Samia Liba ; Alauna Wheeler ; Jocelyn Ochoa ; Ben Stokes ; Tim Atherton ; Linda Hirst; |
| 943 | Mechanical Properties of Adipose Tissue Mediate Breast Cancer Invasion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that increasing the adipocyte stiffness strongly suppresses breast cancer invasion. |
Dong Wang ; Yitong Zheng ; Garrett Beeghly ; Brianna Knode ; Claudia Fischbach ; Mark D Shattuck ; Corey O’Hern; |
| 944 | Migration of Circulating Tumor Cells Through A Heterogeneous Constriction Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we will present preliminary data showcasing the coupling effect between CTCs and the fluid flow, shedding light on the development of a statistical model to predict CTC breakthrough through the network. |
Ankur Bordoloi ; Tim Winkel ; Kristian Thijssen ; Amin Doostmohammadi ; Pouyan Boukany; |
| 945 | Transport of Cancer Cells in Shear Flows Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our preliminary work ( Akerkouch et al., Ann Biomed Eng 51, 1199–1215 (2023)) suggested a potential link between cancer cell growth and the fluid flow pattern. |
TRUNG LE ; Tam Nguyen ; Lahcen Akerkouch ; Amanda Haage; |
| 946 | Using Cancer Cell Motility to Predict The Final Morphology of The Tumor Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we generate three-dimensional engineered spheroids of triple-negative breast cancer cells, comprising two clonal subpopulations with epithelial and mesenchymal characteristics. |
Carolina Trenado Yuste ; Samhita Banavar ; Celeste Nelson; |
| 947 | Investigating Glioblastoma Growth and Metabolism Via MNK-eIF4E Pathway Modulation Using NMR Spectroscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The study will include the presentation and discussion of data obtained from NMR spectroscopy and other relevant sources. |
Kathleen Cate Domalogdog ; Lloyd Lumata; |
| 948 | Biophysical Modeling Identifies An Optimal Hybrid Amoeboid-mesenchymal Phenotype for Maximal T Cell Migration Speeds Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we have developed a hybrid stochastic-mean field biophysical model of bleb-based cell motility to study the potential for adhesion-free bleb-based migration. |
Roberto Alonso Matilla ; David Odde ; Paolo Provenzano; |
| 949 | Computational Modeling of Breast Cancer Cell Invasion Into Adipose Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed novel discrete element method (DEM) simulations of tumor cell invasion into adipose tissue in three dimensions. |
Yitong Zheng ; Dong Wang ; Garrett Beeghly ; Claudia Fischbach ; Mark D Shattuck ; Corey O’Hern; |
| 950 | Optimizing Prostate Cancer Treatment: High-Frequency Adaptive Therapy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present analytical estimations and justifications for high-frequency adaptive therapy, and provide proposals for how it can be implemented through open-loop observations of patients in clinical practice. |
Trung Phan ; Shengkai Li ; Benjamin Howe ; Robert Gatenby ; Joel Brown ; Sarah Amend ; Kenneth Pienta ; Robert Austin ; Yannis Kevrekidis; |
| 951 | Mathematical Model for Pancreatic Cancer in Early Intraepithelial Neoplasia Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present the effects of a gene regulatory network of pancreatic cells when some genes have a delay actions. |
Jose-Roberto Romero-Arias ; Guillermo Ramirez-Santiago; |
| 952 | Traveling-wave Strategy for Plant-mycorrhizal Trade Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To monitor the construction of a living trade network, we built a custom-designed robot for high-throughput time-lapse imaging that could track >500,000 fungal nodes simultaneously. |
Thomas Shimizu ; Loreto Oyarte Galvez ; Corentin Bisot ; Philippe Bourriane ; Howard Stone ; E. Toby Kiers; |
| 953 | Physical Learning in Dynamical Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we generalize a contrastive learning approach for equilibrium systems, Coupled Learning, to derive local, physically realizable rules for training general dynamical systems described by sets of ordinary differential equations. |
Menachem Stern ; Andrea Liu ; Vijay Balasubramanian; |
| 954 | Waddington Differentiation and Saddle Bifurcation in Generalized Hopfield Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study the learning dynamics of Generalized Hopfield networks, which allow for a visualization of internal memories. |
Nacer Eddine Boukacem ; Allen Leary ; Paul Francois ; Madhav Mani ; Felix Gottlieb ; Robin Thériault; |
| 955 | The Restricted Kirchhoff Machine: Self-learning Electrical Circuits for Unsupervised Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce the Restricted Kirchhoff Machine (RKM), an electrical self-learning circuit with variable resistors that employs local rules to infer patterns from data. |
Marcelo Guzmán ; Simone Ciarella ; Andrea Liu; |
| 956 | Adaptation and Loop Stabilization in Periodically Driven Elastic Flow Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present an improved theory for adaptation with a remodeling signal that incorporates a comprehensive model of short-term pulsatile dynamics in elastic vessels, and hence more closely resembles actual biological remodeling at long time-scales. |
Purba Chatterjee ; Sean Fancher ; Eleni Katifori; |
| 957 | Adaptation Maximizes Information and Minimizes Dissipation Across Biological Scales Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Biological and living systems possess the inherent capacity to process information across spatiotemporal scales, displaying the hallmark ability to constantly adapt their responses to ever-changing and complex environments. We show that adaptation is a fundamental mechanism that spontaneously emerges when the system seeks to both maximize its information on external environments and minimize the unavoidable dissipation of its receptors. |
Daniel Maria Busiello ; Giorgio Nicoletti; |
| 958 | Adaptation, Fluctuating Landscapes and Heavy-tails in Animal Behavior Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The slow mode dynamics exhibits heavy-tailed first passage time distributions and correlation functions, and we show that such heavy tails can be explained by dynamics on a time-dependent potential landscape. Inspired by these results, we introduce a generic model in which we separate faster mixing modes that evolve on a quasi-stationary potential, from slower non-ergodic modes that drive the potential landscape, and reflect slowly varying internal states. |
Antonio Carlos Costa ; Massimo Vergassola; |
| 959 | Nonlinear Dynamics of Habituating Systems: Learning to Ignore Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In particular, we introduce an extensible family of nonlinear modules that can hierarchically implement various hallmarks. |
Matthew Smart ; Stanislav Shvartsman ; Martin Mönnigmann; |
| 960 | Predicting Cellular Regulation from Natural Selection, Thermodynamics and Control Theory Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We provide examples in both bacteria and fungi. |
William Cannon; |
| 961 | Discovering Plasticity Rules That Organize and Maintain Neural Circuits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Drawing inspiration from a recent study in zebra finch demonstrating the resilience of the song premotor area HVC after significant cell perturbation (Wang et al, 2022), we employ a meta-learning approach to find robust sets of unsupervised, online rules that can organize and maintain the dynamics of a similar circuit. |
David Bell ; Alison Duffy ; Adrienne Fairhall; |
| 962 | Modeling Stochastic Phenotypic Adaptation to Predict Enzalutamide Resistance in Prostate Cancer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop and apply a stochastic decision-making model to study the dynamics of Enza-resistant and Enza-sensitive cells. |
Zahra Ghoreyshi ; Shibjyoti Debnath ; Jason Somarelli ; Jason George; |
| 963 | Generalized End-product Feedback Circuit Senses High Dimensional Environmental Fluctuations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we extend this analysis to higher dimensions. |
Fang Yu ; Mikhail Tikhonov; |
| 964 | A Fractional Calculus Model of Bacterial Adaptation to Fluctuating Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To this end, we introduce a variable-order fractional model of growth control in which growth is dependent not only on the current metabolic state but also on previous history. |
Josiah Kratz ; Shiladitya Banerjee; |
| 965 | A Physics-based Model for Predicting Temperature-dependent Phase Behavior of Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have developed a quantitatively accurate residue-level coarse-grained model to predict temperature-driven protein condensation. |
Ananya Chakravarti ; Jerelle Joseph; |
| 966 | Investigating The Molecular Driving Forces of Liquid-liquid Phase Separation in Intrinsically Disordered Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Hence, an enhanced understanding of these determinants could offer insight into cellular organisation, as well as shedding light on the pathogenesis of protein condensation diseases. We have investigated these molecular drivers using a model for intrinsically disordered proteins. |
Ellen Carrick ; Jennifer McManus; |
| 967 | Modeling Phase Separation of Proteins with Compact Native States Using LatticePy, A Package for MCMC Simulations on Lattices Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Implementing standard moves for lattice proteins and simple energy functions, we explore the conditions under which proteins with a well-defined, compact native state instead adopt unfolded conformations as part of multiprotein oligomers or condensates. |
Sohit Miglani ; Ned Wingreen ; Benjamin Weiner; |
| 968 | Multiscale Approaches to Model The Functions of Ubiquitin and SUMO Modifications in Protein Phase Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we employed a multiscale simulation approach that encompasses atomistic to different level coarse-grained modeling techniques with data-driven machine-learning methods, to explore the structural differences and multidimensional energy landscape of ubiquitin and SUMO and their conjugates. |
Supriyo Naskar ; Kurt Kremer ; Oleksandra Kukharenko; |
| 969 | Thermodynamics and Transport Properties of Pure RNA Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To this end , building on previous work, we have implemented and optimized a model for probing RNA condensation. |
Dilimulati Aierken ; Jerelle Joseph; |
| 970 | RNA-driven Percolation Transitions in Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate RNA-driven percolation transitions in the context of multicomponent protein-RNA condensates that closely mimic intracellular ribonucleoprotein (RNP) granules. |
Tharun Selvam Mahendran ; Gable Wadsworth ; Anurag Singh ; Priya Banerjee; |
| 971 | Active Remodeling of RNA Interactions Facilitates Nonequilibrium Steady States of Protein-RNA Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we assess the effects of active RNA remodeling by a DEAD-box helicase on condensate structure, composition, and phase behavior. |
Sebastian Coupe ; Nikta Fakhri; |
| 972 | Modulating Condensate Properties and Catalytic Activity with Peptide Sequence in Coacervate Dispersions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To simultaneously explore both the potential influence of droplet physical properties on biochemical reactions in demixed systems as well as the control of those properties through polypeptide sequence, we use polyelectrolyte complex coacervate microdroplets prepared from an RNA enzyme and a small library of prebiotic peptide sequences as a minimal model system. |
Patrick McCall ; Basusree Ghosh ; Lars Hubatsch ; T-Y Dora Tang; |
| 973 | Functional Membraneless Organelles Formed By De Novo Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In my talk, I will describe the design of genetically encoded de novo polypeptides that form membraneless organelles in Escherichia coli and how the designed polypeptide can co-compartmentalize a functional enzyme pair, to create functional membraneless organelle with product formation close to the theoretical limit. |
Jennifer McManus ; Alexander Hilditch ; Andrey Romanyuk ; Ragesh Kumar Thelakkadan Puthiyaveettil ; Stephen Cross ; Richard Obexer ; Derek Woolfson; |
| 974 | Synchronization of Chemical Reactions in A Population of Phase-separated Droplets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this project, we explore whether biomolecular condensates formed via liquid-liquid phase separation could act as a means for collective behaviour to emerge within a cellular environment to enable population-level control of chemical reactions relevant to complex biological processes. |
Alisdair Stevenson ; Sudarshana Laha ; Christoph Weber ; Thomas Michaels; |
| 975 | Diffusiophoresis Promotes Phase Separation and Transport of Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report how ion gradients impact the transport processes of biomolecular condensates on the mesoscale and biomolecules on the microscale. |
Viet Sang Doan ; Ibraheem Alshareedah ; Anurag Singh ; Priya Banerjee ; Sangwoo Shin; |
| 976 | Buffering of Biomolecular Condensate Volume and Mass in Multi-component Mixtures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides new insights into the potential role of biomolecular condensates in functional biology. |
Logan de Monchaux-Irons ; Thomas Michaels ; Nina Han ; Benjamin Frühbauer ; Leonidas Emmanouilidis ; Madhav Jagannathan ; Frederic Allain ; Giulia Celora; |
| 977 | Physical Mechanisms of Protofilament Formation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a novel coarse-grained model for amyloidogenic polypeptides [1] and use Brownian dynamic simulations [2] to gain insight into the physical mechanisms of assembly into oligomeric species. |
Ioana Ilie; |
| 978 | Developing Methods to Classify Protein Clusters As Liquid-liquid Phase Separated Biomolecular Condensates in Vivo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: LLPS is now believed to play a role in many key cellular processes including gene regulation. To test this hypothesis, we are studying the transcription factor Bicoid (Bcd) in fly embryos which has structural properties important for LLPS. |
Alex Verbeem ; Lydia Hodgins ; Cécile Fradin; |
| 979 | Abnormal Vein Geometry and Pathologic Blood Flowrates in Dialysis Patients Create Complex Hemodynamics and Loss of Dialysis Access Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a novel method for device fabrication and imaging that recreate complex hemodynamics in large blood vessels at high flowrates in vitro. |
Anindita Basu ; Bingqing Xie ; Dylan Cook ; Mary Hammes; |
| 980 | Bilayered Tubes Display Internal Undulations As Arteries Do Under Pressure Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work shows that a synthetic inner-lined elastic tube with a stiffness mismatch between the lining and the support displays similar behavior. |
Leonardo Gordillo ; Alicia Castro-Montes ; Damyan Santander ; Javier Maldonado ; Ben Foster; |
| 981 | Modeling The Mechanics of Cell-cell Junction Formation and Dynamics in Vascular Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Starting with a simple case of a two-body problem of cells, we study the mechanics of junction formation and how it is controlled by protrusive activity and cell-cell interactions. |
Suraj Sahu ; Ajay Gopinathan; |
| 982 | Neuronal Growth Investigated By Traction Force and Atomic Force Microscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here I will present experimental results obtained by measuring traction forces and stresses exerted by neurons on the growth substrate during axonal extension. |
Cristian Staii; |
| 983 | Probing Effects of Vimentin on Cell Cytoskeleton Dynamics Through Differential Dynamic Microscopy (DDM) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our research reveals that cells lacking vimentin show 1.5 times higher decay times compared to cells with vimentin, which suggest that vimentin enhances the dynamics of microtubule filaments in the cell. |
Renita Saldanha ; Ryan McGorthy ; Rae Robertson-Anderson ; Alison Patteson; |
| 984 | Osmotic Pressure Microscopy: New Method to Quantify Cellular Mechanical Properties in Walled Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We are developing a new method, Osmotic Pressure Microscopy (OPM) to measure in living cells the parameters most relevant to understand plant movements and growth. |
Mohammad Haque ; Mandar Deshpande ; Sylvia Silveira ; Constance Le Gloanec ; Anne-Lise Routier; |
| 985 | Reverse-engineering Plant Cell Mechanical Properties Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed a novel method to reverse engineer the cellular mechanical properties using osmotic treatments and Finite Element Method(FEM) simulations of pressurized cells. |
Mandar Deshpande ; Muhammad Sahil Haque ; Anne-Lise Routier-Kierzkowska ; Loann Collet; |
| 986 | The Mechanical Behavior of Arabidopsis Cotyledons with Genetic Mutations Affecting Cell Structure and Cell Adhesion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To address the current gap, we perform mechanical testing on the cotyledons of Arabidopsis mutants. |
Michael Wilson ; Juan Pablo Jaimes Bermonth ; Alexander Howell ; Daniel Szymanski ; Chelsea Davis; |
| 987 | Investigation of Adhesion Forces on The Surface of Borrelia Burgdorferi Using AFM Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: The Lyme disease spirochete, Borrelia burgdorferi (Bb), is the leading cause of arthropod-borne disease in the USA. Adhesion is important to the establishment of infection and … |
Carlos Munoz ; Mehmet Ozdogan ; Yvonne Tourand ; Timothy Casselli ; Catherine Brissette ; Nuri Oncel; |
| 988 | A General Solution of A Regular 2D Spring Network to Model The E. Coli Peptidoglycan Shell Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We derive general constitutive laws, valid for large deformations, non-linear responses, and arbitrary anisotropies. |
Octavio Albarran ; renata garces ; Jeff Eldredge ; Giacomo Po ; Christoph Schmidt; |
| 989 | IPF ECM-Derived Hydrogels Promote The Inflammatory Cytokine Expression of Cultured IPF Fibroblasts and Trigger An Inflammatory and Proliferative Immune Cell Profile Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To better understand fibroblast biology in IPF, we developed a 3D hydrogel model derived from human fibrotic lung tissue that allows us to study the effects of fibroblast activation and cytokine expression without the confounding influence of mechanosignaling from stiff plastic substrates. |
Jeffrey Moran ; Jorge Fernandez ; Amit Singh ; Luis Rodriguez ; Geraldine Grant ; Joseph Kim ; Durwood Moore ; Jawad Khan; |
| 990 | Oral: A Mathematical and Computational Model to Study The Role of The Cardiac Jelly During Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we introduce a detailed mathematical model to describe the dynamics of the cardiac jelly. |
Daniel Santos-Olivan ; Alejandro Torres Sánchez; |
| 991 | Reproducing Experimentally Observed Alternans in Cardiac Tissue Using Fractional Diffusion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Computational studies have shown mechanisms behind the dynamics of alternans, however to date they fail to reproduce the dynamics quantitatively, requiring much larger tissue domains compared with experiments. In this talk we argue that the voltage propagation in cardiac tissue in the mesoscopic scale can be described by fractional diffusion and this allows for models to be fitted in tissue sizes as in experiments. |
Lynn Jin ; Elizabeth Cherry ; Flavio Fenton ; Ilija Uzelac ; Alessio Gizzi; |
| 992 | A Modified Fitzhugh-Nagumo Model That Reproduces The Action Potential and Dynamics of The Ten Tusscher Et. Al. Cardiac Model in Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We created a modified FHN model that matches most of the AP shape of the TNNP model for a large range of periods and dynamics in space. |
Evan Rheaume ; Hector Velasco-Perez ; Darby Cairn ; Maxfeild Comstock ; Elisa Rheaume ; Abouzar Kaboudian ; Ilija Uzelac ; Elizabeth Cherry ; Flavio Fenton; |
| 993 | Topological Structures in Polar Liquid Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigated how topological defects in the N F liquid crystals can be affected and controlled by the orientation fields at confining flat surfaces. |
Qi-Huo Wei; |
| 994 | Influence of Confining Surface Gaussian Curvature on The Winding Character of Nematic Disclination Lines Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we use Landau-de Gennes numerical modeling to investigate how Gaussian curvature at the boundary surface influences the winding characters of disclination lines in the bulk. |
Jane Bernadette Denise Garcia ; Mohamed Amine Gharbi ; Daniel Beller; |
| 995 | Numerical Study of Chiral Structures from Achiral Liquid Crystals Using Ball-Majumdar Singular Potential Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These configurations are made possible by the small twist elastic constants of LCLCs relative to their bend and splay elastic constants, though energetic arguments on this point are still under debate. We present a study of these systems using a Ball-Majumdar singular potential computational field theory. |
Lucas Myers ; Jorge Vinals; |
| 996 | Complementary Tensorial Measures of Disclination Line Winding Character Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we demonstrate that the rotation vector can also be calculated from an alternative measure, based on a second-rank pseudotensor defined on either the director field or the Q-tensor field. |
Daniel Beller ; Jane Bernadette Denise Garcia ; Robert Pelcovits ; Thomas Powers ; Jonathan Selinger; |
| 997 | Elasticity and Topological Defects: A Common Thread Between Soft and Hard Materials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The resulting model will be illustrated through select examples of disclination statics and dynamics in nematic liquid crystals and, separately, experimentally observed grain and subrain boundaries in a hard metal. |
Amit Acharya; |
| 998 | Analytical Predictions of Topological Defect Interactions in Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By using appropriate approximations for the nematic order parameter and velocity fields, we find analytical expressions for the velocity of +1/2 and -1/2 winding number topological defects as a function of their distance and orientation. |
Cody Schimming ; Cynthia Reichhardt ; Charles Reichhardt; |
| 999 | Exploring The Formation of Initial Disclination Loops of Active Nematics Through Particle-Based Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we propose a simple model for the formation of an initial disclination loop within the framework inspired by biaxial nematics. |
Yingyou Ma ; Michael Hagan ; Aparna Baskaran; |
| 1000 | Cooperative Motion and Granule Rotation During Rapid Grain Shrinking in Colloidal Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that the periods of rapid dissolution involve the cooperative motion of particles together in rotating, hexagonal ‘granules.’ |
Avani Anne ; Eric Corona ; Helen Chaffee ; Chris Couto ; Elizabeth Rogers ; Aaron Galper ; Conor Floyd ; Ananya Venkatachalam ; Sharon Gerbode; |
| 1001 | Inducing Point Defects in 3D Colloidal Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed a model system in which point defect formation in 3D colloidal crystals can be controlled in-situ. |
Max Schelling ; Janne-Mieke Meijer; |
| 1002 | Controlling Topological Defects in Colloidal Crystal Shells of Hard Superballs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use hard particle Monte Carlo simulations to determine the effect of particle shape and lattice preference in flat space on the structure and distribution of defects in spherical shells filled densely with colloidal particles whose shape varies continuously from a sphere to a cube. We describe defect scar analogues for these systems and show how the scar pattern relates to particle shape. |
Gabrielle Jones ; Philipp Schönhöfer ; Sharon Glotzer; |
| 1003 | Model Predictive Control of Active Brownian Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we propose a feedback control framework for controlling noninteracting Active Brownian Particles (ABPs) at the population level. |
Titus Quah ; Sho Takatori ; James Rawlings; |
| 1004 | Using Potentials to Model The Crystallography of Bee Honeycomb Under Geometric Frustration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: When faced with various geometric constraints, such as boundaries or connecting combs with different orientations, the resulting comb is irregular, with several topological defects. In this work, we study this process using 3D-print experimental frames with imprinted foundations, which impose a precise geometric frustration. |
Francisco Lopez Jimenez ; Yasara Dharmadasa ; Golnar Gharooni Fard ; Orit Peleg; |
| 1005 | Design of Functional Disordered Solids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a novel numerical approach, which directly connects interactions with their effect on emergent elastic properties, to study the self-assembly of disordered solids. |
Mengjie ZU ; Carl Goodrich; |
| 1006 | Nonequilibrium Interfacial Properties of Chemically Driven Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we employ a minimal model of chemically driven fluids in order to study changes in the interfacial tension away from equilibrium. |
Yongick Cho ; William Jacobs; |
| 1007 | Control of Cohesive States in Colloidal Chiral Fluids Through Chemical Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a novel approach to externally govern the collective behavior of spinning colloids by introducing additional diffusiophoretic interactions amongst geometrically anisotropic colloidal components. |
Jaideep Katuri ; Navneet Kaur ; Allison Cornelius ; David Quashie ; Jamel Ali; |
| 1008 | Acoustic Parametric Pumping for Precise Control in A Multi-particle System with Tunable Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The precise control of such a system becomes even more challenging when its interactions are strongly correlated, nonlinear, non-pairwise additive, and non-conservative. Here, we introduce a general method combining parametric pumping and quenching to non-invasively control the configuration of such a multi-particle system and demonstrate it with an acoustically levitated small cluster of particles. |
Qinghao Mao ; Brady Wu ; Bryan VanSaders ; Heinrich Jaeger; |
| 1009 | Active Gas-to-solid Phase Transitions Ruled By Responsive Active Pumping Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work highlights the importance of responsive active pumping in dictating the collective behaviors of active agents. |
Alexandre Morin ; Marine Le Blay; |
| 1010 | Local Curvature Directs Active Particles in Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For this purpose, we conducted simulations (in Julia) on active Brownian particles subjected to hard elliptical confinement. |
Jyoti Sharma ; Francesco Bianciardi ; Lapo Corti ; Stefano Palagi; |
| 1011 | Self-organization of Self-propulsion Forces in A Persistent Active Liquid Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have used Langevin dynamics simulations to study the effects of activity in a two-dimensional dense glass-forming system of Lennard-Jones particles at zero temperature. |
Chandan Dasgupta ; Suman Dutta ; Pinaki Chaudhuri ; Madan Rao; |
| 1012 | Aggregate Morphing of Self-aligining Soft Active Disks in Semi-confined Geometry Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: As the softness parameter decreases, the system’s intriguing structural and dynamical features become more apparent, such as the appearance and disappearance of layered structure. Several of these insights concerning the behavior of self-aligning soft active particles in confined spaces, as well as the possibilities for manipulating their structure via box geometry, will be presented in this work. |
Anshika Chugh ; Soumen Karmakar ; Rajaraman Ganesh; |
| 1013 | Spontaneous Shock Waves in Pulse-stimulated Flocks of Acitive Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report on the emergence of shock wave patterns composed of coherently moving particles energized by a pulsed electric field. |
Bo Zhang ; Andreas Glatz ; Igor Aranson ; Alexey Snezhko; |
| 1014 | Evaporation of Colloidal Suspensions of Aspherical Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent studies have shown that size-dependent stratification can occur in a rapidly drying suspension of a polydisperse mixture of spherical colloids. In this work we utilize molecular dynamics simulations based on an implicit solvent model to investigate the role of particle shape in such far-from-equilibrium processes. |
Binghan Liu ; Gary Grest ; Shengfeng Cheng; |
| 1015 | Birth of Marine Snow Aggregates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We recently discovered that marine snow is a multiphase comet-shaped particle that consists of mucus and particulate organic matter [R. Chajwa et al. arXiv:2310.01982 (2023)]. To understand the formation of these aggregates, we numerically study how the multiphase structures spontaneously form in Stokesian suspension in the non-linear regime of number-density perturbations; and find merging and fracture dynamics at long times with a steady state size distribution. |
Rahul Chajwa ; Manu Prakash; |
| 1016 | Density-dependent Emergent Dynamics of Sea Urchin Embryos Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report on the dynamics and emergent phases of sea urchin embryo assemblies. |
Lisa Lin ; Yu-Chen Chao ; Yuchao Chen ; Farzan Vafa ; Nikta Fakhri; |
| 1017 | Soft Mechanisms of Escape in Geometrically Frustrated Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In a previous work [1], we developed a minimal lattice model of frustrated assembly —focusing on the case of fixed frustration — where the super-extensive accumulation of strain persists to infinite size. |
Nicholas Hackney ; Chris Amey ; Gregory Grason; |
| 1018 | Chloroplasts’ Choreography: On Mechanisms of Light Adaptation in Plant Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using experiments and mathematical models, we will discuss how plants re-arrange the internal structure of cells by the active motion of chloroplasts, to remain efficient during photosynthesis. |
Nico Schramma ; Maziyar Jalaal; |
| 1019 | Tickling Plant Veins with Electroshock to Manipulate Vascular Traffic Lights Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Hence, we propose to overstimulate the plant using continuous electroshocks. |
Sabrina Gennis ; Kaare Hartvig Jensen; |
| 1020 | Biomechanics of Fast Actuation in Mimosa Pudica Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: The "touch-me-not" plant, Mimosa pudica, folds its leaves in less than a second in response to mechanical or electrical stimuli. This movement is reversible, and the … |
Joel Marthelot ; Mathieu Rivière ; Collins Keith ; Ethan Wavra ; Yoël Forterre; |
| 1021 | Cracking The Code of Foliar Desalination: The Structural Basis of Reverse Osmosis in Chambered Salt Glands Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have developed a steady-state, multicompartment, mathematical model to explore how the size and distribution of cuticle fractures affect the balance of pressure- and osmotically-driven fluxes through the gland. |
Melissa Mai ; Fulton Rockwell ; Noel Michele Holbrook; |
| 1022 | How The Softest Part of The Plant Cell Wall Makes It Strong: Pectin-Cellulose Entanglement Prevents Embolism Spread in The Plant Vascular System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In contrast, we hypothesize that the pectin network plays a critical role in preventing embolism spread by locally stabilizing the dynamic cellulose network via polymer entanglements and calcium crosslinks. |
Zhe He ; Fulton Rockwell ; Noel Michele Holbrook; |
| 1023 | Modelling and Inferring Protein Dynamics in Fission Yeast Mechanosensing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work aims at describing clustering by building a mathematical model based on reaction-diffusion equations that take into account the interactions between cell wall polysaccharides and Wsc1. |
Enrico Lorenzetti ; Arezki Boudaoud ; Antoine Fruleux; |
| 1024 | Pattering and Growth Are Coordinated Early in The Cell Cycle Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the model system – Arabidopsis thaliana, SHORTROOT (SHR) and SCARECROW (SCR) are transcription factors (TFs) that regulate the decision-making process of whether to divide formatively or proliferatively. Using an inducible SHR system, we followed the dynamics of these TFs and observed the cell outcome in long timelapses with high temporal resolution of more than 1000 cells. |
Pablo Szekely ; Cara Winter ; Vladimir Popov ; Heather Belcher ; Raina Carter ; Matthew Jones ; Scott Fraser ; Thai Truong ; Philip Benfey; |
| 1025 | Stochastic Simulations of Cortical Microtubule Dynamics Using Cytosim to Derive Biophysical Principles of Morphogenesis in Arabidopsis Leaf Trichomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Such a framework is crucial to investigate cytoskeleton’s regulatory role in cell growth. This study establishes a biophysical link between CMT-CSC dynamics and wall structure in Arabidopsis trichomes – an ideal system because they are single-celled, easily accessible, and reproducible. |
Eashan Saikia ; francois nedelec; |
| 1026 | Peristaltic Flow in Nonlinear Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A theory of peristaltic fluid flow through vessels with a nonlinear pressure-flow relationship is developed, and it is argued that coordination in valve placement is vital for the system to operate, while coordination between contractions is less important than in the linear network. |
Aaron Winn ; Eleni Katifori; |
| 1027 | Quantifying Metastasis Heterogeneity in Colorectal Cancer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We are taking advantage of a unique collection of multi-region sampled metastatic colorectal cancer cases that we have been building over years, encompassing more than 1000 distinct tumor samples from more than 100 patients. |
Kamila Naxerova; |
| 1028 | Quantifying The Somatic Evolution Occurring in Healthy and Pre-malignant Human Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk I will describe how large-scale sequencing data from hundreds of thousands of individuals can be used to provide quantitative estimates for the key parameters governing clonal evolution including the “fitness effects” conferred by specific variants, the mutation rates of alterations and the population sizes of cycling stem cells. |
Jamie Blundell; |
| 1029 | Predicting Cancer Evolution: Quantifying Immune Selection and Other Selective Pressures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we develop a biophysically grounded model to quantify immunogenicity of tumor neoantigens. |
Marta Luksza; |
| 1030 | Characterizing The T Cell Response to A Personalized Cancer Vaccine Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk I will discuss how to leverage T cell receptor (TCR) repertoire sequencing to characterize and monitor responses to the vaccine. |
Zachary Sethna; |
| 1031 | Finding Mechanisms of Resistance In Cancer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, I will discuss different approaches for finding mechanisms of resistance, including studying pre-treatment and post-resistance samples; estimating clonal fitness; and identifying convergent evolution across subclones. |
Gad Getz; |