Highlights of Biological Physics (DBIO) Talks @ APS 2023 March Meeting
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TABLE 1: Highlights of Biological Physics (DBIO) Talks @ APS 2023 March Meeting
| Paper | Author(s) | |
|---|---|---|
| 1 | Metabolic Constraints in The Evolution of Biochemical Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss the significance of this contribution from metabolic expenditures in the course of evolution, by considering the population dynamics. |
Efe Ilker; |
| 2 | From Metabolites to Cells: A Perspective on Non-Equilibrium Thermodynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we will provide an overview of field from the perspective of cells as chemical factories and discuss a selection of methods used to study cell systems. |
Connah Johnson; |
| 3 | Efficient Two-Dimensional Control of Barrier Crossing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We design minimum-dissipation protocols for harmonic trapping potentials under two-dimensional control (of both trap center and stiffness), for driven barrier crossing. |
Steven Blaber; David Sivak; |
| 4 | Stochasticity and Homeostasis in Macromolecular Crowding and Its Effects on The Rates of Reproduction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we will present our recent results on how the mother’s mass and macromolecular load is also not necessarily divided equally between daughter cells. |
Andreas Vasdekis; Shahla Nemati; Abhyudai Singh; Scott Dhuey; Armando McDonald; Daniel Weinreich; |
| 5 | Quantifying Biochemical Reaction Rates from Static Population Variability Within Incompletely Observed Complex Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show how incompletely specified mechanistic models can be used to translate qualitative knowledge of molecular interactions into reaction rate functions from covariability data between pairs of components. |
Andreas Hilfinger; Nava Leibovich; Timon Wittenstein; |
| 6 | How to Suppress Stochastic Fluctuations While Achieving Adaptation with Biologically Realistic Integral Controllers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, recent work has suggested that such robustness comes at the expense of increased stochastic fluctuations. We present theoretical results that support and quantify this trade-off for the commonly analyzed AIF variant in the non-biological limit with perfect annihilation. |
Brayden Kell; Andreas Hilfinger; Ryan Ripsman; |
| 7 | Degrading A Gradient: Information Transmission in Yeast Mating Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using both stochastic spatiotemporal modeling and tools from information theory, we find that the answer is yes: both the signal-to-noise ratio and information transmission increase with degradation. |
Ryan LeFebre; Joseph Landsittel; David Stone; Andrew Mugler; |
| 8 | Analysis of The Dynamics of The Growing and Branching Network of 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 filamentous fungus Podospora anserina under controlled culture conditions. |
Thibault Chassereau; Éric Herbert; Florence Chapeland-Leclerc; |
| 9 | Modeling Protein Dynamics from Brownian Motions to Transcription Regulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How to achieve biological regulations out of thermal motions are of high interest as we model the proteins from atomic to coarse-grained (CG) and from molecular dynamics (MD) to stochastic simulations. |
Jin Yu; |
| 10 | Binding Mechanism of Different Variants of SARS-CoV(-2) Virus with HACE2 Receptor Protein Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have investigated the binding mechanism of different variants of SARS-CoV(-2) virus with hACE2 receptor protein. |
Narayan Adhikari; Bidhya Thapa; Shyam Khanal; Lokendra Dhami; Jhulan Powrel; Prabin Dahal; Rajendra Koirala; Ashmita Shah; |
| 11 | Geometric Signatures of Switching Behavior in Mechanobiology Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These force-activated switching behaviors are important in various biological functions, from cell adhesion and mechanosensing, to molecular motors, proofreading, and antigen discrimination. We develop a theoretical framework that unifies these switching behaviors and identifies the signatures of a system’s free energy landscape that generate specific switches. |
Casey Barkan; Robijn Bruinsma; |
| 12 | Protein Dielectrophoresis in An Exact Nanotrap Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we propose an explicit geometry within which the correction may be put to the test. |
Taylor Colburn; |
| 13 | Dynamic Allosteric Modulation of G-Protein-Coupled Receptors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will present our recent studies in allosteric modulation of adenosine and muscarinic GPCRs by combining cutting-edge cryo-electron microscopy, Gaussian accelerated molecular dynamics (GaMD) simulations and pharmacology experiments 1,2. |
Yinglong Miao; |
| 14 | Analysis of Zika Virus’ Electrostatic Features Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By using several computational methods, we calculated electrostatic properties that allowed us to understand the interactions among multiple E proteins on the Zika virus capsid. |
Cassandra Del Rio De Avila; Lin Li; |
| 15 | Markovian Modeling of Coupled Global and Internal Dynamics in Freely Diffusing Molecules Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present progress on a Langevin formalism for coarse-graining of macromolecules that allows for viscous coupling between global diffusion and internal dynamics as well as an inertial transition between underdamped and overdamped internal motions. |
Jesse Hall; Marina Guenza; |
| 16 | Deciphering Active Site Strain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, quantum chemical calculations form an essential bridge connecting available crystallographic data with vibrational spectra. |
Wouter Hoff; Masashi Unno; Tomotsumi Fujisawa; Takahito Shingae; Jie Ren; Shojiro Haraguchi; Takeshi Hanamoto; |
| 17 | Amide-I Vibrational Entanglement for A 2-State Crossing Point Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Vibrational Manifolds of the Amide I band in both crystalline analogs and protein films show a curious sharp isosbestic point in absorbance as a function of temperature, … |
Robert Austin; Ramzi Khuri; |
| 18 | Computational Modelling of Protein Structure and Stability Using Molecular Dynamics Simulations with Enhanced Sampling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we carry out extensive molecular dynamics simulations with enhanced sampling methods based on potential energy rescaling and Hamiltonian replica exchange to determine the accuracy of measurements of the melting temperature T m. |
Zhuoyi Liu; Alex Grigas; Jake Sumner; Edward Knab; Catlin Davis; Corey O’Hern; |
| 19 | The Dynamic Softening and Intrinsic Stiffening Effect of Cholesterol on Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Small patches of the plasma membrane of the cell must be reshaped from a nearly flat geometry into a sphere (vesicle) as part of the normal transport of proteins and lipids inside … |
Alexander Sodt; Amirali Hossein; Teshani Kumarage; Rana Ashkar; |
| 20 | Cholesterol Hydrogen Bonding Interactions in Lipid Membranes: Insights from Raman Fingerprint Modes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we will show that time-dependent density functional theory (TDDFT) can calculate accurate Raman spectra for molecules up to 100 atoms, including the effects of conformational variation and hydrogen bonding. |
Jason Hafner; Mathieu Simeral; Steven Demers; Kyle Sheth; |
| 21 | Scaling Relations of Elastic and Structural Properties in Cholesterol-rich Lipid Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the interplay between cholesterol-driven lipid packing and emergent elastic properties of lipid membranes remains largely unexplored. Theories based on mean field calculations have predicted different dependences of the membrane bending modulus, κ, and the area compressibility modulus, K A, on A L. Here, we examine these relations in cholesterol-rich lipid membranes with various degrees of acyl chain unsaturation using neutron spin-echo spectroscopy (NSE), solid-state 2H NMR relaxometry, and molecular dynamics simulations. |
Teshani Kumarage; Sudipta Gupta; Fathima Doole; Milka Doktorova; Haden Scott; Laura-Roxana Stingaciu; John Katsaras; George Khelashvili; Michael Brown; Rana Ashkar; |
| 22 | Soft Meshes for Soft Matter: A Molecular Dynamics Approach to Simulating Continuum Models of Fluid Bilayer Vesicles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce a Molecular Dynamics simulation method called dynamic area redistribution that can be used to simulate the fluid behavior of biomembranes using two-dimensional meshes with fixed connectivity. |
Ali Farnudi; Ralf Everaers; Mohammad Reza Ejtehadi; |
| 23 | Thermosensing Through Membrane Mechanics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore here the possibility that thermal and mechanical activation of ion channels, as well as other membrane proteins, may be coupled through the physical properties of lipid bilayer membranes. |
Carlos Alas; Christoph Haselwandter; |
| 24 | Direct Quantification of Ligand-induced Lipid and Protein Microdomains with Distinctive Signaling Properties Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While lipid rafts are believed to exist in cells and to serve as signaling platforms through their enrichment in signaling components, they have not been directly observed in the plasma membrane without treatments that artificially cluster GM1 into large lattices. Here, we report that microscopic GM1-enriched domains can form, in the plasma membrane of live mammalian cells expressing the EphA2 receptor tyrosine kinase in response to its ligand ephrinA1-Fc. |
Kalina Hristova; |
| 25 | Force-sensing in Piezo Ion Channels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We thus derive a force-distortion relationship for the Piezo dome, from which we infer the Piezo dome’s intrinsic radius of curvature and bending stiffness in free-standing lipid membranes mimicking cell membranes, and predict Piezo’s gating curve, with no free parameters. |
Christoph Haselwandter; |
| 26 | The Role of Protein Constriction in The Fission of Membrane Tubes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work investigates the influence of proteins, such as dynamin, which constrict membrane tubes in order to lower the barrier to fission. |
Russell Spencer; Marcus Mueller; |
| 27 | A Dynamic and Mechanical Membrane Model to Study Membrane Remodeling Kinetics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this research, we bridge the gap between protein and membrane dynamic models with a mechanical membrane model that integrates reaction-diffusion dynamics to investigate the mechanisms of protein driven membrane remodeling. |
Yue Ying; YIBEN FU; |
| 28 | Lipid Number Asymmetry: The Hidden Dimension of Mammalian Plasma Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We confirm that cholesterol increases membrane tolerance for PL imbalances in model membranes and cells. |
Ilya Levental; Milka Doktorova; Jessica Symons; Kandice Levental; |
| 29 | In Vitro Living Neurons in A Reservoir Computing Framework Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Nonetheless, the choice of the reservoir is critical, and a good reservoir requires the ability to express complex dynamics with sufficient non-linearity and separation properties. In this work, we target live in vitro neuron cultures, known for their scalable hypernetworks and complex spiking dynamics, making them potentially suitable for constructing quality reservoirs. |
Zhi Dou; Seung-Hyun Kim; Gaurav Upadhyay; Xiaotian Zhang; Mattia Gazzola; |
| 30 | Collective Dynamics of Astrocytes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we analyze the collective calcium dynamics of astrocytes in three distinct states: (1) stellate, (2) polygonal, and (3) reactive that correspond to immature, mature, and injured astrocytes, respectively. |
Nicholas Mennona; Sylvester Gates; Kate O’Neill; Wolfgang Losert; |
| 31 | A Versatile, Accurate, Low-cost and Open-source Electrophysiology Solution for In-vitro Neuronal Cultures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a versatile, accurate, and low-cost in-vitro electrophysiology solution based on open-source electronics, fully customizable recording platforms, and in-house micro-electrode arrays (MEAs) substrates. |
Xiaotian Zhang; Zhi Dou; Gaurav Upadhyay; Seung-Hyun Kim; Daniel Havert; Kai Yu Huang; Austin Ellis-Mohr; Raymond Huang; Onur Aydin; Sehong Kang; Taher Saif; Hyun Joon Kong; John Beggs; Mattia Gazzola; |
| 32 | A Functional Connectivity Atlas of C. Elegans Measured By Neural Activation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By measuring responses to neural activation, we extracted the strength, sign, temporal properties, and causal direction of the connections and created an atlas of causal functional connectivity. |
Francesco Randi; Anuj Sharma; Sophie Dvali; Andrew Leifer; |
| 33 | Olfactory Learning and Navigation Behavior of C. Elegans in A Controlled Odor Environment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: With our apparatus and proposed model, we will discuss progress towards quantitatively characterizing the bi-directionally modulated navigation strategies in learned odor-guided navigation. |
Kevin Chen; Rui Wu; Marc Gershow; Andrew Leifer; |
| 34 | Touch Inhibits Feeding Via A Neural Bottleneck in C. Elegans Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Estimating information compression requires a large amount of measurements of both the input and output signals. Therefore, we implemented a high-throughput assay to supply substrate vibrations with tunable amplitude and frequency as mechanical stimulus while observing pumping in C. elegans populations. |
Monika Scholz; Elsa Bonnard; |
| 35 | Turning-associated Neurons Gates A Sensorimotor Response in C. Elegans Upstream of Neuron AVA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: But precisely how neural circuits integrate sensory and behavior signals remains unknown. To address this, we investigated C. elegans response to touch. |
Sandeep Kumar; Anuj Sharma; Andrew Leifer; |
| 36 | Statistical Significance Analysis of Functional Connectivity Measurements of The Brain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we discuss a statistical framework for accurately conveying our confidence in attributing one neuron’s response to the activation of another. |
Francesco Randi; Anuj Sharma; Sophie Dvali; Andrew Leifer; |
| 37 | Adaptive Robustness Through Incoherent Signaling Mechanisms in A Regenerative Brain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a high-content imaging platform and quantitative behavioral analysis framework that enable us to measure a previously uncharacterized long-lasting latent memory state in planarian flatworms during their whole-brain regeneration with unprecedented precision. |
Bo Wang; Samuel Bray; Livia Wyss; Chew Chai; Maria Lozada; |
| 38 | Network Properties The Whole-brain Drosophila Connectome Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The FlyWire project has completed the proofreading of a connectome for a Drosophila female brain (FAFB) which contains both complete hemispheres of the central brain and includes neurons that receive inputs in the optic lobes. |
Albert Lin; Runzhe Yang; Sven Dorkenwald; Arie Matsliah; David Deutsch; Sebastian Seung; Mala Murthy; |
| 39 | Coordinated Neural Activity in Freely Behaving Drosophila Larvae Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand how brains encode and coordinate behaviors, we seek to follow neural activity in organisms behaving in naturalistic manners. |
Paul McNulty; Rui Wu; Akihiro Yamaguchi; Doycho Karagyozov; Mirna Mihovilovic Skanata; Marc Gershow; |
| 40 | Neural Navigation: Rapid Learning in Complex Partially Observed Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, I leverage the natural propensity of rodents to explore and memorize complex environments. |
Matthew Rosenberg; |
| 41 | A Family of Neurodevelopmental Biomarkers Extracted from A Statistical Analysis of Kinematic Data Measured with High-definition Sensors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our previous studies [1,2] of subjects with Autism Spectrum Disorder (ASD) , we analyzed the randomness of maximal velocity. We reported that the probability distribution for its maximum can be mapped directly to ASD diagnosis. |
Jorge Jose; Khoshrav Doctor; Aditya Phadnis; Chaundy McKeever; Martin Plawecki; |
| 42 | Linear Viscoelastic Properties of The Vertex Model for Biological Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We showed that the linear rheological response of the system can be described using the normal mode formalism, where each normal mode responds with a characteristic relaxation timescale. |
Andrej Kosmrlj; Sijie Tong; Rastko Sknepnek; |
| 43 | Brain Organoids: New Models to Study Neural Development and Disease Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We established reproducible and efficient methods for cortical organoid differentiation that faithfully recapitulate in vivo neocortical development transcriptionally, structurally, and functionally. |
Momoko Watanabe; Jessie Buth; Neda Vishlaghi; Felix Turcios; Ranmal Samarasinghe; Bennett Novitch; |
| 44 | Brain Folds and The Extracellular Matrix: Lessons from Brain Organoids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using different brain organoid models, we detected changes in the matrisome, which includes components of the extracellular matrix (ECM) and their modulating enzymes. |
Orly Reiner; |
| 45 | Functional Neuronal Circuitry and Oscillatory Dynamics in Human Brain Organoids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: With high-density CMOS microelectrode arrays and shank electrodes, we captured spontaneous extracellular activity from brain organoids derived from human induced pluripotent stem cells. |
Kenneth Kosik; |
| 46 | Towards Building Brains Using in Vitro Biology Across Scales Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss work on building minimal, multiscale computational models to predict the structure of a brain organoids early on in development with an eye towards designing new brain organoid structures, or architectures, that are optimized to solve a particular class of computational problems. |
J. Schwarz; |
| 47 | The Role of Vimentin in Transmitting Forces to The Nucleus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study we investigate how vimentin mediates force transmission to the nucleus by examining nuclear morphology, chromatin expression, and response to external stress created by compression or geometric constraints. |
Maxx Swoger; Daniel Conway; Heidi Hehnly; Alison Patteson; |
| 48 | A Nuclear Jamming Transition in Embryonic Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By introducing nuclei as repulsive soft particles that interact with cell junctions in Active Foam model, we study how nuclei alter tissue architecture and dynamics. |
Sangwoo Kim; Rana Amini; Otger Campas; |
| 49 | Stress Fibers and Cortical F-actin Coordinate The Mechanical Anisotropy in Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Likewise, how distinct F-actin architectures contribute to the generation and transmission of mechanical stress is unclear. Therefore, to measure mechanical stresses internally, we have developed a novel tension sensor that embeds into the F-actin cytoskeleton. |
Sorosh Amiri; Camelia Muresan; Michael Murrell; |
| 50 | Measuring The Variability in Individual Fibrin Fiber Mechanics By AFM Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Previous research has reported the mechanical properties of fibrin fibers formed from a single set of conditions. Here we expand on these findings and show variability in the mechanical properties of fibers when formed under various constituent concentrations. |
Christine Helms; |
| 51 | A Simple Active Gel Model for Optogenetic Control of Cell Migration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Cell motility is one of the hallmarks of life and often results from flow in the actin cytoskeleton that is driven by myosin II motors. The natural model to describe such flows is active gel theory, in which myosin II contractility enters as active stress. |
Oliver Drozdowski; Falko Ziebert; Ulrich Schwarz; |
| 52 | Cell Packings and Myosin Network Architectures Underlie Local Tissue Mechanical Behaviors in The Fly Embryo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a framework for analyzing regional cell packings and supracellular myosin network architectures in the fly embryonic epithelium during ventral furrow formation and body axis elongation. |
Christian Cupo; Cole Allan; Vikram Ailiani; Sassan Ostvar; Karen Kasza; |
| 53 | Neuronal Biomechanics Measured Using Combined Atomic Force – Traction Force Microscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk I will present a novel experimental approach which integrates three different high – resolution techniques on the same platform, namely: traction force, fluorescence and atomic force microscopy. |
Cristian Staii; |
| 54 | Traction Force Microscopy Experiments to Measure Axonal Dynamics During Neuronal Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we use traction force microscopy (TFM) to measure traction forces exerted by the growth cones of cortical neurons cultured on poly-acrylamide hydrogels. |
Udathari Kumarasinghe; |
| 55 | Role of Different Cytoskeleton Filaments in The Mechanical Property of The Cytoplasm of A Live Cell Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we combine magnetic tweezer with live cell imaging techniques to directly visualize the deformation of the cytoskeleton networks under load. |
Sijie Sun; qiaoling Huang; David Weitz; |
| 56 | Light, Proteins, and Shape: Exploiting Pattern Formation for Light-controlled Cell Deformations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By coupling a reaction-diffusion model to a dynamic geometry, we analytically explore the potential of the protein reaction network responsible for surface contraction waves (SCWs) in starfish oocytes. |
Tom Burkart; Jinghui Liu; Alexander Ziepke; Nikta Fakhri; Erwin Frey; |
| 57 | Modeling Wound Healing Using Active Deformable Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we employ the deformable particle (DP) model to simulate the mechanics of wound healing in cell monolayers. |
Andrew Ton; Mark Shattuck; Corey O’Hern; |
| 58 | Determining The Mechanical Properties of Hair-Bundle Components From Physiological Measurements in Outer Hair Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesize that measurement uncertainties and morphological assumptions cause uncertainties in the estimated values of a bundle’s mechanical properties. |
Rayan Chatterjee; Daibhid O Maoileidigh; |
| 59 | Second Order Rigidity in Small Underconstrained Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By studying small toy networks with only a single junction, we attempt to develop a mean-field description of the geometry near the critical point. |
Tyler Hain; M Lisa Manning; Christian Santangelo; |
| 60 | Phase Field Modelling of The Mechanics of Nucleated Cells in Confined Spaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present an extension of our elastic phase field method [1] to also include the nucleus. |
Robert Chojowski; Ulrich Schwarz; Falko Ziebert; |
| 61 | Macroscopic Conductivity of Tissues from Microscopic Electrolyte Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This presentation discusses the frequency dependence of impedance, conductivity, and permittivity of an aggregate of confined electrolytes as a model for tissues. |
Francisco Solis; Vikram Jadhao; |
| 62 | Fatal Attraction: Electrostatic Forces Pull Jumping Nematodes Directly to Their Charged Prey Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present experimental results of how flow currents and exposure to electrically charged insects affect jumping Steinernema carpocapsae nematodes. |
Victor Ortega-Jimenez; Sunny Kumar; Saad Bhamla; |
| 63 | Water Surface Swimming Dynamics Via Continuous Contact in Lightweight Centipedes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we discovered that a centipede, L. forficatus (N=8, L=2.3±0.3 cm, 14 leg-pairs), uses body-surface interactions to locomote at the water surface via direct waves of body curvature. |
Baxi Chong; Kelimar Diaz; Steven Tarr; Eva Erickson; Daniel Goldman; |
| 64 | Phase Transition in A Non-Markovian Animal Exploration Model with Preferential Returns Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study a non-Markovian and nonstationary model of animal mobility incorporating both exploration and memory in the form of preferential returns. |
ohad vilk; Michael Assaf; ran nathan; Daniel Campos; Vicenc Mendez; |
| 65 | Thermodynamics of Animal Locomotion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Introducing the energy cost of effort as the generalization of the well-known oxygen cost of transport in the frame of our compact locally linear nonequilibrium thermodynamics model, we analyze oxygen consumption measurement data from a documented experiment on energy cost management and optimization by horses moving at three different gaits. |
Éric Herbert; Christrophe Goupil; |
| 66 | 3-D Pose Estimation of Larval Zebrafish Using An Artificial Neural Network and A Physical Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present (i) a physical model-based method to generate realistic, annotated larval images in novel behavioral contexts, useful to train machine-learning algorithms, among other applications; (ii) an automated method to record and track the posture of individual larval zebrafish in a 3-D environment, applicable when accurate human labeling is too time-consuming; and (iii) a rich annotated dataset of 3-D larval poses for ethologists and the general zebrafish and machine learning community. |
Aniket Ravan; Martin Gruebele; Yann Chemla; |
| 67 | From 100k Pigment Cells to Skillful Camouflage: The Role of Skin Color Changes in Sleeping Octopuses Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study camouflage behavior in the octopus during wake and sleep. |
Leenoy Meshulam; Aditi Pophale; Kazumichi Shimizu; Tomoyuki Mano; Sam Reiter; |
| 68 | Sound of A Handclap: An Elastic Helmholtz Resonator Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In preliminary studies, we observed an order of magnitude change in frequency with different cavity volumes and an amplitude change as a function of clapping speed. |
Yicong Fu; Akihito Kiyama; Sunghwan Jung; |
| 69 | A Hinged Jumping Appendage Helps Terrestrial Springtails Direct Their Ultrafast Jumps Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using high speed video, we analyzed the takeoff kinematics of a terrestrial springtail ( Tomoceridae) leaping off of rigid substrates. |
Jacob Harrison; Adrian Smith; Hungtang Ko; Saad Bhamla; |
| 70 | Strong Environmental Forces Induce A Loss of Wave Coherence in C. Elegans Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The presence of strong environmental perturbations, such as obstacles or highly resistive media (e.g. packed soil), can disrupt wave coherence, producing more complex body kinematics (e.g. multi-frequency undulation, wave interference, quasi-periodicity, and aperiodic states). We describe the origin of these behaviors in the mm-scale nematode C. elegans moving in viscoelastic gels (bulk modulus ~1-50nN/ μm 2) by isolating environmental effects on the various control systems. |
Christopher Pierce; Lucinda Peng; Xuefei Lu; Daniel Goldman; Hang Lu; |
| 71 | Turning Behavior of Freely-walking Drosophila in Response to The Timing of Odor Encounters Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: To survive, insects must use information from complex odor plumes to navigate to their source. In natural plumes, turbulence breaks up smooth odor regions into discrete packets, … |
Viraaj Jayaram; Aarti Sehdev; Nirag Kadakia; Ethan Brown; Thierry Emonet; |
| 72 | Long Term Recordings of Drosophila Melanogaster Behavior at High Temporal Resolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have developed a method to take continuous, high-dimensional, high-resolution behavioral data of the freely moving fruit fly Drosophila melanogaster spanning days and weeks. |
Grace McKenzie-Smith; Scott Wolf; Julien Ayroles; Joshua Shaevitz; |
| 73 | Integrating Pose Estimation with Tag-based Tracking to Capture Dense Social Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present NAPS (NAPS is ArUco Plus SLEAP), a hybrid behavioral tracking framework that combines state-of-the-art, deep learning-based methods for pose tracking (SLEAP) with unique markers for identity persistence (ArUco) and show that we are able to capture pose and identity within dense social networks in complex environments. |
Scott Wolf; Dee Ruttenberg; Daniel Knapp; Andrew Webb; Ian Traniello; Grace McKenzie-Smith; Sophie Leheny; Joshua Shaevitz; Sarah Kocher; |
| 74 | Emergence of Long Time Scales in A Fluctuating Landscape Picture of Animal Behavior Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we hypothesize that the multiplicity of scales inherent to behavior effectively breaks ergodicity, preventing the system from reaching a steady state within experimental time scales. |
Antonio Carlos Costa; Massimo Vergassola; |
| 75 | Data-driven Discovery of Long Timescale Behavioral Strategies During Sensory Evoked Locomotion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To identify the internal states that modulate behavior across scales, we require an understanding of how short timescale behaviors are chained to generate long sequences. We leverage the larval zebrafish to characterize such sequences because of the availability of high-resolution, high throughput recordings in various sensory conditions. |
Gautam Sridhar; Antonio Carlos Costa; Massimo Vergassola; Claire Wyart; |
| 76 | Robust Control of Replication Initiation in The Absence of DnaA-ATP ? DnaA-ADP Regulatory Elements in Escherichia Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we show that the intrinsic ATPase activity of DnaA itself is sufficient for robust and precise initiation control. |
Suckjoon Jun; |
| 77 | Beyond G1/S Regulation: How Cell Size Homeostasis Is Tightly Controlled Throughout The Cell Cycle? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that cell mass homeostasis is robustly maintained, despite disruptions of the normal G1/S transition or cell growth rate. |
Xili Liu; Jiawei Yan; Marc Kirschner; |
| 78 | Cell-cycle Dependent Growth Regulation in Bacterial Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In particular, while the exponential growth rate of E. coli increases during the cell cycle irrespective of nutrient or temperature conditions, the behavior of B. subtilis is non-monotonic. We propose a mechanistic model that explains the emergence of these growth patterns from autocatalytic production of ribosomes, coupled to the rate of cell elongation and surface area synthesis. |
Callaghan Cylke; Shiladitya Banerjee; |
| 79 | A Preservation of Macromolecular Densities Defines Cell Width in Escherichia Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Seminal studies on cell size in rod-shaped, gram-negative organisms such as E. coli have culminated in a series of descriptive phenomenological models which capture important scaling relations, but remain separate from molecular details. Here, we present a novel model where the cell width is precisely adjusted such that macromolecular density within the periplasmic space is maintained across growth conditions. |
Griffin Chure; Roshali De Silva; Jonas Cremer; |
| 80 | Adder Minimizes Cell Size Noise in Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we investigate a simple mechanistic model for exponentially growing cells whose division is triggered at a molecular abundance threshold. |
Motasem ElGamel; Andrew Mugler; |
| 81 | Dynamic Proteome Trade-offs Regulate Cell Size and Growth in Fluctuating Nutrient Conditions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we develop a dynamic coarse-grained proteome sector model which connects growth rate and division control to proteome allocation in time-varying environments in both exponential and stationary phase. |
Josiah Kratz; Shiladitya Banerjee; |
| 82 | Using Simulations to Investigate The Mechanical Properties of Peptidoglycan Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a coarse-grained molecular simulation model for the PG mesh in Gram negative bacteria such as Escherichia coli. |
Marco Mauri; Abimbola F. Adedeji Olulana; Jamie K. Hobbs; Sheila Hoshyaripour; Rosalind Allen; |
| 83 | Teichoic Acids As Organizing Centers for Growth and Shape in Bacillus Subtilis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We used dynamical, quantitative microscopy to demonstrate that inhibiting wall teichoic acid synthesis causes a fundamental re-organization of peptidoglycan synthesis. |
Felix Barber; Zhe Yuan; Enrique Rojas; |
| 84 | Direct Measurement of Turgor Pressure in E. Coli and B. Subtilis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a micromanipulation technique using an atomic force microscope (AFM) that allows us to directly measure and track turgor pressure on a living bacterium. |
Octavio Albarran; Christoph Schmidt; renata garces; Jeff Eldredge; Harold Erickson; |
| 85 | Coarse-grained Simulations of Bacterial Cell-wall Mechanics and Failure Under Extreme Conditions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We characterize stress-strain relationships, anisotropy, pore size distributions, and failure susceptibility and geometry as a function of the crosslink density, length distribution of glycan strands and angular alignment. |
Xiaoxuan Jian; Christoph Schmidt; renata garces; Jeff Eldredge; Octavio Albarran; Giacomo Po; |
| 86 | Mapping Nanostructural Changes in E.coli Peptidoglycan Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To this end, we utilized high-resolution atomic force microscopy (AFM) to map the changes in the PG organization from the pole to the cylindrical section of the rod. |
Abimbola Olulana; Jacob Biboy; Oliver Meacock; Laia Pasquina-Lemonche; William Durham; Simon Foster; Waldemar Vollmer; Jamie Hobbs; |
| 87 | Systems-Level Robustness and Fragility in The Cellular Organelle Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we aim to address the systems-level role organelle interactions play in regulating organelle composition and metabolic flows in the model system Saccharomyces cerevisiae. |
Aline Arra; |
| 88 | Spatial Allocation Rules Governing Systems-level Organelle Biogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Uncovering the functional rules by which the eukaryotic cell controls the size of its organelles is a fundamental problem in cellular biophysics. Here we aim to elucidate one such rule, namely how the budding yeast Saccharomyces cerevisiaecoordinates the size of its organelles with the size of the cytoplasm within which they reside. |
Shankar Mukherji; Deepthi Kailash; |
| 89 | How Type 1 Fimbriae Help E. Coli Adhere to Interfaces? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a tunable approach to quantify how changes in the expression level of type 1 fimbriae alter the ability of bacteria to adhere to interfaces. |
Udayanidhi Ramesh Kumar; Jacinta Conrad; Patrick Cirino; Nam Nguyen; |
| 90 | The Role of Surface-surface Interactions and Growth Media in Antibacterial Action of Microscale ZnO Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Particularly, the nature of interactions between ZnO surfaces, cellular membranes and bacterial growth media remain unambiguous. To address this matter, we employ ZnO microparticles synthesized hydrothermally and subjected to Staphylococcus aureus biological assays with different microbial growth media. |
Yuri Strzhemechny; Dustin Johnson; John Reeks; Alexander Caron; Iman Ali; Shauna McGillivray; Abagael Speights; |
| 91 | Mechanics of Nuclear Deformation in Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This model explains how nuclei can easily flatten on surfaces during cell spreading or elongate as cells move through pores until the lamina smooths out and becomes tense. |
Tanmay Lele; |
| 92 | Active Mechanics of Sea Star Oocytes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While the molecular players underlying actomyosin contractility have been well characterized, how cellular-scale deformation in disordered actomyosin networks emerges from filament-scale interactions is not well understood. Here, we address this question in vivo using the meiotic surface contraction wave of Patiria miniata oocytes. |
Peter Foster; Jinghui Liu; Alexandra Zampetaki; Sebastian Fürthauer; Nikta Fakhri; |
| 93 | Investigating The Control Principles Behind Formation of Stress Fibers By Probing Their Response to External Forces in Silico Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our work, we modify the molecular dynamics simulation engine Cytosim [Nedelec et al. |
Alexandra Lamtyugina; Yuqing Qiu; Suriyanarayanan Vaikuntanathan; |
| 94 | Ultrafast Contraction: Investigating The Structures Underlying Myoneme Force Generating Networks in Spirostomum Sp Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that the appearance of these fibers changes from a loose network in uncontracted cells to a denser, more well-defined fiber when contracted. These structural changes shed a new perspective on how myonemes may generate force. |
Joseph Lannan; Jerry Honts; Saad Bhamla; Mary Elting; |
| 95 | Roles of Catch Bond Dynamics in Cytoskeletal Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we employed an agent-based computational model to understand better how and when weak bonds can make a stronger material by exploring parametric spaces consisting of F-actin length, actin concentration, and the density and kinetics of cross-linking proteins. |
Md Foysal Rabbi; Taeyoon Kim; |
| 96 | Force Transmission Via Dynamic Stretching of Talin As Revealed By Live-cell Single-molecule ImagingSawako Yamashiro (Kyoto University) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How can FA molecules simultaneously maintain the connection to moving F-actin and transmit forces to integrins? In this study, we address this issue by performing Single-Molecule Speckle (SiMS) microscopy which elucidates true functions and kinetics of individual Talin molecules in live cells. |
Dimitrios Vavylonis; Sawako Yamashiro; David Rutkowski; Kelli Ann Lynch; Ying Liu; Naoki Watanabe; |
| 97 | A Universal Form for Heavy-tailed Fluctuations in The Actomyosin Cortex Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we report that, after accounting for static heterogeneity in cell–micropost contacts, the displacement distribution of the fluctuations displays a universal form across time, cell type, and substrate stiffness, resembling an exponentially truncated stable distribution (ETSD). |
Shankar Sivarajan; Yu Shi; Katherine Xiang; John Crocker; Daniel Reich; |
| 98 | Myosin-I Modulates The Dynamics and Architecture of Motile Actin ‘comet Tails’ Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We site-specifically coupled a range of densities of myosin-Is to the bead surface and assessed their effects on actin polymerization, network architecture, and symmetry breaking. |
Mengqi Xu; Luther Pollard; Grzegorz Rebowski; Malgorzata Boczkowska; Roberto Dominguez; Michael Ostap; |
| 99 | Thermodynamic Framework for Nonequilibrium Self-assembly of Branched Actin Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent experimental work has described growth and force feedback mechanisms in these systems. We seek to create a minimal model of this nonequilibrium self assembly process incorporating these mechanisms. |
Elisabeth Rennert; |
| 100 | Bio-inspired Fiber Networks Using Peptide-DNA Nanotechnology Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce DNA crosslinkers into peptide-based fibrous networks to construct the mesoscale’s structural hierarchy. |
Kengo Nishi; Margaret Daly; Stephen Klawa; Kameryn Hinton; Yuan Gao; Ronit Freeman; |
| 101 | Impacts of Biosurfactants on Bacterial Spreading in Soil Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we first demonstrate that rhamnolipids and surfactin, biosurfactants with different chemical structures, can generate corner flows. We identified the critical concentrations of these two biosurfactants to generate corner flow. |
Judy Yang; Yuan Li; Joe Sanfilippo; Daniel Kearns; Howard Stone; Bonnie Bassler; Niki Abbasi; Zemer Gitai; |
| 102 | Emergent Behavior Driven By Self-generated Gradients: from Active Droplets to Bacterial Suspension Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present our analysis of this communication mechanism quantitatively both on the scale of individual agent–trail collisions as well as on the collective scale where droplets actively remodel their environment while adapting their dynamics to that evolving chemical landscape. |
Babak Vajdi Hokmabad; |
| 103 | The Collective Movement of Chemotactic Bacterial Cells Along Self-generated Gradients Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The movement is driven by a combination of flagella-driven propulsion along sensed gradients in nutrient availability and the consumption of nutrients which shape these gradients. I discuss in this talk recent progress in understanding this navigated migration process and the cell-physiological and environmental factors which shape it. |
Jonas Cremer; |
| 104 | Secreted Footprints Organize Complex Cell Migration Patterns Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we explore through mathematical modeling how footprint secretion affects cell motility patterns. |
Emiliano Perez Ipiña; Brian Camley; |
| 105 | Understanding The Emergence of Microbial Collective Behaviors in The Wild Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have designed a naturalistic environmental system where we can quantify how cellular changes such as number and density and environmental features such as particle size perturb collective outcomes. |
Allyson Sgro; Emily Hager; |
| 106 | How Amoeboid Cells Can Modify Their Environment and Can Coordinate Their Motion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Upon starvation, and as part of a survival mechanism, these cells aggregate into large clusters, requiring robust coordination of signaling and motion. We will present two examples how experiments and modeling can shed light on this coordination. |
Wouter-Jan Rappel; Richa Karmakar; Timothy Tyree; Man-Ho Tang; Richard Gomer; Albert Bae; Brian Camley; |
| 107 | Nuclear Mechanotransduction & Stem Cell Fate Regulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Collectively this work reveals a universal mechanism by which nuclear deformation triggers changes in |
Yekaterina Miroshnikova; |
| 108 | Epigenetic Reactions and Chromatin-lamina Interactions Synergistically Regulate The Morphology of Lamina-associated Domains Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To elucidate the mechanisms underlying the morphological modulation of LADs, we propose a theoretical model incorporating chromatin-chromatin interactions, chromatin-lamina interactions, and epigenetic regulations. |
Zixian Guo; Aayush Kant; Vivek Shenoy; |
| 109 | Polymer Model Predicts History Dependent Epigenetic and Lamin-associated Domain Sizes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Although correlated changes in 3D organization and epigenetics in response to stimuli have been observed, current physical models cannot explain this behavior. To tackle this problem, we develop a dynamic, reaction-based polymer model which takes input from ChIP-seq data to identify the initial active and repressed beads on a string to represent the chromatin. |
Vinayak Vinayak; Ramin Basir; Lucas Sant’Anna; Vivek Shenoy; |
| 110 | Chromosome Modeling on Downsampled Hi-C Enhances Compartmentalization Signal Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Aided by recently developed models for chromatin folding and structure, we develop a framework to enhance the compartments’ information far from the diagonal observed in experimental sparse matrices. |
Antonio Oliveira Jr; |
| 111 | Contrasting The Organization and Dynamics in Normal and Cancer Cell Chromosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We used the knowledge-based potential in Chromosome Copolymer Model (CCM) to generate the structural ensemble of chromatin. |
Kiran Kumari; Sucheol Shin; Devarajan Thirumalai; |
| 112 | Image-based Spatial Genomics in Health and Disease Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In sum, the talk will focus on our efforts on: 1) characterizing the 3D genome with new technology developments, 2) understanding 3D genomic functions in the native tissue context in health and disease, and 3) building the 3D genomic “regulatome” to manipulate the 3D genome. |
Siyuan Wang; |
| 113 | A Computational Model for Correcting Intrinsic Enzymatic Biases in Chromatin Accessibility Profiling Data Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a computational method for correcting intrinsic biases from both bulk and single-cell sequencing data. |
Chongzhi Zang; Shengen Shawn Hu; |
| 114 | Live-cell Magnetic Micromanipulation of A Genomic Locus Reveals Interphase Chromatin Mechanics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce an approach to actively manipulate a genomic locus using controlled magnetic forces inside the nucleus of a living human cell. |
Simon Grosse-Holz; Veer Keizer; Maxime Woringer; Laura Zambon; Koceila Aizel; Maud Bongaerts; Fanny Delille; Lorena Kolar-Znika; Vittore Scolari; Sebastian Hoffmann; Edward Banigan; Leonid Mirny; Maxime Dahan; Daniele Fachinetti; Antoine Coulon; |
| 115 | Bridging Nano- and Mesoscale Nuclear Organization with Single-molecule Microscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine high-resolution lattice light sheet microscopy, super-resolution localization microscopy, and single particle tracking to investigate the relationship between chromatin structure, nucleosome dynamics, and biological functions. |
Yu Shi; Timothy Daugird; Wesley Legant; |
| 116 | Positional Information Transfer By Sub-micron Transcription Factor Clusters Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recently clustering of the molecules inside the nucleus has been observed, but whether these clusters report directly on the extra-nuclear information is unclear. By imaging fluorescently-labelled TF molecules in live embryos, we show that clustering only occurs at target genes and this gives rise to the observed heterogeneity in nuclear TF distribution. |
Rahul Munshi; Sergey Ryabichko; Eric Wieschaus; Thomas Gregor; |
| 117 | Single-molecule Tracking Reveals Two Low-mobility States for Chromatin and Transcriptional Regulators Within The Nucleus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using single-molecule tracking, coupled with machine learning, we examined the mobility of multiple transcription factors and coregulators. |
Kaustubh Wagh; Diana Stavreva; Rikke AM Jensen; Ville Paakinaho; Gregory Fettweis; R Louis Schiltz; Daniel Wüstner; Susanne Mandrup; Diego Presman; Arpita Upadhyaya; Gordon Hager; |
| 118 | Modeling Pairing Dynamics of Homologous Chromosomes During Prophase I in Saccharomyces Cerivisae Using Polymer Physics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Pairing occurs in Prophase I, during which linkages tether and align the homologs together. We explore the dynamics associated with this pairing process in Saccharomyces cerevisiae through a polymer physics model of two randomly linked flexible polymers. |
Ariana Tse; Trent Newman; Bruno Beltran; Sean Burgess; Andrew Spakowitz; |
| 119 | Interpretable and Tractable Probabilistic Models for Single-cell RNA Sequencing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present computationally facile solutions to generic biological systems, which couple stochastic transcriptional driving to downstream RNA processing. |
Gennady Gorin; Lior Pachter; Meichen Fang; John Vastola; |
| 120 | Evaluating The Logic of Selection in Germinal Centers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discuss ramifications of different evolutionary models, and encourage thinking about evolutionary fitness as more than a singular number. |
Bertrand Ottino-Loffler; Gabriel Victora; |
| 121 | Lineage Frequency Fluctuations Reveal The Spatial Dynamics of Disease Transmission in SARS-CoV-2 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a data-driven method that uses time series neutral lineage frequencies data to infer an infectivity matrix, which describes the transmission rates between individuals in different locations. |
Takashi Okada; Giulio Isacchini; QinQin Yu; Oskar Hallatschek; |
| 122 | Comparative Efficacy of Antiviral Strategies Targeting Different Stages of The Viral Life Cycle: A Viral Quasispecies Dynamics Study Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use a model of viral quasispecies dynamics to examine the efficacy of antiviral strategies targeting three critical aspects of the viral life cycle: fecundity, reproduction rate, or infection rate in individuals with varying degree of immunity [1]. |
Pancy Lwin; Greyson Lewis; Moumita Das; Barbara Jones; |
| 123 | The Dynamics of LINE-1 Retrotransposition in Cellular Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite these associations, a quantitative understanding of the dynamics and diversity of LINE-1 insertions in somatic tissue is lacking. In order to address this gap, we present a population dynamic model of LINE-1 retrotransposition in individual cells. |
Stephen Martis; Alexander Solovyov; Jayon Lihm; Hao Li; Benjamin Greenbaum; |
| 124 | Influence of Cross Immunoreactive Network Topology and Internal Dynamics of The Immune System on Antigenic Cooperation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: It remains unclear whether the LI emerges solely from the topology of the CRN or if the intricate inner functioning of the immune system has a significant contribution. We investigate these inquiries on LI by fine-graining the immune system dynamics and by exploring the influence of network topology on AC. |
Kevin Ng Chau; Jason George; Herbert Levine; |
| 125 | Eco-evolutionary Stable Strategies of Antigenically Escaping Viruses Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We observe that the antigenic evolution induced by the immune pressure is characterized by a traveling wave of adaptation whose speed and size are primarily ruled by the efficiency of cross-reactive immunity. |
Victor Chardès; Andrea Mazzolini; Aleksandra Walczak; Thierry Mora; |
| 126 | Spatiotemporal Population Dynamics of Native and Engineered Bacteria in The Gut Microbiome Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: As part of the theory and modeling, we use a generalized model of population dynamics that extends the Lotka-Volterra equations beyond the usual predator-prey dynamics to include other types of interactions between engineered and native bacterial species. |
Alberto Alonso; Moumita Das; |
| 127 | Tuning Spatial Distributions of Selection Pressure to Suppress Emergence of Resistance Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Motivated by the control of pests in agriculture, we employ a one-dimensional model with agents diffusing and selection applied temporarily on a sub-region only. |
Thomas Tunstall; Philip Madgwick; Ricardo Kanitz; Wolfram Moebius; |
| 128 | Heterogeneity in Bacterial Filamentation Survival Dynamics Decrease in Response to Increased Stress Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Through the use of a novel dual reporter strain of E. coli we show that increased survival is correlated with continued DNA replication at both moderate and high levels of ciprofloxacin treatment but that the heterogeneity in response is increased at the lower treatment level. |
Robert Austin; Julia Bos; George Butler; Kenneth Pienta; Sarah Amend; |
| 129 | Dynamic Trait Shift and Its Effects on Biological Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Through a simple predator-prey model that explicitly tracks the trait distribution of the prey, we explore the implications of trait shifts. |
Zachary Jackson; BingKan Xue; |
| 130 | Commuter Interactions Shape Disease Spread Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The emergent dynamics depend crucially on the commuting distribution of a population, that is how the probability to travel to a destination decays with distance from home. Applying this idea to epidemics, we will demonstrate the qualitatively different infection dynamics emerging from populations with different commuting distributions. |
Aaron Winn; Eleni Katifori; |
| 131 | Emergent Spatiotemporal Communication Patterns in Insect Swarms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will focus on two types of communication in insect swarms: visual communication, in which fireflies communicate over long distances using light signals, and chemical communication, in which bees serve as signal amplifiers to propagate pheromone-based information about the queen’s location. |
Orit Peleg; |
| 132 | Nonequilibrium Force Fluctuations of Micro Swimmers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate the stochastic force fluctuations of micro swimmers in two scenarios: (1) a single swimmer navigating through a passive fluid; (2) a dense suspension of swimmers surrounding a passive tracer. |
Wylie Ahmed; |
| 133 | The Collective Motion and Merging of Macroscopic Bacterial Aggregates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we report collective behaviors exhibited by the bacteria Enterobacter cloacae. |
James Boedicker; |
| 134 | Spatiotemporal Dynamics of Metabolite Gradients Control The Emergent Morphology of A Bacterial Colony on Hard Agar Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The growth of an E. coli colony on hard agar exhibits robust expansion kinetics and morphology despite the complex interactions between millions of cells experiencing compact confinement under a spatiotemporally varying nutrient gradient. To probe the mechanistic origins of such robust colony characteristics, an agent-based model along with a set of reaction-diffusion equations to model the spatiotemporal dynamics of extracellular metabolites is employed. |
Harish Kannan; Paul Sun; Tolga Caglar; Daotong Ge; Kinshuk Sahu; Jiajia Dong; Bo Li; Terence Hwa; |
| 135 | Mechanical Information Processing By The Actin Cytoskeleton Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we demonstrate tunability of LIM domain protein localization and function in endothelial cells by altering various intracellular and extracellular mechanical cues such as shear stress, contractility, and matrix rigidity. |
Shailaja Seetharaman; Theresa Chmiel; John Devany; Anthony Carlos; Raymond Moellering; Margaret Gardel; |
| 136 | Graph Identification of Proteins in Tomograms (GRIP-Tomo) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We systematically introduced data distortion or defects such as missing fullness of data, the tumbling effect, and the missing wedge effect into the simulated volumes, and varied the distance cutoffs in pixels to capture the varying connectivity between the density cluster centroids in the presence of defects. |
Margaret Cheung; August George; Doonam Kim; Trevor Moser; James Evans; Ian Gildea; |
| 137 | Building Differentiable Kinetic Models to Improve Yield of Finite Sized Assemblies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we use deterministic reaction simulations to quantify how kinetic trapping regimes can emerge in finite sized assemblies based on topology, size and interaction strengths. |
Adip Jhaveri; |
| 138 | Manipulating Polydispersity of Lens Β-crystallins Using Divalent Cations Demonstrates Evidence of Calcium Regulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We assayed hydrodynamic behavior and assembly mechanics of crystallins in different salts and observed altered protein polydispersity in vitro. |
Michael Bergman; Leila Deravi; |
| 139 | Learning and Controlling Phase Separation in Complex Geometries with Differentiable Physics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, starting with general theories from nonequilibrium thermodynamics, we write a differentiable physics simulator using adjoint methods for phase separation that can be used in learning, optimization, and control applications. |
Alexander Cohen; Jorn Dunkel; Martin Bazant; |
| 140 | Vimentin Intermediate Filaments Increases Collective Cell Migration Through Extracellular Matrix Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that loss of vimentin significantly impairs the ability of the spheroid to collectively expand through collagen networks and remodel the collagen network. |
Alison Patteson; Minh-Tri Ho Thanh; |
| 141 | Modeling Collective Interactions Between Embedded Spheroids and Collagen Fibers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand the complex interplay between tumor spheroids and ECM, we construct and study a three-dimensional vertex model for tumor spheroids. |
Tao Zhang; J. Schwarz; |
| 142 | An Agent-based Model of The Tumor Microenvironment Predicts Hallmarks of Cancer and Sets The Stage for Model-driven Experimental Design of CAR T Cell Therapy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, I introduce a multiscale agent-based model of a cell population that integrates subcellular signaling and metabolism, cellular level decision processes, and dynamic vascular architecture and function to interrogate regulation among heterogeneous cell agents. |
Neda Bagheri; |
| 143 | Infiltration of Immune Cells Into Tumors; A Necessary Part of Immunotherapy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk will focus how one can use computational models to better understand the factors governing infiltration dynamics. |
Herbert Levine; |
| 144 | Killer Immune Cell Swarming and Solid Tumor Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The mechanisms and cellular forces that underpin the coordinated movements and interactions of killer immune cells and tumor cells are incompletely understood. We investigate the intercellular signaling and mechanical forces that these killer immune cells employ to effectively infiltrate and attack solid tumors. |
Maté Biro; |
| 145 | Scaling Laws in Deep Neural Networks: Insights from Statistical Mechanics and Exactly Solvable Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A full understanding — and in particular, a prescriptive theoretical framework — for what governs this scaling is lacking. Towards this end, I will discuss our work introducing a classification of different regimes of behavior — notions of "resolution-limited" and "variance-limited" regimes — based on the mechanistic origins behind the scaling. |
Yasaman Bahri; |
| 146 | Results from A Mapping Between Reinforcement Learning and Non-Equilibrium Statistical Mechanics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this setting, we derive results in RL that are analogous to the Gibbs-Bogoliubov’s inequality in equilibrium statistical mechanics. We propose methods to iteratively improve this bound based on results from RL. |
Jacob Adamczyk; Argenis Arriojas Maldonado; Stas Tiomkin; Rahul Kulkarni; |
| 147 | The Onset of Variance-Limited Behavior for Neural Networks at Finite Width and Sample Size Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, at a training set size, the finite-width network generalization begins to worsen compared to the infinite width performance. We empirically study the transition from the infinite width behavior to this variance-limited regime as a function of training set size and network width and network initialization scale. |
Alexander Atanasov; Cengiz Pehlevan; Blake Bordelon; Sabarish Sainathan; |
| 148 | Feature Learning and Overfitting in Neural Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Yet, understanding when and how this feature learning improves performance remains a challenge: for example, for a fixed task such as classifying images, feature learning is beneficial in modern architectures but detrimental in standard fully-connected feed-forward networks. Here we propose an explanation for this puzzle, by showing that feature learning can result in poor generalization performances as it leads to a `sparse’ neural representation, where only a fraction of the connection in the original network are active. |
Francesco Cagnetta; |
| 149 | Flatter, Faster; Scaling Momentum for Optimal Speedup of SGD Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we study implicit bias arising from the interplay between SGD with label noise and momentum in the training of overparametrized neural networks. |
Aditya Cowsik; Tankut Can; Paolo Glorioso; |
| 150 | Statistical Mechanics of Infinitely-Wide Convolutional Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce a stylised teacher-student framework where a CNN is trained on the output of another CNN with random weights. |
Alessandro Favero; Francesco Cagnetta; Matthieu Wyart; |
| 151 | Phase Diagram of Training Dynamics in Deep Neural Networks: Effect of Learning Rate, Depth, and Width Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We systematically analyze optimization dynamics in deep feed-forward neural networks (DNNs) trained with stochastic gradient descent (SGD) over long time scales and study carefully the effect of learning rate, depth, and width of the neural network. |
Dayal Singh Kalra; Maissam Barkeshli; |
| 152 | Generative Probabilistic Matrix Model of Data with Different Low-dimensional Latent Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The model’s special cases include hierarchical clusters, sparse mixing, and non-negative mixing. We describe the correlation and eigenvalue distributions of these patterns within the general model and discuss how our model can be used to generate structured training data for supervised learning. |
Philipp Fleig; Ilya Nemenman; |
| 153 | The Evolution of The Fisher Information Matrix During Deep Neural Network Training Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: al. 2021), but further study is required. Here, we study the evolution of the Fisher Information Matrix throughout training in both the early and late phase, and identify a number of dynamical signatures of its behavior. |
Chase Goddard; David Schwab; |
| 154 | When Does Dual Dimensionality Reduction Perform Better Than Single Dimensionality Reduction? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use a generative model of multivariate correlated data and linear dimensionality reduction approaches to carefully explore under which conditions DDR methods outperform independent approaches. |
Eslam Abdelaleem; K. Michael Martini; Ahmed Roman; Ilya Nemenman; |
| 155 | Physics-Informed Featurization of Spectral Functions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate two methods for approximating spectral functions via rational approximations, i.e., approximations as a ratio of two polynomials. |
Shubhang Goswami; Kipton Barros; Matthew Carbone; |
| 156 | Efficient Modelling of Ge15Te85 Using Active Learning Methods Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discuss active learning, compare training methods, and evaluate the ability of trained MLIPs to match experimentally known quantities of Ge 15Te 85. |
Thomas Arbaugh; Francis Starr; |
| 157 | A Simple Model for Grokking Modular Arithmetic Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk I will present a simple neural network that groks a variety of modular arithmetic tasks. |
Andrey Gromov; |
| 158 | Mechanobiology of Collective Cell Migration Under Physical Confinements Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we obtained biological insights into the kinematic behavior of collectively migrating cell cohorts under a series of well-defined geometrical and physical confinements such as on narrow strips and on out-of-plane curved surfaces. |
Chwee Teck Lim; |
| 159 | Strain Response of Epithelial Cell Trains Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by recent in vitro studies of epithelial monolayers on 1D micro-patterned substrates, we use continuum and mesoscopic models of a linear array of cells to examine their response to externally applied mechanical perturbations. |
Toshi Parmar; Liam Dow; Beth Pruitt; M Cristina Marchetti; |
| 160 | Intercellular Adhesion Mediates Non-monotonic Growth of Cell Collectives Due to Biomechanical Feedback Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By implementing a minimal computational model for three-dimensional multicellular spheroids (MCS), we determine how intercellular adhesive interactions and mechanical pressure on single cells regulate cell division. |
Abdul Malmi Kakkada; |
| 161 | Strain-Tension Feedback Leads to Sustained Pulsing Activity in Epithelial Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The mechanistic basis of this tissue-wide pulsing activity remains unknown. To capture this phenomenon, we have developed a vertex model of epithelial tissues with mechanochemical feedback, where junctional active tension is controlled by junction strain. |
Sam Banks; Fernanda Pérez Verdugo; Shiladitya Banerjee; |
| 162 | Mechanical Basis for Epithelialization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work suggests that cell density is the primary factor in cell-cell border development and that cell-cell adhesion is subordinate. |
Christian Cammarota; Nicole Dawney; Mimi Jüng; Dan Bergstralh; |
| 163 | Vertex Modeling of Epithelial Tissues: Structural Changes from Out-of-plane Mechanics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show here that the quantitative predictions of a two-dimensional approach fail to agree with experimental data on MDCK epithelia, predicting floppy mechanics where the tissues are stable and rigid. We identify the cause of this discrepancy as the presence of actin stress fiber bundles near the basement membrane, breaking the apical-basal symmetry and leading to significant, systematic changes in cell outline as a function of the apical-basal coordinate. |
Sascha Hilgenfeldt; Mayisha Nakib; Jairo Martin Rojas Huamaní; William Brieher; |
| 164 | Dynamic Remodeling of Fiber Networks with Stiff Inclusions Under Compressive Loading Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A model tissue system consisting of a fibrin network imbedded with inert stiff beads replicates this compression stiffening behavior. We employ bulk rheology and a custom imaging device to investigate the response of these fibrin-bead networks to uniaxial compression. |
Bobby Carroll; Minh-Tri Ho Thanh; Alison Patteson; |
| 165 | Finite Elasticity and Interplay Between Curvature and Rigidity in Vertex Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a mean field approach, we study the finite mechanical response of the vertex model (VM) of biological tissue to compression and dilation and compare our analytical results to simulations. |
Arthur Hernandez; M Cristina Marchetti; Michael Moshe; Michael Staddon; |
| 166 | Generating Convergent-extension Flows in A Model Epithelial Tissue with Active Feedback Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a continuum model for an epithelial tissue with catch-bond type feedback for the actomyosin cortex, due to an anisotropic distribution of myosin molecular motors regulated by tension. |
Aondoyima Ioratim-Uba; Tanniemola Liverpool; Silke Henkes; |
| 167 | T1 Transitions As Active Hexatic Defect Annihilations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show, analytically and numerically, that T1 transitions in epithelial tissue monolayers can be accurately and predicatively described by the annihilation dynamics of an active, hexatic defect quadrupole. |
Dimitrios Krommydas; Livio Nicola Carenza; Luca Giomi; |
| 168 | Compression Induced Fluidization in Vertex Models of Epithelial Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we show that compression-induced fluidization is in fact an exact consequence of the most common vertex model free energy. |
Avik Mondal; David Lubensky; |
| 169 | The Role of Collective Cellular Rearrangements in The Rheology of Dense Biological Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use the vertex model to study the collective cell rearrangements and the tissue rheological response of a monolayer under external shear. |
Anh Nguyen; Dapeng(Max) Bi; |
| 170 | Cell Dissociations in Collective Invasion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To better understand the results, we propose a theoretical model with the phase field approach, and recapitulate the experimental results by introducing three different cell types (follower, guided, and a high-motility metabolically active subset of cells) based on their spatial position. |
Wei Wang; Robert Law; Konstantinos Konstantopoulos; Brian Camley; |
| 171 | Probing Allosteric Communication of Bacterial ClpP Peptidase Using Dynamic Network Analysis and Machine Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To elucidate the gating mechanism, we performed all-atom molecular dynamics simulations and normal mode analysis of both "closed" and "open" states of wild-type (wt) ClpP and several mutants. |
Ashan Dayananda; Timothy S. Dennison; Riina Tehver; George Stan; |
| 172 | Superdiffusive Motion of Influenza A Viruses on Surfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a stochastic model that captures the fundamental mechanism of IAV motion on surfaces. |
Siddhansh Agarwal; Greg Huber; Daniel Fletcher; |
| 173 | Stochastic Dynamics and Ribosome-RNAP Interactions in Transcription-Translation Coupling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and binding). |
Xiangting Li; Tom Chou; |
| 174 | The Mammalian Meiotic Spindle: A Living Material Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While we have a (nearly) complete "parts list" of the dozens of bio-molecules that make up the spindle, it is far from clear how these molecules self-organize to create the material properties that allow the spindle to produce forces and transmit them to chromosomes over the required length- and time-scales. In this talk, I will present data and analysis that suggests that, despite its formidable bio-molecular complexity, important aspects of the large-scale structure and dynamics of spindles in living cells can be understood via a relatively simple continuum picture in which the spindle is modeled as an active nematic liquid crystal. |
Colm Kelleher; Daniel Needleman; |
| 175 | Protein Remodeling and Translocation Mediated By AAA+ Nanomachines in The Degradation and Disaggregation Pathways: Computational Studies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In coarse-grained models of protein degradation mediated by the 26S proteasome, we use machine learning approaches to characterize dynamic competition between GFP refolding and translocation in sequence direction-dependent (N-C and C-N) mechanisms. |
George Stan; |
| 176 | Probing Severing Enzyme’s Functional States with Molecular Simulations and Machine Learning Approaches Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we built a Markov State Model of all-atomistic simulations of the spastin motor in order to identify kinetically relevant protein conformations. |
Maria Kelly; |
| 177 | Determining Quaternary Allostery of The Spastin Motor Through Bioinformatics and Graph Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We employed a coevolutionary mutual information analysis, integrated with our molecular dynamics simulations of the bound and unbound ligand states, and we built a mathematical graph to visualize the allosteric networks based on learned parameters. |
Amanda Macke; Maria Kelly; Shehani Kahawatte; Abigail Miller; Ruxandra Dima; |
| 178 | Effect of Molecular Walkers on Microtubule Substrates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present simulation results for a coarse-grained microtubule model that responds to the stepping of molecular walkers and investigate the character and range of the conformational changes. |
Jutta Luettmer-Strathmann; Matthew Murrow; |
| 179 | Kinesin Model for Brownian Dynamics Simulations of Stepping Efficiency Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we develop a 3D model of kinesin stepping on a rigid microtubule substrate that can be simulated efficiently with Brownian dynamics simulations. |
Matthew Murrow; Jutta Luettmer-Strathmann; |
| 180 | Inferring Subsystem Efficiencies in Bipartite Molecular Machines Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we derive upper and lower bounds on the subsystem efficiencies of individual components of a bipartite molecular machine. |
Matthew Leighton; David Sivak; |
| 181 | Effects of Membrane Viscoelasticity on The Red Blood Cell Dynamics in A Microcapillary Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present a computational study based on the boundary integral method and thin-shell mechanics to examine how membrane viscoelasticity influences the dynamics of RBCs flowing through straight and constricted microcapillaries. |
Ali Gurbuz; On Shun Pak; Michael Taylor; Mettupalayam Sivaselvan; Frederick Sachs; |
| 182 | Lipid Bilayer Thickness Effects on Spectroscopic Measurements Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Dynamics on the order of membrane thickness are commonly described by phenomenological models and are attributed to competition between bending relaxation and intermonolayer friction. In this work, we provide a theory that explicitly accounts for finite membrane thickness effects, and we show that the linear response at these lengthscales is dominated by a non-equilibrium shear mechanism different from the commonly assumed intermonolayer friction. |
Zachary Lipel; Dimitrios Fraggedakis; Yannick Omar; Kranthi Mandadapu; |
| 183 | Sensing A Little Friction: How Interleaflet Friction Depends on Membrane Composition and Controls Membrane Bending Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In particular, we observe dramatic changes to friction when cholesterol is included in the bilayer. |
Aurelia Honerkamp-Smith; |
| 184 | The Effects of Domain Formation on Lipid Membrane Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use neutron spectroscopy and molecular dynamics (MD) simulations to selectively study the dynamic response of the lipid matrix to the formation and growth of ordered domains. |
Rana Ashkar; Sudipta Gupta; Henry Lessen; Frederick Heberle; Alexander Sodt; |
| 185 | Effect of Bottlebrush Poloxamer Architecture on Binding to Liposomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We found that the binding affinity of a bottlebrush poloxamer (BBP) is about three times higher than a linear poloxamer with a similar composition and number of PPO units. |
Joseph Hassler; Adelyn Crabtree; Lucy Liberman; Frank Bates; Benjamin Hackel; Timothy Lodge; |
| 186 | Phospholipid Flipping Into The Outer Leaflet of The Bacterial Outer Membrane Compensates for Severe Reduction in Protein Content Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we characterized an E. coli mutant with a global reduction in OM proteins due to the deletion of bamD, which causes reduction in OM stiffness, increased membrane permeability, and OM rupture in spent medium. |
Jiawei Sun; Kerwyn Huang; |
| 187 | Disruption Without Disintegration: How Are Membranes Targeted By Antimicrobial Peptides Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: With neutron spectroscopic techniques such as quasi-elastic neutron scattering and neutron spin echo, we found that Aurein 1.2 restricts the lipid lateral motion in the fluid phase significantly and modifies the elasticity of membranes. |
Shuo Qian; Veerendra Sharma; Piotr Zolnierczuk; Durgesh Rai; |
| 188 | Erythro-PmBs: A Selective Polymyxin B Delivery System Using Antibody-conjugated Hybrid Erythrocyte Liposomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a novel PmB delivery system constructed by conjugating hybrid erythrocyte liposomes with antibacterial antibodies to combine a high loading efficiency with guided delivery. |
Hannah Krivic; |
| 189 | Probing Interactions of PQS Analogs with Outer Membranes of Pseudomonas Aeruginosa Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: It has been shown that this signaling molecule can also stimulate OMV formation in other closely related organisms, suggesting small molecule induced OMV biogenesis is a widely conserved process. This work aims to provide fundamental insight into the effect of key functional groups of PQS on its interaction with the bacteria OM by investigating a variety of structural analogs. |
Emad Pirhadi; Hasan Al Tarify; Jeffrey Schertzer; Xin Yong; |
| 190 | Effect of Weak Magnetic Field on The Antibacterial Properties of Antibiotics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We are conducting a comparative study of weak electromagnetic field on inhibitive properties on antibiotics and see if an exposure to weak magnetic field can enhance the bacterial inhibition of pathegenic bacterial and reduce the side effects of drugs. |
Samina Masood; |
| 191 | Specific Iron Binding to Natural Sphingomyelin Membrane Induced By Non-specific Co-solutes in Solutions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, using spinal bovine SPM as a model system, we form and study a monomolecular layer (ML) at a physiological solution interface to determine the effect of various ions and their complexes on the PC-template formed by the SPM. |
David Vaknin; Honghu Zhang; Wenjie Wang; |
| 192 | Glycocalyx-induced Cell Membrane Protrusions at The Cell-substrate Interface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work examines the interplay of hyaluronan-rich glycocalyx with the cell membrane and its role in generating membrane protrusions. |
Ethan Coburn; Shlomi Cohen; Yu Jing; Jennifer Curtis; |
| 193 | Detecting Assemblies of Coordinated Neurons with A Novel Family of Maximum Entropy Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a novel method based on Bayesian inference of maximum entropy models for detecting and modeling cell assemblies from population activity. |
Clelia de Mulatier; |
| 194 | Baseline Control of Optimal Performance in Recurrent Neural Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the benefits of these modulations using a reservoir computing approach, modeling a sensory area as a recurrent neural network, and changes in brain state as modulations of its baseline inputs. In our brain-inspired framework for reservoir computing, we found that the dynamical phase of a recurrent neural network is controlled by modulating the mean and quenched variance of its baseline inputs. |
Luca Mazzucato; Francesco Fumarola; Shun Ogawa; |
| 195 | Pitch Acts As A Distractor in Optimal Estimation of Yaw in Dynamic Natural Scenery Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: One possible explanation for this is these biases arise in response to features of the statistics of natural scenes. Here, we computationally investigate this problem in the context of the blowfly ( Calliphora vicina) visual system. |
Charles Edelson; Robert de Ruyter; William Bialek; Shiva Sinha; |
| 196 | On The Context-dependent Efficient Coding of Olfactory Spaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present an integrative approach combining normative theories of context-enhanced efficient coding and mechanistic models of neural circuits to generate predictions that will be tested in electrophysiology and behavioral experiments. |
Gaia Tavoni; ShiNung Ching; Baranidharan Raman; |
| 197 | Emergent Neural Network Behavior in Dynamically Driven Superconducting Loop Disordered Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a system of superconducting loops coupled through Josephson junctions with disorder introduced into the geometry of the loops and junctions. |
Uday Goteti; Shane Cybart; Robert Dynes; |
| 198 | Grid Cell Percolation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The percolation perspective casts a new light on the role of grid cells in organizing spatial cognition and helps understanding several neurophysiological mechanisms of spatial information processing, such as path integration, spatial planning and establishing global spatial scales. |
Yuri Dabaghian; |
| 199 | Flexible Multitask Computation in Recurrent Networks Utilizes Shared Dynamical Motifs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a conceptual framework that establishes dynamical motifs as a fundamental unit of computation, intermediate between the neuron and the network. |
Philipp Fleig; Laura Driscoll; Eugenio Piasini; |
| 200 | Theory of Coupled Neuronal-Synaptic Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In neural circuits, synapses influence neurons by shaping network dynamics, and neurons influence synapses through activity-dependent plasticity. Motivated by this fact, we study a network model in which neurons and synapses are mutually coupled dynamic variables. |
David Clark; Larry Abbott; |
| 201 | Potential Landscapes and The Visual Cortex: A Study of Brain Wave Entrainment Using Neural Mass Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work [1] suggests that NMMs may be capturing features of underlying effective landscapes that help shape brainwaves and may affect sensory information processing. |
Richa Phogat; P. Parmananda; Ashok Prasad; |
| 202 | MiV-Simulator: A Computational Framework to Simulate Exact Scale In-vitro Neuronal Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, in vitro experiments can be demanding in terms of resources and technical skills. To complement experiments, aid their design, and overall accelerate investigation, we present an open-source computational framework for the simulation and analysis of these systems. |
Gaurav Upadhyay; Seung Hyun Kim; Frithjof Gressmann; Ivan Raikov; Zhi Dou; Xiaotian Zhang; Ivan Soltesz; Lawrence Rauchwerger; Mattia Gazzola; |
| 203 | High Frequency Deep Brain Stimulation Reduces Exaggerated Synchronization in Biophysically Realistic Spiking Neural Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The methods in this study serve as biophysically realistic building blocks of DBS network models, and MI was seen to be a promising measure for network synchronization. |
AmirAli Farokhniaee; |
| 204 | Variational Onsager Neural Networks (VONNs): A Thermodynamics-Based Variational Learning Strategy for Non-Equilibrium Material Modeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a variational learning strategy for the discovery of non-equilibrium equations, through the variational action density from which these equations may be derived. |
Shenglin Huang; Zequn He; Bryan Chem; Celia Reina; |
| 205 | Enhancing Prediction Performance of Reservoir Computing By Multiple Delayed Feedbacks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: As a result of adding delays with small spacing to the Electro-optic oscillator model with filter, a stronger feedback coefficient is needed to destabilize the system’s dynamics. Our study examined the impact of the time delays and the spacing between them on the reservoir computing device’s performance. |
Seyedkamyar Tavakoli; Andre Longtin; |
| 206 | Towards Better Physics Extraction in Images Via Unsupervised Custom Loss Shift- Variational Autoencoders Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a shift invariance variational autoencoder (sh-VAE) with a customized loss function, in an attempt to learn more physically meaningful features. |
Arpan Biswas; Sergei Kalinin; Maxim Ziatdinov; |
| 207 | Dynamical Models from Data, Including Constants of Motion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The FJet method is introduced for modeling a dynamical system from data; it is based on using machine learning to model the updates of the phase space variables. |
Michael Zimmer; |
| 208 | Machine Learning Inverse Problem Solving for Optical Constants Determination Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we employ machine learning based methods to solve the inverse problem of determining the thickness and optical constants of a material from reflectance and transmittance measurements only. |
Mariana Fazio; Kieran Craig; Marwa Ben Yaala; Bethany McCrindle; Chalisa Gier; Callum Wiseman; Stuart Reid; |
| 209 | Magnetic Iron-cobalt Silicides Discovered Using Machine-learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We employ a machine learning (ML) framework coupled with first principles calculations to discover rare-earth-free magnetic iron-cobalt silicide compounds. |
Timothy Liao; Weiyi Xia; Masahiro Sakurai; Renhai Wang; Chao Zhang; Huaijun Sun; Kai-Ming Ho; Cai-Zhuang Wang; James Chelikowsky; |
| 210 | Development of Ensemble Models for The Growth of Colloidal Spin-on-Glass Materials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using the sol-gel method to establish versatile functional modifications on various surfaces is furthermore a straight-forward and cost-efficient approach. |
Tim Erdmann; |
| 211 | Exploring Materials Dataspaces By Combining Supervised and Unsupervised Machine Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we discuss a rarely addressed topic – the development of automatic tools to explore the available materials-science data. |
Andreas Leitherer; Angelo Ziletti; Christian Liebscher; Timofey Frolov; Luca Ghiringhelli; |
| 212 | Development of Deep Learning Potentials to Investigate Initial Corrosion Mechanisms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we develop and assess the applications of Deep Learning Potentials to investigate corrosion mechanisms via Molecular Dynamics (MD) simulations. |
Ridwan Sakidja; Hendra Hermawan; Ayoub Tanji; Peter Liaw; Xuesong Fan; |
| 213 | Machine Learning Potentials for Accelerated Nuclear Fuel Qualification Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To this end, we derive new accurate machine learning (ML) potentials for actinides that provide high-fidelity reproduction of quantum mechanical (QM) forces at the same low cost of classical force fields. |
Richard Messerly; Leidy Lorena Alzate Vargas; Roxanne Tutchton; Michael Cooper; Sergei Tretiak; Tammie Gibson; |
| 214 | Reinforcement Learning Mimicking Sperm Chemotaxis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce an alternative approach to develop navigation strategies of sperm cells based on reinforcement learning. |
Alan C. H. Tsang; Omar Mohammed; Henry C. W. Chu; |
| 215 | Phase Relationships in Phototaxis of Microswimmers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study will provide insight about the switching of phototaxis in microswimmers, informing the design and control of light-guided microswimmers. |
Zhao Wang; Alan C. H. Tsang; |
| 216 | Predicting The Distribution of Mechanical Stresses in The S. Aureus Cell Wall During The Cell Cycle Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we used concepts from mechanical engineering to create an elastic model of the cell wall, in order to predict the spatial distribution of stress in the cell wall, and the induced deformations, during the cell cycle. |
Marco Mauri; Sheila Hoshyaripour; Abimbola F. Adedeji Olulana; David Owen; Jamie K. Hobbs; Simon Foster; Rosalind Allen; |
| 217 | Effects of Chromatin-Nuclear Envelope Interactions on Long-Range Chromatin Interactions and Chromatin Accessibility at Single-Cell Level Through Ensemble Analysis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, how chromatin spatial accessibilities in 3D space at the single-cell level are dictated by these interactions is not well understood beyond Mb-scale A/B compartments. We study this problem using a model incorporating chromatin-nuclear envelope interactions via LAD regions mapped by the DamID assay. |
Pourya Delafrouz; Hammad Farooq; Lin Du; Jie Liang; |
| 218 | Multi-plasmid Localization and Dynamics in Nanocavity Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Plasmids usually possess multiple copies in bacteria to ensure their successful partitioning and inheritance. While sophisticated active partitioning mechanisms exist for low-copy … |
Zezhou Liu; Sarah Christensen; Xavier Capaldi; Seyed Imman Isaac Hosseini; Lili Zeng; Rodrigo Reyes-Lamothe; Walter Reisner; |
| 219 | Microscopic Modeling of Mitotic Spindle Reveals The Function of Its Chiral Shape Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the microscopic explanation of torques in the mitotic spindle is still missing. To address this question, we have developed a model that represents microtubules as flexible rods, which are cross-linked by motor proteins and passive linkers. |
Maja Novak; Arian Ivec; Nenad Pavin; Iva Toli?; |
| 220 | Conversion-limited Phase Separation in Biological Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Phase separation is not only ubiquitous in diverse physical systems, but also plays an important organizational role inside biological cells. However, experimental studies of … |
Chiu Fan Lee; |
| 221 | X-ray Reflectivity Study of Structural Modifications to Supported Phospholipid Bilayers Due to Interactions with The Antimicrobial Peptide, Indolicidin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In order to investigate the details of the membrane-peptide interaction, we have fabricated biometric phospholipid membranes supported on atomically flat silicon substrates and characterized their structure using x-ray reflectivity in the presence and absence of Indolicidin. |
Gobind Basnet; Jonathan Maloney; Elizabeth Gaillard; Laurence Lurio; |
| 222 | Theory of Self-organized Cell Fate Specification Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In an attempt to unify the zoo of chemical and mechanical signaling processes that feed into fate decisions, we develop an information-theoretic approach to quantify reproducibility and robustness of fate patterns. |
David Brückner; Gasper Tkacik; |
| 223 | Spatial Organization of A Heterogeneous Polymer in A Crowded Medium Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study the spatial organization of a heterogeneous polymer (with ring topology) by crowding effects, using molecular dynamics simulations. |
Amir Hosein Sadeghi Isfahani; Bae-Yeun Ha; Youngkyun Jung; |
| 224 | Statistical Physics and Geometry of Overparameterization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Modern machine learning often employs overparameterized statistical models with many more parameters than training data points. In this talk, I will review recent work from our group on such models, emphasizing intuitions centered on the bias-variance tradeoff and a new geoemetric picture for overparameterized regression. |
Pankaj Mehta; |
| 225 | Zipf’s Criticality in Learning Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recently, Zipf’s law has been observed in the distribution of functions which may be produced by a neural network of a given architecture. We show that these results hold true for many learning machines (not necessarily deep networks) in regimes where learning is possible. |
Sean Ridout; Ilya Nemenman; |
| 226 | How SGD Noise Affects Performance in Distinct Regimes of Deep Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Understanding when the noise in stochastic gradient descent (SGD) improves generalization of neural networks remains a challenge, complicated by the fact that nets can operate in distinct training regimes. Here we study how the magnitude of this noise or `temperature’ T affects performance as the scale of initialization α is varied. |
Antonio Sclocchi; Mario Geiger; Matthieu Wyart; |
| 227 | Stochastic Gradient Descent Introduces An Effective Landscape-dependent Regularization Favoring Flat Solutions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The key question is which solution is more generalizable. Empirical studies showed a strong correlation between flatness of the loss landscape at a solution and its generalizability, and stochastic gradient descent (SGD) is crucial in finding the flat solutions. |
Ning Yang; Yuhai Tu; Chao Tang; |
| 228 | Contrastive Learning Through Non-equilibrium Memory Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we show how the simplest form of non-equilibrium memory in each `synapse’ of a network allows for contrastive rules such as equilibrium propagation. |
Arvind Murugan; Adam Strupp; Benjamin Scellier; Martin Falk; |
| 229 | Data-driven Irreversibility Measurement for Biological Patterns Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use deep learning to reveal tractable, low-dimensional representations of patterns in a canonical protein signaling process, Rho-GTPase system as well as complex Ginzburg-Landau dynamics. |
Junang Li; Chih-Wei Joshua Liu; Michal Szurek; Nikta Fakhri; |
| 230 | Training Elastic Neural Networks with The Hamiltonian Monte Carlo Sampling Algorithm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we train resource-constrained elastic ANNs by applying the Hamiltonian Monte Carlo method, a variant of the Metropolis-Hastings algorithm used in statistical physics to sample probability distributions presenting a large number of local minima. |
Théophile Louvet; Vincent Maillou; Finn Bohte; Lars Gebraad; Marc Serra-Garcia; |
| 231 | Scalable and Interpretable Machine Learning for Inference in Stochastic Transcriptional Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use physics-informed machine learning to develop a scalable and general approach for high-throughput inference of transcriptional system kinetics. |
Maria Carilli; |
| 232 | Finding The Function-Determining Subset of Amino Acids in Protein Sequence Data Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Specifically, we consider EBMs’ ability to capture protein sectors, roughly 10 to 20 percent of total sequence positions that correlate strongly with biological functions. |
Peter Fields; Vudtiwat Ngampruetikorn; Rama Ranganathan; David Schwab; Stephanie Palmer; |
| 233 | Engineering High-precision, Dynamic Genetic Control Systems Via Supercoiling-guided Design Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that gene syntax—the relative ordering and orientation of genes—defines the expression profiles, variance, burst dynamics, and intergene correlation of two-gene systems. |
Kate Galloway; |
| 234 | Using Optogenetics to Find The Signal That Maintains The DNA Damage Checkpoint Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To test which model is correct, we measured the rate of DNA resection using single-cell probes. |
Sahand Rahi; Marco Labagnara; |
| 235 | Rules of Transcriptional Bursting Revealed By Absolute Quantification of Nascent RNA in Living Fly Embryos Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, these reductionist insights have not yet been successful in adding up to a coherent biophysical model that links molecular mechanisms to empirical bursting dynamics. In this work, we provide a unified perspective on this problem by quantifying transcriptional activity in live Drosophila embryos with single RNA detection sensitivity. |
Po-Ta Chen; Benjamin Zoller; Michal Levo; Thomas Gregor; |
| 236 | DNA Supercoiling-transcription Interplay in The Presence of Nucleosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Overall, we present a mechanistic description of the supercoiling-transcription interplay in eukaryotes. |
Shubham Tripathi; Sumitabha Brahmachari; Jose Onuchic; Herbert Levine; |
| 237 | Self-assembly of DNA Binding Proteins Can Help Control Transcription Initiation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we implemented a rigid-body reaction-diffusion model to quantify how interactions between GAF proteins and between GAF to DNA control residence times, as measured by single-particle tracking experiments. |
Mankun Sang; Margaret Johnson; |
| 238 | Discovery of An Endogenous Cellular Pathway That Regulates Transcriptional Noise to Promote Cell-fate SpecificationLeor WeinbergerUniv. of California San Francisco (UCSF); Gladstone Institutes Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Stochastic fluctuations in gene expression (‘noise’) are often considered detrimental but, in other fields, fluctuations are harnessed for benefit (e.g., ‘dither’ or amplification … |
Leor Weinberger; |
| 239 | Reconstructing Chromatin Structural Connectivity from Sparse Locus Tracking Experiments Using Polymer Dynamics Modeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, visualization of chromatin is mostly limited to live imaging of a few fluorescently labeled chromosomal segments (or loci) or high-resolution reconstruction of multiple loci from a single time frame. In this study, we present an exact analytical framework that provides a probabilistic description of the time evolution of a flexible polymer structure given its structure at an earlier time point. |
Sayantan Dutta; Jude Lee; Liang-Fu Chen; Alistair Boettiger; Andrew Spakowitz; |
| 240 | A Multicolour Polymer Model for The Prediction of 3D Structure and Transcription in Human Chromatin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce a polymer model which accounts for multiple types — or “colours” — of DNA-binding proteins. |
Giuseppe Negro; Massimiliano Semeraro; Antonio Suma; Giuseppe Gonnella; Peter Cook; Davide Marenduzzo; |
| 241 | Structural Integrity and Relaxation Dynamics of Axially Stressed Chromosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use a data-driven, coarse-grained polymer modeling approach, capable of generating ensembles of chromosome structures that are quantitatively consistent with experiments, to explore the relationship between the spatial organization of individual chromosomes and their emergent mechanical properties. |
Sumitabha Brahmachari; Benjamin Ruben; Vinicius Contessoto; Ryan Cheng; Antonio Oliviera Jr.; Michele Di Pierro; Jose Onuchic; |
| 242 | 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; Ailun Wang; Michele Di Pierro; |
| 243 | Engineering CRISPR/dCas Based Toggle Switches in Escherichia Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we first develop a thermodynamic model to investigate parameters that affects the bistability of toggle switches based on CRISPR binding. We later use a massively parallel assay called X-seq to efficiently characterize these parameters for hundreds of toggle-switch constructs. |
Yasu Xu; |
| 244 | Kinetics of PHILIP Insertion Into A Membrane with Varying Model Parameters Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk will mainly focus on kinetics of pHILIP insertion into a membrane with varying model parameters that control level of pH and value of pKa. |
Ganga Sharma; |
| 245 | Intramolecular Structural Vibrations of Triose Phosphate Isomerase Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: TIM SSATM measurements were done on large crystals made using a batch microseeding method. |
Alexander McNulty-Romaguera; |
| 246 | Effects of Salt and Lipids on Conformational Dynamics of The Aβ42 Protein Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show that salt facilitates long-range tertiary contacts in Aβ42 and more compact conformations. |
Brian Andrews; Thomas Ruggiero; Brigita Urbanc; |
| 247 | Triggered Functional Dynamics of AsLOV2 By Time-resolved Electron Paramagnetic Resonance at High Magnetic Fields Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Such techniques exist, and include time-resolved (tr) X-ray spectroscopy, tr IR spectroscopy, tr NMR, and Förster resonance energy transfer, though each presents challenges when working with light-activated proteins in vitro. To mitigate these challenges, we present rapidscan-enabled, high-field, 240 GHz Gd-Gd tr EPR (TiGGER) and demonstrate it on AsLOV2, a light-activated protein found in oats. |
Shiny Maity; Brad Price; C. Blake Wilson; Arnab Mukherjee; Matthieu Starck; David Parker; Maxwell Wilson; Janet Lovett; Songi Han; Mark Sherwin; |
| 248 | Molecular Dynamics (MD) Study of The Structural and Dynamical Properties of An Intrinsically Disordered Protein (IDP) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present results on structure factor, intermediate scattering function, and backbone N-H vector correlations for pristine and metal-bound Nvjp -1. |
Selemon Bekele; Kristi Singh; Sanaz Farajollahi; Patrick Dennis; Nancy Kelley-Loughnane; Hao-Bo Guo; Rajiv Berry; |
| 249 | Integrating Machine Learning and Molecular Modelling for Predicting Protein-Ligand Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Computational approaches have increasingly become an indispensable part in predicting protein-ligand interactions and attracted much attention. In this talk, I will present our most recent progress along this direction by integrating machine learning and molecular modeling. |
Yingkai Zhang; |
| 250 | Robustness of Min Protein System In Vivo Pattern Formation on [MinE] Vs. [MinD] Phase Space Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: (3) How do the answers change under different growth conditions? In this work, we answer these questions by constructing a phase diagram in the MinD vs. MinE space, two key Min proteins required for the reaction-diffusion system. |
Ziyuan Ren; Henrik Weyer; Laeschkir Würthner; Daniel Villarreal; Dongyang Li; Cindy Sou; Erwin Frey; Suckjoon Jun; |
| 251 | Interfacial Charge Transfer of Amyloid-β Proteins with Graphene Examined Using Raman Spectroscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we investigate the electronic states of Aβ proteins at different fibrillization stages. |
Wujoon Cha; Chaejeong Heo; Sang Hyub Lee; Seok Joon Yoon; Byeong Wook Cho; Taewoo Ha; Young Hee Lee; |
| 252 | Hard X-ray Spectroscopy: A Versatile Tool for Biophysicists Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For determining the spin states of the associated metalloenzyme reaction we collected the Fe Kβ main line emission from crystals of the IDO using a specially designed von Hamos spectrometer. |
Olga Maximova; Sahand Emamian; Katherine Davis; Kendra Ireland; Vatsal Purohit; Kirklin McWhorter; Winter Allen; Scott Jensen; Diego Casa; Yulia Pushkar; |
| 253 | Graphene-Based Field Effect Transistors for Use in Biodetection of Hemoglobin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Hemoglobin as a measurable particle is of particular interest, as it has an absorbance spectrum in the visible range, meaning that it will readily create a large electrical signal when combined with graphene and illuminated with visible light. We have fabricated graphene field-effect transistor devices and use them to detect the concentration of hemoglobin in aqueous solutions. |
Vinh Nguyen; Leslie Howe; Yifei Wang; Ho Vinh; Jiarong Cui; |
| 254 | Microbial Diversification in Experimentally Evolved Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We studied a commensal interaction between two bacterial species in which Acinetobacter cross-feeds resources to Pseudomonas. |
Alejandra Rodriguez Verdugo; |
| 255 | The Interplay Between Growth Rate and Antibiotic Susceptibility in Community Response to Antibiotic Exposure Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we studied how bacterial growth dynamics can overcome differences in antibiotic susceptibility in determining community resilience: the recovery of the original community state following antibiotic exposure. |
Daniel Amor; Jeffrey Gore; |
| 256 | High-Diversity Coevolutionary Dynamics in A Model of Interacting Bacteria and Phage Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These processes motivate the question: how do ecology and evolution interact in microbial communities, and what are the characteristic patterns of diversity they produce? We explore this question in the context of a toy model of a single bacteria and phage species, each of which is comprised of many closely related strains. |
Aditya Mahadevan; Daniel Fisher; |
| 257 | Co-existence of Multiple Microbial Strains on The Same Resource in Boom-and-bust Environments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, using a consumer-resource model of microbial ecosystems, we propose that by differentiating on Monod parameters characterizing microbial growth rates in high and low nutrient conditions, strains can coexist in patterns similar to those observed. |
Sergei Maslov; Yulia Fridman; Akshit Goyal; Zihan Wang; |
| 258 | Spatial Drug Heterogeneity Changes The Bacteria Persistence in A Deleterious Diffusive Environment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we study the interplay of migration and spatial heterogeneity in an experimental meta-community of E. faecalis, a Gram-positive opportunistic pathogen. |
Zhijian Hu; Yuzhen Wu; Tomas Freire; Erida Gjini; Kevin Wood; |
| 259 | A Biophysical Threshold for Biofilm Formation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work thus provides a key step toward quantitatively predicting and controlling biofilm formation in diverse and complex settings. |
Sujit Datta; Jenna Ott; Selena Chiu; Daniel Amchin; Tapomoy Bhattacharjee; |
| 260 | Selection for Faster Microbial Expansion on Surfaces Causes Heritable Changes in Cell Shape That Feedback on The Population Genetics of Expanding Colonies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We found that cells selected for faster expansion on surfaces evolved an elongated cell shape and a bipolar budding pattern, in which daughter cells bud at the pole opposite to the birth scar. |
Katie Randolph; Andrea Giometto; |
| 261 | The Evolution of Context-dependent Altruism Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use computer simulations to determine the circumstances under which context dependence is actually favored over simple hard-coded strategies. |
Linnea Bavik; |
| 262 | Environmental Vs Demographic Noise in The Genetic Structures of Range Expansions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the context of neutral evolution, we examine the interplay between intrinsic noise caused by stochastic variation in growth processes, e.g. genetic drift, and extrinsic noise caused by spatially heterogeneous environments. |
Jimmy Gonzalez Nunez; Jayson Paulose; Wolfram Möbius; Daniel Beller; |
| 263 | Microbial Population Dynamics and Selective Advantage in Microchannels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this project, we explore bacteria Escherichia coli proliferating in rectangular microchannels with two open ends. |
Anzhelika Koldaeva; |
| 264 | The Fate of Beneficial and Deleterious Mutations in Range Expansions Driven By Long-range Dispersal Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Range expansions can leave behind signals that mimic local adaptation via founder events either at the expansion frontier in populations with only short-range dispersal or due to recurrent seeding of satellite outbreaks away from the core population when individuals are capable of long-range dispersal. In this simulation study, we introduce a fitness-affecting mutation in one individual during range expansions driven by long-range dispersal in order to learn about when "survival of the fittest" actually holds in these populations replete with founder events, or if the founder events generally cause "survival of the luckiest" dynamics to win out. |
Nathan Villiger; Jayson Paulose; |
| 265 | Speciation at An Expanding Front Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce and explore a model for speciation at the front of a colony expanding synchronously into new territory. |
Lauren Li; Mehran Kardar; |
| 266 | Mechanical Heterogeneity and Directional Cues in The Fibrous Extracellular Matrix Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our experiments use microspheres made of poly(N-isopropylacrylamide), an active hydrogel that contracts when heated. With these particles, we can apply well-controlled displacements of large magnitude at scales of tens of microns. |
Jacob Notbohm; |
| 267 | Tutorial Calculations for Force-sensing Proteins, Catch Bonding, and Other Elements of Cell–matrix Adhesion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Students can observe all of those phenomena in simple kinetic simulations and compare them to experiment. Along the way, they also gain skills by implementing the stochastic simulation algorithm in a sequence of problems: * Simple Brownian motion; * Brownian motion with a linear potential landscape; * Brownian motion in a potential well with escape; * Brownian motion in a double-well potential, modeling a two-state system. |
Philip Nelson; |
| 268 | Mediating Cell Adhesion Using Surface Microtexture Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we investigated the use of microtexture alone to control cell adhesion. |
Caroline McCue; Kripa Varanasi; Sean Parks; Moony Tseng; Adel Atari; |
| 269 | Probing Cell-matrix Interactions in 3D at The Local Scale Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will introduce our recent works in quantitatively studying how cells interact with their surrounding extracellular matrix. |
Ming Guo; |
| 270 | Local Nonlinear Elastic Response of Extracellular Matrices Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, to understand how a living cell feels the nonlinear mechanical resistance from the ECM, we mimic the cell-applied local force using optical tweezers; we report that the local stiffening responses in highly nonlinear ECM are significantly weaker than responses found in bulk rheology, across two orders of magnitude of the locally applied force since the onset of stiffening. |
Haiqian Yang; Estelle Berthier; Chenghai Li; Pierre Ronceray; Yulong Han; Chase Broedersz; Shengqiang Cai; Ming Guo; |
| 271 | Engineering Dynamic Cell-Material Interfaces to Decode How Cells Communicate with Their Environment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss the development of DNA/peptide-based stimuli-responsive interfaces as in vitro model systems able to recapitulate the dynamic cell-matrix interface. |
Ronit Freeman; |
| 272 | A Multiscale Whole-cell Theory for Cell Migration Under Geometric Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To explain the experimental observations of the regulatory roles of the ECM mechanics and geometry in mesenchymal migration, we have developed a multiscale whole-cell theory that considers the sensing of the constricted ECM domains. |
C. Nadir Kaplan; Wenya Shu; |
| 273 | Hyaluronan Glycocalyx Mechanically Modulates Cell Shape and Focal Adhesion Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Given the range of biological processes that involve hyaluronan-rich glycocalyx, from synaptogenesis to cell migration to immune cell interactions, this work provides new insight into the impact on cells exposed to their own changing glycocalyx or that of others. |
Yu Jing; Jessica Faubel; Katherine Powell; Shlomi Cohen; Jennifer Curtis; |
| 274 | Modelling Cell Trapping Phenomenon and Sub-diffusive Cell Migration on Slow Relaxing Substrates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand the migration transition induced by stress relaxation, we have developed a cell migration model based on the motor clutch framework by introducing stochastic adhesion dynamics and membrane/cortex deformation. |
Vivek Sharma; Ze Gong; Omkolade Adebowale; Ovijit Chaudhuri; Vivek Shenoy; |
| 275 | Probing Mechanical Interactions Between Lamellipodia and Surrounding Mechanical Environment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To better understand the mechanical interaction between cells and their surrounding environment, we developed an agent-based model of a branched actin network consisting of F-actin, Arp2/3, actin cross-linking protein, myosin motor, and an underlying substrate. |
June Hyung Kim; Taeyoon Kim; |
| 276 | Model of How Septin Ring Compartmentalization Aids T-cell Circumnavigation in Extracellular Matrices Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The resulting septin/F-actin rings subdivide the volume of the cell into separate compartments, with potentially different microenvironments. We developed a 2D computational model to test how such compartmentalization aids cell motility. |
Sami Alawadhi; David Rutkowski; Alexander Zhovmer; Erdem Tabdanov; Dimitrios Vavylonis; |
| 277 | Statistical Thermodynamics and Data Ad Infinitum Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Generalizing ideas of Szilard (1925), Mandelbrot (1964) and Hill (1964), we show that a statistical thermodynamic structure can emerge purely from the infinitely large data limit under a probabilistic framework independent upon their underlying mechanistic details. |
Hong Qian; Ying-Jen Yang; |
| 278 | Energy Costs of Coupled Metabolic and Genetic Information Processes in A Living Minimal Bacterial Cell: Life at The Edge Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: We recently published a 4D whole cell model (4DWCM) of a minimal bacterial cell (with only 493 genes) growing in a rich medium. Time-dependent behaviors of concentrations and … |
Zaida Luthey-Schulten; |
| 279 | Predicting Cellular Regulation By Combining Statistical Thermodynamics, Control Theory, and Optimization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In that light, we present methods for inference of the distribution of flux through metabolic networks using the principle of maximum entropy production. |
Ethan King; |
| 280 | Nonequilibrium Thermodynamics of Chemical Reaction Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: I will first briefly review the fundamentals of thermodynamics of open chemical reaction networks (CRNs). I will then present a circuit theory of CRNs which, like electrical … |
Massimiliano Esposito; |
| 281 | Recent Progress in The Statistical Physics of Real Neural Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: After some initial uncertainties, it now is clear that these models can provide extraordinarily precise descriptions of ~100 cells, for example correctly predicting the ~100,000 triplet correlations in such networks within experimental errors. When models work this well it makes to take them seriously as statistical mechanics problems and ask, for example, where real networks are in phase diagram of possible networks. |
William Bialek; |
| 282 | Multi-Relevance: Coexisting But Distinct Notions of Scale in Large Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Next, we introduce a method of calculating the cutoff scheme to be used based on the structure of the model at hand. In doing so, we demonstrate that some models support multiple notions of scale, and term this property "multi-relevance". |
Adam Kline; Stephanie Palmer; |
| 283 | Exploring Criticality in Markovian Brain Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, the model is advanced in order to discuss the effect of matrix asymmetry, which is important for certain measures in stochastic thermodynamics (ex: detailed balance). We introduce a new parameter that controls the asymmetry of these discrete Markovian systems and show that when varied over an appropriate scale this factor is able to collapse Shannon entropy measures. |
Faheem Mosam; Eric De Giuli; |
| 284 | Sparse, Consistent Correlation Structure in The Retinal Population Code Across Natural Movies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We analyze data from the larval salamander retina responding to five different natural movies, and use maximum entropy models to characterize the population in terms of activations and couplings between neurons. |
Caroline Holmes; Benjamin Hoshal; Michael Berry; Olivier Marre; Stephanie Palmer; |
| 285 | Coarse-graining Facilitates Generalization in Populations of Retinal Ganglion Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The joint probability distribution of these outputs, retinal ganglion cells (RGCs), is known to change with the statistics of the scene driving retinal activity. This creates a significant challenge in creating generative models of population activity that generalize to new types of stimuli. |
Kyle Bojanek; Olivier Marre; Michael Berry; Stephanie Palmer; |
| 286 | Brain Network Dynamics for Navigational Learning and Memory Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Together, the brain and behavioral dynamics in this study provide rich insight into navigational learning and memory. |
Jean Carlson; Erica Ward; Robery Woodry; Elizabeth Chrastil; |
| 287 | Heavy-tailed Neuronal Connectivity Arises from Hebbian Self-organization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we propose a minimal model of synaptic self-organization: connections are pruned at random, and the synaptic strength rearranges under a mixture of Hebbian and random dynamics. |
Christopher Lynn; Caroline Holmes; Stephanie Palmer; |
| 288 | Signatures of Criticality in The Physical Structure of The Brain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent experimental and computational advances have enabled the three dimensional reconstruction of millimeter-scale brain volumes of multiple organisms at the cellular level [1-3], thereby allowing for detailed investigation of the structure of brain tissue. Here we utilize these datasets to examine physical properties of the structure of the brain using techniques from statistical physics. |
Helen Ansell; Istvan Kovacs; |
| 289 | Early Path Dominance As A Principle for Neurodevelopment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand how the neural networks of brains acquire their topological structures upon development, we perform a computational study of human diffusion MRI across adults (UK Biobank, N =19,380, adolescents (Adolescent Brain Cognitive Development Study, N =15,593) and neonates (Developing Human Connectome Project, N =758), as well as mouse viral tracing (Allen Institute). |
Rostam Razban; Jonathan Pachter; Ken Dill; Lilianne Mujica-Parodi; |
| 290 | Multistable Irregular Activity in Large Winner-take-all Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Identifying multistable network models producing cortical-like irregular spiking is an unsolved challenge in neuroscience. |
Rich Pang; |
| 291 | A Random Matrix Theory in Eigenspace Enables Direct Control of Collective Network Activity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A common approach to analytically treat neural network models is to assume a random connectivity matrix. |
Lorenzo Tiberi; David Dahmen; Moritz Helias; |
| 292 | Learning Dynamic Graphs, Too Slow Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we model the learning of linear algebra textbooks with finite length random walks over the corresponding semantic networks. |
Andrei Klishin; Nicholas Christianson; Cynthia S.Q. Siew; Dani Bassett; |
| 293 | Thermal Management in Neuromorphic Materials, Devices, and Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: [1,2,3] In this talk, we describe the current state of thermal management of neuromorphic systems; the role of the brain criticality and resistive switching-based neuromorphic devices [4, 5]; the energy and electrical considerations for spiking-based computation and their relation with fundamental features of the brain’s thermo regulation [6]; graph neural networks models in neuromorphic computing [7]; and thermoelectric control of materials and neuromorphic devices. |
Felipe Torres; ALI BASARAN; IVAN SCHULLER; |
| 294 | AC-mode Graphene Field-Effect Transistors for Sensing Stress Biomarkers in Physiologically Relevant Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A simple analytical model can well explain the frequency and salt concentration-dependent sensor response. |
Biddut Sarker; Ahmad Islam; Reeshav Shrestha; Lawrence Drummy; |
| 295 | ANTIBODY/APTAMER-BASED AFFINITY PURIFICATION WITH RAMAN LABEL FOR SENSITIVE DETECTION OF CA 125 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study investigates the affinity of antibody and aptamer towards CA 125 and the sensitivity of each approach using affinity purification with gold nanoparticles (AuNps) with Raman-label. |
Robinson Karunanithy; Torrey Holland; Sivakumar Poopalasingam; |
| 296 | Investigating The Assembly of Multiple Nanoparticles Encapsulated in A Viral Capsid Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A coarse-grained model is developed to capture the steric and electrostatic interactions between NPs, and between NPs and the capsid. |
Kristen White; Vikram Jadhao; Bogdan Dragnea; Ayesha Amjad; |
| 297 | Delivery of Microcargoes By Artificial Microtubules Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Thus inspired, here we developed an artificial microtubule (AMT), a structured microfibre with embedded micromagnets that serve as stepping stones to guide particles rapidly through flow networks. |
Arnold Mathijssen; Hongri Gu; Bradley Nelson; |
| 298 | Experimental Studies of Graphene Transport in Lung-surfactant Monolayers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work seeks to improve our understanding of the way 2D particles, or particles of atomic-scale thickness, interact with certain biological membranes composed of lipid molecules. |
Joseph Samaniuk Samaniuk; |
| 299 | Using Mixed Monolayer Nanoparticles to Probe The Role of Surface Forces in Protein Corona Formation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Langmuir-like behavior and approach to saturation are only reliably observed at low salt concentration, where Coulombic forces are expected to dominate. |
Robert Costin; Miles Willis; Jennifer Hanigan-Diebel; Matthias Carrol; Sam Lohse; |
| 300 | "Defect States Study and Surface Patching in ZnO Nanoparticles Via Nano-bio Interaction with DNA Bases" Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: ZnO nanostructures with varying annealing temperatures are synthesized using the hydrothermal method. |
Ummay Honey; |
| 301 | Single-Molecule Atomic Force Microscopy Force Spectroscopy of Modified Phytoglycogen Nanoparticles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work shows the effectiveness of simple modifications in tuning the properties of PG nanoparticles and highlights PG as a novel, sustainable nanotechnology. |
Benjamin Baylis; Yasmeen El-Rayyes; Ashley Geddes; Laura Roman; Mario Martinez; Carley Miki; John Dutcher; |
| 302 | Disorder in I-WP TPMS-like Photonic Networks Creates Angle-independent Colors in Sternotomis Virescens Longhorn Beetles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work illustrates the complex interplay of structural and pigmentary color in longhorn beetles and shows how angle-independence in optical response is achieved by the novel PAI-WP networks. |
Viola Bauernfeind; Kenza Djeghdi; Ullrich Steiner; Bodo D. Wilts; |
| 303 | Polymorphism, Structure, and Nucleation of Cholesterol·H2O at Aqueous Interfaces and in Pathological Media: Revisited from A Computational Perspective Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We revisit the important issues of polymorphism, structure, and nucleation of cholesterol·H 2O using first principles calculations based on dispersion-augmented density functional theory. |
Margarita Shepelenko; Anna Hirsch; Neta Varsano; Fabio Beghi; Lia Addadi; Leeor Kronik; Leslie Leiserowitz; |
| 304 | Investigation of Lipid-based Drug Delivery Vehicle Using Molecular Dynamics Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, I will present the interactions of the various constituent molecules with the two different lipid membranes and the effect that their insertion into the membrane has on the two different membranes. |
Jun Xie; |
| 305 | Self-assembly of Virus Like Particles and Their Biomedical Applications Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, both bacterial phage MS2 protein and shrimp white spot syndrome VP28 are recombinantly expressed in a heterologous system. |
Chia-Ching Chang; Pragati Vishwakarma; Hussein Reda Hussein; Chia-Yu Chang; Yini Zhang; Chih-Yu Yang; Yu-Chaun Liang; Fu-Rong Chen; Tapan Kumar Chaudhuri; |
| 306 | Theoretical Simulations for The Effect of Lattice Vibration on The Transport Properties of Biological Nanowires Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a tight biding model Hamiltonian, we examine the diffusing of wave pockets through a one-dimensional lattice with randomized on-site and hopping energies. |
Ruqian Wu; Sahar Sharifzadeh; Rafael Umeda; Luke Nambi Mohanam; |
| 307 | Benchmarking Biomaterials for Quantum Information Processing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The results from Nuclear Magnetic Resonance (NMR) measurements of T2 and T2* on various phosphate compounds in different chemical environments will be explored. The aim of this research is to delineate the influence of molarity, molecular correlation time, and dipole-dipole interaction through NMR, and to learn how these parameters can be used to manipulate correlation times between phosphorus spins. |
Donovan Davino; Edward Walsh; G. Tayhas Palmore; Vesna Mitrovic; |
| 308 | Explore DNA Nanostructures for Controlling Multienzyme Assembly and Modulating Catalysis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we described a robust strategy for DNA-scaffolded assembly and confinement of biochemical reactions. |
Jinglin Fu; |
| 309 | Coupling Reactive and Diffusive Fluxes to Predict Catalysis-driven Chemotaxis at The Nanoscale Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We adopt Mielke’s framework, which models the conventional reaction-diffusion equation as a gradient descent of the Helmholtz free energy with respect to an Onsager-type dissipation potential. We introduce a new term into this potential that couples the diffusive flux of an enzyme to a simple chemical reaction. |
Kathleen Krist; William Noid; |
| 310 | Mechanochemical Active Nematics: How to Design Topology Sensing Enzymes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Active nematic fluids are an important class of materials whose dynamics are intrinsically chaotic. Towards developing bioinspired signaling pathways that shape these flows into desired configurations, we aim to design feedback loops that spatiotemporally modulate active stress in response to structural cues from the nematic. |
Michael Norton; Piyush Grover; |
| 311 | The Concept of A Chemical Temperature from Optical Tweezers Experiments Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: It is fundamental to consider that the random forces giving rise to thermal fluctuations generate both diffusion and dissipation. Our optical tweezer experiments suggest that … |
Tian Huang; Jin Tae Park; Hyuk Kyu Pak; Steve Granick; |
| 312 | A Background Enzymatic Active Bath Affects Liquid-Liquid Phase Separation of Protein 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; Diego Luna; Anthony Estrada; Sarthak Gupta; J. Schwarz; Jennifer Ross; |
| 313 | Active Boundary Layers in Confined Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we work with the well-known kinesin/tubulin active nematic under confinement and show that the self-sustained flows can develop active boundary layers that topologically polarize the confining walls and determine the bulk flows. |
Jordi Ignés-Mullol; Jérôme Hardoüin; Claire Doré; Justine Laurent; Teresa Lopez-Leon; Francesc Sagués; |
| 314 | Onset of Homochirality in Cell Monolayers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a simple model to describe the possible origin of homochirality in cells. |
Ludwig Hoffmann; Luca Giomi; |
| 315 | Enhanced Swimming Behavior of Active Hematite Microparticles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Calcined particles have an average 28-fold rise in MSD at 1-minute lag times. This simple approach makes hematite more accessible to key areas of soft matter and photocatalysis research. |
Sarah Schyck; Silvana Caipa Cure; Laura Rossi; stefano sacanna; |
| 316 | Dynamics, Scaling Behavior, and Control of Nuclear Wrinkling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine live-imaging experiments, theory, and simulations to characterize the onset and dynamics of nuclear wrinkling during egg development in the fruit fly, Drosophila melanogaster, when nurse cell nuclei increase in size and display stereotypical wrinkling behavior. |
Nicolas Romeo; Jonathan Jackson; Alexander Mietke; Keaton Burns; Jan Totz; Adam Martin; Jorn Dunkel; Jasmin Imran Alsous; |
| 317 | Synthesis and Hydrogelation of Bioinspired Block Copolymers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report the preparation of symmetric polyethylene glycol (PEG) block copolymers containing well-defined number and location of unprotected catechol groups. |
Fahed Albreiki; Samanvaya Srivastava; |
| 318 | Coexistence in Diverse Communities with Higher-order Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides needed theoretical expectations for how higher-order interactions impact species coexistence in diverse communities. |
Theo Gibbs; Simon Levin; Jonathan Levine; |
| 319 | Emergent Competition Shapes The Ecological Properties of Multi-trophic Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A fundamental question in theoretical ecology is to understand how the interplay between trophic structure, diversity, and competition shapes the ecological properties of ecosystems. To address this problem, we analyze a generalized Consumer Resource Model with three trophic layers using the cavity method and numerical simulations. |
Zhijie Feng; Pankaj Mehta; Jason Rocks; Robert Marsland; |
| 320 | Predicting Microbial Community Compositions Using Compressive Sensing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present a new model-agnostic approach to predicting community compositions using compressive sensing. |
Shreya Arya; Ashish George; James O’Dwyer; |
| 321 | A New Geometric Framework for Niche Theory and Consumer Resource Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a new, simple yet powerful, geometric framework for understanding species coexistence in CRMs based on convex polytopes in the space of consumer preferences. |
Emmy Blumenthal; Pankaj Mehta; |
| 322 | Predicting The First Steps of Evolution in Randomly Assembled Microbial Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a replica-theoretic approach for predicting the first steps of evolution in randomly assembled communities that compete for substitutable resources. |
John McEnany; Benjamin Good; |
| 323 | Effects of A Periodically Changing Environment on A Predator-prey Ecology Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the Lotka-Volterra model for predator-prey competition subject to a periodically varying carrying capacity. |
Mohamed Swailem; Uwe Tauber; |
| 324 | Theory: Predicting and Controlling Evolving Ecological Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present general analytical solutions to Adaptive Dynamics equations and present formulas that govern how equilibrium abundances shift over evolutionary time scales. |
Dervis Vural; Vu Nguyen; |
| 325 | Dynamical Phase Transitions in The Eco-evolutionary Dynamics of Complex Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Species respond and adapt to their surroundings by modifying their phenotypic traits, which in turn alters their environment and the resources available. To study this interplay between ecological and evolutionary mechanisms, we construct a consumer-resource model coupled with phenotypic mutations. |
Jim Wu; Trevor GrandPre; Anne-Florence Bitbol; David Schwab; |
| 326 | An Age-structured Lotka-Volterra Model and The Emergence of Overcompensation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We construct an age-structured single-species population model that incorporates a Lotka-Volterra-type cannibalism interaction. |
Mingtao Xia; Xiangting Li; Tom Chou; |
| 327 | Impact of Oceanic Frontal Divergence on Phytoplankton Community Composition Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine observations, simulations, and theory to consider the impact of realistic flow fields with resolved submesoscale dynamics on plankton community composition. |
Abigail Plummer; Mara Freilich; Roberto Benzi; Chang Jae Choi; Lisa Sudek; Alexandra Worden; Federico Toschi; Amala Mahadevan; |
| 328 | Dynamic Coexistence Due to Growth Succession in Cyclic Microbial Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a phenomenological model to gain insight into the dynamic coexistence of microbes due to changes in physiological states in cyclic environments. |
Avaneesh Narla; Terence Hwa; Arvind Murugan; |
| 329 | Quantitative Physiology: Predictive Understanding of Living Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will review several quantitative physiological studies of bacterial systems which led to the elucidation of the underlying regulatory strategies and mechanisms, as well as other studies for which mechanistic understandings are still outstanding. |
Terence Hwa; |
| 330 | The Proteome Acts As A Terminal Electron Acceptor Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: At the same time, metabolic transformations convert nutrients – e.g. ammonia, phosphate, and sugars – into the macromolecules that build cells, e.g. proteins, nucleic acids, and lipids. I will describe a simple mathematical model of resource allocation during microbial growth that explicitly accounts for these dual roles by tracking the nominal oxidation state of carbon (NOSC) in nutrients (e.g. glucose), intermediates (amino acids), products (CO 2), and biomass (proteins). |
Abraham Flamholz; |
| 331 | Functional Decomposition of Metabolism Reveals Gross Imbalance in The Energy Budget of Aerobically Growing Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We established a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to cellular metabolic functions, e.g., the synthesis of metabolic building blocks such as amino acids and the generation of bioenergy such as ATP. |
Matteo Mori; Chuankai Cheng; Brian Taylor; Terence Hwa; |
| 332 | Effect of Cell-to-cell Variability on The Signal Transduction Capability of An Isogenic Population Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: With E.Coli chemosensory signaling pathway as our model system, we addressed the general question of how the nonlinear signal transduction capabilities of a diverse population and those of the mean phenotype differ and what are the physiological implications. |
Swayamshree Patra; Jeremy Moore; Nirag Kadakia; Keita Kamino; Agastya Rana; Thierry Emonet; |
| 333 | The Physiological Response of Bacterial Cells to Temperature Shock Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed a device that allows us to track the growth of single cells during rapid temperature shifts. |
Kerwyn Huang; |
| 334 | Biomass Transfer on Autocatalytic Reaction Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, I characterized the biomass transfer process for autocatalytic, growing systems with scalable reaction fluxes. |
Wei-Hsiang Lin; |
| 335 | On The Physiology of Vibrio Natriegens and The Possible Costs of Growing "too Fast" Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, even though it is able to grow so fast, V. natriegens is not a dominant species in the marine environments where it was isolated from. To see whether this may arise from possible tradeoffs between fast growth with other physiological characteristics, we characterized various aspects of V. natriegens’ growth physiology, including yield, death, and lag times when switching between nutrients. |
Leonardo Pacciani-Mori; Terence Hwa; |
| 336 | Principles of Resource Allocation Under The Active Control of Ribosome Synthesis in Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, testing these predictions has been a major experimental challenge. Here, we show that Bacillus subtilis, another model bacterial organism, deviates from this growth maximization paradigm. |
Ryan Thiermann; Jin Yang; Farshad Abdollah-Nia; John Sauls; Taylor Rytlewski; Sarah Cox; James Williamson; Zulfar Ghulam-Jelani; Jue Wang; Victoria Castillo; Suckjoon Jun; |
| 337 | Dynamic Allocation of Proteomic Resources By E. Coli in Rich and Minimal Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A coarse-grained kinetic model quantitatively captures the enzyme recovery kinetics across many pathways, based solely on snapshots of the proteome right before and long after the transition, without invoking any ad hoc fitting parameters. |
Terence Hwa; Chenhao Wu; Matteo Mori; Christina Ludwig; |
| 338 | Adaptability and Sensitivity in Gene Regulatory Responses Out of Equilibrium Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we study the control of a simple, ubiquitous gene regulatory motif to explore the consequences of departing equilibrium in kinetic cycles. |
Gabriel Salmon; Sara Mahdavi; Patill Daghlian; Hernan Garcia; Rob Phillips; |
| 339 | Cellular Adaptations of Yeast to Freeze-thaw Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the survival of Saccaromyces cerevisiae when exposed to cycles of freeze (77K) and thaw (298 K), followed by growth. |
Charuhansini Kulkarni; Nithila Kumar; Ankita Ray; Zeenat Rashida; Shashi Thutupalli; |
| 340 | A Novel Electrical Device Demonstrates Localized Stimulation Triggers Cell-type-specific Proliferation in Biofilms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work thus reveals that an electronic interface can selectively target bacterial cell types, enabling control of biofilm composition and development. |
Colin Comerci; Alan Gillman; Leticia Galera-Laporta; Edgar Gutierrez; Alex Groisman; Joseph Larkin; Jordi Garcia-Ojalvo; Gürol Süel; |
| 341 | Dynamical States of Self-Organised Waves in A Giant Single-Celled Organism Feeding on Light Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Time-keeping and synchronization are recurring themes in the research of Living Systems as contributors to Homeostasis — biological self-stabilization far-from-thermal-equilibrium, as well as to Anticipatory Behaviour. |
Eldad Afik; Tony Liu; Elliot Meyerowitz; |
| 342 | Utilizing Massively Parallel CRISPRi Assays to Investigate Antibiotic Tolerance Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate that this approach can be used to investigate antibiotic tolerance and persisters by controlling the cas protein using an inducible promoter and thereby allowing for the reversal of growth based effects. |
Keiran Stevenson; Guillaume Lambert; Louis Cortes; |
| 343 | Growth Rate of Pathogenic Bacterial Species in The Presence of Zinc Oxide Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We plan to extend this research to bacterial species with differing morphological and Gram-staining characteristics. |
Ahmed Majgaonkar; |
| 344 | Active Transport and Self-organization in Living Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Efficient control of mass, energy, and information flows is critical for the robust function of large complex systems. Cities, for example, can come to a standstill when power … |
Michael Shelley; |
| 345 | Individual-based Biophysical Modeling of Spatial Dynamics of Chemotactic Microbial Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present an individual-based, biophysical computational framework for mechanistic and multiscale simulation of the spatiotemporal dynamics of motile and chemotactic microbial populations. |
Congjian Ni; |
| 346 | Combining Mechanistic and Statistical Models to Enable Nascent Chain Tracking for Multiple MRNAs Using A Single Color Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present a hybrid computational pipeline where detailed mechanistic simulations produce realistic NCT videos and machine learning is used to assess experimental designs for their potential to resolve multiple mRNA species sharing a single fluorescent color. |
William Raymond; |
| 347 | 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; |
| 348 | Stochastic Models of Cellular Survival and Evolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We verify that the average, standard deviation, and autocorrelation coefficient correspond to expectations for the Ornstein-Uhlenbeck process. |
Christopher Siebor; Gabor Balazsi; |
| 349 | Oxygen Delivery to Tissue Via A Complex Branched Cellular Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand what structural features allow for adequate supply of the system, we investigate the steady-state tissue oxygen gradient arising from a tree-like distribution network with a single point of entry. |
Tatyana Gavrilchenko; Pauline Hansen; Daniel Fortunato; Alex Barnett; Stanislav Shvartsman; |
| 350 | Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on An Epithelial Tissue Patch Infected By SARS-CoV-2 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We extend our established agent-based multiscale computational model of infection of lung tissue by SARS-CoV-2 to include pharmacokinetic and pharmacodynamic models of remdesivir. |
Juliano Ferrari Gianlupi; Tarunendu Mapder; T.J. Sego; James Sluka; Sara Quinney; Morgan Craig; Stratford; Jr; Robert; James Glazier; |
| 351 | Ab Initio Investigation of Bio-interfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Therefore, an atomistic understanding of nano clay interaction with biologically relevant materials is of great importance. In this respect, we investigated the interaction of eleven unnatural amino acids with Fe and Mg co-doped montmorillonite clay using density functional theory calculations. |
Deniz Cakir; Ashan Fernando Warnakulasuriya; Mark Hoffmann; |
| 352 | Contrasting Self-assembly Pathways at The Membrane Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, these assemblies differ in how they couple to co-factors that can separately promote either protein-protein assembly or protein-membrane recruitment. We discuss similarities between these systems that can help them to efficiently assemble only on membranes, highlighting how cooperativity plays a key role in avoiding kinetic traps. |
Margaret Johnson; |
| 353 | Enhancement of Information Transmission Efficiency Via Feedback in Synapses of The Fly Early Visual System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Weckström and Laughlin (2010) show that significant electric potentials are generated in the photoreceptor-LMC extracellular space as a response to visual activity. We propose that regularization of vesicles occurs through the control of the voltage sensors responsible for vesicle release by these feedback potentials. |
Golam Kashef; Robert de Ruyter; |
| 354 | Energetic and Kinetic Criteria for Assembling HIV-1 Gag Lattices in Solution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This strategy can mimic mechanisms used by cells, where co-factors and membrane binding can provide similar time-dependent mechanisms of cooperative control. Our work provides a foundation for predicting how these essential factors regulate Gag lattice formation. |
Yian Qian; Margaret Johnson; Daniel Evans; |
| 355 | Visualizing Self-generated Gradients of Chemoattractants By Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Chemotactic bacteria such as E. coli can bias their motility in response to local concentrations of chemicals, which are also influenced by the bacteria themselves. Here, we … |
Trung Phan; Henry Mattingly; Jonathan Marvin; Lam Vo; Loren Loogan; Thierry Emonet; |
| 356 | What Shapes Bacterial Biofilms? A Physics Perspective Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work aims to understand how the material properties of the biofilm matrix determine biofilm morphology and mechanical properties. |
Eleonora Secchi; |
| 357 | The Role of Viscoelasticity of Gel-like Biofilms on Mechanical Clearance By Immune Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we investigate the individual and combined effects of eDNA and alginate on biofilm structure, the impact of polymer-specific enzymes as mechanically compromising agents, and the role of viscoelasticity of calcium-gelled biofilms in the success of mechanical clearance by neutrophils. |
Marilyn Wells; Vernita Gordon; Isabella Chavez; Hailey Currie; |
| 358 | Jump-start and Push-start: How Signal Crosstalk Can Drive The Activation of Quorum Sensing Pathways Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we explore the effect of intracellular signal crosstalk on quorum sensing using a simple model. |
Joseph Sanders; Hoda Akl; Stephen Hagen; BingKan Xue; |
| 359 | Computational Modelling to Predict How Extracellular Polymeric Substances Production on Biofilm Mechanics and Detachment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, a three-dimensional individual-based model (IbM) of biofilm was developed by coupling the computational fluid dynamics approach (CFD) with the discrete element method (DEM). |
Jinju Chen; yuqing xia; Jayathilake Pahala Gedara; Bowen Li; Paolo Zuliani; David Deehan; Jennifer Longyear; Paul Stoodley; |
| 360 | Orientational Dynamics of Bacterial Active Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We build a variable-step multichannel imaging setup for the observation of fluorescent cell body, stained flagellar and phase contrast. |
Kaiwei Wang; |
| 361 | Comparison Between Phase-field Model and Coarse-grained Model for Characterizing Cell-resolved Morphological and Mechanical Properties in A Multicellular System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this paper, we study two popular computational models for multicellular systems, i.e., the phase-field model and the coarse-grained model, and compare their performance in characterizing the cell morphologies, cell adhesion, and cell stiffness in a real C. elegans embryo. |
Guoye Guan; |
| 362 | Receptor Promiscuity and Feedback Control Mediate Accurate and Robust Encoding and Decoding of Positional Information During Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we show how receptor promiscuity and feedback control on receptors can act as local cell autonomous control mechanisms that allow for sculpting of morphogen profiles in tandem with accurate and robust positional inference. |
Krishnan Iyer; Madan Rao; |
| 363 | Machine-learning Drosophila Embryogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study incorporates neural networks as an integral part of a framework for constructing predictive phenomenological models in biology and biophysics. |
Jonathan Colen; Noah Mitchell; Nikolas Claussen; Marion Raich; Sebastian Streichan; Vincenzo Vitelli; |
| 364 | Topological Defects in The Nematic Order of Actin Fibres As Organization Centres of Hydra Regeneration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we utilize the fresh water animal Hydra as a model system, focusing on the dynamics of the actin cytoskeleton during a regeneration process which is akin to development. |
Yonit Maroudas-Sacks; Lital Shani-Zerbib; Liora Garion; Anton Livhsits; Erez Braun; Kinneret Keren; |
| 365 | Degradable X-Ca-Alginate Aerogels As Neuronal Scaffolds-investigation of Pc12 Cells-substrate Interface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, the suitability of X-Ca-Alg aerogels as neuronal scaffolds is examined. |
Martina Rodriguez Sala; Firouzeh Sabri; Omar Skalli; Grigorios Raptopoulos; Patrina Paraskevopoulou; |
| 366 | Impairment of Entropy Regulation in Humans Associated with Age and Illness: A Calorimetric Approach Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, we will introduce our experimental approach for the continuous measurement of entropy flows in the human body, here considered as a non-equilibrium and non-stationary system. |
Nicolas Brodeur; |
| 367 | Disease Prediction By Detecting and Integrating Connectomic Networks and Marginally Weak Signals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we hypothesize that a large portion of the predictiveness of disease outcomes attributes to inter-marker connections as well as marginally weak signals. |
Yanming Li; |
| 368 | An Updated Computer Model of Type 1 Diabetes Mellitus in Neonatal Patients Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The study focused on a DNA triplet involved in the translation of the preproinsulin precursor peptide mRNA into the mature bioactive insulin protein. |
Robert Goshen; Harriet Papernick; |
| 369 | Atomic Level Fluctuations of Connectivity in The Structure Network of SARS-CoV2-Human ACE2 Receptor Complex Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we study the non-covalent connectivity of the SARS-CoV2-Human ACE2 receptor complex, as obtained from molecular dynamics simulations, through graph spectral analysis and show the effects of connectivity strength and dynamic stability on the interface region. |
Saraswathi Vishveshwara; Varsha Subramanyan; Arinnia Anto; Moitrayee Bhattacharyya; Smitha Vishveshwara; |
| 370 | Particle-Resolved Holographic Molecular Binding Assays Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate this technique with probe beads functionalized with protein A that are immobilized with holographic optical traps while being incubated with target antibodies. |
Kaitlynn Snyder; David Grier; |
| 371 | An Elastic Lattice Polymer Model of Bacterial Chromosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Bacterial DNA often adopts tree-like double-folded branching configurations due to DNA supercoiling. In this context, we propose a framework to generate expected bacterial chromosome structures at multiple scales. |
Elham Ghobadpour; Ralf Everaers; Ivan Junier; |
| 372 | The Other Side of Entropy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The role of entropy has since moved beyond the traditional boundaries of equilibrium thermodynamics, towards problems for which the development of a statistical mechanical theory seems plausible but the a-priori probabilities of states are not known, making the definition and calculation of entropy-like quantities challenging. In this talk, I will discuss information theoretic ideas and methods that enable these computations. |
Stefano Martiniani; |
| 373 | First Law of Thermodynamics with Strong Coupling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we discuss how the problem can be solved by a concise and simple mathematical description for classical systems in which the change in interaction energy between the two systems can be decomposed into energy flows related to state changes of each one of the systems alone. |
Susanne Still; Gavin Crooks; |
| 374 | Information and Optimal Inference Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Physics works because it ignores microscopic details, not because they are small, but because they are unimportant. This idea of importance has a natural interpretation in information theory, and in earlier work we showed that omitting detail isn’t a trade-off: A model which includes many irrelevant parameters captures much less information than a simpler model without them, when both are fitted to the same limited noisy data [1]. |
Michael Abbott; Julian Rubinfien; Benjamin Machta; |
| 375 | Data Efficiency of The Symmetric Information Bottleneck Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore the data size requirements of both methods by analytically calculating error bounds and mean squared errors in the estimation of mutual information terms used in both bottlenecks. |
K. Michael Martini; Ilya Nemenman; |
| 376 | Machine-Learning Surrogates for Information Geometric Analysis of Multi-parameter Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, many models are available only as "legacy code" to which AD methods are difficult to apply. To utilize these AD methods, we propose a general method in which a machine learned model is used as a surrogate model for these legacy models. |
Jay Spendlove; Mark Transtrum; Tracianne Neilsen; |
| 377 | Optimal Compression and Transcriptional Control Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: If conditional distributions are Gaussian and effective noise levels are small, we derive a scaling relation onto which all optimal bottleneck curves collapse. |
Marianne Bauer; William Bialek; |
| 378 | The Information Bottleneck and The Double Pendulum: Using Machine Learning to Study How Chaos Destroys Information Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show how machine learning presents new opportunities for the study of information loss in chaotic dynamics, with a double pendulum serving as a model system. |
Kieran Murphy; Dani Bassett; |
| 379 | What Does It Mean to Invert An Exact Renormalization Group Flow? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this note, we demonstrate how the Dynamical Bayesian Inference equation is, itself, equivalent to a continuity equation which we dub Bayesian Diffusion. |
Marc Klinger; |
| 380 | An Equivalence Between The Exact Renormalization Group and Continuous Entanglement Renormalization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we attempt to fill the gap and show that for free field theories one may develop a "Hilbert space picture" of the ERG, giving a direct equivalence of entanglement renormalization and a subclass of ERG flows. |
Samuel Goldman; |
| 381 | Information Driven Renormalisation Group on Irregular Lattices Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This inherent difficulty made it elusive to develop a model-independent paradigm for RSRG in inhomogeneous systems. In this work we address this gap by extending the recent information-theoretical formulation of RSRG to arbitrary irregular lattices. |
Doruk Efe Gokmen; Maciej Koch-Janusz; Zohar Ringel; Sounak Biswas; Felix Flicker; |
| 382 | Constrained Models on Quasicrystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Treating the vertices and edges of AB as those of bipartite graphs, we (i) prove the existence of Hamiltonian cycles (visiting each vertex precisely once), an NP-complete problem in general graphs, and thereby construct polynomial-time solutions in AB to a range of NP-complete problems with applications in adsorption, catalysis, scanning tunneling microscopy, and elsewhere; (ii) demonstrate the existence of fully-packed loops on Ammann Beenker tilings, and study their statistics numerically, giving a generalisation of ice-type models to aperiodic settings; (iii) apply MPS-DMRG to study the quantum dimer model; we are able to apply this technique in 2D owing to structures emerging naturally from the dimer constraint. |
Felix Flicker; |
| 383 | Phase Transition in The Computational Complexity of The Shortest Common Superstring and Genome Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite this fact, high-throughput technologies and modern algorithms currently allow bioinformaticians to produce and assemble datasets of billions of reads. Using methods from statistical mechanics, we address this conundrum by demonstrating the existence of a phase transition in the computational complexity of the problem and showing that practical instances always fall in the ‘easy’ phase (solvable by polynomial-time algorithms). |
David Yllanes; Victor Martin-Mayor; Luis Antonio Fernandez; |
| 384 | First Passage Time and Information of A One-dimensional Brownian Particle with Stochastic Resetting to Random Positions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We explore the different entropy regimes, namely, the externally-driven, the zero-entropy and the Maxwell demon regimes. |
Javier Toledo-Marin; Denis Boyer; |
| 385 | Surface Fluctuating Hydrodynamics Methods for The Drift-Diffusion Dynamics of Proteins and Microstructures Within Curved Lipid Bilayer Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce surface fluctuating hydrodynamics approaches for investigating transport and fluid-structure interactions arising in cell mechanics within curved lipid bilayer membranes. |
Paul Atzberger; |
| 386 | Modeling The Assembly of Curvature Inducing Proteins in SARS-CoV-2 Budding at Multiple Scales Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This phase separation can be demonstrated analytically by modeling the coupled evolution of M protein density and membrane shape, where proper parameterization requires a microscopic understanding of the interactions and dynamics of M proteins. To help develop this understanding, we utilize a multiscale modeling approach. |
Joseph McTiernan; Michael Colvin; Roya Zandi; Ajay Gopinathan; |
| 387 | Curvature Sensing As An Emergent Property of Multi-scale Assembly of Septins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These experiments unexpectedly indicated that septins’ curvature preference is not absolute but rather sensitive to the combinations of membrane curvatures present in a reaction, suggesting there is competition between different curvatures for septin binding. To understand the physical underpinning of this result, we developed a kinetic model that connects septins’ self-assembly and curvature sensing properties. |
Wenzheng Shi; Ehssan Nazockdast; Christopher Edelmaier; |
| 388 | Influence of Thermal Fluctuations on The Association and Localization of Proteins Onto Curved Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we extend these results to develop models that predict single-protein association rates to membrane-adhered beads of different curvatures. Referring to experiments on the association of septin proteins, we propose two classes of predictive models: i) for proteins with a maximal association rate to a preferred membrane curvature, and ii) for proteins with enhanced association rates above a threshold curvature. |
Indrajit Badvaram; Brian Camley; |
| 389 | A Bifurcation Amplifies and Integrates A Noisy Signal from Many Molecular Thermo-receptors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Single neurons in the organ reliably respond to mK temperature increases, 1000 times more sensitive than single thermo-TRP ion channels, whose opening probability barely rises – by less than 0.1%. Here, we propose a mechanism for the integration of this molecular information into an amplified neural response. |
Isabella Graf; Benjamin Machta; |
| 390 | Probing Surface-mediated Protein Aggregation Via FRET-induced Lifetime Changes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We describe progress on the detection and understanding of surface-mediated aSyn aggregation on artificial membranes made from anionic phospholipids. |
Paula-Marie Ivey; Magaly Guzman Sosa; Arjun Krishnamoorthi; Justin Patel; Jean-Christophe Rochet; Kevin Webb; |
| 391 | The Mechanical Basis for Single Amphipathic Helix Engagement with Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present research into how AH-domains interact with cellular membranes at the atomistic scale. |
Christopher Edelmaier; |
| 392 | All Atom Simulations Reveal Adaptive and Multimodal Membrane Binding of Contractile Ring Anchoring Protein Mid1 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In order to elucidate Mid1’s membrane binding mechanism, we used the available structural information of the PH, C2, and CNCT in all atom molecular dynamics simulations of Mid1 near membrane compositionally based on experimental measurements. |
Aaron Hall; Yeol Kyo Choi; Wonpil Im; Dimitrios Vavylonis; |
| 393 | Atomic Insights Into Amyloid-Induced Membrane Damage Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we perform the first all-atom simulations in which membrane-bound amphipathic peptides self-assemble into β-sheets that subsequently either form stable pores inside the bilayer or drag lipids out of the membrane surface. An analysis of these simulations shows that the acyl tail of lipids interact strongly with non-polar side chains of peptides deposited on the membrane. |
Yanxing Yang; |
| 394 | Investigation of The Synergistic Antimicrobial Effect of Winter Flounder Peptides Using Molecular Dynamics Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we report the results of all-atom molecular dynamics simulations of the interaction of 10 different two-way combinations of Winter Flounder peptides, a family of cationic AMPs found in the epithelial mucous cells of winter flounder, against membrane models representative of gram-positive bacteria (100% POPG), gram-negative bacteria (POPE:POPG = 3:1) and red blood cells (RBC). |
Miruna Serian; |
| 395 | Exploring Specific and Non-specific Membrane Binding Targets of Self-assembling Human Islet Amyloid Polypeptide Oligomers on Phase-Separated Lipid Domains Using MD Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Self-aggregation of human Islet Amyloid Polypeptide (hIAPP) is linked to type 2 diabetics (T2D). Recent cellular studies indicate that the small, disordered hIAPP oligomers are … |
Kwan Cheng; Angela Graf; Aakriti Acharya; Thuong Pham; |
| 396 | Antibody Binding Regulates The Dynamics of The Membrane-bound Prion Protein Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the influence of the POM1 and POM6 antibodies on the flexibility and the interaction with the membrane of the mouse PrP C by molecular dynamics simulations. |
Ioana Ilie; Marco Bacci; Andreas Vitalis; Amedeo Caflisch; |
| 397 | Force Probing Ligand-receptor Interactions on Cells and Exosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using the single-molecule force spectroscopy method, we probed dynamic ligand-cellular receptor interactions and found important physical parameters associated with binding and unbinding thermodynamics. |
sakurako tani; Lina Alhalhooly; Yongki Choi; |
| 398 | The Structure-function Problem in Microbial Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How does Nature construct such robustly functional communities? In this talk, I will present our recent work on this ‘structure-function problem’ in communities. |
Seppe Kuehn; |
| 399 | Global Patterns in Gene Content Soil Microbiomes Emerge from Ecological Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, leveraging a global dataset of soil metagenomes, we identify a pattern in gene content of soil microbiomes. |
Kyle Crocker; Milena Chakraverti-Wuerthwein; Madhav Mani; Karna Gowda; Seppe Kuehn; |
| 400 | Mapping Prediction Error Versus Information Content of Coarse-grained Descriptions of Microbial Ecosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We build on this work to systematically compare all possible coarse-grained descriptions by explicitly quantifying their prediction power and information content. |
Jacob Moran; Mikhail Tikhonov; |
| 401 | Ecosystems Self-organize to Capture Atypically Large Energy in A Model of Coupled Redox Transformations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we systematically study the energy capture efficiency and convergent features of self-organized ecosystems, by means of a new conceptual model which combines ecology with thermodynamically-constrained redox transformations. |
Akshit Goyal; Avi Flamholz; Alexander Petroff; Arvind Murugan; |
| 402 | How Does Toxin Production Maintain Diversity in Ecological Systems? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Specifically, by using a coarse-grained model of metabolism which satisfies proteome constraints, we show transitions from low to high diversity, and suggest diversity can be maintained by toxin production through two routes: (i) coexistence at steady state, and (ii) persistence through oscillations or chaos. |
Ga Ching Lui; Sidhartha Goyal; |
| 403 | Multi-strain Phage-induced Clearance of Pseudomonas Aeruginosa Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we address quantitatively how to design a phage cocktail efficient against Pseudomonas aeruginosa infections. |
Jacopo Marchi; Sophia Zborowsky; Laurent Debarbieux; Joshua Weitz; |
| 404 | Recovering Population and Growth Rate of Bacteria Within A Two-Tank Interconnected Chemostat Model Using Data Assimilation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we consider a two-tank gradostat model where data is collected from the outflow of the second tank. |
Susan Rogowski; Nick Cogan; Aseel Farhat; |
| 405 | Additivity and Asymmetricity in Microbial Community Coalescence Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using both theory and experiment with bacterial microcosms, we show that species pool size and interspecies interaction strengths determine the additivity and asymmetricity in community coalescence. |
Jinyeop Song; Jiliang Hu; Jeffrey Gore; |
| 406 | Nutrients’ Control Over Microbial Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By experimentally manipulating the quality and quantity of available nutrients in natural microbial microcosms, my work aims at bridging the gap between theory and experiments and gaining a mechanistic understanding of the principles governing how available nutrients shape microbial communities. |
Martina Dal Bello; |
| 407 | Competition at The Edge of Expanding Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These mutants may colonize new territory either faster or slower than their wildtype ancestors, leading to a nontrivial morphology of the expansion front near the mutant colony. In this work, we couple a model of surface growth to a model of one-dimensional competition to describe this behavior. |
Daniel Swartz; Hyunseok Lee; Kirill Korolev; Mehran Kardar; |
| 408 | Lab-evolved Multicellular Organisms Exhibit Long-range Flows That Overcome Nutrient Diffusion Limits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a possible mechanism for this: live clusters exhibit metabolically-driven flows when cultured in liquid media. |
Emma Bingham; Nishant Narayanasamy; William Ratcliff; Peter Yunker; Shashi Thutupalli; |
| 409 | Cell Size Regulation and Growth Control in Crowded Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using parameters determined from experiments on cultured epithelial cells, we develop a multi-scale Cellular Potts model that describes the dynamics of a tissue transitioning from a sub-confluent state to a state of arrested growth. |
Logan Carpenter; Shiladitya Banerjee; |
| 410 | Adding Learning Degrees of Freedom in Biological Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that the rigidity transition can be shifted by introducing the preferred cell perimeters as transient degrees of freedom. |
Sadjad Arzash; Indrajit Tah; Andrea Liu; M Lisa Manning; |
| 411 | Cellular Cruise Control: Energy Dissipation Regulates Collective Migration in Epithelia Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a data-driven agent-based model that predicts collective migratory behavior from past energy dissipation alone, considering cell-substrate friction and viscous cell-cell interactions. |
Isaac Breinyn; Simon Martina-Perez; Daniel Cohen; Ruth Baker; |
| 412 | Investigating The Effects of Laser Induced Cavitation Bubbles and Fast Calcium Influx in Wound Healing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Combining the displacement fields and patterns of fast calcium influx, we can relate shear-stress to damage around the wound and on to the pattern of cell behaviors observed on longer time scales. |
Mia Grace Cantrell; |
| 413 | A Mathematical Model for Tissue Growth in A Tissue-engineering Scaffold Pore Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Growth of the tissue is affected by a number of factors, including the flow rate and concentration of nutrients in the feed, the elasticity of the scaffold, and the properties of the cells. Many studies have examined these factors separately, but in this project, we aim to examine all of them together. |
Haniyeh Fattahpour; Pejman Sanaei; |
| 414 | Time-dependent Impact of Texture Sensing and Adhesion on Guided Epithelial Cell Migration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have investigated the interplay among three processes: sensing of, adhesion to, and guidance by the microenvironment. |
Corey Herr; Matt Hourwitz; Abby Bull; John Fourkas; Wolfgang Losert; |
| 415 | A Biomechanical Model for Epithelial Defense Against Cancer Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we study in detail the contribution of tissue mechanics towards regulating non-proliferative cell competition in vitro and in silico. |
Sayantani Kayal; Praver Gupta; Shilpa Pothapragada; Tamal Das; Dapeng Bi; |
| 416 | Dynamics of Cytokinesis Failure in Individual Tumorigenic Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigated the spatiotemporal dynamics with which a mother cell fails to undergo cytokinesis and gives rise to multinucleated progeny. |
Maryam Kohram; Celeste Nelson; |
| 417 | Substrate-mediated Mechanical Interactions Induce Multicellular Network Formation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show, through agent-based simulations of cells modeled as motile, contractile force dipoles on elastic substrates, that mechanical interactions result in cell networks. |
Patrick Noerr; Farnaz Golnaraghi; Ajay Gopinathan; Kinjal Dasbiswas; |
| 418 | Tension Remodeling Controls Topological Transitions in Confluent Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Existing vertex-based models of confluent tissues with constant and uniform tension are unable to account for the observed phenomena. We, therefore, present a new dynamic vertex model of epithelial tissues, where the tension in the intercellular junction is remodeled depending on the magnitude and direction of the local strain. |
Fernanda Pérez Verdugo; Shiladitya Banerjee; |
| 419 | Competition Between Activity and Shear in Biological Tissues: Yielding, Shear Thinning and Discontinuous Shear Thickening Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we study numerically the yielding behaviour of biological tissues using a minimal vertex-based model, in which a 2D layer of confluent cells is represented by a tiling of polygons, defined by the positions of the vertices [1]. |
Michael Hertaeg; Suzanne Fielding; Dapeng Bi; |
| 420 | Probing Dynamic Structure-Function Relationship of Bone at The Nanoscale Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we will employ in situ experimental nanomechanical experiments to tackle: how does the nanostructure of bone respond to cycling physiological loading? |
Ottman Tertuliano; |
| 421 | Flow and Deformation of Tumor Spheroids Through Constricted Microchannels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have demonstrated that many spheroids (~50-80 spheroids) can be aspirated on a chip for multiple runs per day. |
Pouyan Boukany; |
| 422 | Cell Deformation Signatures Along The Apical-Basal Axis: A 3D Continuum Mechanics Shell Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesize that this discrepancy is due to mechanical effects in the third (apical-basal) dimension, caused by actin stress fibers near the basal membrane. To fundamentally understand the effect of such additional stress on the shape of a cell, we develop a 3D continuum mechanics model of an epithelial cell as an elastic cylindrical shell, with appropriate boundary conditions reflecting the action of the basal fiber bundles. |
Jairo Martin Rojas Huamaní; Mayisha Nakib; William Brieher; Sascha Hilgenfeldt; |
| 423 | Cell Shape Changes Driven By Actomyosin Contractility Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To better understand an intrinsic mechanism for bleb formation, we developed an agent-based cell-like model by incorporating our well-established actomyosin network model with a cell membrane simplified into a triangulated mesh. |
Fahmida Sultana Laboni; Makito Miyazaki; Taeyoon Kim; |
| 424 | Twist Response of Actin Filaments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work explains how contractile forces generated by myosin motors accelerate filament severing by cofilin and establishes a role for filament twisting in the regulation of actin filament stability and assembly dynamics. |
Enrique De La Cruz; |
| 425 | Active Microrheology of Actin-vimentin Intermediate Filaments Composite Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Central to this multifunctionality are the inherent stiffness of each filament and the myriad binding proteins that serve to crosslink, bundle, and stabilize these filaments. Exploring the mechanics and dynamics of in vitro reconstituted networks consisting of only one of these cytoskeletal components has been the subject of extensive experimental work. |
Julie Pinchiaroli; Robert carrol; Alison Patteson; Bekele Gurmessa; |
| 426 | Collective Behaviors of Actin Filaments in The Motility Assay with Mobile Myosin Motors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We employed our computational model for the motility assay with consideration of motor mobility. |
Taeyoon Kim; Brandon Slater; |
| 427 | Stress Relaxation in 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. |
Prathamesh Kulkarni; Frederick MacKintosh; Anatoly Kolomeisky; |
| 428 | Range and Distribution of Forces Induced By Myosin Motors in The Disordered Actin Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We model myosin motors as contractile force dipoles embedded in a bond-diluted triangular lattice, representing the actin network, with bonds that resist bending and stretching. |
Abhinav Kumar; David Quint; Kinjal Dasbiswas; |
| 429 | Cell Polarity, Motility, and Shape Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This shape sensing can lead to surprising new behaviors, like single cells developing a spontaneous circular motion, but can be disrupted by membrane roughness. I will discuss the implications of this idea both for how cells respond to electrical cues and how cells in different environments polarize. |
Brian Camley; |
| 430 | Filament Sliding in Simulations of CaMKII-actin Bundles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We modeled CaMKII-actin bundles using a coarse-grained model of four particles per actin promoter and a docking simulation performed in our group. |
Carlos Bueno; Nicholas Schafer; Neal Waxham; Margaret Cheung; Peter Wolynes; |
| 431 | Coarse-grained Molecular Dynamics Modeling of Actin Self-assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A coarse-grained model is developed to capture the geometric features of G-actin and the assembly characteristics of microfilaments. |
Grant Davis; Christopher Grosenick; Shreya Dayal; Mark Stevens; Shengfeng Cheng; |
| 432 | Shape Change in Cytoskeleton Surface By Active Self-organization of Nematic Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we propose a theoretical model to explore the physical mechanisms, regulated by the aforementioned interplay, that leads to self-organized shape changes in a cytoskeleton surface. |
Waleed Mirza; Marino Arroyo; Alejandro Torres-Sánchez; Marco De Corato; |
| 433 | Cytoskeletal Networks at Interfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recently, a continuum theory has been developed [1], allowing for the prediction of the material properties of highly crosslinked cytoskeletal networks from a phenomenological modelling of the microscopic interactions between the cytoskeleton filaments. We extend this theoretical framework to account for external forces, allowing us to explore how the properties of cytoskeletal networks are affected by the presence of various interfaces. |
Alexandra Zampetaki; Sebastian Fürthauer; |
| 434 | Simulating Confined Cytoskeletal Structures with Explicit Motors and Crosslinkers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use this method to show how confined actin filaments form structures such as contractile rings or bundled networks in the presence of myosin motors, passive crosslinkers, and surface-attached linkers or motors. |
Dimitrios Vavylonis; Adam Lamson; Bryce Palmer; Michael Shelley; David Rutkowski; |
| 435 | Program Director: Dr. Anne Gershenson Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Program Directors (also called Program Officials or POs) in the NIGMS Division of Biophysics, Biomedical Technology and Computational Biosciences (BBCB) will present funding … |
Anne Gershenson; |
| 436 | Following The Binding and Dissociation Kinetics of Unlabeled Transcription Factors at The Single Molecule Level Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a single-molecule optical-tweezers assay that exploits the thermal fluctuations of a DNA hairpin to detect the association and dissociation of individual, unlabeled transcription factors. |
Ariel Kaplan; |
| 437 | Importance of Many Body Interactions in DNA Synthesis Initiation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this contribution we will present the molecular basis for the primase synthesis mechanism of the CRISPR-associated primase-polymerase from Marinitoga piezophila (Mp). |
G. Andrés Cisneros; |
| 438 | Investigating Recognition and Sequence Preference of Kaiso Interactions with Methylated DNA Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we performed molecular dynamics simulations to investigate recognition mechanism and binding of Kaiso to two distinct meDNA sequences, MeCG2 and MeECad. |
Bidhya Thapa; Narayan Adhikari; Purushottam TIwari; Prem Chapagain; |
| 439 | Amino Acid Characteristics in Protein Native State Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We consider the magnitude and direction of protrusion along with a simplified chemical attribute captured by a hydrophobic scale. |
Tatjana Škrbic; Achille Giacometti; Amos Maritan; Trinh Hoang; Jayanth Banavar; |
| 440 | Computational Analysis of The Effects of The Early Effects of Disulfide Bonds Cleavage on The Structure of Human Serum Albumin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we did not attempt to simulate the photoinduced mechanisms but only their effects. |
Kiara Fenner; |
| 441 | Mode Projected Dynamics of Globular and Membrane Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we performed simulations of opsin as a model membrane protein and ovalbumin using CHARMM35b2 to understand the projected mode dynamics, which is useful to analyze intramolecular energy transfer in proteins. |
Saravana Prakash Thirumuruganandham; |
| 442 | Modeling Current Blockade in A Dual Nanopore Device Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The volumetric CB algorithm is quite general, and we choose the model parameters by comparing the exact CB data from simulation of an electrokinetic BD model (EKBD) where the co-ions and counter-ions flow through the NP provides the CB directly. |
Aniket Bhattacharya; Swarnadeep Seth; |
| 443 | Principles of Cellular Control of Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, it is unclear why particular condensates form at particular locations and times. To unveil part of this mystery, I will present two principles that cells use to control condensates. |
David Zwicker; |
| 444 | Identifying Temporal Neural Firing from Images Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: In order to better understand information processing of neural systems and the neural interactions, the simultaneous activity of its individual neurons needs to be known. Optical … |
Dominika Lyzwa; |
| 445 | Photonic Probing of Structural Alteration in DNA Molecular Spatial Mass Density Fluctuations in The Nuclei of Human Brain Cells in Progressive Alzheimer’s Disease Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Alzheimer’s disease (AD) is one of the most common neurodegenerative disorders worldwide and a leading cause of death among the elderly. It is characterized by the accumulation of … |
Fatemah Alharthi; Ishmael Apachigawo; Prabhakar Pradhan; Mohammad Moshahid Khan; |
| 446 | Synaptic Reshaping of Plastic Neuronal Networks By Periodic Multichannel Stimulation with Single-pulse and Burst Stimuli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study synaptic reshaping by periodic multichannel stimulation (PMCS). |
Justus Kromer; Peter Tass; |
| 447 | Extrinsic Vs Intrinsic Criticality In Systems With Many Components Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Some biological systems with many components exhibit seemingly critical behaviors, causes of which are unclear. Here we argue that although signatures of criticality are indicative of atypically large fluctuations coupled to observable degrees of freedom, they are agnostic about the origins of such fluctuations. |
Vudtiwat Ngampruetikorn; Ilya Nemenman; David Schwab; |
| 448 | Mechanics of Memory of An Information Engine Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: As a biological process typically involves transition among multiple states spanning over widely different timescales, the cumulative outcome is naturally expected to depend crucially on the memory of the dominant previous states. We attempt to model such intrinsic memory by introducing a two-step fast transition where the two steps are separated by a waiting time. |
Tamoghna Das; Tsvi Tlusty; |
| 449 | A Universal Theory of The Sensory Response Requiring No Free Parameters Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A theoretical approach governing the rate response of peripheral neurons is described. |
Willy Wong; |
| 450 | A Framework for Solving Time-delayed Markov Decision Processes Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Reinforcement learning has revolutionized our understanding of evolved systems and our ability to engineer systems based on a theoretical framework for understanding how to … |
Sarah Marzen; Yorgo Sawaya; George Issa; |
| 451 | How Toe Spacing Affects Impact Dynamics During Passive "foot" Intrusions Into Granular Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand how toe spacing influences the intrusion dynamics of lizard feet, we studied 3D printed models of a simplified 3-toed "foot" dropped vertically into poppy seeds. |
Simon Thill; |
| 452 | Noise and Local Interactions in Milling Whirligig Beetles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study shows the surprising possibility of inferring underlying modes of interactions between individuals via analysis of noise. |
Vishwesha Guttal; Shashi Thutupalli; Jitesh Jhawar; |
| 453 | Pattern Dynamics and Stochasticity of The Brain Rhythms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We offer a methodology that is sensitive to individual, time localized features and yet allows describing a given waveform as a single entity, without defeaturing, putting each pattern, as a whole, into a statistical perspective. |
Yuri Dabaghian; Clarissa Hoffman; Daoyn Ji; Jingheng Cheng; |
| 454 | How Recurrent Neural Networks Infer Dynamical Models from Data for Prediction, Inference, and Source Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I introduce a framework that allows randomly constructed neural networks to learn and manipulate dynamical models from data via generalized synchronization. |
Zhixin Lu; |
| 455 | The Dynamics of Recurrent Neural Networks Throughout Learning at The Edge of Chaos Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we demonstrate that intrinsic excitability enables RNNs to form more stable and robust internal representations whose geometry converges throughout learning. |
Tala Fakhoury; |
| 456 | Robust Memory Manifolds in Neural Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a general principle that we refer to as frozen stabilization (FS), which allows a family of neural networks to self-organize to a dynamically critical state exhibiting multiple memory manifolds without parameter fine-tuning or symmetries. |
Tankut Can; Kamesh Krishnamurthy; |
| 457 | Mean Field Trajectories in A Spin Model for Decision Making on The Move Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work demonstrates the rich space of trajectories that emerge from the model. |
Dan Gorbonos; Nir Gov; Iain Couzin; |
| 458 | Transitions in Classical Dynamical Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For the circle map, aka, climbing sine map, we focused on the properties of trajectories evolving in one cell or the ones transitioning to the neighboring cells for different order parameters. |
Negin Moharrami Allafi; Enrique Pujals; Vadim Oganesyan; |
| 459 | Frequency Shifting and Induced Stability in Systems of Asymmetrically Coupled Oscillators Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, in natural systems such as social systems and the brain, influences between components are often unequal. In the present work, we generalize our previous work by allowing each oscillator’s coupling strength to be asymmetrical, where a given oscillator may be more sensitive to the influence of its partners than vice versa. |
Joseph McKinley; Mengsen Zhang; Alice Wead; Christine Williams; Emmanuelle Tognoli; Christopher Beetle; |
| 460 | Dynamics of Model Oscillatory Neuronal Networks with Adaptive Synaptic Weights and Structure Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the dynamics of phase oscillator networks with variable coupling strength and structure that can represent oscillatory neuronal networks where the spiking dynamics, synaptic weights, and network structure influence each other. |
Kanishk Chauhan; Ali Khaledi-Nasab; Alexander Neiman; Peter Tass; |
| 461 | High-Order Accuracy Computation of Coupling Functions for Strongly Coupled Oscillators Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop a general framework for identifying phase-reduced equations for finite populations of coupled oscillators that is valid far beyond the weak coupling approximation. |
Youngmin Park; |
| 462 | Interpreting Polychronization Through The Lens of Tropical Geometry Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the temporal coding regime, synaptic delays become crucial for understanding cognitive dynamics, and spiking neural networks with nontrivial synaptic delays are known to express certain complex behaviors such as polychronization. In this talk, we explore the link between such delay networks and a field of mathematics called tropical algebra, which has found applications in fields from optimization and control to field theory. |
Matthew Daniels; Advait Madhavan; Mark Stiles; |
| 463 | High-order Phase Reduction Applied to Remote Synchronization Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we analytically demonstrate the role of two factors promoting remote synchrony. |
Michael Rosenblum; |
| 464 | Theory of Communication Subspaces for Stochastic Recurrent Neural Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To fully understand and replicate this ability of the brain in artificial systems, we need a deeper understanding of information transfer across cortical areas. We reduce this gap by developing analytical tools to analyze interareal communication in terms of coherence and noise correlations in subpopulations of neurons within and across areas. |
Shivang Rawat; David Heeger; Stefano Martiniani; |
| 465 | Modulation of Synaptic Signaling By Calcium Feedback Loops in Dendritic Spines Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This electric isolation can be a mechanism for neuromodulation to control the regime of a cortical circuit’s effective recurrence. In this project, we simulate a spatial neuron model with a single spine on a dendrite and a minimal set of channels to study how voltage-dependent calcium feedback loops and calcium-dependent potassium channels in the spine can modify the neuron synaptic potential, and the implications this may have on cortical circuits like attractor networks. |
Harper Cho; |
| 466 | Neurodynamical Computing at The Information Boundaries of Intelligent Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By integrating the dynamical systems view of cognition with the distributed feedback of perceptual control, we highlight theoretical gaps in understanding neurodynamical function. |
Joseph Monaco; Grace Hwang; |
| 467 | Probing The Material Properties of Multi-component and Multi-phasic Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we aim to establish a molecular grammar of sequence-encoded and structure-specific protein-protein and protein-RNA interactions that governs the biomolecular condensate phase behavior and dynamical properties. |
Priya Banerjee; |
| 468 | Characterizing The Structural Dynamics of Nucleolus During Cell Cycle Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we used 4D live-cell imaging and histogram-based image analysis to quantify the structural dynamic of nucleolus during the cell cycle. |
Truong An Pham; Madhav Mani; XIAOZHONG Wang; Reza Vafabakhsh; |
| 469 | The Effect of Cell to Cell Variablilty in Multicomponent Protein Phase Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Given that concentrations of proteins vary substantially from cell to cell, we investigated how cellular variability affects protein phase separation. |
Kamal Bhandari; |
| 470 | Composition Tunes Physical Properties of Multi-component Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In multi-component systems, one possible route is through modulation of condensate composition. To explore this, we employ quantitative phase imaging and thermodynamic tie-line measurements to measure the stoichiometry inside model multi-component condensates containing full-length FUS protein and RNA. |
Patrick McCall; Anthony Hyman; Jan Brugues; |
| 471 | Catalysis-Induced Phase Separation and Autoregulation of Enzymatic Activity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that the catalytic activity alone can induce phase separation for sufficiently active systems and large enzymes, without any equilibrium interactions between components. |
Matthew Cotton; Ramin Golestanian; Jaime Agudo-Canalejo; |
| 472 | Conformational Entropy of Intrinsically Disordered Proteins Bars Intruders from Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that at realistic IDR densities, particles as small as the size of a typical protein (5 nm in diameter) can be more than 90% excluded from condensates. |
Vladimir Grigorev; Ned Wingreen; Yaojun Zhang; |
| 473 | Theory of Rheology and Aging of Protein Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we develop a rheological model of biological condensates which shows the experimentally observed features. |
Ryota Takaki; Marko Popovic; Louise Jawerth; Frank Jülicher; |
| 474 | Material Properties of Rubisco-EPYC1 Condensates in An Algal Pyrenoid Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In order to understand the steady-state and dynamical properties of Rubisco-EPYC1 condensates, we developed a coarse-grained model of interacting Rubisco and EPYC1, with bonding kinetics and molecular details learned from experiments. |
Trevor GrandPre; Yaojun Zhang; Andrew Pyo; Benjamin Weiner; Ned Wingreen; |
| 475 | Engineering Biomolecular Condensate Surfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How the interfaces between these distinct sub-phases might control transport and reactivity is important for ribosome biogenesis, and how these interfaces might be modulated to control cancer and other diseases, remains unknown. Here we discuss our work to address this challenge, inspired by native proteins that are specifically enriched at the nucleolar periphery. |
Amal Narayanan; Anita Donlic; David Sanders; Amy Strom; Ke Xu; Cliff Brangwynne; |
| 476 | Proximity to Criticality Determines Surface Tension of Biomolecular Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Near the critical point, the complex mapping from microscopic features to macroscopic properties can be simplified in terms of a small number of parameters, making it easier to identify underlying principles – but how far does this critical region extend for biomolecular condensates? To address this question, we employed coarse-grained molecular dynamics simulations and found that the critical region is sufficiently large to cover the full physiological range of temperatures. |
Andrew Pyo; Yaojun Zhang; Ned Wingreen; |
| 477 | Single-molecule Trajectories in Chemically Active Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The fluorescent labeling of molecules enables molecular tracking and provides an invaluable tool to probe key processes in cell biology. We discuss how biomolecular condensates govern the kinetics of chemical reactions and how this is reflected in the dynamics of labeled molecules. |
Stefano Bo; Frank Jülicher; |
| 478 | Prewetting of Critical Membranes & Collapsed Polymers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we propose a minimal theory for phase separation at biological surfaces by cytoplasmic & nuclear proteins. |
Mason Rouches; Sarah Veatch; Benjamin Machta; |
| 479 | Pattern Formation of Phase-separated Lipid Domains in Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a theoretical model that explains existing observations and makes predictions for future experiments. |
Qiwei Yu; Andrej Kosmrlj; |
| 480 | Torsional Mechanics of Fundamental Processes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will discuss our effort to develop single-molecule tools tailored for torsional mechanical studies. |
Michelle Wang; |
| 481 | Physical Mechanisms for DNA Twist Changes and Supercoiling Induced By Salt and Temperature Changes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We determined that the coupling constant is 4.5 ± 0.8 kBT/(degrees·nm) for one base pair. |
Liang Dai; |
| 482 | Tensile Force in A Single-stranded DNA Gap Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This result is consistent with the presence of ~1pN of tensile force in the ssDNA gap. We hypothesized that this tensile force arises from the steric repulsion between the double-stranded DNA (dsDNA) segments flanking the gap. |
Harold Kim; |
| 483 | Detecting Poloidal Bias In DNA Minicircles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a single-molecule fluorescence method to measure the poloidal bias in DNA minicircles. |
Tony Lemos; |
| 484 | Stability of DNA Double Helix Under Sharp Bending Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, we report extensive molecular dynamics (MD) simulations of double-stranded DNA (dsDNA) minicircles with lengths between 64 and 106 bp, investigating the stability of the DNA double helix under various extents of DNA bending. |
Jun Soo Kim; |
| 485 | Multiscale Modeling of Chromatin: from Fibers to Genes to Chromosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe our coarse-grained mesoscale chromatin model and novel equilibrium and dynamics algorithms to sample higher-order chromatin structure as a function of internal and external parameters and fold genes from first principles, interpret folding mechanisms relevant to cell differentiation and cancer progression, and simulate chromatin conformations consistent from experimental chromosome conformation capture contact maps. |
Tamar Schlick; Zilong Li; Stephanie Portillo-Ledesma; |
| 486 | Understanding Transcriptional Regulation By Characterizing Gene Regulatory Functions of Synthetic Loci in Mammalian Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, endogenous mammalian gene loci exhibit complex pleiotropic regulatory interactions that limit our ability to decouple underlying mechanisms governing their GRFs. To overcome this limit, we constructed a fully-composable synthetic reporter locus that enables single-cell fluorescent measurement of steady-state and dynamic transcriptional activities. |
Zheng Diao; Oleg Igoshin; Caleb Bashor; |
| 487 | A Differentiable Model of Nucleic Acid Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present an implementation of oxDNA, a popular force field for modelling nucleic acids, in JAX-MD, a state of the art differentiable molecular dynamics library. |
Ryan Krueger; Megan Engel; Michael Brenner; |
| 488 | Structural and Dynamic Signatures of Active Chromatin Polymers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose activity as an important force regulating genome structural characteristics, such as chromosome compaction and nuclear positioning. |
Sumitabha Brahmachari; Tomer Markovich; Frederick MacKintosh; Jose Onuchic; |
| 489 | The Role of Dynamics Is Self-organizing Biological Flow Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk we will provide a brief overview and introduction of self-organization and pattern formation in flow systems, and describe the role of local adaptive rules in pattern formation and solving complex optimization problems. |
Eleni Katifori; |
| 490 | Evolution of Aortic Geometry Modeled with Morphoelastic Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the evolution of the largest blood vessel in the human body, the aorta. |
Luka Pocivavsek; Kameel Khabaz; Junsung Kim; David Jiang; Alyssa Varsanik; Kayla Polcari; Nhung Nguyen; |
| 491 | Experimental Quantification of Chaos in Cardiac Tissue; Examples of Period 3 and Other Complex Dynamics 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 stimuli. |
Mikael Toye; Conner Herndon; Molly Halprin; Eva Greiner; Flavio Fenton; |
| 492 | Excitability at The Interface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we show the following: two media that are individually non-excitable can become excitable at their interface when a fast degree of freedom is diffusively coupled. |
Colin Scheibner; Adam Cohen; Hillel Ori; Vincenzo Vitelli; |
| 493 | Light-induced Cortical Excitability Reveals Programmable Shape Dynamics in Starfish Oocytes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop an optogenetic method to qualitatively explore the mechanism responsible for coordinating surface contraction waves that are generic to sea star oocytes during meiotic cell division. |
Jinghui Liu; Tom Burkart; Alexander Ziepke; Tzer Han Tan; S. Zachary Swartz; Erwin Frey; Nikta Fakhri; |
| 494 | Exploring Regular, Exotic and Turbulent Flow States in Active Fluids Via The Framework of Exact Coherent Structures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The ECS framework enables a fully nonlinear but highly reduced-order description in terms of a directed graph. |
Piyush Grover; Rumayel Pallock; Michael Norton; Caleb Wagner; Jae Sung Park; |
| 495 | On The Mechanical Origins of Waving, Coiling and Skewing Patterns in Arabidopsis Thaliana Roots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present theory and simulations of the well-known waving, coiling and skewing patterns presented by roots of Arabidopsis thaliana when grown on inclined agar substrates. |
Yasmine Meroz; Amir Porat; Arman Tekinalp; Yashraj Bhosale; Mattia Gazzola; |
| 496 | Elasticity of Spheres with Buckled Surfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, by exploiting well-known properties of the solid harmonics, we present a simple, direct method for solving the elastic problem of spheres and spherical voids with surface deformations, described by a real spherical harmonic. |
Yingzhen Tian; Megan McCarthy; Megan King; Simon Mochrie; |
| 497 | Invasion in Breast Cancer Organoids As A Mechano-biological Instability Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: It is known that the ability of cells to sense the mechanical propertis of the matrix and react to these mechanical signals is crucial during invasion, but why some cells adopt an invasive phenotype or the physical mechanism by which the cell mass invades the matrix are not well understood. To address this question in a controlled and accessible system, we focus on in vitro breast cancer organoids embedded in collagen matrices. |
Marino Arroyo; Giancarlo Cicconofri; Pau Blanco; Guillermo Vilanova; Pablo Saez; |
| 498 | Cdc42 Mobility and Membrane Flows Regulate Fission Yeast Cell Shape and Survival Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To investigate the self-organizing properties of the Cdc42 secretion-polarization system, we developed a stochastic particle model implementing the reaction-diffusion of Cdc42. |
David Rutkowski; Vincent Vincenzetti; Dimitrios Vavylonis; Sophie Martin; |
| 499 | The Alternate Ligand Jagged Enhances The Robustness of Notch Signaling Patterns Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By solving a system of 12 coupled ordinary differential equations, we calculate the phase space across different parameters for hexagonal ordered states. |
Mrinmoy Mukherjee; Herbert Levine; |
| 500 | Configurational Entropy As A Driver of Tissue Structural HeterogeneityVasudha Srivastava, Jennifer L. Hu, Sundus F. Shalabi, James C. Garbe, Boris Veytsman, Martha R.Stampfer, Matt Thomson, Greg Huber, Mark A. LaBarge, ZevJ. Gartner Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate that the observed structural ensemble follows Boltzmann statistics, corresponding to the maximum entropy distribution subject to the energetic constraints derived from interfacial mechanics. |
Zev Gartner; |
| 501 | Strain Response to Energy Consumption in Contractile Acto-Myosin Gels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present the first direct simultaneous measurements of ATP consumption and strain in a reconstituted in-vitro acto-myosin network. |
Francis Cavanna; José Alvarado; |
| 502 | Emergent Programmable Behavior and Chaos in Dynamically Driven Active Filaments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A remarkable example of single-celled behavior is seen in the ciliate Lacrymaria olor, which uses rapid shape changes to an active, slender protrusion, many times the cell size, to hunt for prey. Here, inspired by these extreme behaviors in L. olor, we present an active filament model wherein behavior (filament shape dynamics) is mechanistically linked to the underlying physical properties and motile ciliary dynamics of the cell. |
Deepak Krishnamurthy; Manu Prakash; |
| 503 | Sensing Physical Signals with Cytoskeletal Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Chemical signals have been found to trigger and steer these waves, facilitating the guidance e.g. of immune cells to their target. Here we consider the role of these cytoskeletal dynamics in sensing of the physical microenvironment. |
Wolfgang Losert; |
| 504 | Geometric Trade-off Between Contractile Force and Fluid Drag Determines The Motility of Actomyosin Droplets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To decouple the mechanics from biochemical regulations, here we develop an in vitro biomimetic migratory cell model by encapsulating actomyosin networks into water-in-oil droplets covered with a lipid monolayer [1]. |
Ryota Sakamoto; Ziane Izri; Yuta Shimamoto; Makito Miyazaki; Yusuke Maeda; |
| 505 | F-actin Architecture Governs Self-organized Criticality in The Cytoskeleton Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Self-Organized criticality (SOC) is observed across diverse natural phenomena, including earthquakes, avalanches, and landslides. Signatures of critical phenomena include fractal … |
Zachary Sun; Michael Murrell; |
| 506 | Motor-driven Advection Competes with Macromolecular Crowding to Drive Spatiotemporally Heterogeneous Transport in Cytoskeleton Composites Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate diffusive transport of spherical particles and DNA through in vitro motor-driven cytoskeleton composites using single particle tracking and differential dynamic microscopy. |
Janet Sheung; Jonathan Garamella; Stella Kahl; Brian Lee; Nadia Schwartz Bolef; Daisy Achiriloaie; Jennifer Ross; Ryan McGorty; Rae Robertson-Anderson; |
| 507 | Competition of Convection and Diffusion in The Self-mixing of Microtubule-kinesin Active Fluid with Non-uniform Activity: Experiment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work will inform the design of future microfluidic mixing applications and provide insight into intracellular mixing processes. |
Teagan Bate; Megan Varney; Ezra Taylor; Joshua Dickie; Chih-Che Chueh; Michael Norton; Kun-Ta Wu; |
| 508 | Competition of Convection and Diffusion in The Self-mixing of Microtubule-kinesin Active Fluid with Non-uniform Activity: Simulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our second model introduces a spatiotemporally varying ATP field to an existing nematohydrodynamic active fluid model and then couples the active stresses to local ATP concentrations. |
Joshua Dickie; Teagan Bate; Megan Varney; Ezra Taylor; Chih-Che Chueh; Michael Norton; Kun-Ta Wu; |
| 509 | Kinesin-driven Microtubule Flows Drive Elastic Structural Transitions in Actin Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we describe how active consituents of a cytoskeletal composite material are reorganized into a steady-state structure through the action of molecular motors. |
John Berezney; Itamar Kolvin; Seth Fraden; Zvonimir Dogic; |
| 510 | Extensile to Contractile Transition in Active Networks of Microtubule and Molecular Motors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the microscopic origin of the extensile to contractile transition in active gels composed of microtubule bundles and multivalent clusters of kinesin-1 motors. |
Guillaume Duclos; Bibi Najma; Peter Foster; Aparna Baskaran; |
| 511 | Toward Rational Design of Biotic-Abiotic Machines Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We consider an active gel made of actin crosslinked and driven by myosin II minifilaments, bound to PEG-DA hydrogel slabs using the biotin-streptavidin system. |
Jonathan Michel; Michael Rust; Jennifer Ross; Megan Valentine; Rae Robertson-Anderson; Timothy Atherton; Moumita Das; |
| 512 | Extracting Active Fluctuating Forces from Fluctuating Motions of An Active Particle in Viscoelastic Medium A Quadratic Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study uses 1064nm and 980nm wavelength lasers to create an optical trap and to serve as a tracking beam, respectively. |
Simin Xia; Chong Shen; H Daniel Ou-Yang; |
| 513 | Growing A Network Via Oscillations on Nodes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We conclude by proposing extensions of our model to the cases of germline cysts in mammals and annelid worms. |
Hayden Nunley; Matthew Smart; Stanislav Shvartsman; |
| 514 | Mechanisms of Mammalian Drug Resistance Acquired During Long-term Evolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose DNA amplification around resistance genes as one of the major causes of drug resistance in cancer and other diseases, and suggest corresponding measures to improve treatment efficiency. |
Yiming Wan; Quanhua Mu; Rafa? Krzyszto?; Joseph Cohen; Damiano Coraci; Christopher Helenek; Annie Lin; Kevin Farquhar; Jiguang Wang; Gabor Balazsi; |
| 515 | Specificity, Cooperativity, Synergy, and Mechanisms of Splice-modifying Drugs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce a biophysical modeling framework that quantitatively describes the sequence-specific and concentration-dependent behavior of splice-modifying drugs. |
Justin Kinney; |
| 516 | Experimental Quantification of Model Identifiability and Information Loss Due to Distortions in Fluorescence Microscopy and Image Processing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this presentation, we experimentally analyze single-cell preparations using smFISH and MS2-MCP labeling and for many different microscopy and image processing settings. |
Michael May; |
| 517 | Computational Agent-based Modelling Reveals The Role of Tumour Microenvironment on The Success of Combination Chemotherapy/immunotherapy to Treat Glioblastoma Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To this end, we develop a novel agent-based model of glioblastoma dynamics that accounts for the interactions between GBM and immune cells and its effects on the treatment efficacy. |
Anudeep Surendran; |
| 518 | Using The Finite State Projection Based Fisher Information Matrix to Optimize Single-cell Experiment Designs Under Different Combinations of Discrete Stochastic Models and Measurement Errors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To find which experiments are best suited to identify a model, we adopt the chemical master equation framework to define likelihood functions, and we calculate the Finite State Projection based Fisher Information Matrix (FSP-FIM) to estimate and compare information for different experiment designs (Fox, 2019, Fox 2020). |
Joshua Cook; |
| 519 | Live Imaging of Gut-associated Innate Immune Cell Motion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How these physical behaviors are manifested inside a living host remains unclear. We therefore examined innate immune cells – neutrophils and macrophages – in larval zebrafish, a model vertebrate. |
Piyush Amitabh; Jonah Sokoloff; Raghuveer Parthasarathy; |
| 520 | Identifying The Transition Genes and State Specific Gene Regulation from Single-cell Transcriptome Data with SpliceJAC Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present spliceJAC, a method to quantify the multivariate mRNA splicing from single cell RNA sequencing (scRNA-seq). |
Federico Bocci; |
| 521 | Analytical Model for Vaccination Protocols That Optimally Produce Broadly Neutralizing Antibodies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: One way that the adaptive immune system responds to infectious pathogens is by creating antibodies (Ab) that can bind specifically to the associated antigens (Ag). |
Saeed Mahdisoltani; Mehran Kardar; Arup Chakraborty; |
| 522 | A Model for How T Cell-mediated Autoimmunity Can Be Triggered By Persistent Viral Infections Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Specifically, we describe how T cell activation by multiple foreign antigens can result in weakly autoreactive T cells exceeding the quorum threshold and mounting a response to self-antigens. |
Rose Yin; Sam Melton; Arup Chakraborty; Mehran Kardar; Eric Huseby; |
| 523 | Optimal Design of Cocktail Boosters to Elicit A Polyclonal Response Against Related Viral Strains Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By exploiting a mapping of models describing the evolutionary dynamics of B cells during affinity maturation to a simple quantum mechanical analog, we investigate the optimal antigen composition of the cocktail vaccine in order to best exploit immune memory generated by previous encounters of related pathogen strains. |
Federica Ferretti; Arup Chakraborty; Mehran Kardar; |
| 524 | Stochastic Modeling for Studying The Effects of BET Inhibitors on The Modulation of P-TEFb Levels Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Aimed at quantitative understanding of how BET inhibitors affect the statistics of PTEFb level, we develop a coarse-grained stochastic model. |
Miranda Harkess; Niraj Kumar; |
| 525 | Lower Bounding Variability in Microbiome Acquisition and Exponential Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Data from microbiome assembly in fruit flies and growth experiments in E. coli, S. aureus, and L. minor empirically demonstrate that replicates of identically prepared experimental systems are nonetheless variable. We employ theoretical microscopic models that lower bound the variability associated with these processes and show they are consistent with experiments. |
Eric Jones; |
| 526 | Statistical Theory of Asymmetric Damage Segregation in Clonal Cell Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we focus on the statistical properties of damage in individual lineages and the overall damage distributions in growing populations for a variety of ADS models with different rules governing damage accumulation, segregation, and the lifetime dependence on damage. |
Lev Tsimring; Arkady Pikovsky; |
| 527 | Background-dependent Sensory Bet-hedging in Chemotactic Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: That is, transitioning to tracking one ligand does not compromise the population’s ability to hedge its bets across other future ligands. Remarkably, we found that populations maintain this bet-hedging capability even if the background and foreground ligands compete for receptor binding sites. |
Jeremy Moore; Keita Kamino; Thierry Emonet; Thomas Shimizu; |
| 528 | Physical Limits on Size Precision in Single-celled Microorganisms 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% in a constant environment. To investigate the origins of this precision, we study the fundamental physical limits on setting a size in single cells. |
Daniel McCusker; David Lubensky; |
| 529 | Kinship Effects in Stochastic Antibiotic Killing of Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We analyzed the growth and death of individual cells and turned the dataset into a genealogical tree, precisely identifying the relationship between bacterial cells. |
Wesley Stine; Tats Akiyama; Minsu Kim; |
| 530 | Precise Spatial Scaling in The Early Fly Embryo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show that boundaries of gap gene expression also scale, and more strongly that local gene expression levels provide information about relative position but no additional information about absolute position or embryo length. |
Milos Nikolic; William Bialek; Thomas Gregor; |
| 531 | Investigating The Importance of Migration and Spatial Heterogeneity in Emerging Spatial Patterns of Host-parasitoid Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use a discrete time metapopulation model on a square lattice, with diffusive migration to adjacent sites. |
Appilineni Kushal; |
| 532 | Variability in Responses to Random Perturbations Constrain Biomolecular Network Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work can help analyse large-scale drug perturbation studies where the exact nature of each perturbation is unknown. |
Seshu Iyengar; Andreas Hilfinger; |
| 533 | Examining Variation in Gene Expression and Co-expression Using Single-cell Genomics and Method of Moments Estimators Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, it remains challenging to distinguish biological and technical sources of cell-cell variability and to assess the statistical significance of quantitative comparisons between groups of cells. We introduce memento to address these limitations and enable accurate and efficient differential expression analysis of the mean, variability, and gene correlation from scRNA-seq. |
Min Cheol Kim; |
| 534 | Exploiting Fluctuations in Gene Expression to Infer Causal Interactions Between Genes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a novel approach to use naturally occurring stochastic fluctuations in cells to infer causal interactions between genes, without the need to perturb cells or follow cells over time. |
Euan Joly-Smith; Paige Allard; Fotini Papazotos; Laurent Potvin-Trottier; Andreas Hilfinger; |
| 535 | Probing The Role of “power Strokes” in A Molecular Motor with Nonequilibrium Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a coarse-grained classical approach to explicitly simulate the nonequilibrium dynamics of a catenane-based molecular motor under chemical fueling. |
Emanuele Penocchio; Geyao Gu; Alex Albaugh; Todd Gingrich; |
| 536 | Controlling Molecular Heat Conduction Using Temperature Modulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The broad class of molecular structures that can be realized through advanced molecular synthesis techniques in inorganic, organic, and material chemistry provide possibilities for fabricating molecular structures that could be used to advance the field phononics, that is, using phononic heat transfer to perform complex logic operations. To control these phononic molecular devices, we propose manipulating the heat current through the device by modulating its temperature. |
RENAI CHEN; Tammie Gibson; Galen Craven; |
| 537 | Evolutionary Dynamics of Homeostasis Mechanisms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: What are the basic principles that govern their evolution? This talk examines this question using simulations and theory. |
Edo Kussell; Spencer Hobson-Gutierrez; |
| 538 | Theoretical and Experimental Investigation of Dynein-mediated Transport and Positioning of The Nucleus Prior to First Division in The Early C. Elegans Embryo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a combination of stochastic and continuum models with experimental validation in early C. elegans embryos, we demonstrate that centrosome asymmetry and the geometry of the early embryo are both critical for proper centrosome positioning in the early C. elegans embryo. |
Adriana Dawes; |
| 539 | Length-dependent Poleward Flux of Sister Kinetochore Fibers Promotes Chromosome Alignment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we introduce a flux-driven centering model that relies on flux generated by forces within the overlaps of bridging and kinetochore fibers. |
Nenad Pavin; |
| 540 | A Model for Microtubule-mediated Deformation of A Nucleus Membrane Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent experiments show that loss of the lamin network results in nuclear deformations and rupture. To understand the mechanistic basis of this phenomenon, we developed a mathematical model that accounts for, and couples, the fluid flows around and through the permeable membrane, and the pulling on the membrane by membrane-bound, but mobile, molecular motors attached to impinging microtubules. |
Yuan-Nan Young; Reza Farhadifar; Michael Shelley; |
| 541 | Microtubule Organization Into Tactoids with Active and Passive Crosslinkers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have observed in vitro formation of microtubule tactoids, whose shape is reminiscent of the mitotic spindle. |
Prashali Chauhan; J. Schwarz; Jennifer Ross; |
| 542 | Effects of The GTPs Concentration and Variation Length on The Dynamics of Microtubules Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we investigate the effects of the variable length of the microtubule and the GTPs concentration during the growth and shrink regimes, the cap length variations and the catastrophe phenomenon. |
NGANFO YIFOUE WILLY ANISET; |
| 543 | Emergent Dynamics in Motor-free Active Contractile Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our results demonstrate that this Ca 2+-triggered network exhibits viscoelastic behaviors that under certain conditions can be reversed. We propose a unifying phase diagram for this calcium-driven contractile dynamics. |
Xiangting Lei; Tuhin Chakrabortty; Jerry Honts; Saad Bhamla; |
| 544 | Identifying The Control Knobs of Cytoskeletal Flow Using Simulations and Representation Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we combine physical modeling and representation learning (a convolutional autoencoder) to identify a useful latent representation that detects the mechanisms of contractility contributing to large-scale flow. |
Yuqing Qiu; Elizabeth White; Suriyanarayanan Vaikuntanathan; Aaron Dinner; |
| 545 | DNA Transport Within Confined Motor-driven Cytoskeletal Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Previously, we showed how macromolecular crowding and confinement synergistically couple to dramatically slow the diffusion of crowded DNA molecules that are confined by lipid membranes to cell-sized volumes. Here, we build on this work by incorporating motor-driven cytoskeletal composites into this platform. |
Mehdi Shafiei Aporvari; Philip Neill; Daisy Achiriloaie; Ryan McGorty; Rae Robertson-Anderson; |
| 546 | Biodynamic Monitoring of Bacterial Invasion of Living Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we describe the use of BDI to monitor the infection of 3D living tissue by bacteria. |
Zhen Hua; John Turek; Fernanda Cunha; Michael Ladisch; David Nolte; |
| 547 | Revisiting The Temperature Dependence of Protein Diffusion Inside Bacteria: Validity of The Stokes-Einstein Equation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we applied single-particle tracking photoactivated localization microscopy (sptPALM) to investigate the diffusion of histone-like nucleoid structuring (H-NS) proteins and free dyes in bacterial cytoplasm at different temperatures. |
Yong Wang; Asmaa Sadoon; William Oliver; |
| 548 | The Effect of Nanoparticle Charge and Size on 3D Diffusion in Live Escherichia Coli Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the rheology of the bacterial cytoplasm using a combination of biplane microscopy and single particle tracking. |
Diana Mendez; Alp Sunol; Benjamin Bratton; Joseph Sheehan; Liam Holt; Zemer Gitai; Roseanna Zia; Joshua Shaevitz; |
| 549 | Hydrodynamic Modelling and Experiment of Spiroplasma’s Cytoskeletal Driven Motility Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This mechanism allows for motility, yet the interaction between the filaments and spiroplasma’s membrane is unclear. We model this motility using a regularized stokeslet approximation to hydrodynamic interactions and investigate the cell’s ability to deform its membrane using torsion and bend-based modalities. |
Paul Ryan; |
| 550 | Stochastic Model and Optimization of SELEX Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this paper, we develop a fully discrete stochastic model of SELEX. |
Yue Wang; |
| 551 | Crowd Control: Organizing Gene Expression in Cell-sized Vesicles with Macromolecular Crowding Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work demonstrates a straightforward way to control the organization of gene expression in cell-sized vesicles and provides insight into the spatial regulation of gene expression. |
Gaurav Chauhan; Elizabeth Norred; Michael Simpson; Steven Abel; |
| 552 | An Inducible and Titratable Site-specific in Vivo Recombination System in Escherichia Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed and characterized a Cre/lox system that allows us to perform in vivo recombineering at tunable, low rates in Escherichia coli, using chemically inducible promoters with low leakage and a degradation tag on the Cre recombinase. |
Elisa Garabello; Andrea Giometto; |
| 553 | Atomic Force Microscopy Experiment and Monte-Carlo Study of The Elasticity of Exosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In particular, we consider two classes of exosomes; i) the wild type and ii) a special case where expression of Pan protein is artificially reduced. |
Vikash Pandey; Hanna Kylhammar; Vipin Agrawal; Fredrik Stridfeldt; Apurba Dev; Dhrubaditya Mitra; |
| 554 | Excitation and Inhibition Imbalance Affects Dynamical Complexity Through Symmetries Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Broadly, our work reveals a class of hidden symmetries in biology, present in the network of interactions among system components, and it underscores their functional importance. |
mathieu ouellet; Jason Kim; Harmange Guillaume; Sydney Shaffer; Lee Bassett; Dani Bassett; |
| 555 | Microbial Division of Labor for Mixed Sugar Fermentation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we develop a theoretical framework for microbial mixed-sugar fermentation and use it to compare the performances of the superbug and DOL strategies in chemostats. |
Siqi Liao; Ting Lu; |
| 556 | Molecular Analysis of The Type III Interferon Complex and Its Applications in Protein Design and Engineering Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using molecular modeling and simulations, we quantify differences in residue contact and strain fluctuation, produce detailed free-energy landscapes, and reveal previously unknown structural features of the engineered and wild type extracellular signaling complexes; we then leverage this information to guide engineering at the receptor-receptor interface, increasing complex formation by as much as 2.5-fold and identifying hot spots of interactions between the ligands and receptors. This two-pronged approach to protein design and engineering enables analysis of inaccessible protein complexes to generate molecular insights into IFNL behavior, elevating approaches to harness their therapeutic potential. |
William Grubbe; Fabian Byléhn; Walter Alvarado; Juan Mendoza; Juan De Pablo; |
| 557 | Competitive Binding Facilitates Oscillations in A Non-Cooperative Repressilator Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a repressilator made from deactivated CRISPR cas proteins, which, despite binding non-cooperatively to their target sites, nevertheless exhibit sustained oscillations over many cellular generations as observed in single cell microfluidics experiments. |
Miles Rouches; Louis Cortes; Guillaume Lambert; |
| 558 | Untangling The Regulatory Role of Individual TFs in E. Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Predicting the effect of individual TFs on gene regulation can be challenging due to their entanglement with promoter specific effects such as TF-TF interactions, or network interactions (feedback, etc). To overcome this limitation, we have developed an approach using systematically designed synthetic gene targets in E. coli to quantify the pure regulatory function of individual TFs and to remove the “context dependent” entanglements of natural promoters. |
Robert Brewster; |
| 559 | 3D Genome Organization in The Epithelial-mesenchymal Transition Spectrum Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a novel workflow coupling immunofluorescence and dielectrophoresis to unravel EMT heterogeneity at single-cell resolution. |
Ruby Huang; |
| 560 | Inferring Single-cell Transcriptomic Dynamics with Structured Dynamical Representations of RNA Velocity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have developed "LatentVelo" to generalize RNA velocity with deep learning. |
Spencer Farrell; Madhav Mani; Sidhartha Goyal; |
| 561 | Bursty RNA Velocity of Gene Programs for Trajectory Inference Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce a new RNA velocity model which accounts for transcriptional bursting and infers kinetic parameters using the joint distributions of counts. |
Frank Gao; Suriyanarayanan Vaikuntanathan; Samantha Riesenfeld; |
| 562 | Cancer Cell States in A Perturbed Epigenetic Landscape Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, the epigenetic landscape is described using a Hopfield model originating from cooperative feedback loops with master regulator genes [1]. |
Andreas Kraemer; |
| 563 | Bifurcation and Multistability in Three-gene-driven Network Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work uses a geometric approach grounded in bifurcation theory to study the stability profile of a mutually repressing three-gene network across different regions of an unconstrained parameter space. |
Rebecca Rousseau; Rob Phillips; |
| 564 | Single Cell Dynamics of The Lac Operon Induction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we designed mother machine devices to directly observe the switch-like behaviour of the lac operon at the single cell level. |
Louis Cortes; Guillaume Lambert; |
| 565 | Coupling Between Epithelial-to-mesenchymal Transition and Cell Cycle Progression Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: From the obtained vector fields, we applied the transition path analyses, which are originally developed in studying chemical reactions, on simulated single cell trajectories. |
Jianhua Xing; |
| 566 | A Novel FRET-based Reporter for Real Time Interrogation of P38-mediated Stress Response in Human Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we demonstrate a novel FRET-based p38 reporter that allows us to simultaneously visualize p38 activation state and intracellular localization. |
Thomas Kuhlman; Michael Worcester; |
| 567 | ScTOP: Physics-inspired Order Parameters for Cell Fate Classification and Visualization of Single Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present single-cell Type Order Parameters (scTOP): a statistical-physics-inspired approach for constructing "order parameters" for cell fate given a reference basis of cell types. |
Maria Yampolskaya; Pankaj Mehta; |
| 568 | Phenotypic Consequences of Gene Expression Driven By Positive and Negative Feedback Gene Circuits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the influence of common network motifs, such as negative or positive feedback regulation, on the ectopic expression of the metastasis-related TF, Bach1. |
Rafal Krzyszton; Joshua Azukas; Yiming Wan; Helmut Strey; Gabor Balazsi; |
| 569 | Critical Growth of Cerebral Tissue in Organoids: Theory and Experiments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop a Fokker-Planck theory of tissue growth with three types of cells (symmetrically dividing, asymmetrically dividing and non-dividing) as main agents to study the growth dynamics of human cerebral organoids. |
Egor Kiselev; Arndt von Haeseler; Florian Pflug; |
| 570 | Models of Branching Morphogenesis of Dendrites in Fly Sensory Neurons Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To test models of morphogenesis, we have developed a mean-field, continuum model of dendrite growth in which polar branch segments grow at one end (the tip), stochastically nucleate new segments, and disappear randomly at a rate proportional to branch density (to simulate contact-triggered retraction). |
Xiaoyi Ouyang; |
| 571 | Minimal Model for Emergent Spatiotemporal Patterning of Synthetic Notch Expression in Vivo Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the mechanisms that regulate the dynamics of a activated synthetic signal in a growing tissue is not well understood. Towards this goal, we present a vertex-based model of spatio-temporal synthetic Notch (synNotch) activation in the epithelium of the Drosophila wing imaginal disc. |
Jonathan Dawson; Paul Langridge; Abdul Malmi-Kakkada; |
| 572 | Cytoskeletal Dynamics Generate Active Liquid-liquid Phase Separation.Alexandra Tayar, Weizmann Institute of Science Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we study the impact of mechanical activity on LLPS. |
Alexandra Tayar; |
| 573 | Self-organization and Hydrodynamics of Active Rods on Fluid Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use a combination of continuum modeling and particle simulations based on slender-body theory to study the collective dynamics of a suspension of pusher and puller rods in a fluid membrane submerged in bulk fluid, as a simplified model for the assembly of cytoskeletal biopolymers on the cell membrane. |
Arijit Mahapatra; Wenzheng Shi; Ehssan Nazockdast; |
| 574 | Defect Dynamics in Viscoelastic Passive and Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we explore a hydrodynamic model of nematics that includes a single relaxation time through linear stability analysis and simulation. |
Michael Norton; Moumita Das; |
| 575 | Motility Induced Patterning in Range Expansions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By using numerical simulations and analysis of a continuum model, we demonstrate activity induces finite wavelength patterns that can strongly affect colony expansion for both pulled and pushed waves. |
Suraj Shankar; Julien Tailleur; David Nelson; |
| 576 | Self-organization and Control in Acoustically Coupled Active Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we study the collective behavior of self-propelled active agents communicating with each other by means of acoustic signals. |
Alexander Ziepke; Ivan Maryshev; Igor Aranson; Erwin Frey; |
| 577 | Spontaneous Flow Transition in Confined Active Nematic Droplets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we present an analog of the active Fréedericksz transition and probe independently how the interplay between confinement, active stress, and nematic elasticity controls the flow to no-flow transition and investigate the rate of energy consumption in the observed states. |
Salman Alam; Bibi Najma; Jeremy Laprade; Peter Foster; Guillaume Duclos; |
| 578 | Pair Interactions of Bacterial Active Droplets in Nematic Liquid Crystals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we report on the interaction of two active droplets moving: (1) in the same direction, (2) in opposite directions. |
Hend Baza; Mojtaba Rajabi; Sergij Shiyanovskii; Oleg Lavrentovich; |
| 579 | E. Coli Through Obstacles: Fluxes, Entropy Production and Extractable Work in Active Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a minimal mechanical model to quantitatively capture experimentally measured local fluxes at funnel tips. |
Satyam Anand; Xiaolei Ma; Shuo Guo; Stefano Martiniani; Xiang Cheng; |
| 580 | Spontaneous Flow Created By Active Topological Defects Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite this importance, few analytical results have been obtained on the flow-field and active-stress patterns around active topological defects. Using the generic hydrodynamic theory of active systems, we investigate the flow and stress patterns around these topological defects in unbounded, two-dimensional active nematics. |
Louis Brezin; Thomas Risler; Jean-François Joanny; |
| 581 | Chiral Symmetry Breaking and Vortical States in Bacterial Biofilm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work we make use of experimental, theoretical and computational techniques to investigate the transition between the swarming and biofilm regime in a system of genetically modified Bacillus subtilis. |
Livio Nicola Carenza; Mustafa Basaran; Tevfik Can Yüce; Luca Giomi; Askin Kocabas; |
| 582 | Novel Critical Phenomena in Compressible Polar Active Fluids: A Functional Renormalization Group Approach Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Similar studies on the more general compressible PAFs have been hindered by technical difficulties, except for rare cases. Using functional RG methods, we are able to overcome some of these issues and reveal for the first time critical phenomena in compressible PAFs. |
Patrick Jentsch; Chiu Fan Lee; |
| 583 | Structural States and Conservation Laws in A System of Two-dimensional Active Swimmers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Ensembles of motile microswimmers display complex collective dynamics. Nonetheless, when confined to two dimensions, we show they can be expressed using a unifying formalism. |
Naomi Oppenheimer; Yuval Shoham; |
| 584 | COLLOIDAL PHYSICS THAT INSTANTIATE LIFE IN BIOLOGICAL CELLS Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: More generally, our computational study of protein synthesis in E. coli from the tandem perspective of cell biology and meso-scale physics presents a unique opportunity to broadly explore how the physical state of the cell impacts biological function. |
Roseanna Zia; |
| 585 | Design, Construction, and Analysis of A Synthetic Minimal Bacterial Cell Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: That minimal cell has about half of the genes that are in the bacterium on which it was based, Mycoplasma mycoides JCVI syn1.0, the so-called synthetic bacteria we reported on in 2010. |
John Glass; |
| 586 | Physical Modeling of The Three-Dimensional Architecture of The Human Genome 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; Sumitabha Brahmachari; |
| 587 | Universality Vs. Specificity in Synaptic Transmission Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a statistical-mechanical analytic theory of the action-potential-triggered neurotransmitter release at the chemical synapse. |
Olga Dudko; Bin Wang; |
| 588 | Dynamics of Water Around Intrinsically Disordered Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Results of several studies have indicated water dynamics around IDPs to be more restricted than around structured proteins of similar size, but reasons for this difference are less clear. I will discuss computational studies of water around several IDPs and structured proteins of similar size, and companion megahertz-to-terahertz dielectric spectroscopic measurements [1], which together provide a detailed picture of the extent to which dynamics of water around IDPs is more restricted as well as its origins. |
David Leitner; |
| 589 | Physical Characteristics of Some Intrinsically Disordered Proteins from Simulation Studies Using Mesoscale Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will report our simulation results using coarse-grained models of IDPs. |
Joshua Ashby; Amrit Vignesh; Swarnadeep Seth; Aniket Bhattacharya; |
| 590 | Emergent Thermophoretic Behavior in Non-equilibrium Chemical Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we show that thermophoresis can be observed in any system having internal states with different transport properties, and temperature-modulated rates of transitions between the states. |
Daniel Maria Busiello; Shiling Liang; Paolo De Los Rios; |
| 591 | Searching for Colored Noise in Enhanced Diffusion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Focusing on the “click” chemical reaction consisting of copper-catalyzed alkyne-azide cycloaddition, CuAAC, we confirm enhanced fluctuations of the colloidal particle uniformly at all frequencies – which amounts to a shift in the frequency of crossover from ballistic to diffusive motion. |
Jin Tae Park; Tian Huang; Steve Granick; |
| 592 | Stochastic Thermodynamics of Resetting with Imperfections Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Fully developing stochastic thermodynamics for systems undergoing resetting has been difficult, as conventional resetting breaks microreversibility; time-reversed trajectories have vanishing probability. Two approaches that circumvent this issue are discussed. |
Kristian Stølevik Olsen; Francesco Mori; Supriya Krishnamurthy; |
| 593 | Thermodynamic Trade-off Relation in Stochastic Resetting Process Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We consider a paradigm of overdamped Brownian particle undergoing a stochastic resetting process in a thermal environment. |
Jae Sung Lee; Priyo Pal; Hyunggyu Park; |
| 594 | Highly Nonequilibrium Steady State Induced By A Locally Nonchaotic Energy Barrie Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this research, we investigate the concept of locally nonchaotic energy barrier, e.g., a narrow step in an external force field. |
Yu Qiao; Zhaoru Shang; |
| 595 | Heterogeneous Particle Dynamics Driving Macroscopic Degradation in Porous Electrodes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A Fokker-Planck model that describes the resistance evolution of a population of battery particles is formulated from the idea of a fitness landscape, borrowed from ideas in population genetics. |
Debbie Zhuang; Martin Bazant; |
| 596 | Neuron Operations Compatible with The Physics of A Super-Turing Computational Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A. Newell developed an early cognition theory which he completely described in a 1990 book. |
Emmett Redd; |
| 597 | Connecting Structure of Individual Networks to Dynamics in Oscillator Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a new mathematical approach to go from the connectivity of an individual network – for example the realization of a random graph on an individual trial or the precise connection patterns in an experimental reconstruction – to the spatiotemporal pattern of oscillations in a neural system. |
Lyle Muller; Roberto Budzinski; Alexandra Busch; Gabriel Benigno; Ján Minác; |
| 598 | Non-Gaussian Random Matrices Predict The Stability of Feasible Lotka-Volterra Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will show how tools from the theory of disordered systems can be used to account for non-Gaussian features of the interactions, and to obtain the spectra of the community matrix of survivors. |
Tobias Galla; Joseph Baron; Thomas Jun Jewell; Christopher Ryder; |
| 599 | Population Diversity and Fitness Uncertainty Allow for Faster Evolutionary Rates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I show uncertainty relations that bound the rate of evolutionary processes driven by natural selection, mutations, or by stochastic forces. |
Luis Pedro Garcia-Pintos; |
| 600 | A Simplified Drift-diffusion Model for Pandemic Propagation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a simplification of the susceptible-infected-recovery (SIR) and SIRS models for pandemic propagation that allows a quasi-analytical treatment of COVID-19 propagation across multiple countries. |
Abhimanyu Ghosh; Clara Bender; Preetam Ghosh; Hamed Vakili; |
| 601 | Synthetic Gene Circuits: Evolution of Drug Resistance Evolution in Fluctuating Drug Conditions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigated drug resistance arising from gene expression noise using genetically engineered yeast (S. cerevisiae) exposed to fluctuating drug conditions. |
Harold Flohr; |
| 602 | High-dimensional Characterization of Phototroph-heterotroph Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work presents a new view of how the chemical environment impacts phototroph-heterotroph interactions. |
Chandana Gopalakrishnappa; Zeqian Li; Seppe Kuehn; |
| 603 | Structured Interactions Explain The Absence of Keystone Species in Synthetic Marine Microcosms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By mathematically modeling communities with interspecies interactions, we show how progressively structured interactions, as opposed to independent interactions, can systematically reduce the incidence of keystone species. |
Sivan Pearl; Hyunseok Lee; Akshit Goyal; Jeffrey Gore; |
| 604 | Optical Reflection Statistics from A Thin Weakly Disordered Optical Media: Application to Detection of Structural Alterations in Cells/tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the disordered thin-film limit, a linearized one-dimensional stochastic model is introduced to derive the full statistics of the reflected light. |
Alexander Punnoose; Shirsendu Nanda; Prabhakar Pradhan; |
| 605 | Flow Physics Explains Morphological Diversity of Ciliated Organs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose that convergence of ciliated organ designs follows functional constraints rather than phylogenetic distance, and we present universal design rules that can also guide the design of synthetic ciliary pumps. |
Feng Ling; Eva Kanso; Janna Nawroth; |
| 606 | Influence Maximization in Boolean Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will introduce an alternative method inspired by those used in the solution of the well-studied problem of influence maximization for spreading processes in social networks. |
Filippo Radicchi; |
| 607 | Percolation in Borromean Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by experiments on topologically linked DNA networks, we consider the connectivity of Borromean networks, in which no two rings share a pairwise-link, but groups of three rings form inseparable triplets. Specifically, we focus on square lattices at which each node is embedded a loop which forms a Borromean link with pairs of its nearest neighbors. |
Donald Ferschweiler; Ryan Blair; Alexander Klotz; |
| 608 | No Free Lunch for Avoiding Clustering Vulnerabilities in Distributed Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use methods of statistical physics to show that clustering vulnerabilities arise from generic interactions among competing degrees of freedom that describe the placement and connection of distributed system elements. |
Pheerawich Chitnelawong; Andrei Klishin; Greg Van Anders; |
| 609 | The Journal Φ Index and Highly Cited Papers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This question matters for research assessment, because of the increased difficulty for transformative, groundbreaking papers —many of which become highly cited eventually —to appear in high Impact Factor journals. To answer this question we analyze papers that were cited at the 99 th percentile in their academic field per publication year, and were designated as "highly cited papers" by Clarivate Analytics’ Essential Science Indicators. |
Manolis Antonoyiannakis; |
| 610 | Self-linking Duplication-divergence Model for Protein Interaction Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we extend and analyze the duplication-divergence model with self-linking nodes. |
Leopold Bilder; Istvan Kovacs; |
| 611 | A Mutation-selection Paradigm for The Dynamics of Biological Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We assume that the same paradigm can model the short-term dynamics of biological networks. |
Vito Dichio; Fabrizio De Vico Fallani; |
| 612 | Structure of Brain Connectome and Contactome in Fly, Mouse, and Human Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We analyze various aspects of complex neuronal networks in the fruit fly, mouse, and human brain [1-3] with the goal of gaining insight into their structure and building useful generative models. |
Anastasiya Salova; Istvan Kovacs; |
| 613 | Complex Quantum Networks on A Lattice of Spins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a model of complex quantum communication networks in the context of interacting quantum spin systems on a lattice. |
Ravi Chepuri; Istvan Kovacs; |
| 614 | How Good Is The Overlap Between Two Biological Networks? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Thus, a positive benchmark is needed to quantify how much a network agrees with a gold standard network. Here, we propose such a positive benchmark that captures a best-case scenario by creating an alternative network ensemble. |
Bingjie Hao; Istvan Kovacs; |
| 615 | Applying A Network Reconstruction Method to Reveal Connectivity of In-vitro Neuronal Culture from Measurements Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We discuss our application of a method for reconstructing directed networks from dynamics [Ching and Tam, Phys. |
Emily S.C. Ching; |
| 616 | Bifurcations in The Herd Immunity Threshold for Discrete-Time Models of Epidemic Spread Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We performed a complete sensitivity analysis of the herd immunity threshold for discrete-time SIR compartmental models with a static network structure. |
Maximilian Nguyen; Sinan Ozbay; Bjarke Nielsen; Simon Levin; |
| 617 | Light, CRISPR and DNA Repair Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present multi-target CRISPR, an approach whereby a degenerate gRNA directs Cas9 to simultaneously target a large number of epigenetically diverse genomic locations. |
Taekjip Ha; |
| 618 | Structural Effects of H4K16 Acylations Characterized By Mesoscale Simulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent experimental analysis of key nucleosomal physics through single-molecule force spectrometry and structural probing has allowed the development and validation of fast mesoscale polymer models for chromatin structure which directly incorporate these acylations, providing a potential avenue for understanding their impact on local chromatin structure. In this work, we perform mesoscale simulations of 12-nucleosome chromatin fibers with three different H4K16 acylations, deriving key model parameters directly from experiments performed in concert, analyze the impact of these acylations on fiber structure, and compare our predictions to the available body of experimental data. |
Aria Coraor; Yiheng Wu; Juan De Pablo; |
| 619 | A Polymer Model to Infer 3D Chromosome Structures from Hi-C Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop a polymer physics-based minimalist model, called heterogeneous loop model (HLM), and infer 3D organization of chromatin from Hi-C data. |
Changbong Hyeon; Lei Liu; |
| 620 | On The Origin of The Integrity of A Subset of Topologically Associating Domains Upon Cohesin Loss in Interphase Chromosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, using polymer simulations, we uncovered that TADs with epigenetic mismatches across their boundaries or with physical boundaries in their 3D structures survive upon loop deletion. |
DAVIN JEONG; Guang Shi; Xin Li; Devarajan Thirumalai; |
| 621 | Investigating The Epigenetic Code Through Data-driven Chromosome Structure Modeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a model for chromosome architecture at nucleosome resolution, using maximum entropy methods to recapitulate experimental Hi-C contact maps. |
Soren Kyhl; |
| 622 | Interaction Energy Scales Intrinsic to The Structural Ensemble of Chromosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we extend the idea and calculate the statistical potential (SP) between various locus types in order to predict the organization of chromosomes. |
Sucheol Shin; Guang Shi; Devarajan Thirumalai; |
| 623 | FRAP Calibrated Polymer Model of Chromatin with HP1a Predicts Heterochromatin Domain Sizes, 3D Organization, and Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We develop a simple model containing spherical particles to mimic HP1a protein and a single-chain polymer representing the chromatin. |
Ramin Basir; Vivek Shenoy; Vinayak Vinayak; |
| 624 | Extended and Dynamic Linker Histone-DNA Interactions Control Chromatosome Compaction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using single-molecule optical tweezers to address the thermodynamics and kinetics of protein-DNA interactions, we reveal that linker histone interactions with DNA are remarkably extended, with the C-terminal domain binding both DNA linkers as far as ~ ±140 bp from the dyad. |
Ariel Kaplan; |
| 625 | Quantitative Link Between Chromatin Compaction and Epigenetic Memory at The Single-cell Level Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We found that KRAB recruitment, known to cause H3K9me3 modifications and epigenetic memory, leads to chromatin compaction around 20kb, and that compaction is retained in permanently silenced cells even after releasing KRAB from the genome. |
Taihei Fujimori; Minhee Park; Derek Le; Antonia Hafner; Joydeb Sinha; Alistair Boettiger; Lacramioara Bintu; |
| 626 | Higher-order Genetic Interactions in Sequence-function Relationships Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, modern high-throughput phenotyping assays have shown that genetic interactions among three or more loci also frequently occur. In this talk, I will present ongoing work on modeling these higher-order interactions based on either high-throughput experimental assays or the analysis of collections of functional sequences. |
Juannan Zhou; |
| 627 | Multi-scale Simulations to Assess Chromatin Organization Along The Nuclear Periphery Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work provides accurate chromatin maps showing different types of LADs, highlighting chromosome conformation and positioning as important factors in LAD strength. |
James Glazar; Vivek Shenoy; |
| 628 | Investigating Human Chromosome Organization By Whole-genome Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we use the Open-MiChroM software to simulate the 46 chromosomes of a GM12878 human cell at 50 kb resolution, seeking to understand whether the nuclear organization of the whole genome would rely on the same principles observed for the organization of a single chromosome. |
Matheus Mello; Esteban Dodero Rojas; Antonio Oliveira Junior; Vinicius Contessoto; Jose Onuchic; |
| 629 | Statistical Physics Models of Transcriptional State Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use ideas from statistical physics to describe the distribution of ~100 genes from ~80,000 human cells. |
Camilla Sarra; Yaojun Zhang; William Bialek; Trevor GrandPre; |
| 630 | Chain Flexibility Effect on Complex Coacervate Core Micelles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we investigated the structure of C3Ms formed by mixing of block copolyelectrolytes having different lengths characterized by dynamic light scattering (DLS) and small angle X-ray scattering (SAXS) measurements. |
Taeyoung Heo; SooHyung Choi; |
| 631 | Surface Layer Adsorption and Bulk Association of Mucins in Human Airway Mucus Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: The airway surface layer lines the respiratory tract, simultaneously trapping inhaled particulates and facilitating their removal from the lung. Secreted gel-forming mucins, which … |
Scott Danielsen; Michael Rubinstein; |
| 632 | Membrane-mediated Interactions Between Deformable Nanoparticles on Membranes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use computer simulations to investigate the interactions between deformable, hinge-like nanostructures and lipid membranes. |
Nikhil Nambiar; Steven Abel; |
| 633 | Relaxational Dynamics of The Size Interconversion of Virus Capsids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We apply a simple relaxational model that ignores the impact of any nucleation barriers, and finds a reasonable agreement between theory and experiment with a minimal number of adjustable parameters. |
Alexander Clark; Paul Van der Schoot; Roya Zandi; |
| 634 | Thermal Stability and Secondary Aggregation in Geometrically-frustrated Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We here consider a simple model of a frustrated 1D incommensurate chain at finite temperature. |
Michael Wang; Gregory Grason; |
| 635 | Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a model to explore the mechanisms of RNA condensation by structural proteins, protein oligomerization and cellular membrane–protein interactions that control the budding process and the ultimate virus structure. |
Siyu Li; Roya Zandi; |
| 636 | Impact of Cross-linking on The Structural and Interfacial Properties of Surfactant Micelles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Structural analysis shows that pure tyloxapol systems are relatively spherical in shape and become more aspherical by replacing tyloxapol molecules with a corresponding number of Triton X-100 monomers. |
Hrachya Ishkhanyan; |
| 637 | Aggregation Vs. Condensation in A Lattice Model of Geometrically Frustrated Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We consider a minimal lattice model of geometrically frustrated assembly and use it to study the statistical mechanics of GFA at variable temperature and concentration. In this talk, we focus on how these systems can escape this size limitation via a condensation transition to a macroscopic bulk phase that is characterized by a finite density of topological defects. |
Nicholas Hackney; Chris Amey; Gregory Grason; |
| 638 | High-precision Measurement and Inference of Short-ranged Colloidal Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We demonstrate an alternative method based on holographic microscopy and Bayesian inference. |
Caroline Martin; Solomon Barkley; Lev Bershadsky; Ella King; Michael Brenner; Vinothan Manoharan; |
| 639 | End-to-end Base Stacking Drives Liquid Crystalline Phase Formation in "gapped" DNA Constructs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By performing SAXS/WAXS measurements for temperatures in the range of 5 to 65°C, we determined the thermal melting temperature ( Tm) of the end-to-end and side-by-side interactions that stabilize the positional order for DNA constructs, which differ in their terminal base pairs (AT-AT, AT-GC, or GC-GC) but are otherwise identical. We report remarkable variations in thermal stability (up to 25 °C shift in Tm) of these interactions, and the accompanying smectic order, due to these single base-pair alterations. |
Sineth Kodikara; Prabesh Gyawali; Hamza Balci; Samuel Sprunt; |
| 640 | Dynamically Tuning The Membrane Lipid Composition Can Control Macromolecular Assembly Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use computational modeling to quantify how macromolecular self-assembly can be dynamically tuned via the composition of the plasma membrane and protein stoichiometry. |
Jonathan Fischer; |
| 641 | The Role of Inter-particle Cohesive Stiffness in Determining The Size and Nature of Self-limiting, Geometrically-frustrated Assemblies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recently, the “curvamer” model was introduced to study self-limitation in 1D stacks of deformable, shell-like particles, where an elastic energy emerges from bending costs in stacks of uniformly spaced particles. |
Kyle Sullivan; Nabila Tanjeem; Montana Minnis; Ryan Hayward; Gregory Grason; |
| 642 | Frustrated Self-Assembly of Hyperbolic Crystals from Icosahedral Nanoparticles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we present an analytical theory of icosahedral NP self-assembly based on the non-Euclidean crystal {3,5,3} in 3-hyperbolic space. |
Nan Cheng; Kai Sun; Xiaoming Mao; |
| 643 | Controlled 2D and 3D Self-assembly of Short Fibers for Additive Manufacturing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present an inexpensive method of aligning and consolidating short fibers into different shapes, such as discs, spheres, triangles, and needles. |
Thamires Lima; Zachary Hinton; Clayton Francis; Nicolas Alvarez; |
| 644 | Millisecond Functional Dynamics of RNA Polymerases Elucidated By Markov State Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: RNA polymerase II (Pol II) undergoes a series of conformational changes when actively transcribing genes. I will present our group’s work on constructing Markov State Models (MSMs) from molecular dynamics (MD) simulations to elucidate dynamics of these conformational changes, including forward translocation, backtracking, and pyrophosphate release. |
Xuhui Huang; |
| 645 | Speed Variations of Bacterial Replisomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present a theory that predicts the abundance of DNA fragments in an exponentially growing bacterial population from the dynamics of replisome. |
Simone Pigolotti; Deepak Bhat; Samuel Hauf; Charles Plessy; Yohei Yokobayashi; |
| 646 | Bacterial Replication Initiation As Precision Control in Biology Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a model based on the DnaA flux to explain our results. |
Haochen Fu; Dongyang Li; Fangzhou Xiao; Suckjoon Jun; |
| 647 | DBIO Thesis Prize Winner: Jonathon L. YulyElectron Bifurcation and Correlations in Biological Energy Transduction Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Remarkably, although Boltzmann weights qualitatively capture the impact of the landscape on the short-circuit turnover, mean field transport theories fail to capture the efficient energy transduction, and instead predict short-circuiting, implying that correlations between redox cofactors cannot be naïvely neglected. Upon further exploration, this seems general for all energy transducing systems: mean field transport theory cannot capture the efficient energy transduction observed in biology. |
Jonathon Yuly; Peng Zhang; Kiriko Terai; David Beratan; |
| 648 | A Free-energy Profile Study of A Bipedal Single-stranded DNA Nanowalker’s Walking Gaits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we conducted a systematic free energy profile study on a 15nt long ssDNA nanowalker on a dsDNA track using oxDNA, a coarse-grained DNA model. |
Too Hon Lin; |
| 649 | How Do Self-assembled Virus-like Particles Break Open to Expose Their Cargo? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By measuring the rate of binding of fluorescent molecules to the viral RNA, we indirectly explore the effects of chemical environments on capsid integrity. |
Amelia Paine; Camila Cersosimo; Vinothan Manoharan; |
| 650 | Speedy Synthetic DNA Motors Are on A Roll Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will describe the development of DNA-based machines that roll rather than walk, and consequently have a maximum speed and processivity that is three orders of magnitude greater than the maximum for conventional DNA motors. |
Khalid Salaita; Selma Piranej; |
| 651 | Mechanical Properties of BiP (Binding Immunoglobin Protein) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: One novel approach to study the mechanical properties of BiP considers exploring the changes in the viscoelastic behavior upon ligand binding, using a technique called nano-rheology. |
Zahra Alavi; |
| 652 | A Hybrid Eulerian-Lagrangian Simulation Framework for Heterogeneous Soft Structures Operating in Fluids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Their interaction with surrounding fluids is computationally challenging and expensive to resolve. Here, we mitigate these issues via a hybrid Eulerian-Lagrangian algorithm that combines Cosserat rod theory with vortex methods and immersed boundary techniques. |
Arman Tekinalp; Mattia Gazzola; Yashraj Bhosale; |
| 653 | Physical Model Inspired By Energetic Jumping Nematodes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study sheds insight into both how organisms exploit elastic instabilities for ultrafast motions while offering design motifs for soft jumping robots. |
Sunny Kumar; Victor Ortega-Jimenez; Ishant Tiwari; Saad Bhamla; |
| 654 | Modeling Locomotion of A Hydrogel Crawler Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a new application of data-driven modeling on a soft crawler made of thermo-responsive hydrogels, materials that swell and shrink as a function of temperature. |
Siming Deng; Bibekananda Datta; Junning Liu; Thao (Vicky) Nguyen; Brian Bittner; Noah Cowan; |
| 655 | Kraken – A Multiphysics Soft Robot Simulation Platform Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The primary contributions of this work are capabilities to simulate nonlinear hyperelastic material models, simulation of the dynamics of soft actuators, and the ability to solve complex contact mechanics problems that often emerge when simulating soft robots. |
Kevin Wandke; Y Z; |
| 656 | Deep Learning Force Manifolds from The Physical Simulation of Robotic Paper Folding Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The lack of physical insight on such methods result in a critical lack of generality in terms of material, geometric, and/or environmental (e.g. friction) changes. In regards to this, we propose a novel control strategy for the difficult task of single manipulator paper folding with complete generality. |
Andrew Choi; Dezhong Tong; Demetri Terzopoulos; Jungseock Joo; Mohammad Khalid Jawed; |
| 657 | Single-vertex Origami for Multimodal Locomotion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The ancient art of origami provides an ideal platform for the design of reconfigurable systems, since a myriad of shapes can be achieved by actively folding thin sheets along pre-defined creases. Here, we focus on one of the simplest building blocks of origami-based materials – the rigid, degree-four vertex – and investigate its interactions with a flat surface. |
Davood Farhadi; Laura Pernigoni; David Melancon; Antonio Grande; Katia Bertoldi; |
| 658 | A Principal Bundle Perspective on Differential Flatness in Complex Robotic and Biological Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Specifically, we give a sufficient condition for the direct construction of flat outputs from any section of the system’s principal bundle that is orthogonal to a computable distribution. |
Jake Welde; Matthew Kvalheim; Vijay Kumar; |
| 659 | Topology, Dynamics, and Control of An Octopus Muscular Hydrostat Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Overall, this work significantly advances modeling and simulation abilities in the space of heterogeneous and active structures while exposing design and algorithmic principles pertinent to muscular hydrostats, with implications in biology, robotics, and control. |
Arman Tekinalp; Noel Naughton; Seung-Hyun Kim; Udit Halder; Prashant Mehta; William Kier; Mattia Gazzola; |
| 660 | Connecting Biological Design Principles and Optimal Mechanics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent studies have highlighted that the nonlinear design principles of biological actuators (skeletal muscle) exhibit certain mechanical performance advantages – for example, improved energy economy, improved stability, and reduced information entropy in the control effort. |
Jake McGrath; José Alvarado; |
| 661 | Design and Closed-Loop Motion Planning of An Untethered Swimming Soft Robot Using 2D Discrete Elastic Rods-based Physics Engine Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, a framework for physics-based modeling, motion planning, and control of an untethered swimming soft robot is introduced. |
Xiaonan Huang; Zachary Patterson; Andrew Sabelhaus; Carmel Majidi; Khalid Jawed; Weicheng Huang; Kiyn Chin; Zhijian Ren; |
| 662 | Hierarchical Control and Learning of A Foraging CyberOctopus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by the unique neurophysiology of the octopus, we propose a hierarchical framework that simplifies the coordination of multiple soft arms by decomposing control into high-level decision making, low-level motor activation, and local reflexive behaviors via sensory feedback. |
Chia-Hsien Shih; Noel Naughton; Udit Halder; Heng-Sheng Chang; Seung Hyun Kim; Rhanor Gillette; Prashant Mehta; Mattia Gazzola; |
| 663 | Mean Field Theory for Larval Drosophila Peristalsis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We describe a first-principles theoretical understanding of animal posture, using the Drosophila melanogaster larva (fruitfly maggot) as a model system. |
Jane Loveless; Greg Stephens; |
| 664 | Endowing Soft Robots with Fluidic Counting Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Although useful for accurate estimates and fast response times, such a strategy imposes additional complexity in both hardware and software that often undermines the simplicity, resistance of the soft robotic unit. With the goal to allow soft robots to be autonomous and resilient, we present a smart fluidic circuit that paves the way to such features with no need of electronics. |
Sergio Picella; |
| 665 | Super-resolution Imaging of Intracellular Transport Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present our results on how microtubule post-translational modifications, in particular detyrosination, regulate the transport and fusion of lysosomes with autophagosomes. |
Melike Lakadamyali; |
| 666 | Effects of Network Morphology in Cargo Transport Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we investigate the effects of microtubule network complexity on kinesin mediated cargo transport. |
Nimisha Krishnan; Jennifer Ross; |
| 667 | Impact of The Number of Motors on Cargo on The Switching Probability and Pause Duration at Microtubule Intersections Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work provides new insights into the importance of motor concentration, and network properties on intracellular transport. |
Maria Gamez; Niranjan Sarpangala; Nimisha Krishnan; Jennifer Ross; Ajay Gopinathan; |
| 668 | Kinesin-1, -2 and -3 Motors Use Family-specific Mechanochemical Strategies to Effectively Compete with Dynein During Bidirectional Transport Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Compared to kinesin-1, motors from the kinesin-2 and -3 families display a higher sensitivity to load in single-molecule assays and are thus predicted to be overpowered by dynein complexes in cargo transport. To test this prediction, we used a DNA scaffold to pair DDB with members of the kinesin-1, -2 and -3 families to recreate bidirectional transport in vitro, and tracked the motor pairs using two-channel TIRF microscopy. |
William Hancock; |
| 669 | Optimising Search Times for Motor Driven Cargo Within Cytoskeletal Traps By Tuning Attachment and Detachment Kinetics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In pancreatic beta cells, microtubule traps help regulate insulin secretion. Here we study the effectiveness of such traps using minimal one and two-dimensional models of cargo transport with a basin of attraction created by oppositely oriented microtubules. |
Niranjan Sarpangala; Oleg Kogan; Ajay Gopinathan; |
| 670 | The Differential Roles of Neurofilament Gene Expression and The Slowing of Their Transport in The Radial Growth of Myelinated Axons Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the relative contributions of these two mechanisms are unknown. To address this, we developed a computational model that is constrained by published data on cytoskeletal morphometry and NF transport kinetics to simulate the radial growth of axons in the ventral root and sciatic nerve of rats. |
Rawan Nowier; Anika Friedman; Anthony Brown; Peter Jung; |
| 671 | Reaction Diffusion Model for Understanding The Drug-target Interaction in Single Cell Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: While drug-target binding/unbinding kinetics can inform the interaction, the kinetics have not been well characterized inside the cell. To better understand this, we study the binding/unbinding kinetics of benzimidazole-derivative DNA binding drugs (Hoechst 33342 dye) in E. coli cells. |
Subrata Dev; |
| 672 | Alien Proteomics Reveals Physical Rules for Diffusion Through The Nuclear Pore Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This study demonstrates the integration of biochemical measurements with physical insight to predict cellular biology on a systems level. |
Margarita Gordiychuk; Nishant Pappireddi; Thao Nguyen; Olenka Jain; Andreas Mayer; Marianne Bauer; Alex Johnson; Michael Stadlmeier; Ned Wingreen; Martin Wühr; Yaojun Zhang; |
| 673 | Translocation of A Cone-shaped HIV-1 Capsid Through The Nuclear Pore Complex Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Since the HIV-1 capsid has a cone shape with a narrow tip and a broad back, does translocation efficiency and time depend on the end that enters the NPC first? To answer these questions, we develop an analytical model for the transport of a cone-shaped HIV-1 capsid through the NPC, focusing on the energy barrier created by nups within the pore and the capsid-nup interactions that can reduce the barrier. |
Bhavya Mishra; Roya Zandi; Ajay Gopinathan; |
| 674 | The Endoplasmic Reticulum As A Transport and Delivery Network for Calcium Ions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using genetic perturbation of ER morphogens that lead to fragmentation or increased tubule length in the ER we demonstrate that these morphological changes indeed lead to reduced magnitude in observed localized calcium puffs. Our work highlights the importance of ER morphology in controlling its structure as an intracellular transport hub. |
Elena Koslover; Cecile Crapart; Zubenelgenubi Scott; Laura Westrate; Edward Avezov; |
| 675 | Nonequilibrium Assembly, Maintenance and Control of A System of Golgi Cisternae in The Trafficking Pathway Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How do cellular organelles, such as the Golgi, self-assemble to a specific steady state size and maintain it in the face of a steady trafficking of vesicles? We address this nonequilibrium assembly using a Master equation approach that involves the mechanochemical cycle of active fission-fusion. |
Amit Kumar; Sudipto Muhuri; Madan Rao; |
| 676 | System-scale Quantitative Measurement Recognizes Scaling Exponents Between Multiple Organelle Volumes Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: A fundamental question in cellular biophysics is how the multiple components of the cell are coordinately built to optimize physiological function. A powerful tool to infer the … |
Shixing Wang; Shankar Mukherji; |
| 677 | Interdependence in Organelle Biogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we have characterized the systems-level patterns of interdependence in organelle biogenesis using Saccharomyces cerevisiae as a model system. |
Kiandokht Panjtan Amiri; Shankar Mukherji; |
| 678 | Max Delbruck Prize in Biological Physics: Viruses, Immunity and Vaccines Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The ability to develop effective universal vaccines that protect us from variant strains of mutable viruses will help create a more pandemic-resilient world. I will describe how by bringing together approaches from statistical physics, virology and immunology, progress is being made to address this challenge. |
Arup Chakraborty; |
| 679 | Maturation, Selection and Response in Immune Repertoires Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will present a framework of coevolution between immune systems and viruses in a finite-dimensional antigenic space, which describes the cross-reactivity of viral strains and immune systems primed by previous infections. |
Aleksandra Walczak; |
| 680 | Affinity Maturation of Antibodies Targeting HIV Spikes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This process involves competition between B-cells: those that ingest more Ags receive signals (from T helper cells) to replicate and mutate for another round of competition. Modeling this process, we find that the affinity of the resulting Abs is a non-monotonic function of the target (e.g. viral spike) density, with the strongest binding at an intermediate density (set by the two-arm structure of the antibody). |
Mehran Kardar; |
| 681 | Clonal and Cellular Dynamics of The Antibody Response Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work combines intravital multiphoton microscopy with mouse genetics to study how the dynamics of B and T lymphocytes within germinal centers shapes the evolution of the high-affinity antibodies that are crucial to protection from infectious disease. |
Gabriel Victora; |
| 682 | Visualizing The Conformations and Dynamics of FG-nucleoporins in Situ Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we develop an experimental approach using site-specific fluorescent labeling of IDPs in mammalian cells paired with highly time-resolved fluorescence microscopy. |
Miao Yu; |
| 683 | The Effect of Polymer Length in Phase Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we study a short polymer system of poly-Adenine RNA (polyA n) and peptide ([RGRGG] m) to understand the underlying thermodynamics of LLPS. |
Kasun Gamage; Gilberto Valdes-Garcia; Casey Smith; Karina Martirosova; Michael Feig; Lisa Lapidus; |
| 684 | Early Stages of FUS Protein Aggregation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we perform computer simulation to elucidate the mechanism of the early stage of FUS protein aggregation using a coarse-grained model of intrinsically disordered protein previously developed by our group. |
Abhinaw Kumar; Devarajan Thirumalai; |
| 685 | Molecular Assembly Lines Regulate The Size of Active Droplets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our previous work, we used theory to propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific sequence of assembly steps. |
Tyler Harmon; |
| 686 | Adhesion and Phase Behavior of Adhesive Peptides from Biofilms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Abundant in lysine, tyrosine, tryptophane, and threonine, the sequence shares similarity with mfps but also important differences. In this talk, I am going to describe our recent progress in understanding how this unique sequence balances the tendency to LLPS and to adhere to surfaces in order to maximize its adhesive performance. |
Jing Yan; Xin Huang; Rich Olson; |
| 687 | Instability of Lamellar Phase in Non-equilibrium Liquid-liquid Phase Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We consider an initially lamellar phase-separated microstructure and show that the effective long range interaction which originates in the chemical reactions, gives rise to unstable fluctuation modes that can lead to cylindrical or spherical microstructures. |
Amit Kumar; Dan Deviri; Samuel Safran; |
| 688 | Molecular Dynamics of A FUS Droplet Wetting An Actin Filament Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We analyze the structural and energetic phenomena of liquid phase separating protein droplets in time and space. |
Ulf Schiller; James Andrews; |
| 689 | A Reentrant Transition in RNA Aggregation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our model reveals that the driving force for aggregation is the increased configurational entropy associated with the multiplicity of ways to form bonds in the aggregate. |
Ofer Kimchi; Ella King; Andrew Pyo; Ned Wingreen; Michael Brenner; |
| 690 | RNA Phase Transitions Are Entropically Driven By Phosphate Backbones and Modulated By Nucleotide Sequences Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recently, GC-rich RNAs have been observed to form protein-independent foci in cells, which was conceptualized on the basis of an enthalpic model where base pairing and stacking interactions were postulated as drivers of RNA phase separation. Directly observing these transitions using temperature-controlled microscopy, we surprisingly discover that entropy rather than enthalpy drives RNA phase separation with a variety of RNA displaying system-specific Lower Critical Solution Temperatures (LCSTs) in the presence of Mg 2+. |
Gable Wadsworth; Priya Banerjee; Rohit Pappu; Xiangze Zeng; Walter Zahurancik; Venkat Gopalan; |
| 691 | Stability Analysis of A Phase-separating Droplet with Active Reactions Reveals Rich Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Biomolecular condensates like the nucleolus, transcriptional condensates, and nuclear speckles spatially concentrate proteins and carry out irreversible reactions such as RNA transcription and splicing. To study the different qualitative dynamics that can arise in such active droplets, we consider a minimal two-species model where a conserved protein species phase-separates according to model B dynamics, while actively producing and passively interacting with a non-conserved molecular species (RNA) that slowly decays. |
Pradeep Natarajan; Andriy Goychuk; Arup Chakraborty; Mehran Kardar; |
| 692 | Spatiotemporal Control of Condensates Via Oligomerization-dependent Phase Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we establish a thermodynamic framework for the oligomerization-dependent phase separation and a dynamic model based on Cahn-Hilliard theory to study the partitioning of condensates due to local light activation. |
Hongbo Zhao; Amy Strom; Yoonji Kim; Cornelis Storm; Cliff Brangwynne; Andrej Kosmrlj; |
| 693 | Predicting Biomolecular Phase Separation with Field-theoretic Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Many recent studies have relied on particle-based models, yet computational limitations have restricted these models to approximations such as implicit solvents, Debye-Hückel electrostatics and simplistic treatments of phase equilibrium. In this work, we present a new model for biomolecular phase separation that avoids these approximations by using field-theoretic simulations. |
Joshua Lequieu; Ritvind Suketana; |
| 694 | A Population-level Resolution to The Colonization-dispersal Tradeoff Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: When utilizing solid substrates such as chitin, individual microbial cells must resolve the tradeoff between colonizing them for growth and dispersing from them to explore new nutrient patches. As such, we studied the strategies of chitin utilization of two different bacterial species: one favoring attachment of cells to particles and another, detachment from them. |
Ghita Guessous; |
| 695 | Topographic Changes in Heteroresistant Bacterial Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using white-light interferometry, we examine the spatial structure of bacterial communities with heterogeneous population responses to antibiotics through the surface topography of the community. |
Adam Krueger; Peter Yunker; David Weiss; Bikash Bogati; |
| 696 | Self-organized Canals Enable Long Range Directed Material Transport in Bacterialcommunities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we report a unique form of actively regulated long-range directed material transport in structured bacterial communities. |
Shiqi LIU; Liang Yang; Yingdan Zhang; Zi Jing SENG; Haoran Xu; Yilin Wu; Ye Li; |
| 697 | Morphological Instability of Growing Competing Bacterial Colonies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent experiments on 2D growing multi-strain colonies have shown that cells become segregated into single-strain sectors, developing a morphological instability in which the interface between two sectors forms a dented, rough shape. To understand the mechanisms underlying such instability, we consider a minimal continuum model that incorporates cell growth and cell-substrate friction, both of which can vary between single-strain sectors. |
Alejandro Martinez-Calvo; Carolina Trenado-Yuste; Ned Wingreen; Sujit Datta; |
| 698 | One to Many and Many to One: How Phenotypic Heterogeneity Scaffolds Communal Carbon-harvesting By Marine Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I’ll present recent work on how phenotypic heterogeneity facilitates the collective growth and reproduction of a marine bacterium that eats polysaccharides from brown algae, allowing a division of labor. |
Julia Schwartzman; |
| 699 | Predicting Metabolomic Profiles from Microbial Composition Through Neural Ordinary Differential Equations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we develop a new method — mNODE (Metabolomic profile predictor using Neural Ordinary Differential Equations), based on a state-of-the-art family of deep neural network models. |
Tong Wang; Xu-Wen Wang; Kathleen Lee-Sarwar; Augusto Litonjua; Scott Weiss; Yizhou Sun; Sergei Maslov; Yang-Yu Liu; |
| 700 | Fluctuations in Biofilm Topographies: Characterization and Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We characterize the fluctuations through scale-free metrics like the Hurst exponent and fractal dimension, as well as standard ISO metrics. |
Pablo Bravo; Siu Lung Ng; Kathryn MacGillvray; Brian Hammer; Peter Yunker; |
| 701 | Heterogeneity in A Developing Biofilm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using Vibrio cholerae as a model organism, we aim to reveal the spatiotemporal pattern and heterogeneity of gene expression and second-messenger molecule concentration at the single-cell level. |
Jung-Shen Tai; Jing Yan; Christopher Waters; |
| 702 | Mathematical Modeling of Spatio-temporal Organization of Biofilm Structure Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we developed a mathematical model to describe the spatio-temporal organization of the biofilm components in various settings. |
Mohammad Nooranidoost; NG Cogan; |
| 703 | Force Balance and Surface Interactions Play An Important Role in Determining Bacterial Colony Growth Rate Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use interferometry to measure the three-dimensional surface morphology of biofilms grown on different surfaces. |
Aawaz Pokhrel; Gabi Steinbach; Siu Ng; Brian Hammer; Peter Yunker; |
| 704 | Mechanics of Biofilm Adhesion to Ultra-thick Polymer Brushes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we quantify bacterial adhesion and biofilm state while varying the mechanical properties of the brushes by manipulating their grafting density, growth conditions, and post-growth chemical modification, allowing for the creation of brushes of varying height and stiffness. |
Katherine Powell; Jessica Faubel; Jennifer Curtis; |
| 705 | Rheology of The Environment Regulates Bacterial Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work thus reveals a new mechanism, beyond mechanosensing, by which mechanics modulates microbial behavior. |
Anna Hancock; Sujit Datta; |
| 706 | Structural Changes in Chromosomes Driven By Multiple Condensin Motors During Mitosis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We created a theoretical framework that describes the loop extrusion (LE) by multiple condensin I and II motors in order to investigate the changes in chromosome organization during mitosis. |
Devarajan Thirumalai; |
| 707 | Theory of Chromatin Organization Maintained By Active Loop Extrusion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The active loop extrusion hypothesis proposes that chromatin threads through the cohesin protein complex into progressively larger loops until reaching specific boundary elements. We build upon this hypothesis and develop an analytical theory for active loop extrusion which predicts that loop formation probability is a non-monotonic function of loop length and describes chromatin contact probabilities. |
Brian Chan; Michael Rubinstein; |
| 708 | Inferring Chromatin Loop Configurations Via A Loop Extrusion Factor (LEF) Model Based on Measured LEF Density Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Accordingly, we present modified LEF model simulation in which the position-dependent loop extrusion rate follows directly from cohesin ChIP-seq data. |
Tianyu Yuan; Tianyu Yuan; Hao Yan; Mary Lou Bailey; Jessica Williams; Ivan Surovtsev; Megan King; Simon Mochrie; |
| 709 | The Little Condensins That Could: How Tiny Condensins Move Colossal Chromosomes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, experimental data is available either at the 5nm scale (as single molecule experiments) or at the micron scale (as Hi-C). Thus, we built a kinetic model of multiple condensins that can bridge this gap in length scales. |
Atreya Dey; |
| 710 | Transcription Is A Moving Barrier to Loop Extrusion That Shapes The Genome Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We analyzed chromosome conformation capture (Hi-C) data near active and inactive genes under conditions with normal or altered cohesin dynamics. |
Edward Banigan; Wen Tang; Aafke van den Berg; Roman Stocsits; Gordana Wutz; Hugo Brandão; Georg Busslinger; Jan-Michael Peters; Leonid Mirny; |
| 711 | Active Transcription Regulates Mesoscale Genomic Organization Via Active Extrusion of Chromatin Loops Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a mesoscale phase-field model to explain the underlying physics of nuclear chromatin organization in presence of DNA looping. |
Aayush Kant; Zixian Guo; Vivek Shenoy; |
| 712 | Chromatin Compartments from Correlated Active Processes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Collectively, our work provides new avenues for the interpretation of data on chromosomes, and has broad implications for active polymer systems. |
Deepti Kannan; Andriy Goychuk; Mehran Kardar; Arup Chakraborty; |
| 713 | Organizational Principles of Active Chromatin at Transcription Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use multi-color super-resolution microscopy to investigate the spatial organization of chromatin and transcription condensates. |
Jan-Hendrik Spille; Ganesh Pandey; Alisha Budhathoki; Filmon Medhanie; |
| 714 | Three-dimensional Multiphase Liquid Chromatin Model of Eukaryotic Nucleus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand and disentangle the complex interplay of forces that contribute to the emergent patterns of chromatin organization and dynamics, we have devised a phenomenological field-theoretic model of the nucleus as a multiphase condensate of liquid chromatin types. |
Rabia Laghmach; Michele Di Pierro; Davit Potoyan; |
| 715 | Condensation Dynamics of Sticky Chromatin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For example, rheological properties and collapse times for large lengths of chromatin remain poorly characterized or explained. To study such dynamics, we use a mixture of coarse-grained 3D Brownian dynamics and kinetic Monte-Carlo algorithms to model DNA and associated binding proteins. |
Adam Lamson; Olga Troyanskaya; Michael Shelley; |
| 716 | Intermolecular Interaction and Local Chromatin Density Regulate Biomolecular Condensate Growth Inside The Nucleus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study the growth of biomolecular condensates embedded in the chromatin network inside the nucleus. |
Deb Banerjee; Tafadzwa Chigumira; Josiah Kratz; David Chenoweth; Shiladitya Banerjee; Huaiying Zhang; |
| 717 | Multiscale Modeling of Chromatin Condensates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our work presents a molecular view of chromatin condensates using a multiscale model of chromatin. |
Andrew Golembeski; Joshua Lequieu; |
| 718 | Multivalent Binding Proteins Can Drive Collapse and Reswelling of Chromatin in Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we use Langevin dynamics simulation of a coarse grained chromatin polymer to show that the role of binding proteins can be more nuanced than previously suspected. |
Sougata Guha; Mithun Mitra; |
| 719 | Active and Driven Wave-propelled Interfacial Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: When an asymmetric floating body is internally or externally vibrated, the self-generated capillary wavefield can lead to steady propulsion or rotation. In this talk, I will discuss several related and recently discovered systems that leverage this physical mechanism. |
Daniel Harris; |
| 720 | The Role of Mechanical Properties of The Basilisk Lizard Foot in Rejecting Perturbations While Running at The Air-water Interface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesized that the properties of the foot, particularly the shape and stiffness, can passively correct for kinematic errors which would otherwise result in atypical perturbations to the reaction force. To test this, we developed several robophysical models of the foot varying in fidelity from simple 2D shapes cut from acrylic to 3D-printed and silicone cast feet based on biological scanning and testing of cadaveric specimens. |
Henry Cerbone; Michelle Yuen; Perrin Schiebel; |
| 721 | Robot Doggy Paddle: Modeling and Optimization Reveal Efficient Swimming Gaits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Building on previous work on single leg swimming gaits, this study describes a 7 degree-of-freedom reduced-order dynamic model that captures surface swimming of a bipedal “sagittal quadruped” robot made of two rigidly connected “hip” masses with revolute-revolute legs connected at each hip. |
Sean Gart; Max Austin; Jonathan Clark; Jason Pusey; |
| 722 | Magnetic, Modular, Undulatory Robots As Robophysical Models for Exploration of Fish-inspired Swimming Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, it remains unclear how fish or fish-inspired swimming emerges from the complex physics of FSI which includes interactions among active structures (e.g., fins and elongated bodies), neuromuscular and motor control, and the physics of fluids. We address this problem using robophysical models of undulatory swimming (magnetic, modular, undulatory robots). |
Hankun Deng; Donghao Li; Kundan Panta; Bo Cheng; |
| 723 | Modeling and Characterization of Bi-flagellated Robot with Tumbling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we build a macroscopic bio-inspired robot with two rigid flagella (right-handed helices) connected to a cylindrical head. |
Zhuonan Hao; Sangmin Lim; Mohammad Khalid Jawed; |
| 724 | Data-driven Discovery of Hierarchical Neuromechanical Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The promise of big kinematic datasets from new automated labeling methods motivates the aim for a general, data-driven paradigm to identify templates in motion data. We present a framework for identifying these dynamic posture principles grounded in a local model of the hypothesized template-anchor dynamics, enabling generalization to a range of both periodic and transient locomotion tasks. |
Benjamin McInroe; Yuliy Baryshnikov; Daniel Koditschek; Robert Full; |
| 725 | EMBUR (EMerita Burrowing Robot): A Robophysical Exploration of Mole Crab Burrowing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we discuss prior research on a novel mole crab-inspired robot– EMBUR ( EMerita Burrowing Robot) – and how it has been used as a tool for robophysical exploration of legged burrowing. |
Laura Treers; Benjamin McInroe; Robert Full; Hannah Stuart; |
| 726 | Hopping on Deformable Terrain with State-Based Switching: Dynamics and Implications for Robot Design Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We derive a Poincaré map that captures the hop-to-hop energy dynamics of a monopod hopping on deformable terrain. |
Daniel Lynch; Sean Gart; Jason Pusey; Kevin Lynch; Paul Umbanhowar; |
| 727 | Robotic Morphing in The Aquatic-to-terrestrial Transition Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: ART can swim underwater or at the surface, walk over different terrain, and transition between water and land. We investigated the confluence of robot gait, limb shape, and the environmental medium and found that, by adapting its shape and gait, ART can locomote in different environments with comparable, or in some cases, even better cost of transport than exclusively uni-modal robots. |
Robert Baines; |
| 728 | Flipper-based Locomotion on Muddy Substrates Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, using a turtle-inspired robot, we investigated how the performance of flipper-based locomotion depends on mud properties. |
Boyuan Huang; Shipeng Liu; Jake Futterman; Feifei Qian; |
| 729 | Biological and Robophysical Experiments of Terrestrial Fish Locomotion on Mud of Controlled, Variable Strength Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To fully understand how these locomotor features interact with the environment to permit performance, we need to further quantify the interaction with wet deformable substrates. Here, we used controlled mud as a model wet deformable substrate and developed methods to prepare mud into spatially uniform states and temporally stable states and tools to characterize its strength. |
Divya Ramesh; Gargi Sadalgekar; Qiyuan Fu; Zach Souders; Jack Rao; Chen Li; |
| 730 | Bacterial Biofilms As Model Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We introduce theoretical framework describing the bacterial microcolonies as active viscoelastic materials. |
Vasily Zaburdaev; |
| 731 | Collective Effects in Flow-driven Cancer Cell Migration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a minimal model of autologous chemotaxis, we determine the cell density at which sensing fails, and we find that it agrees with published experimental measurements. We derive a physical limit to autologous chemotaxis in terms of the cell density, the Péclet number, and the length scales of the cell and its environment. |
Louis Gonzalez; Andrew Mugler; |
| 732 | Motility Induced Phase Separation of Deformable Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a multi-phase field model, we examine how particle deformability, which is a proxy for cell stiffness, affects MIPS. |
Austin Hopkins; Benjamin Loewe; M Cristina Marchetti; |
| 733 | Geometric Programming of Collective Sensing of Neural Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In our research, we used cell micropatterning techniques to pattern cell colonies on a grid-shaped maze and we control the connection between each grid by narrow bridges occupied by a small number of cells. |
Guanyu Li; Bo Sun; Andrew Mugler; Patrick Chappell; Ryan LeFebre; Alia Starman; |
| 734 | Sensitivity in The Cochlea Through Local Tuning Rules Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a model where hair cells use only local information, their mean squared displacement in response to thermal noise, to tune the entire cochlea to an array of critical modes. |
Asheesh Momi; Isabella Graf; Julian Rubinfien; Benjamin Machta; |
| 735 | Nuclei Size-regulated Packing and Phase Transition on Multicellular Spheres Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By further artificially applying osmotic shock to increase the nuclei-to-cell size ratio in alveolospheres, we indeed observe that the cell packing become more ordered. |
Wenhui Tang; Jessie Huang; Darrell Kotton; Dapeng Bi; Ming Guo; |
| 736 | Long-range Cellular Wound Response Manifests As Ebb and Flow Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: With time, bulk elastic behavior causes these multiple spots to merge into a single spot: with inward flow towards the damage at early times, followed by later outward flow, mediated by actomyosin contractility. Using a knock-down expression model, we confirm that this in turn is modulated by mechanosensitive channels, Piezo1 and TRPC1, and also by calcium propagation kinetics. |
Sun-Min Yu; Myeonggon Park; Yitan Li; Steve Granick; |
| 737 | Local Vs Central Nervous System Control of Hindgut Motility Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we will discuss the effects of CNS denervation and exogenously applied serotonin (5-HT) on hindgut motility. |
Spandan Pathak; Norma Peña-Flores; Phillip Alvarez; Jenna Feeley; Jens Herberholz; Wolfgang Losert; |
| 738 | Gut Instincts: A Data Driven Approach to Mouse Colon Modeling Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk will discuss statistical analysis of the optogenetic and calcium measurements of mouse colons and how it is implemented in the data-driven modeling of the ICCs and neurons that also capture the global dynamics that are observed in the colon. |
Andrea Welsh; Kristen Smith-Edwards; Brian Davis; Bard Ermentrout; |
| 739 | Emergent Bacterial Dynamics in Self-generated Oxygen Gradients Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Altogether, our work reveals the rich collective dynamics that can emerge for bacterial populations in environments with physicochemical complexity. |
Babak Vajdi Hokmabad; Sebastian Gonzales La Corte; Sujit Datta; |
| 740 | Cooperative T4 Phage Resistance in E. Coli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This begs the question: can a similar application of fundamental theories of evolution in small interconnected populations also be used to accelerate the {em de novo} emergence of phage resistance in E. coli? We do not aim to disprove the classic experiments of Delbruck and Luria of course, they are correct as implemented. |
Robert Austin; Krisztina Nagy; Trung Phan; Ryan Morris; Julia Bos; Peter Galajda; |
| 741 | The Interplay of Behavioral Variability and Response Sensitivity Generates Collective Effects in Host-pathogen Transmission Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a model of pathogen transmission that ties individual behaviors to population-level phenomena. |
Sounok Ghosh; J. Schwarz; Antun Skanata; |
| 742 | Curvature-mediated Bridging Drives Non-adhesive Strip Wound Healing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our experiments show that the epithelial cell re-epithelization is closely regulated by the gap geometry: actin cable accumulates at the two ends of straight stripes and drives gap closure via purse string contraction; straight strips do not facilitate cell migration perpendicular to wound front but wavy strips do, through the complex cell movement patterns induced by curved boundaries; cell bulging and lamellipodium extension can help establish bridges over gap widths in certain range, but not significantly beyond; for the gap size that can be bridged in the present study, actin cables can readily form to spread the bridges, leading to full gap closure. |
Hongmei Xu; |
| 743 | Machine Learning for Scientific Discovery Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work describes how machine learning may be used to develop accurate and efficient nonlinear dynamical systems models for complex natural and engineered systems. |
Steven Brunton; |
| 744 | Multiphysics and Multiscale Modeling of Erythrophagocytosis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Because of the lack of experimental approaches to quantify the chemical kinetics and cell dynamics during phagocytosis, it is not clear how biological signaling pathways cooperate with biophysical alterations of the phagocytes and their targets to ensure the timely and efficient removal of such an immense number of RBCs. To fill this knowledge gap, we develop a new biochemical signaling model to simulate the initiation of erythrophagocytosis by the interaction between the ligands on the RBCs and their receptors on the macrophages. |
He Li; Yu Zhang; Chen Zhao; Ming Dao; Aeksander Popel; George Karniadakis; |
| 745 | Symmetry-informed Model Inference for Living Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will describe our current efforts to develop computational inference frameworks capable of learning interpretable dynamical equations directly from spatio-temporal data provided by our experimental collaborators. |
Jorn Dunkel; |
| 746 | Data-Driven Reduction of Intrisically Nonlinear Dynamics to Spectral Submanifolds: Theory and Applications Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I discuss a recent dynamical systems alternative to neural networks in the data-driven reduced-order modeling of nonlinear phenomena. |
George Haller; |
| 747 | Principles of Cellular Behavior: Integrating Cellular Structure, Dynamics, and Decision Making in A Unicellular Walker Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Ultimately, we aim to elucidate general principles of the regulation and evolution of cellular behavior by integrating understanding across scales of biological organization, linking cellular structure and physiology to patterns of behavior to environmental contexts. |
Benjamin Larson; |
| 748 | A Tool to Sing Louder and An Amplifier to Hear Better Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will present some research which shows how the signallers, the male tree crickets use a behavioural strategy to make themselves louder. |
Natasha Mhatre; |
| 749 | Capturing The Social Spectrum in ASD Rats Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using this method, we acquired a rich dataset of interactions across pairings from autism spectrum disorder (ASD) knockout rats and their wild-type counterparts. |
Ugne Klibaite; Tianqing Li; Diego Aldarondo; Timothy Dunn; Bence Olveczky; |
| 750 | Sworms: How Nematodes Aggregate and Move Together Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using quantitative behavioural imaging and agent-based modeling, we identified three local interactions rules that individual worms follow to aggregate and swarm together. |
Serena Ding; |
| 751 | Exploring Open- and Closed-loop Communication Between Fireflies and LEDs Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present details of the implementation and preliminary results from a pilot field season introducing the system to two species of fireflies. |
Owen Martin; Nataliya Nechyporenko; Sanskar Katiyar; William McDonnell; Kaushik Jayaram; Orit Peleg; |
| 752 | Leveraging Behavioral Variability for Robust Classification of Firefly Flash Signals Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a high-throughput analysis pipeline to extract trajectories and flash patterns of individual fireflies recorded in the field. |
Chantal Nguyen; Owen Martin; Chantal Nguyen; Raphael Sarfati; Murad Chowdhury; Michael Iuzzolino; Dieu My Nguyen; Ryan Layer; Orit Peleg; |
| 753 | The Use of Laser Speckle Spectroscopy for Subtle Detection of Infantile Ants Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To capture delicate movements of different ant infantile stages (i.e., larvae, pupae) buried within ~700 μm glass particles at 1-5 cm depths, we focus a HeNe laser on the medium and digitally capture the backscatter speckle pattern. |
Hosain Bagheri; Paige Caine; Daniel Soto; Michael Goodisman; Daniel Goldman; |
| 754 | Density-Functional Fluctuation Theory (DFFT) Approach to Modeling Basketball Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we extend the application to sports by analyzing highly detailed data of basketball player positions collected over the last decade. |
Boris Barron; Nathan Sitaraman; Tomas Arias; |
| 755 | Crystallography of Honeycomb Formation Under Geometric Frustration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we study how bees collectively adapt to their environment to regulate the honeycomb. |
Golnar Gharooni Fard; Francisco Lopez Jimenez; Orit Peleg; |
| 756 | On The Emergence of Winner and Loser in Zebrafish Fights Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present work quantifying the emergence of a winner and loser in adult male zebrafish fights. |
Liam O’Shaughnessy; Tatsuo Izawa; Joshua Shaevitz; Greg Stephens; |
| 757 | Chimera States Among Synchronous Fireflies Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present evidence for the occurrence of chimera states within swarms of synchronous fireflies. |
Raphael Sarfati; Orit Peleg; |
| 758 | Synchronization of Complex Human Networks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our results may influence numerous fields, including traffic management, epidemic control, and stock market dynamics. In the talk, I will describe our experimental setup, present the results, and discuss all the consequences of these unique dynamics. |
Moti Fridman; |
| 759 | Cell Division and Differential Adhesion Drive Cell Self-segregation During Embryo Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we use a vertex model to investigate cell segregation during embryogenesis. |
Xinzhi Li; Dapeng Bi; |
| 760 | Mechanosensing Directs Invasion and Morphodynamics of Spheroids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By using spheroids as the tumor model, we are able to create a more physiologically relevant model for how tumors react to various mechanical cues in the ECM. |
Austin Naylor; Christopher Eddy; Bo Sun; |
| 761 | Kinetics of Cellular Aggregation: Growth, Power Laws, and Distinct Mechanisms of Cell-cell Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Different interactions give rise to different pathways of cellular rearrangement and the development of specialized tissues. In this theoretical work, we investigate the spontaneous emergence of tissue patterns from an ensemble of single cells on a substrate following three leading pathways of cell-cell interactions: direct cell adhesion contacts, matrix-mediated mechanical interaction, and chemical signaling. |
Rumi De; Debangana Mukhopadhyay; |
| 762 | Instabilities in Hexanematic Models of Epithelia Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By considering a hydrodynamic approach, we investigate the stability of hexanematic liquid crystals identifying the role of activity and flow alignment in the generation of spontaneous flows, which also reflect the interplay between different length scales. |
Josep-Maria Armengol-Collado; Livio Nicola Carenza; Luca Giomi; |
| 763 | Multiscale Measurements of Mechanical Stress in 3D Co-cultures Using A Deformable Micro-device Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a method to actuate and observe many multicellular aggregates, such as spheroids or organoids, within a single deformable micro-device. |
Charles Baroud; Shreyansh Jain; Hiba Belkadi; Martin Genet; |
| 764 | Mechanoregulation of Biofilm Homeostasis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Altogether, our study will highlight the role of mechanics in guiding cellular decisions within a biofilm. |
Sourabh Monnappa Kuppanda Jafri; Selman Sakar; Alexandre Persat; |
| 765 | Theoretical and Computational Modelling of Cell-cell Adhesion Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The main objective is to develop a mathematical and computational model for cell-cell adhesion in full 3D generality coupling the active gel model of the actomyosin cortex to the adhesion dynamics of cell adhesion molecules of the Cadherins family. |
Pradeep Bal; Marino Arroyo; |
| 766 | Rigidity of 3D Confluent Tissue Is Governed By Energy Barriers to Local Reconnection Events Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate three-dimensional vertex model for confluent tissue, where the bulk tissue is represented by a tessellation of polyhedral cells with shared faces, using Brownian dynamics. |
Shabeeb Ameen; J. Schwarz; Tao Zhang; |
| 767 | Investigating The Density Variation of Fibroblasts Near Topological Defects Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Near circular defects the cells reach a higher density than the rest of the monolayer while near the hyperbolic defects the density remains low. We investigate the role of collective migration in this behavior by varying the height of the topographic features and studying their resulting distributions and dynamics. |
Kirsten Endresen; Kurmanbek Kaiyrbekov; Brian Camley; Francesca Serra; |
| 768 | Emergent Chirality in Active Solid Rotation of Pancreas Spheres Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we elucidate the biophysical mechanism underlying rotation in spherical tissues, a phenomenon widely reported both in vivo and in vitro. |
Tzer Han Tan; Aboutaleb Amiri; Irene Seijo-Barandiarán; Michael Staddon; Anne Materne; Charlie Duclut; Sandra Tomas; Marko Popovic; Anne Grapin-Botton; Frank Jülicher; |
| 769 | Dynamics of Exciton Polaron in Microtubule Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this paper, we study the dynamical properties of the exciton-polaron in the microtubule. |
NGANFO YIFOUE WILLY ANISET; |
| 770 | Slicing Softly with Paper Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To explore skin-paper interactions, we designed an experiment in which a piece of paper contacts an artificial finger made from ballistic gelatin. |
Sif Fink Arnbjerg-Nielsen; Matthew Biviano; Kaare Jensen; |
| 771 | Particle Based Simuation of The Assembly and Mechanical Remodeling of Vascular Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using particle based simulation, we model the formation of preliminary vascular networks from individual endothelial cells during embryogenic development. |
Suraj Sahu; Ajay Gopinathan; Suzzane Sindi; Mikahl Banwarth-Kuhn; Jose Zamora; |
| 772 | Stiffness-driven Human Hepatocytes Dysfunction Via Metabolic-Redox Cross Talk in Liver Fibrogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The overall goal of this study is to introduce a new paradigm that LS is a driver of hepatic dysfunction during fibrosis. |
Srivatsan Kidambi; |
| 773 | Cell Shape and Fate Changes in 3D Model of Mammalian Hair Follicle Development Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This collection of cells will compartmentalize, elongate and invaginate into the connective tissue under the epithelial layer to form a structure termed the placode. We investigate two possible mechanisms that might trigger this transition using an extended 3D Vertex model with features specific to skin, including additional heterotypic tension at interfaces between cells of different types. |
Elizabeth Lawson-Keister; Ali Hashmi; Clementine Villeneuve; Sara Wickström; M Lisa Manning; |
| 774 | Exploring Protein Biophysics with Deep Learning Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Beyond structure prediction, deep learning approaches can help to predict mutational effects, protein function, or ligand binding. In all these applications, from a physics perspective, the primary challenge is to understand what the biophysical meaning is of the predictions produced by machine learning, how the machine learning algorithms make their predictions, and how we can curate and select the right training data for obtaining good results. |
Claus Wilke; |
| 775 | GENERALIST: Generative Probabilistic Non-Linear Tensor Factorization Model for Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For large protein sequences with datasets of limited sample size, inference of the protein sequence space could be challenging or infeasible. To address this gap, we present GENERALIST: a generative probabilistic model for protein sequences based on tensor factorization. |
Hoda Akl; Brooke Emison; Xiaochuan Zhao; Purushottam Dixit; |
| 776 | Analyses of The Cores of AlphaFold2 Protein Structure Predictions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the present work, we assess AlphaFold2 computational models using the number of residues in the core, a feature that is strongly correlated with protein stability. |
Jillian Belluck; Alex Grigas; Corey O’Hern; |
| 777 | Evaluating Machine Learning Techniques for Decoy Detection of Protein-Protein Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we constructed a dataset of high-resolution x-ray crystal structures of protein heterodimers and generated PPI models for each experimental target using current computational protein docking methods: ZDOCK, HDOCK, and Rosetta. |
Naomi Brandt; Alex Grigas; Lynne Regan; Corey O’Hern; |
| 778 | Local Deformations of Proteins Through Molecular Simulations Reveal Allosteric Couplings with Implications for Drug Design Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show that the more natural language to describe conformational changes is a local metric based on an elastic strain formalism, that is able to capture local deformations induced by allosteric perturbations such as drug/peptide binding in Molecular Dynamics simulations. |
Fabian Byléhn; Juan De Pablo; Gustavo Perez Lemus; Cintia Menendez; Walter Alvarado; |
| 779 | Characterising The Intrinsically Disordered Region of ORF6 from SARS-CoV-2 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, I present molecular scale detail on the conformational sampling of the ORF6 C-terminal region and provide a comparison of our MD simulations to experimental results. |
Alice Pettitt; Lydia Newton; Stephen McCarthy; Alethea Tabor; Gabriella Heller; Christian Lorenz; D. Flemming Hansen; |
| 780 | Evolution of The Structure and Function of The Cyanobacterial Orange Carotenoid Protein and Its Quenching of The Cyanobacterial Light Harvesting Antenna Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In conjunction with analysis of genomic sequence data from ecophysiologically diverse cyanobacteria we find a variety of carotenoproteins that are single-domains homologs of the OCP. |
Cheryl Kerfeld; |
| 781 | The Molecular Origin of Various DNA-repair Quantum Yields in Photolyases Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we switched two key residues in the active sites of class I (N341, R342 in EcPL from Escherichia coli) and class II photolyases (G381, F382 in AtPL from Arabidopsis thaliana). |
Chao Yang; |
| 782 | Many-body Van Der Waals Forces, Polarization Response and Dynamical Effects in Poly-peptides Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The many-body dispersion (MBD) approach enables the inclusion of non-pairwise contributions that consistently yield more accurate energies and longer ranged forces than standard Lennard-Jones-like potentials. Here we focus on the signatures of such many-body forces on the dynamical properties of small peptides, both in terms of simplified backbone models and for a 15-residue polyalanine within semiempirical quantum mechanics. |
Mario Galante; Alexandre Tkatchenko; |
| 783 | Examining Dynamic Allostery and Communication in Proteins Via Machine Learning and Statistical Analysis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will present results from applying machine learning and statistical techniques to the analysis of molecular dynamics simulations with a particular emphasis on understanding how ensemble change and how different regions of proteins, and protein complexes move and potentially communicate. |
Freddie Salsbury; Dizhou Wu; |
| 784 | Investigating Decoy Detection for Protein-protein Interaction Models Using State-of-the-art Scoring Methods and A Novel Graph Neural Network Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We found that for some targets, the decoy scores were strongly correlated to the structural similarity scores. |
Jacob Sumner; Grace Meng; Alex Grigas; Corey O’Hern; |
| 785 | Information Processing By Heterogeneous Cell Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To explicitly account for cell-to-cell differences in quantifying signaling network fidelity, we develop a novel information theoretic framework, cell-state conditioned mutual information (CeeMI). |
Purushottam Dixit; |
| 786 | Optimal Cellular Adaptation in Fluctuating Metabolic Microenvironments Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a stochastic model to characterize the decision-making employed by systems that optimally navigate fluctuating nutritional environments. |
Jason George; |
| 787 | One Nose But Two Nostrils: Interaction Between Two Hemispheres Aligns Bilateral Responses Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A theory was developed for the (unique) Hebbian solution, and explained two scalings. |
Bo Liu; |
| 788 | Infomation and Evolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a study to experimentally test that asexual populations do not maximize information about their environment. |
Sarah Marzen; Jonathon Soriano; |
| 789 | Do E. Coli Care About Single Molecules? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce an information rate that quantifies how much behaviorally-relevant information (in bits) is encoded per unit time by the receptor associated kinases. |
Henry Mattingly; Keita Kamino; Thierry Emonet; Benjamin Machta; |
| 790 | Alternation Emerges As A Multi-modal Strategy for Turbulent Odor Navigation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand where and when it is more convenient to sniff in the air, we combine fully resolved simulations of turbulent odor transport and Bellman optimization methods for decision-making under partial observability. |
Nicola Rigolli; Gautam Reddy; Massimo Vergassola; Agnese Seminara; |
| 791 | Allostery for Free? Scenarios for The Evolutionary Origin of Allostery in Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here use simplified physical models of proteins to show that allostery can emerge, not from direct selection, but indirectly, from selection on functions of the active site, such as binding specificity. We find that such selections lead to a spatially extended region of mutationally sensitivity where mutations act allosterically to modulate the function of the active site from a distance. |
Eric Rouviere; Olivier Rivoire; Rama Ranganathan; |
| 792 | Optimization and Variability Can Coexist Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show that this intuition is misleading: in problems ranging from transcriptional regulation to neural computation, variability in parameters can coexist with near optimal performance. Abstracting away domain-specific details, we show that this is possible because the parameter spaces of real biological systems are high dimensional. |
Lee Susman; |
| 793 | Training Networks with Internal Prestress Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use disordered elastic networks to model amorphous materials. |
Ayanna Matthews; Sidney Nagel; Margaret Gardel; |
| 794 | Physical Limits on Galvanotaxis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use a physical model to show that stochasticity due to the finite number of sensing proteins limits the accuracy of galvanotaxis via electrophoresis. |
Ifunanya Nwogbaga; Brian Camley; A Hyun Kim; |
| 795 | Bayesian Origins of Growth, Cooperation, and Inequality in Populations of Learning Agents Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we derive a general population dynamics of learning agents leveraging knowledge of their environments to grow and reinvest their resources. |
Jordan Kemp; Luis Bettencourt; |
| 796 | Information Processing in The Adaptive Immune Response Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, using computational and analytic methods, we investigate how the network of agents – antigens, cytokines, naïve, effector, memory and regulatory cells – processes information about antigen features. |
Obinna Ukogu; Armita Nourmohammad; |
| 797 | Increased Dynamic Range As A Driver of ASD Neuronal and Behavioral Differences Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: ASD compared to NT show heightened discriminability between stimuli, higher variance in neuronal activity, slower updating, deficits in learning and generalization, and reduced encoding capacity. Here, we suggest that these myriad of differences stem from a computational principle that relies on the dynamic range of the neuronal population response. |
Yuval Hart; |
| 798 | Sled Dogs As Tethered Active Agents: Part 1 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: With interactions spanning spatial, social, and physical dimensions, this “tethered” collective provides new challenges in terms of description and data collection. Here, we describe how high resolution drone imaging, bespoke animal-borne sensors, and observational behavioral data are used in conjunction to study sprint-racing sled dog teams as they partake in regular training activities. |
Benjamin Seleb; Matthew Bull; Saad Bhamla; |
| 799 | Sled Dogs As Tethered Active Agents: Part 2 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we complement a suite of multiscale fieldwork measurements of sled dog teams (see part 1) during training to understand how dog teams balance responsive agility with stability using harness physics, cyclic gaits, and simplified perceptual decision making rules. |
Matthew Bull; Benjamin Seleb; Saad Bhamla; |
| 800 | Strong Casimir-like Forces in Flocking Active Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work I describe genuinely Casimir-like long-ranged forces that arise when a flocking AM system is confined between flat reflecting boundaries – either elastic or inelastic – in the direction transversal to collective motion. |
Giuseppe Fava; |
| 801 | Fish Shoals Are Viscoelastic Materials Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In the natural world, this leads to fantastic patterns and collective behaviors across many lengthscales. This talk focuses on describing these active systems as amorphous non-equilibrium materials by investigating laboratory schools of fish. |
Pasha Tabatabai; Gabriel Kuntz; Mitchell Rask; |
| 802 | Fluid Circulation Driven By Collectively Organized Metachronal Waves in Swimming T. Aceti Nematodes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This coordinated state consists of metachronal waves that drive fluid circulation inside the drop. We experimentally measure the properties of these flows and compare them to an analytical model. |
Anton Peshkov; Alice Quillen; Brato Chakrabarti; |
| 803 | Collective Behaviors of Elastic Filaments Undulating in Close Proximity Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We focus on the conditions for the formation of meta-chronal waves of multiple filaments aligned at a wall focusing on the regime of a d L. |
Narina Jung; Won Kyu Kim; Changbong Hyeon; |
| 804 | Ecological Context Shapes Collective Turns and Velocity Correlations in Jackdaw Flocks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we report that ecological context can also influent collective turns and velocity correlations for flocks of jackdaws ( Corvus monedula). |
Hangjian Ling; Nicholas Ouellette; Alex Thornton; Guillam Mclvor; Daniel O’Coin; |
| 805 | Global Coordination Using Local Information in Fire Ant Pontoon Bridges Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Over time, most proto-bridges retract and a single final bridge forms, suggesting global coordination. Our agent-based model of the system suggests that the tendency for ants to join proto-bridges more often in areas with stronger food scent is sufficient for them to form a single bridge. |
Noah Egan; Haolin Zeng; Ram Avinery; Shengkai Li; Hosain Bagheri; Takao Sasaki; Daniel Goldman; |
| 806 | Collective Motion of Proteus Mirabilis Swarmer Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We aim to model the collective motion of swarmer cells in the absence of regulation in the precocious mutant in order to understand how wild type regulation of the swarming cycle exploits the collective dynamics of swarmer cells to swarm so effectively. |
Emma Dawson; Minsu Kim; |
| 807 | Three-Dimensional Characterization of Surface Wave Behavior in Dense Colonies of M. 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. |
Aaron Bourque; Joshua Shaevitz; |
| 808 | Morphogenetic Process of A Composite Structure Driven By Contractile Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Concurrently, we developed an agent-based model to mimic the experimental system. |
Donghyun Yim; Youngmin Jo; Pilnam Kim; Taeyoon Kim; |
| 809 | How An Immune Cell Repertoire Physically Computes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Guided by in vivo observations, we build a theoretical framework that maps molecular recognition to clonal fitness via active force usage by the cell during signal acquisition. |
Shenshen Wang; |
| 810 | Dynamics of Immune Memory and Learning in Bacterial Communities Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Despite their vast biological differences, adaptive immunity shares features from microbes to vertebrates such as emergent immune diversity, long-term coexistence of hosts and pathogens, and fitness pressures from evolving pathogens and adapting hosts, yet there is no conceptual model that addresses all of these together. To address these questions, we propose and solve a simple phenomenological model of CRISPR-based adaptive immunity in microbes. |
Sidhartha Goyal; |
| 811 | Optimization and Historical Contingency in Protein Sequences Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: Protein sequences are shaped by functional optimization on the one hand and by evolutionary history, i.e. phylogeny, on the other hand. A multiple sequence alignment of homologous … |
Anne-Florence Bitbol; |
| 812 | Structure, Function and Dynamics of The C. Elegans Nervous System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Yet even with this granular anatomical description, it remains challenging to accurately predict brain wide neural dynamics or detailed circuit function because it is unknown for many neural connections how signals propagate from one neuron to the next. To fill this gap, we created a comprehensive neural response map of the C. elegans head at cellular resolution by measuring network calcium activity in response to single-neuron optogenetic perturbations for more than 10,000 neuron-pairs. |
Andrew Leifer; |
| 813 | Understanding Cellular Decisions in Latent Space Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will show how multicellular signalling dynamics can sometimes be best represented and modelled in a low dimensional « latent space », offering an alternative modeling approach to standard gene networks. |
Paul Francois; |
| 814 | TBD Related Papers Related Patents Related Grants Related Venues Related Experts View |
Knut Drescher; |
| 815 | Substrate Stiffness-dependent Bacterial Growth Dynamics in 3D Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use different microbial strains isolated from red flour beetles and directly quantify their population scale growth dynamics within 3D medium of varying stiffness. |
Sreepadmanabh M; Saheli Dey; Pratibha Sanjenbam; Christina Kurzthaler; Deepa Agashe; Tapomoy Bhattacharjee; |
| 816 | 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; Tapomoy Bhattacharjee; |
| 817 | Cooperation of Motility- and Growth-driven Activity in Biofilm Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We used confocal fluorescence microscopy to capture the spatiotemporal behavior and patterning of Bacillus subtilis biofilms, focusing on the specific contributions of flagella-propelled motile cells and growing chains of matrix-producing cells. |
Kimberly Bowal; Nicolas Ducharme; Louis Brezin; Kirill Korolev; Joseph Larkin; |
| 818 | Instantaneous Polar Order Enhances Cell Aggregation in Thin Myxococcus Xanthus Layers – Experiment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a mutant with fluorescently labeled MglB proteins, we directly measured the polarity of individual cells and revealed a transient local polar order in thin M. xanthus colonies controlled by cell reversal frequency. |
Endao Han; Katherine Copenhagen; Matthew Black; Joshua Shaevitz; |
| 819 | Instantaneous Polar Order Enhances Cell Aggregation in Thin Myxococcus Xanthus Layers – Theory Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We aim to understand the interplay of polar order and nematic defects within M. xanthus layers. |
Katherine Copenhagen; Endao Han; Matthew Black; Joshua Shaevitz; |
| 820 | Self-buckling and Self-writhing of Semi-flexible Swimmers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Modeling the cell body as a semi-flexible Kirchhoff rod driven from equilibrium by a dynamically evolving flagellar orientation field, we derive the Euler-Poincaré equations governing the evolution of the system, and rationalize experimental observations of buckling and writhing of elongated P. mirabilis cells. |
Wilson Lough; Douglas Weibel; Saverio Spagnolie; |
| 821 | Spiral Waves in A Bacterial Population Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we discovered a unique type of spiral waves in a bacterial population resulting from cell density variation. |
Shiqi LIU; Yilin Wu; |
| 822 | Interplay Between Phototaxis and Photosynthesis in A Model Motility Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the links between these strategies is poorly understood. In this work we aim to bridge this gap, combining experimental measurements of the model microswimmer Chlamydomonas reinhardtii and a modelling approach. |
stephen williams; |
| 823 | Nematode Motility in Granular Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We will present how worms smoothly alter their motility pattern in different granular environments. |
Tapomoy Bhattacharjee; Saheli Dey; Sreepadmanabh M; Sandhya Koushika; |
| 824 | Trying So Hard But Going Nowhere: Swimming of Drugged Daphnia Magna Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: These antennae movements change dynamically to achieve particular swimming gaits whose descriptions in the literature have been qualitative and vaguely quantitative. Our study creates a granular level quantitative classification of baseline motion parameters of these swimming gaits. |
Moumita Dasgupta; Edwin Panora; Leon Armbruster; Francesca Savio; Matthew Beckman; |
| 825 | Tracking Bacillus Subtilis in 2D and Study of Its Heterogeneous Motility with Run-and-Tumble Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In RT simulation, we introduce heterogeneity by dispersing the internal speed of particles while stochasticity is reflected through diffusion parameters. |
Joowang Son; Jaeup Kim; |
| 826 | Stress and Alignment Response to Complex Confinement in Bacterial Monolayers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present simulations of colonies subject to external perturbation such as obstacles within the colony and moving boundaries. |
Blake Langeslay; Gabriel Juarez; Will Fahy; |
| 827 | Microstructure-Dependent Optical Properties of Doped Spinel Oxide Nanosystems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Annealing changes the defect structures of Cr and the trap states and the strength of the energy transfer between the different Cr defects and significantly affects the optical properties. We found crystal field decrease at low temperatures caused by quasi-melted pseudocrystalline surface, making them temperature sensitive, an order of magnitude increase in the photon yield upon X-ray or UV illumination, and temperature-dependent LLP. |
David Beke; Adam Gali; Mátyás Rudolf; Bence Markus; |
| 828 | Non-opsin-based Biological Vision: The Physics of Infrared Light Sensing in The Pit Viper Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To address these, we employ an experimental realization of a pit membrane using an InGaAs detector translated within a model pit. |
Zachary Miller; Abby Leung; Trevor Arp; Nathaniel Gabor; |
| 829 | Modular Hyperspectral Imaging System Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this contribution, we present development and characterization of a modular push-broom HSI system for imaging samples in transmission and reflection utilizing the 400 – 1000 nm spectral range. |
Matija Milanic; Jost Stergar; Luka Rogelj; Tadej Tomanic; |
| 830 | State-of-the-Art Technologies for Optical Imaging of Biological Tissues: Contrast, Resolution, and Throughput Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This talk will provide an overview of applications of optical imaging in biological tissues including methods such as fluorescence and nonlinear contrast, super-resolution, and holography and interferometry. |
Yuankai Tao; |
| 831 | Blue-light Optical Coherence Microscopsy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we present a blue-light OCM system with a center wavelength of 450 nm and a 6 nm bandwidth. |
Shanjida Khan; Kai Neuhaus; Omkar Thaware; Shuibin Ni; Myeong Ju; Travis Redd; David Huang; Yifan Jian; |
| 832 | Accurate Henle’s Fiber Layer Measurement By Volumetric Directional OCT Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We proposed a novel imaging technology, Volumetric Directional OCT (VD-OCT), a dedicated OCT system with two sets of optical scanners that can precisely control and continuously and synchronously update the imaging beam entry points during a volumetric OCT scan. |
Shuibin Ni; Shanjida Khan; Thanh-Tin P. Nguyen; Ringo Ng; Brandon Lujan; Ou Tan; David Huang; Yifan Jian; |
| 833 | Larrea Tridentata: A Path to A Non-invasive Brain Cancer Treatment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The plant Larrea tridentata (La Gobernadora in Mexico or Creosote bush in the United States) is known to have medical properties for different disorders, including cancer, due to one of its components, the nordihydroguaiaretic acid (NDGA). By using confocal Raman microscopy to analyze the function of NDGA in normal astrocytes and glioblastoma, we found evidence that this acid does not affect the former, making this a potential non-invasive alternative for cancer treatment. |
Lizbeth Martinez Lopez; Felicia Manciu; Kevin Bennet; Marian Manciu; |
| 834 | Quantification of Malaria Parasite in Blood Smears Using Phase Microscopy Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present the results of phase microscopy using an automated digital processing technique for malaria parasite detection and identification of species and stages. |
Charlotte Kyeremah; David Newey; Albert Adu; Wisdom Mensah; Daniel Haehn; Chandra Yelleswarapu; |
| 835 | The Effects of Hypoxia on Cancer Cell Motility and on Cell Size Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We investigate the effects of hypoxia on cancer cell motility (as a potential indicator of EMT) and on cell size (as a potential indicator of PACC formation). |
Robert Austin; Kimberly Shen; Noreen Hosny; Kenneth Pienta; Sarah Amend; Emma Hammarlund; |
| 836 | Fourier Space Analysis of Tissue Order Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present an approach to determine the overall order of tissue architecture in histology slides of murine abdominal wall samples with induced peritonitis. |
Jost Stergar; Katja Lakota; Martina Perše; Matija Tomši?; Nika Kojc; Matija Milanic; |
| 837 | Hyperspectral Imaging and Optical Profilometry of Murine Tumor Models Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we combined hyperspectral imaging (HSI) with 3D optical profilometry (OP) to image multiple subcutaneously grown murine tumor models. |
Tadej Tomanic; Luka Rogelj; Jost Stergar; Bostjan Markelc; Tim Bozic; Simona Kranjc Brezar; Gregor Sersa; Matija Milanic; |
| 838 | Learning Accurate Closures of A Kinetic Theory of An Active Fluid Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present a learning framework that relies on invariant representation of tensor-valued isotropic functions to learn the closure models directly from kinetic simulations. |
Suryanarayana Maddu; Scott Weady; Michael Shelley; |
| 839 | Data-driven Approaches to Predict and Understand The Dynamics of Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, developing models using traditional statistical physics approaches is challenging because active materials lack the scale separation characteristic of equilibrium systems. In this presentation, I will discuss efforts to use data-driven techniques to address this challenge in the context of a model active material, microtubule-based active nematics. |
Michael Hagan; |
| 840 | Directing Assembly and Encoding Information in Active Matter Via Light Patterns Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, using simulations and data science, we unravel the interplay between the properties of the active particles and the features of the light pattern, propose protocols to control smart templated assembly and motion in active matter, and identify a metric to quantify the amount of information encoded in the active fluid following the application of the light pattern. |
Jerome Delhommelle; Caroline Desgranges; |
| 841 | Learning A Compact Representation of The Nematic Director of Active Nematics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we develop a neural network to learn a compact (reduced-dimension) representation of the Q-tensor field that describes the nematic director of experimental active nematics. |
Phu Tran; Zvonimir Dogic; Aparna Baskaran; Pengyu Hong; Michael Hagan; |
| 842 | Categorizing Spatiotemporal Dynamics of Bacterial Swarm Fronts Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we reduce the complex dynamics of the multicellular system to the time evolution of closed curves by representing the swarms by their moving boundary. |
Alasdair Hastewell; Hannah Jeckel; Andreea-Oana Chelban; Gabriel Rodriguez-Roig; Knut Drescher; Jorn Dunkel; |
| 843 | Predicting Spatio-temporal Patterns of Cells Guided By Time-varying Guidance Cues with Reservoir Computing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This problem is further exacerbated when the training data is short in time and includes a stochastic component. We therefore propose a reservoir computer architecture with an additional input vector that mimics the temporal dynamics of a parameter of the dynamical system. |
Hoony Kang; Keshav Srinivasan; Michelle Girvan; Wolfgang Losert; |
| 844 | Rapid Detection and Classification of Motile Cell Tracks in 3D Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use DHM data as ground truth libraries for a deep learning object detection network. |
Samuel Matthews; Laurence Wilson; James Walker; Victoria Hodge; |
| 845 | Neural Networks for Data-driven Models of Cell Mechanics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show how machine learning can link protein distributions to mechanical forces, leading to data-driven physical models without requiring knowledge at the microscale. |
Matthew Schmitt; Jonathan Colen; Stefano Sala; Margaret Gardel; Patrick Oakes; Vincenzo Vitelli; |
| 846 | Electron Flow in Biofilm Matrix: Impact of Chemical Composition and Context Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To provide a mechanistic understanding of EET in biofilms, we fabricated well-defined synthetic hydrogels mimicking P.a. biofilm matrices, and characterized the mechanisms underpinning EET efficiency of both hydrogels and P.a. biofilms with distinct compositions under different conditions. |
Jinyang Li; |
| 847 | Spontaneous Phase Separation in Vibrio Cholerae Bacterial Biofilms Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our approach addresses the critical need to understand the formation of bacterial biofilms to posteriori use new strategies to disrupt and/or eliminate biofilms by interfering with the PS process. |
Alexis Moreau; |
| 848 | How Bacteria Use Electrochemical Potentials to Solve Complex Problems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In my talk, I will present our recent efforts to uncover the computational power of bacteria and their communities. |
Gurol Suel; |
| 849 | Experimental Macroecology in Microbial Systems Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This approach has achieved considerable success in microbial ecology in recent years, having identified universal patterns of diversity and abundance that can be captured by a single effective model: the stochastic logistic model of growth (SLM). |
William Shoemaker; Alvaro Sanchez; Jacopo Grilli; |
| 850 | Host Heterogeneity in C. Elegans Drives Variation in Gut Microbial Composition Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use a bottom-up experimental approach to understand microbiome assembly rules from in vivo monocolonization of the C. elegans gut by members of the native worm microbiome. |
Satya Spandana Boddu; K. Michael Martini; Ilya Nemenman; Nic Vega; |
| 851 | Mechanics and Microstructure in Biofilms and Their Interactions with The Immune System: Why You Should Care, and Why I Think This Intersection Is Understudied Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: How these myriad parameters interplay in real-world infections, which are polymicrobial and can happen at many different anatomical sites, is not understood at all. In this talk, I will give a synthetic overview of our findings and how they point toward future investigation. |
Vernita Gordon; Gordon Christopher; Kendra Rumbaugh; |
| 852 | Pseudomonas Aeruginosa Contracts Mucus to Rapidly Form Biofilms in Tissue-engineered Human Airways Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To understand how mechanical tissue properties influence biofilm biogenesis, we developed a tissue-engineered airway called AirGel, composed of a tube-shaped epithelium in an optically-clear matrix. |
Tamara Rossy; Tania Distler; Joern Pezoldt; Jaemin Kim; Lorenzo Talà; Nikolaos Bouklas; Bart Deplancke; Alexandre Persat; |
| 853 | Active Bulging Promotes Biofilm Formation in A Bacterial Swarm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Combining multi-mode imaging, single-cell tracking and numerical simulations, here we discovered that an interfacial process denoted as "active bulging" promotes biofilm formation. |
Siyu Liu; Ye Li; Yilin Wu; Daniel Kearns; |
| 854 | Probing Intercellular Interactions in Dynamic Clusters of Swarming Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By observing the collective motion exhibited in the swarms of both species of bacteria, in particular the dynamic packs of motile SM3 cells upon dilution as compared with their motility in the planktonic state, our study demonstrates to what extent cell-cell interactions exist and affect collective behaviors. |
Jay Tang; |
| 855 | Substrate Stiffness Impacts Early Biofilm Formation By Modulating Twitching Motility Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a simple mechanistic model for the function of type-4 pili (T4P) on a deformable substrate, that accounts for the observed results. |
sigolene Lecuyer; Delphine Débarre; Sofia Gomez Ho; Karin John; Lionel Bureau; |
| 856 | Run-and-Tumble Analysis of Enterobacter Sp. SM3 Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present first findings of the run-and-tumble behavior of the newly-discovered, swarm-competent bacterium enterobacter sp. |
Silverio Johnson; Brian Freedman; Sridhar Mani; Jay Tang; |
| 857 | From Run-and-tumble to Hopping-and-trapping: Bacterial Foraging in Porous Landscapes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Additionally, it is unclear whether heightened cell density is perceived as a dynamic porous landscape leading to a foraging switch. In this work we investigate these open-ended questions using porous and patchy microfluidic landscapes. |
Miles Wetherington; |
| 858 | Mesenchymal Cell Motility Is Required for Sacculation During Lung Development Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we build a computational model of sacculation to test our hypothesis that mesenchymal cell motility is required for epithelial expansion and mesenchymal thinning. |
Carolina Trenado Yuste; Sarah Paramore; Rishabh Sharan; Danelle Devenport; Celeste Nelson; |
| 859 | How Do Cell Intrinsic Cues and External Signals Interplay with Cell Motility to Affect Cellular Organization? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we describe a rule based model to investigate how the relative dependence of cellular decisions on intrinsic versus extrinsic cues affects cellular organization, and how is the effect different in organisms with motile versus non-motile cells. |
Somya Mani; Tsvi Tlusty; |
| 860 | Learning About Teeth: Data-driven Continuum Models of Amelogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Based on a minimal set of assumptions about the behavior of individual cells, we develop a coarse-grained continuum model of epithelial front motion and enamel deposition, which we solve using recently developed deep learning techniques for inverse problems. |
Pearson Miller; Mackie O’Hara; |
| 861 | Anisotropic Growth in The Presence of Noise and Mechanical Feedback in Elastic Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We model a growing elastic tissue in two dimensions using continuum mechanics, and study the effects of noise and mechanical feedback on a background of exponential anisotropic growth. |
Minu Varghese; David Lubensky; |
| 862 | A Morphogen Gradient Orchestrates Pattern-preserving Tissue Morphogenesis Via Motility-driven (un) Jamming Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition. |
Diana Pinheiro; |
| 863 | Cell Division and Active Motility Drive Hexatic Order in Biological Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we study the effect of cell division and apoptosis on global hexatic order within the framework of the self-propelled Voronoi model. |
Yiwen Tang; Dapeng(Max) Bi; Mark Bowick; Siyuan Chen; |
| 864 | The Cellular Mechanics of Cephalic Furrow Formation in The Drosophila Embryo Investigated Using An Advanced Vertex Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: An analysis of the cell shape changes that occur in the active region of the epithelial cell layer reveals that the CFF occurs in two distinct phases: the initiation and progression phases. |
Redowan Ahmed Niloy; Michael Holcomb; Jeffrey Thomas; Jerzy Blawzdziewicz; |
| 865 | A Mechanical Finger-trap Mechanism Controls Cell Width in Bacillus Subtilis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By studying the mechanical properties of the cell wall using osmotic shocks, we found that the cell responded to an increase in turgor pressure with longitudinal stretching and circumferential compaction. |
paola bardetti; |
| 866 | Receptor Promiscuity and Feedback Control Mediate Accurate and Robust Encoding and Decoding of Positional Information During Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this study, we show how receptor promiscuity and feedback control on receptors can act as local cell autonomous control mechanisms that allow for sculpting of morphogen profiles in tandem with accurate and robust positional inference. |
Krishnan Iyer; Madan Rao; |
| 867 | Control of Tissue Fluidity By Optogenetic Manipulation of Actomyosin Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use optogenetic tools to manipulate actomyosin contractility in the germband epithelium, which exhibits rapid flow during Drosophila body axis elongation. |
Marisol Herrera Perez; Karen Kasza; Christian Cupo; |
| 868 | An Action Principle for The Morphogenesis of Thin Sheets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose that nature settles on the ‘simplest’ growth patterns. |
Dillon Cislo; Boris Shraiman; |
| 869 | Hatching on A Budget: The Economized Energy Expenditure of Beetle Embryos Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study extra-embryonic tissue dynamics in two key processes during embryo development, gastrulation and dorsal closure, in the serosa membrane of the red flour beetle Tribolium castaneum. |
Zoë Lange; |
| 870 | Fish-inspired Robot Manipulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We employed suction flow at the fingertips of a humanoid hand and found that gentle suction conditions, on the order of 1N of force, improve the rapid capture of floating objects up to 10 kg. |
Hannah Stuart; Juan Romero; Peter Wainwright; Stanley Wang; |
| 871 | A Shannon-inspired Framework for Multi-legged Matter Transport Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we establish an analogous framework to describe matter transport, in the manner of robot locomotion, over noisy landscapes. |
Baxi Chong; Juntao He; Daniel Soto; Tianyu Wang; Daniel Irvine; Daniel Goldman; |
| 872 | Emergent Gait Transitions of A Quadrupedal Robot Under Obstacle Modulation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Recent biological studies (Wilshin et al., 2017) demonstrated that when moving from flat ground to rough terrains, dogs would shift from walk-like gaits to trot-like gaits. Inspired by this result, we use a quadrupedal robot as a robophysics model, to study how a ”soft’’ feedforward gait is affected by repeated ”phase perturbations’’, as the robot traverses an array of evenly spaced half-cylindrical obstacles. |
Xingjue Liao; Feifei Qian; |
| 873 | RoboPhysics Inspired Experiments to Understand How Canines Move Over Regular Obstacle Arrays Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Surprisingly, they did not exhibit large changes in gait. Therefore, in this study we step back to characterize changes in basic stride parameters and spatial aspects of locomotion. |
Benjamin Doshna; Michelle Joyce; Haodi Hu; Feifei Qian; Simon Wilshin; Andrew Spence; |
| 874 | Using An Insect-scale Robot to Explore The Impact of Limb Number and Length on Locomotion in Unstructured Terrain Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We included limb and gait combinations which result in body-terrain contact to explore whether using the body as an additional point of support could help ensure robust locomotion. |
Perrin Schiebel; Velin Kojouharov; Robert Wood; |
| 875 | Terrestrial Swimming in Multilegged Robots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Numerical simulations and theoretical analysis demonstrate that periodic leg-substrate contact allows for analysis via an effective Resistive Force Theory akin to that in flowable media where the system experiences an effective viscous drag and acquired drag anisotropy. |
Juntao He; Baxi Chong; Shengkai Li; Eva Erickson; Kelimar Diaz; Tianyu Wang; Daniel Soto; Daniel Goldman; |
| 876 | Multi-robot Connection Towards Collective Obstacle Field Traversal Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by ants collectively traversing obstacles through physical connections with each other, we study the locomotion performance of a group of "connectable” robots over an obstacle field filled with half-cylindrical "boulders”. |
Haodi Hu; Elliott Meeks; Feifei Qian; |
| 877 | Force Sensing Can Help Robots Reconstruct Potential Energy Landscape and Guide Locomotor Transitions to Traverse Large Obstacles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: When viewed on a potential energy landscape of the system, which results from physical interaction with obstacles, these locomotor transitions are strenuous barrier-crossing transitions between landscape basins. Because potential energy landscape gradients are conservative forces, we hypothesize that sensing obstacle interaction forces allows landscape reconstruction, which can guide robots to cross barriers at the saddle to make transitions more easily (analogous to crossing a mountain ridge at its saddle). |
Yaqing Wang; Chen Li; |
| 878 | Connection-Based Data-Driven Gait Modeling of A Quadruped Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We report initial results from a Ghost Robotics Vision 60 robot, measuring ego motion using iterative closest point (ICP) estimation from LIDAR data to solve for the body velocity, and using encoder data for body shape. |
Ziyou Wu; Shai Revzen; |
| 879 | An Autonomous Tensegrity Robot with Closed-loop Control and Real-time State Estimation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we present an autonomous 3-bar tensegrity robot with elastic sensor tendons for closed-loop control and sim2real transfer. |
William Johnson; |
| 880 | Compliant Cable-driven Limbless Robot for Complex Terrain Navigation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The robot also features an elastic mesh skin for smooth robot-environment contact and detachable modular wheels for variable drag anisotropy. The cable-driven mechanism allows variation of body stiffness, and we study how such mechanics facilitate terrain traversal in model laboratory complex terrains (i.e., lattices, channels, granular media). |
Velin Kojouharov; Tianyu Wang; Christopher Pierce; Kelimar Diaz; Baxi Chong; Daniel Goldman; |
| 881 | Lattice Transport Via Mechanical Intelligence in Undulatory Locomotors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our observations of nematode locomotion in obstacle lattices suggest that many collision-instigated behaviors occur passively, thus we hypothesize that the bilateral muscle actuation mechanism provides favorable passive mechanics for heterogeneity navigation. |
Tianyu Wang; Christopher Pierce; Velin Kojouharov; Kelimar Diaz; Baxi Chong; Hang Lu; Daniel Goldman; |
| 882 | Robophysical Modeling of Dynamic Posture Modulation of Vibration Sensing in Orb Weaving Spiders Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, whether this is true and how it works is poorly understood, due to difficulty of measuring the dynamics of the entire prey-web-spider interaction system all at once. Here, we developed a robophysical model of the system to test this hypothesis of active sensing and discover its principles. |
Eugene Lin; Yishun Zhou; Luke Moon; Andrew Gordus; Chen Li; |
| 883 | Early Career Award for Biological Physics Research: Life in A Tight Spot: How Bacteria Navigate Crowded Spaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will summarize my group’s work unravelling how confinement in a crowded 3D space changes how bacteria behave. |
Sujit Datta; |
| 884 | Cell-cell Collisions: Wetting, Speed, and Acceleration Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Can we predict collision outcomes by leveraging cell shape and speed? |
Pedrom Zadeh; Brian Camley; |
| 885 | A Coarse-grained Model for Cytoplasmic Streaming Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we theoretically investigate the transition to streaming and the consequent transport and mixing. |
Brato Chakrabarti; Michael Shelley; |
| 886 | Diffusion Maps for Collective Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show that a coarse-grain description of a high-dimensional dynamical system can be found by defining a measure of similarity between the different possible states that the system can achieve. |
Christian Esparza Lopez; Greg Stephens; |
| 887 | AI-enabled Analysis of Collective Cell Dynamics Driven By Electric Fields Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In PIV-based analysis, dynamic information is collected based on small segments of the image, regardless of the local cell density. We present an AI-based cell segmentation and tracking workflow that can identify the motion of individual cells in a group from phase contrast images, and demonstrate its capability of providing detailed cell scale information on the link between individual and collective behavior. |
Shuyao Gu; Kan Zhu; Min Zhao; Wolfgang Losert; |
| 888 | Unveil Microscopic Mechanism from Collective Behaviors Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we will present a generic neural network architecture to solve the inverse problem—revealing dynamical mechanisms of individual cells from their collective behaviors that are easily accessible in experiment. |
Ming Han; John Devany; Margaret Gardel; Vincenzo Vitelli; |
| 889 | Learning Mechanisms for Collective Multicellular Behavior with Differentiable Molecular Dynamics Simulations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we leverage advances in machine learning technologies to optimize over physics and biology based molecular dynamics (MD) simulations of individual cells, to learn mechanisms that can drive collective behavior. |
Ramya Deshpande; |
| 890 | Collective Behavior of Model Swimmers at Intermediate Reynolds Numbers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using computational fluid dynamics approaches, we examine how the collective behaviors emerge in a mixture of a simple mesoscale model swimmer immersed in a viscous incompressible fluid under the increasing effect of inertia. |
Hong Nguyen; Daphne Klotsa; |
| 891 | Chemotactic Motility-induced Phase Separation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we combine continuum models for MIPS and chemotaxis and use linear stability analysis and numerical simulations to study chemotactic MIPS. |
Hongbo Zhao; Andrej Kosmrlj; Sujit Datta; |
| 892 | Anomalous Collective Dynamics of Auto-chemotactic Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present the adapted phase diagram as well as a a novel nonlinear mechanism that could stabilize the continuous transition against a pattern forming instability. |
Richard Swiderski; Florian Raßhofer; Jasper van der Kolk; Abhik Basu; Astik Haldar; Erwin Frey; |
| 893 | Toward Ideal Gas Law for Crowds with Large Pressures Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our study reveals the criterion for crowd speed (corresponds to fluctuation velocity) to follow the Maxwell-Boltzmann distribution. |
Lei Fang; |
| 894 | Stochastic Bounds of Aggregation Dynamics Distinguish Near-wild-type from Wild-type Strains in Social Bacteria Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To study this problem, we use the model organism Myxococcus xanthus, a bacterial species that exhibits a rudimentary but robust form of development in the form of fruiting body aggregation, wherein cells in a low-nutrient environment spontaneously organize from a homogeneous, flat swarm into a discrete number of mound-shaped aggregates harboring thousands of cells. We present a high-throughput imaging setup and analysis pipeline to produce a dataset of these aggregation events that is sufficiently large to use data-driven statistics to quantify the bounds of wild-type behavior. |
Merrill Asp; |
| 895 | Autonomous Waves and Global Motion Modes in Living Active Solids Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using a biofilm-based bacterial active solid, here we discovered self-sustained elastic waves with unique wave properties not seen in passive solids, such as power-law scaling of wave speed with activity. |
Haoran Xu; Yulu HUANG; Rui Zhang; Yilin Wu; |
| 896 | Two Dimensional Bacterial Turbulence at A Liquid-air Interface Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use Serratia marcescens bacteria that swim at a water-air interface to study 2D bacterial turbulence. |
Yuanfeng Yin; |
| 897 | Size-distribution Dynamics in Growing Bacterial Colonies with Mechano-sensing Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Inspired by our recent work on smectic liquid crystals in extreme confinement [1-2], we develop a microscopic theory for growing bacteria colonies based on classical dynamical density functional theory (DDFT). |
René Wittmann; Fabian Jan Schwarzendahl; Hartmut Löwen; |
| 898 | Energy Profiles and Statistics of Spontaneous T1 Transitions in Confluent Tissues Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We use a multi phase field model to study spontaneously generated T1 transitions under different regimes of cell deformability and cell-cell interaction. |
Harish Pruthviraj Jain; Luiza Angheluta; Axel Voigt; |
| 899 | Characteristics of Growing, Tangled Branches Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we use a combination of experiments and simulations to show that entanglement through growth is easy to achieve, can result in configurations that are impossible to access through mechanical agitation alone, and can be tuned through branch geometric changes. |
Thomas Day; Peter Yunker; William Ratcliff; G. Ozan Bozdag; Seyed Alireza Zamani Dahaj; |
| 900 | The Secret Life of Sarcomeres: Stochastic Heterogeneity of Sarcomeres in Beating Stem-cell Derived Cardiomyocytes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show that a simple dynamic model reproduces crucial experimental findings by assuming non-monotonic force-velocity relations for single sarcomeres, as previously predicted for ensembles of motor proteins. |
Christoph Schmidt; Daniel Haertter; Wolfram-Hubertus Zimmermann; Lara Hauke; Til Driehorst; Branimir Berecic; Lukas Cyganec; Malte Tiburcy; |
| 901 | Spatial Patterning of Mitochondrial Metabolism in Mouse Oocytes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I am using quantitative microscopy, molecular perturbations, and biophysical modeling to decipher the mechanism behind the formation of subcellular spatial patterns of mitochondrial metabolism in mouse oocytes. |
Yash Rana; Xingbo Yang; Daniel Needleman; |
| 902 | Effects of Obesity on The Dynamics of Cancer Cell Invasion Into Adipose Tissue Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have developed discrete element method (DEM) simulations of tumor cell invasion into WAT. |
Yitong Zheng; Dong Wang; Garrett Beeghly; Claudia Fischbach; Mark Shattuck; Corey O’Hern; |
| 903 | Modeling Collective Cell Behavior in The Presence of External Stimuli Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Controlling collective movement, arrangement and affecting proliferation of cell monolayers via external stimuli could be useful in organoid development, wound healing, and drug discovery research. A plethora of experiments have focused on these topics, here we present a computational model that simultaneously captures cell motility, division, and nematic order within the cell monolayer. |
Kurmanbek Kaiyrbekov; Kirsten Endresen; Francesca Serra; Brian Camley; |
| 904 | Topology Protects The Emergence of Coherent Oscillations in The Circadian Rhythm Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a topological model that demonstrates emergent oscillations at the network boundary, effectively reducing the system dynamics to a lower-dimensional space. |
Chongbin Zheng; Evelyn Tang; |
| 905 | Effect of Boundary Elastic Interactions on Motile Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Cells have been observed to perform durotaxis or preferential migration towards a stiffer substrate region. We explain this with a physical model where cells are described as motile agents that exert contractile, traction forces on the underlying substrate, which lead to elastic forces and torques on the cells at boundaries. |
Subhaya Bose; Haiqin Wang; Xinpeng Xu; Arvind Gopinath; Kinjal Dasbiswas; |
| 906 | TBD Related Papers Related Patents Related Grants Related Venues Related Experts View |
Thomas Lecuit; |
| 907 | Nontrivial Effects of Activity on The Glassy Dynamics of Active Self-propelled Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, activity has nontrivial complex effects on the dynamical heterogeneity. In this talk, I will discuss some of these effects and show that mode-coupling theory, extended for active systems, can surprisingly capture both these aspects of activity. |
Saroj Nandi; |
| 908 | Criticality of Isotropic Stress Percolation During Glass to Fluid Transition in Active Cell Layers Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Our findings provide a new perspective on the fundamental mechanical mechanisms associated with the solid-like to fluid-like transition in active cell layers. |
Siavash Monfared; Guruswami Ravichandran; Jose Andrade; Amin Doostmohammadi; |
| 909 | From Cells to Tissue: Decoupling Cell-adhesion and Contractile Forces in A Model Epithelial Tissue Framework Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we propose a framework to model epithelial cells and tissues as deformable polygons(DP) with precise control over single-cell properties such as their elasticity, surface tension, and motility as well as their interactions in a dense 2D monolayer. |
Anshuman Pasupalak; |
| 910 | Glass-like Dynamics in Plant Cells Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we study the collective re-arrangements of chloroplasts in the water plant Elodea densa. |
Maziyar Jalaal; Nico Schramma; Cintia Perugachi Israels; |
| 911 | Distinguishing Jammed Monomer and Polymer Packings in Three Dimensions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we seek to discern the fundamental differences between packings of spherical monomers and packings of polymers with short-range attractive interactions. |
Jack Logan; Alex Grigas; Mark Shattuck; Corey O’Hern; |
| 912 | Emergence of Bacterial Glass: Two-step Glass Transition in 2D Bacterial Suspension Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Bacterial populations are particularly interesting in this context, as they are known to show a plethora of collective phases, yet it remains challenging to characterize dense states of bacteria, partly because it is experimentally difficult to realize a uniform growth condition for dense populations. Here we overcome this by a recently developed membrane-based device [1] and report the emergence of glassy states in two-dimensional suspension of Escherichia coli [2]. |
Kazumasa Takeuchi; Hisay Lama; Masahiro Yamamoto; Yujiro Furuta; Takuro Shimaya; |
| 913 | Polymer Collapse and Jamming: The Role of The Backbone Connectivity and Adhesive Interactions in Determining The Properties of The Cores of Collapsed Polymers and Folded Proteins Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To this end, we analyze the interior packing fraction, number of contacts above isostaticity, and the emergence of excess low-frequency modes in the vibrational density of states. |
Alex Grigas; Mark Shattuck; Corey O’Hern; |
| 914 | How Do Changes in The Spatial and Temporal Correlations Arising from Activity Affect The Glass Transition? Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: This work offers fundamental insights into the differences between the glassy dynamics that occurs in thermal energy-driven versus activity-driven systems, an important step forward in modeling active motion in living and non-living materials. |
Francesco Arceri; Corey O’Hern; Mark Shattuck; |
| 915 | Branching Fractional Brownian Motion As A Model of Serotonergic Neurons Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To better represent the biological process we are trying to simulate, we introduce the concept of branching FBM (bFBM). |
Reece Beattie-Hauser; Gaurav Khairnar; Jonathan House; Skirmantas Janusonis; Ralf Metzler; Thomas Vojta; |
| 916 | Topological Packing Statistics Distinguish Living and Non-living Matter Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: By introducing a mathematical framework for measuring topological distances between general 3D point clouds, we construct a universal topological atlas encompassing bacterial biofilms, zebrafish brain matter and embryonic tissues as well as colloidal packings, glassy materials, and stellar configurations. |
Dominic Skinner; Hannah Jeckel; Adam Martin; Knut Drescher; Jorn Dunkel; |
| 917 | Rheological Aging of Viscoelastic Glasses Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we present a theory of aging for viscoelastic glasses that incorporates both relaxation processes. |
Andrei Gasic; Peter Wolynes; |
| 918 | Ecological Feedbacks in Evolutionary Rescue Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: The speed of adaptive evolution can be remarkably fast, yet may sometimes fail to keep pace with rapidly changing environments. Quantifying the evolvability of populations is a … |
Jeremy Draghi; |
| 919 | Self-propelled Adaptive Evolution on Malleable Dynamic Fitness Landscapes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Evolving populations, from cells to organisms, adapt to the demands of their environment, yet in modifying their environment, they directly alter the selective pressures they experience, thereby reshaping their local fitness landscape. Here we present a minimal two-field model to capture this eco-evolutionary feedback loop. |
Alexander Heyde; L Mahadevan; |
| 920 | Frequent Hybridization and Gene Sweeps Shape Evolution of A Natural Bacterial Population Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Earlier work found that Yellowstone cyanobacteria comprise two distinct clusters adapted to different temperatures. |
Gabriel Birzu; Daniel Fisher; Devaki Bhaya; |
| 921 | Characterizing Diversity and Genetic Exchange in Marine Prochlorococcus Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: I will describe our recent efforts using hundreds of single cell genomes to elucidate a quantitative description of horizontal transfer of core genes in Prochlorococcus. |
Alana Papula; Daniel Fisher; |
| 922 | Evolution of Microbial Growth Dynamics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Like all biological traits, the nutrient-growth relationship is subject to the fundamental evolutionary processes of mutation, selection, and genetic drift. Using a combination of empirical data and mathematical models, I will show how these evolutionary processes address two longstanding questions about the nutrient-growth relationship. |
Michael Manhart; |
| 923 | Inferring Epistasis for HIV Evolution Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we describe the epistatic effects of mutations inferred from HIV evolution, where many mutations are present, using modified, computationally-efficient approach. |
Kai Shimagaki; John Barton; |
| 924 | Inferring Mutation Rates from Evolutionary Histories with Path Integral Methods Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, these models depend on knowing detailed properties of a pathogen, such as its mutation rate and how mutations affect its fitness. Here we study how such properties can be inferred from data, in particular, genetic sequences collected over time from a population. |
Uchenna Nwaege; John Barton; |
| 925 | Quantifying Adaptive Landscapes of Commensal Gut Bacteria Using High-resolution Lineage Tracking Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: However, the evolutionary dynamics of process are difficult to characterize in dominant gut species in their complex in vivo environment. In this talk, I will show how the fine-scale dynamics of genome-wide transposon libraries can enable quantitative inferences of these in vivo evolutionary forces. |
Daniel Wong; Benjamin Good; |
| 926 | Evolution of Evolvability in Rapidly Evolving Populations Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we develop a mathematical framework for predicting the fates of mutations that modify the rates and fitness benefits of future mutations. |
James Ferrare; Benjamin Good; |
| 927 | Linkage Equilibrium Between Rare Alleles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here, we introduce an alternative metric ("linkage equilibrium") that vanishes in the absence of recombination and approaches one for unlinked loci. |
Anastasia Lyulina; Zhiru Liu; Benjamin Good; |
| 928 | Predicting The Structure of GxE and GxGxE Interactions in Saccharomyces Cerevisiae Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find that our predictions explain a substantial fraction of measured GxE and GxGxE effects. |
Sarah Ardell; Alena Martsul; Milo Johnson; Sergey Kryazhimskiy; |
| 929 | Limit Cycles Turn Odd Active Matter Into Robots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, I will discuss how odd active matter—media in which energy conservation and chiral symmetries are simultaneously broken—can be used to steer mechanical waves in unprecedented ways. |
Corentin Coulais; |
| 930 | Coordinated Collective Behavior Through Contact Interactions and Adaptive Oscillators Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk we present design principles for high density collectives to achieve phase synchronized motion through contact interactions. |
Nick Gravish; |
| 931 | Stigmergic Formation of Soft Matter Structures in A Robophysical Collective Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: A single agent transports ~10% of the initial staple mound over 4 hours. We aim to assign these robots with low level tasks such as material transport coordinated by the environment (i.e., "stigmergy") and posit that the resulting structures will facilitate higher level tasks. |
Daniel Daniel Soto; Joonha Hwang; Michael Goodisman; Daniel Goldman; |
| 932 | Towards A Colloidal Crystal Robot Gripper Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this computational project, we decompose the geometry of the cluster of swelling particles into basic elements such as angle, edge length and cluster asymmetry. We show how these geometric elements control where dislocations form and how they move in the 2D crystallite. |
Corwin Kerr; Nipuli Gunaratne; Philipp Schönhöfer; Sharon Glotzer; |
| 933 | Swarms of Optically Controllable Electrokinetic Microrobots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we show a new class of photovoltaic-powered, electrochemically propelled microrobots that are compatible with CMOS electronics and are fabricated in parallel using standard lithography techniques. |
William Reinhardt; Lucas Hanson; Scott Shrager; Tarunyaa Sivakumar; Maya Lassiter; Marc Miskin; |
| 934 | Granulobots: Leveraging Mechanical Properties of A Decentralized, Multi-unit, Dense Robotic Aggregate for Sensorless Tasks Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we use a new decentralized and modular robotic platform that we recently developed, Granulobot, to demonstrate tasks based on aggregate mechanical properties. |
Baudouin Saintyves; Matthew Spenko; Heinrich Jaeger; |
| 935 | Fabricating Reprogrammable Solar Powered Microscopic Robots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We show progress towards programmable, autonomous microscopic robots. |
Maya Lassiter; |
| 936 | Collective Chase: Emergent Dynamics of Braitenberg’s Vehicle 2b (aggression) Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this talk, we study the dynamics of a different collective system, inspired by Braitenberg’s "aggression" vehicles. |
Rundong Yang; Wei Zhou; Nick Gravish; |
| 937 | Adaptable Force Chains in Granular Assemblies Using Variable Stiffness Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we fabricate variable stiffness particles, whose stiffness can be reversibly changed on demand to tune the force network in a packing. |
Sven Witthaus; Atoosa Parsa; Nidhi Pashine; Jerry Zhang; Corey O’Hern; Rebecca Kramer-Bottiglio; |
| 938 | Guided Motion of Kinked Vesicles By Active Particles Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Collective motion of active particles has been studied extensively, yet effective strategies to navigate active particle swarms are still rare and rely on external guidance. We introduce a method to control the trajectories of swarms of active rod-like particles by confining them within a rigid bounding membrane (vesicle) of non-uniform shape. |
Sophie Lee; Philipp Schönhöfer; Sharon Glotzer; |
| 939 | Emergent Swarm Robot Behaviors Induced By Confinement and Contact Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Building on our study of phase changes in contact-mediated robot collectives [Li et al, Science Advances 2021], we study the dynamics and task capabilities of a confined programmable swarm of twelve disk-shaped (8 cm diameter) wheel-driven robots that make decisions based on local collisions. |
Zhexin Shen; Ram Avinery; Hosain Bagheri; Daniel Soto; Daniel Goldman; |
| 940 | Recipes for Emulating Nonlinear Active Materials with Robotics Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we demonstrate that programmable interactions between undulatory robots can be a versatile tool for studying nonlinear wave propagation that relaxes the limits necessitated by constituent materials and geometry. |
Kai Qian; Phoenix Stout; Gustav Blankenberg; Wei Zhou; Jihad Alqasimi; Nicholas Gravish; Nicholas Boechler; |
| 941 | Modeling and Analysis of Mesophyll Tissue Development in Leaves and Flowers Across Species Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We hypothesize that the differences in the structural properties of mesophyll tissue are primarily driven by differences in cell stiffness, growth rate, and adhesion. |
Arthur MacKeith; Allison Culbert; John Treado; Adam Roddy; Craig Brodersen; Mark Shattuck; Corey O’Hern; |
| 942 | A Hybrid Model Framework for Studying Mechanics of Epithelial Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we present a simulation framework for modeling morphogenetic events in early embryogenesis from a mechanics perspective. |
Joseph Sutlive; Tony Zhang; Bing He; Zi Chen; |
| 943 | Epithelial Geometry Reveals How Positive Tension Feedback Drives Active Cell Intercalations During Tissue Convergence Extension: Theory Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a positive tension feedback loop, primed by initial tension anisotropy, that leads to spatially coordinated junction collapses and thus cell intercalations. |
Nikolas Claussen; Fridtjof Brauns; Matthew Lefebvre; Sebastian Streichan; Boris Shraiman; |
| 944 | Epithelial Geometry Reveals How Positive Tension Feedback Drives Active Cell Intercalations During Tissue Convergence Extension: Experiment Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In contrast, in a living tissue, internally stresses generated by molecular motors can drive active intercalations. Using gastrulation of drosophila embryos as a model system, imaged, segmented, and tracked in toto, we show how tension inference can be used to distinguish between these two processes purely based on the local geometry of the cell array. |
Fridtjof Brauns; Nikolas Claussen; Matthew Lefebvre; Sebastian Streichan; Boris Shraiman; |
| 945 | From Genes to Geometry: How A Visceral Organ Takes Form Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Using deep tissue light-sheet microscopy for whole-organ live imaging, we find a mechanical program folding the embryonic midgut of Drosophila: hox genes control the emergence of high-frequency calcium pulses, which trigger muscle contractions. |
Noah Mitchell; |
| 946 | Modeling Cell Shape Changes in The Zebrafish Embryo Using A 3D Vertex Model Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we focus on Kupffer’s vesicle (KV) in the zebrafish embryo as a model organ, as it undergoes programmed asymmetric cell shape changes to establish the left-right axis of the embryo. |
Raj Kumar Manna; Emma Retzlaff; Elizabeth Lawson-Keister; Michael Bates; Yiling Lan; Heidi Hehnly; Jeffrey Amack; M Lisa Manning; |
| 947 | 3D Cell Packing Dynamics in Converging and Extending Epithelial Sheets Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Here we study cell shape changes and rearrangements in two model tissues undergoing convergent extension flows: the mouse neural plate, a proliferating pseudostratified epithelium, and the fruit fly germband, a non-proliferating columnar epithelium. |
Sassan Ostvar; Erika Kusaka; Xun Wang; Alyssa Lesko; Ann Sutherland; Karen Kasza; |
| 948 | Activity and Topological Defects in 3D Morphogenesis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We now extend it to include the presence of a diffusive chemical agent, activity, and parameter dependence on topological defects in polarity. |
Richard Ho; Luiza Angheluta-Bauer; |
| 949 | A Mechanochemical Model Recapitulates Distinct Vertebrate Gastrulation Modes Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We derive a minimal theoretical framework that couples actomyosin activity to tissue flows, thus providing the basis for gastrulation dynamics. |
Mattia Serra; |
| 950 | Branching Morphogenesis of Sea Cucumber Ossicles in Multi-cellular Syncytial Confinement Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In holothurians, biomineralization occurs in the form of discrete ~100 um length scale structures called ossicles that diversify in shapes not only across species but even within an individual animal. Through live and fixed microscopy techniques, we establish that these structures grow from individual crystalline seeds inside a multi-cell syncytial complex with the biomineralized phase completely covered with a membrane-coated cytoplasmic sheath. |
Pranav Vyas; Charlotte Brannon; Laurent Formery; Christopher Lowe; Manu Prakash; |
| 951 | Recording Symmetry Breaking During Gastruloid Morphogenesis with Recombinase Circuits Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We study symmetry breaking in the gastruloid model of axial morphogenesis using genetic circuits recorders of signaling histories. |
Harold McNamara; Jared Toettcher; |
| 952 | Pushing The Envelope: Force Balance Between The Spindle and Nuclear Envelope During Fission Yeast Closed Mitosis Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We find differences in spindle mechanics between the two species, suggesting how features of spindle organization may evolve to match their mechanical constraints. |
Marcus Begley; Christian Pagán Medina; Parsa Zareiesfandabadi; Matthew Rapp; Abhimanyu Sharma; Mary Elting; |
| 953 | Modeling The Spongy Mesophyll in Plant Leaves in Three Dimensions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: In this work, we perform structural characterizations of mature mesophyll tissues using micro-CT scans from multiple species. |
Allison Culbert; Arthur MacKeith; Adam Roddy; Corey O’Hern; Mark Shattuck; |
| 954 | Sap Flow and Sugar Transport in A Pine Needle: How to Deal with An Adverse Environement Related Papers Related Patents Related Grants Related Venues Related Experts View Abstract: The survival of green plants depends on efficient use of photosynthesis in the leaves, where sunlight, water, and CO 2 are transformed to sugar – the raw material, which builds up … |
Tomas Bohr; |
| 955 | Marchantia Polymorpha Gemmae Interact As Capillary Multipoles on Fluid Interfaces Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: Gemmae have long been assumed to be passive agents, but their capillary interactions while attached to the air-water interface suggest they play a much more active role in liverwort reproduction. To investigate this, we directly measure capillary interactions of gemmae on both flat and curved fluid interfaces using brightfield and phase contrast microscopy as well as optical profilometry, and find that gemmae adsorbed to the water surface interact as capillary multipoles with a dominant quadrupolar character. |
Katharine Jensen; Katie Nath; Caroline Tally; Alex Kim; Justyn Friedler; Anneliese Silveyra; James Fortin; |
| 956 | Biogirders: How The Leaves of The Giant Amazonian Waterlily Occupy A Large Surface Area at An Economical Material Cost Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: The giant Amazonian waterlily (genus Victoria) produces the largest floating leaves of all plants. We studied how the structural form of the vasculature system underpins gigantism in these extraordinary leaves. |
Finn Box; Alexander Erlich; Jian Guan; Chris Thorogood; |
| 957 | Dehydration-induced Corrugated Folding in Shape-morphing Leaves Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: For example, the leaves of Rhapis excelsa fold into a corrugated structure with the loss of water. To understand this interesting phenomenon, we explore the mechanical basis and the cellular mechanism of the corrugated leaf folding. |
Kexin Guo; Mingchao Liu; K. Jimmy Hsia; |
| 958 | Drought-induced Curvature Changes in Leaf Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: There were several non-destructive approaches suggested to utilize the relationship between water stress and leaf vibration frequency, but the tendency of the frequency due to the dryness was controversial. Here, we proposed a new perspective of leaf surface curvature effect to vibration frequency in order to understand this discrepancy. |
Sunghwan Jung; Jisoo Yuk; Joseph Lee; Crystal Fowler; |
| 959 | Rearrangement of Primary Cell Wall Polymers During Mechanical Stretch Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We have developed a method to stretch onion epidermal wall to various levels of longitudinal strain to examine both reversible and irreversible structural change of wall polymer architecture. |
Joshua Del Mundo; Jingyi Yu; Guillaume Freychet; Mikhail Zhernenkov; Eric Schaible; Chenhui Zhu; Daniel Cosgrove; Esther Gomez; Enrique Gomez; |
| 960 | Frequency Response Analysis of Gravitropism in Rice Roots Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present a control model to characterize root sensory response and describe how plant growth trajectory is impacted by periodic stimuli using frequency response techniques such as Bode analysis. |
Madison Hales; Aradhya Rajanala; Christopher Pierce; Ram Avinery; Mingyuan Zhu; Isaiah Taylor; Philip Benfey; Daniel Goldman; |
| 961 | Plant Root Inspired Protrusions Enhance Intruder Anchoring Force in Dry Granular Media Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To discover the principles for biological and engineering anchoring resistance, we study forces experienced by rigid cylinders (8.3mm diameter) incorporating rigid protrusions (3mm by 5mm) as it is pulled from a model noncohesive soft substrate, dry granular media (1mm diameter particles). |
Deniz Kerimoglu; Aradhya Rajanala; Nicholas Naclerio; Daniel Goldman; Elliot Hawkes; Alexa Mathis; |
| 962 | Principles in Plant Roots Enable Robotic Self-anchoring Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: And 4), radial expansion increases soil loading and anchoring force. In our study, we have developed a soft, pneumatic device capable of all four of these plant-inspired behaviors. |
Nicholas Naclerio; Deniz Kerimoglu; Sean Chu; Daniel Goldman; Elliot Hawkes; |
| 963 | Emergent Behaviors of Heterogeneous Cell Growth Patterns in Plant Root Growth Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: To investigate the effects of cell growth on circumnutation, we developed a multiparticle Discrete Element Method (DEM) simulation in which each "particle" represents a single root cell. |
Aradhya Rajanala; Christopher Pierce; Deniz Kerimoglu; Mingyuan Zhu; Madison Hales; Isaiah Taylor; Philip Benfey; Daniel Goldman; |
| 964 | Experiments and Simulations of Turing Patterns in Vegetation Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We present controlled experiments of Chia seeds growing in half-meter square domains growing in four different substrates with different diffusion coefficients, amounts of daily irrigation and evaporation that display evolving transitions that include Turing patters ranging from spots, labyrinth, and mazes to continuum. |
Flavio Fenton; Brendan Daquino; Mikael Toye; |
| 965 | The Network Architecture of Plant-pathogen Interactions Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We propose a simple model to study how networks of interacting molecules can be used to build an immune sensor. |
Benjamin Weiner; |
| 966 | Improving The Water Solubility of Hydrophobic Carotenoids Through Association with Phytoglycogen Related Papers Related Patents Related Grants Related Venues Related Experts View Highlight: We developed a method to produce lyophilized powders of ASX associated with PG (ASX-PG) that can be easily redispersed in water, increasing the solubility of ASX by a factor of 10 9. |
Nicholas van Heijst; John Dutcher; |