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Encounter rates between bacteria and small sinking particlesAug 22 2019Bacteria in aquatic environments often interact with particulate matter. A key example is bacterial degradation of marine snow responsible for carbon export from the upper ocean in the biological pump. The ecological interaction between bacteria and sinking ... More
Evolution of specialization in dynamic fluidsAug 21 2019Previously we found mechanical factors involving diffusion and fluid shear promote evolution of social behavior in microbial populations (Uppal and Vural 2018). Here, we extend this model to study the evolution of specialization using realistic physical ... More
Non-affinity and fluid-coupled viscoelastic plateau for immersed fiber networksAug 21 2019We employ a matrix-based solver for the linear rheology of fluid-immersed disordered spring networks to reveal four distinct dynamic response regimes. One regime - completely absent in the known vacuum response - exhibits coupled fluid flow and network ... More
How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kineticsAug 20 2019Dimeric molecular motors walk on polar tracks by binding and hydrolyzing one ATP per step. Despite tremendous progress, the waiting state for ATP binding in the well-studied kinesin that walks on microtubule (MT), remains controversial. One experiment ... More
Thermodynamics of switching in a multistable systemAug 20 2019Multistable nonequilibrium systems are abundant outcomes of nonlinear dynamics with feedback but still relatively little is known about what determines the stability of the steady states and their switching rates in terms of entropy and entropy production. ... More
Sampling protein-ligand binding pathways to recover crystallographic binding poses using interactive molecular dynamics in virtual realityAug 20 2019Using molecular dynamics (MD) to simulate drug binding & unbinding is a challenge. Because it requires sampling rugged energy landscapes that separate bound and unbound states, it has a high cost and consumes significant computational resources. Here, ... More
Pattern localization to a domain edgeAug 20 2019The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how patterns can emerge from a homogenous steady state when two reactive components have different ... More
Spectral theory for the stability of dynamical systems on large oriented locally tree-like graphsAug 19 2019We develop a mathematical theory for the linear stability of stationary states in large dynamical systems modelled by a set of randomly coupled differential equations on a locally tree-like network. Our approach provides analytical expressions for the ... More
A Modified Ising Model of Barabási-Albert Network with Gene-type SpinsAug 19 2019The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in quasi-steady ... More
The Weighted Mean Curvature Derivative of a Space-Filling DiagramAug 19 2019Representing an atom by a solid sphere in $3$-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. ... More
The Weighted Gaussian Curvature Derivative of a Space-Filling DiagramAug 19 2019The morphometric approach [HRC13,RHK06] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the ... More
Network constraints in scale free dynamical systemsAug 19 2019Scale free dynamics are observed in a variety of physical and biological systems. These include neural activity in which evidence for scale freeness has been reported using a range of imaging modalities. Here, we derive the ways in which connections within ... More
Epiphoresis: a nonequilibrium mechanism for fast search on DNAAug 19 2019Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "epiphoresis", the dynamics of DNA-binding proteins up ... More
Applying the Method of Critical Fluctuations on Human ElectrocardiogramsAug 18 2019In this work we apply the Method of Critical Fluctuations (MCF)on human Electrocardiogram (ECG) time-series. The method is able to reveal critical characteristics, in terms of physical behavior, in experimentally recorded signals. Using the concept of ... More
Brownian motion and beyond: first-passage, power spectrum, non-Gaussianity, and anomalous diffusionAug 17 2019Brownian motion is a ubiquitous physical phenomenon across the sciences. After its discovery by Brown and intensive study since the first half of the 20th century, many different aspects of Brownian motion and stochastic processes in general have been ... More
Controlling distant contacts to reduce disease spreading on disordered complex networksAug 16 2019Disorder is a characteristic of real social networks generated by heterogeneity in person-to-person interactions. This property affects the way a disease spreads through a population, reaches a tipping point in the fraction of infected individuals, and ... More
Topotaxis of active Brownian particlesAug 16 2019Recent experimental studies have demonstrated that cellular motion can be directed by topographical gradients, such as those resulting from spatial variations in the features of a micropatterned substrate. This phenomenon, known as topotaxis, is especially ... More
Generalized group-based epidemic model for spreading processes on networks: GgroupEMAug 16 2019We develop a generalized group-based epidemic model (GgroupEM) framework for any compartmental epidemic model (for example; susceptible-infected-susceptible, susceptible-infected-recovered, susceptible-exposed-infected-recovered). Here, a group consists ... More
Evolution of cooperation in networks: well-connected cooperators can enhance cooperation but are counteracted by Trojan horsesAug 16 2019Cooperative behaviour is widespread in nature, but explaining how cooperation evolves constitutes a major scientific challenge. Simulation models has shown that social network structure plays a key role in rendering cooperation evolutionarily stable. ... More
$θ$-curves in proteinsAug 16 2019Apart from the knots formed by the main-chain, the proteins can form numerous topological structures, when included the covalent and ion-mediated interactions. In this work, we define the protein non-trivial $\theta$-curves and identify 7 different topologies ... More
Organization of fast and slow chromatin revealed by single-nucleosome dynamicsAug 16 2019Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal nature of ... More
Algebraic Coarse-Graining of Biochemical Reaction NetworksAug 15 2019Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive coarse-graining ... More
Cooperative metabolic resource allocation in spatially-structured systemsAug 14 2019This paper extends a framework for dynamic metabolic resource allocation based on the maximum entropy principle to spatiotemporal models of metabolism with cooperation. Much like the maximum entropy principle encapsulates `bet-hedging' behaviour displayed ... More
Structure and efficiency in bacterial photosynthetic light-harvestingAug 14 2019Photosynthetic organisms use networks of chromophores to absorb sunlight and deliver the energy to reaction centres, where charge separation triggers a cascade of chemical steps to store the energy. We present a detailed model of the light-harvesting ... More
Cardiac Mechano-Electrical Dynamical InstabilityAug 14 2019In a computational study we reveal a novel dynamical instability of excitation waves in the heartmuscle. The instability manifests itself as gradual local increase in the duration of the actionpotential which causes formation and hypermeandering of spiral ... More
Thermodynamics of the S2-to-S3 State Transition of the Oxygen-Evolving Complex of Photosystem IIAug 14 2019The room temperature pump-probe X-ray free electron laser (XFEL) measurements used for serial femtosecond crystallography provide remarkable information about the structures of the catalytic (S-state) intermediates of the oxygen-evolution reaction of ... More
Migration and accumulation of bacteria with chemotaxis and chemokinesisAug 14 2019Bacteria can chemotactically migrate up attractant gradients by controlling run-and-tumble motility patterns.In addition to this well-known chemotactic behaviour, several soil and marine bacterial species perform chemokinesis: they adjust their swimming ... More
Detachment of fluid membrane from substrate and vesiculationAug 14 2019The detachment dynamics of a fluid membrane with an isotropic spontaneous curvature from a flat substrate are studied by using meshless membrane simulations. The membrane is detached from an open edge leading to vesicle formation. With strong adhesion, ... More
Architecture and evolution of semantic networks in mathematics textsAug 14 2019Knowledge is a network of interconnected concepts. Yet, precisely how the topological structure of knowledge constrains its acquisition remains unknown, hampering the development of learning enhancement strategies. Here we study the topological structure ... More
Random walk on a lattice in the presence of obstacles: The short-time transient regime, anomalous diffusion and crowdingAug 14 2019The diffusion of a particle in a crowded environment typically proceeds through three regimes: for very short times the particle diffuses freely until it collides with an obstacle for the first time, while for very long times diffusion the motion is Fickian ... More
Multilevel and multifidelity uncertainty quantification for cardiovascular hemodynamicsAug 13 2019Standard approaches for uncertainty quantification (UQ) in cardiovascular modeling pose challenges due to the large number of uncertain inputs and the significant computational cost of realistic 3D simulations. We propose an efficient UQ framework utilizing ... More
Semigroup Models for Biochemical Reaction NetworksAug 13 2019The CRS (chemical reaction system) formalism by Hordijk and Steel is a versatile method to model self-sustaining biochemical reaction networks. Its distinguishing feature is the explicit assignment of catalytic function to chemicals that are part of the ... More
A simple model for pattern formation in clonal-growth plantsAug 13 2019Clonal plants reproduce by generating new plants from a piece of an existing one without the need of producing seeds or spores. They form a whole family of plants, including terrestrial and marine species. However, the specific features of clonal growth ... More
Beyond local gradient-sensing: memory effects in bacterial chemotactic navigationAug 12 2019The response of microbes to external signals is mediated by biochemical networks with intrinsic timescales. These timescales give rise to a cellular memory that plays a pivotal role in controlling cellular behaviour. Here we study the role of cellular ... More
Enabling Simulation of High-Dimensional Micro-Macro Biophysical Models through Hybrid CPU and Multi-GPU ParallelismAug 12 2019Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional configuration space at ... More
Deep learning brain conductivity mapping using a patch-based 3D U-netAug 12 2019Purpose: To investigate deep learning electrical properties tomography (EPT) for application on different simulated and in-vivo datasets including pathologies for obtaining quantitative brain conductivity maps. Methods: 3D patch-based convolutional neural ... More
Loops versus lines and the compression stiffening of cellsAug 10 2019Both animal and plant tissue exhibit a nonlinear rheological phenomenon known as compression stiffening, or an increase in moduli with increasing uniaxial compressive strain. Does such a phenomenon exist in single cells, which are the building blocks ... More
Dynamic Force Measurements on Swimming Chlamydomonas Cells using Micropipette Force SensorsAug 09 2019Flagella and cilia are cellular appendages that inherit essential functions of microbial life including sensing and navigating the environment. In order to propel a swimming microorganism they displace the surrounding fluid by means of periodic motions, ... More
Target search on DNA by interacting molecules: First-passage approachAug 09 2019Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular complexes. While the ... More
Extreme-Value Statistics of Molecular MotorsAug 09 2019We derive exact expressions for the finite-time statistics of extrema (maximum and minimum) of the spatial displacement and the fluctuating entropy flow of biased random walks modelling the dynamics of molecular motors at the single-molecule level. Our ... More
Can endogenous fluctuations persist in high-diversity ecosystems?Aug 09 2019When can complex ecological interactions drive an entire ecosystem into a persistent non-equilibrium state, where species abundances keep fluctuating without going to extinction? We show that high-diversity spatially-extended systems, in which conditions ... More
The Heat of Nervous Conduction: A Thermodynamic FrameworkAug 08 2019Early recordings of nervous conduction revealed a notable thermal signature associated with the electrical signal. The observed production and subsequent absorption of heat arise from physicochemical processes that occur at the cell membrane level during ... More
Preferences for efficiency, rather than preferences for morality, drive cooperation in the one-shot Stag-Hunt GameAug 08 2019Recent work highlights that cooperation in the one-shot Prisoner's dilemma (PD) is primarily driven by moral preferences for doing the right thing, rather than social preferences for equity or efficiency. By contrast, little is known on what motivates ... More
Population collapse in Elite-dominated societies: A differential equations model without differential equationsAug 07 2019The HANDY model of Motesharrei, Rivas, and Kalnay examines interactions with the environment by human populations, both between poor and rich people, i.e., "Commoners" and "Elites". The Elites control the society's wealth and consume it at a higher rate ... More
Environmental Disorder Regulation of Invasion and Genetic LossAug 07 2019Many physical and natural systems, including the population of species, evolve in habitats with spatial stochastic variations of the individuals' motility. We study here the effect of those fluctuations on invasion and genetic loss. A Langevin equation ... More
Predicted disease compositions of human gliomas estimated from multiparametric MRI can predict endothelial proliferation, tumor grade, and overall survivalAug 06 2019Background and Purpose: Biopsy is the main determinants of glioma clinical management, but require invasive sampling that fail to detect relevant features because of tumor heterogeneity. The purpose of this study was to evaluate the accuracy of a voxel-wise, ... More
Water-assisted electronic transport in graphene nanogaps for DNA sequencingAug 06 2019Innovative methodologies for reliably and inexpensively sequencing DNA can lead to a new era of personalized medicine. In this work, we performed a theoretical investigation of a nanogap-based all electronic DNA sequencing device. To do so, we used a ... More
Quantum Mechanics of Proteins in Explicit Water: The Role of Plasmon-Like Solute-Solvent InteractionsAug 06 2019Quantum-mechanical van der Waals dispersion interactions play an essential role for both intra-protein and protein-water interactions $-$ the two main driving forces for the structure and dynamics of proteins in aqueous solution. Typically, these interactions ... More
Streaming Potential in Bio-mimetic Microvessels Mediated by Capillary GlycocalyxAug 05 2019Implantable medical devices and biosensors are pivotal in revolutionizing the field of medical technology by opening new dimensions in the field of disease detection and cure. These devices need to harness a biocompatible and physiologically sustainable ... More
A trial for theoretical prediction of microalgae growth for parallel flowAug 05 2019Many models established for solving the problem of the prediction of microalgae growth. However, the models are semi-empirical or considerable fitting coefficients exist in the theoretical model. Therefore, the prediction ability of the model is reduced ... More
Identify the stiffness of DNA via deep learningAug 04 2019DNA detection is of great significance in the point-of-care diagnostics. The stiffness of DNA, varying with its sequence and mechanochemical environment, could be a potential marker for DNA identification. The steric configurations of DNA fragments with ... More
Cross-validation tests for cryo-EM maps using an independent particle setAug 02 2019Cryo-electron microscopy is a revolutionary technique that can provide 3D density maps at near-atomic resolution. However, map validation is still an open issue in the field. Despite several efforts from the community, it is possible to overfit the reconstructions ... More
Could short-lasting non-specific immunity explain seasonal spacing of epidemic diseases?Aug 02 2019Common respiratory viruses cause seasonal epidemics in sequential patterns. The underlying mechanisms for this pattern have been debated for some time. For influenza, contenders include temperature, humidity, and vitamin D levels. While such seasonal ... More
Interplay between surface and bending energy helps membrane protrusion formationAug 02 2019We consider a one-dimensional elastic membrane, which is pushed by growing filaments. The filaments tend to grow by creating local protrusions in the membrane and this process has surface energy and bending energy costs. Although it is expected that with ... More
Fractional Order Models of Arterial Windkessel as an Alternative in the Analysis of the Left Ventricular AfterloadAug 01 2019In this paper, a new fractional order generalization of the classical Windkessel arterial model is developed to describe the aortic input impedance as an assessment of the left ventricular after-load. The proposed models embeds fractional-order capacitor ... More
Modeling Tumor Angiogenesis with Cellular AutomataAug 01 2019Angiogenesis is the formation of new blood vessels from the existing vessels. During tumor angiogenesis, tumor cells secret a number of chemical substrates called tumor angiogenic factors (TAFs). These factors diffuse through the extracellular matrix ... More
Correlation Tensor Magnetic Resonance ImagingJul 31 2019Diffusion Kurtosis MRI (DKI) quantifies the degree of non-Gaussian water diffusion -a sensitive biomarker for microstructure in health and disease. However, DKI is not specific to any microstructural property per se since kurtosis might emerge from different ... More
Chiral active matter: microscopic `torque dipoles' have more than one hydrodynamic descriptionJul 31 2019Many biological systems, such as bacterial suspensions and actomyosin networks, form polar liquid crystals. These systems are `active' or far-from-equilibrium, due to local forcing of the solvent by the constituent particles. In many cases the source ... More
From Logistic Growth to Exponential Growth in a Population Dynamical ModelJul 31 2019Dynamics among central sources (hubs) providing a resource and large number of components enjoying and contributing to this resource describes many real life situations. Modeling, controlling, and balancing this dynamics is a general problem that arises ... More
Binary pusher-puller mixtures of active microswimmers and their collective behaviorJul 31 2019Microswimmers are active particles of microscopic size that self-propel by setting the surrounding fluid into motion. According to the kind of far-field fluid flow that they induce, they are classified into pushers and pullers. Many studies have explored ... More
Proteins: the physics of amorphous evolving matterJul 31 2019Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function performed by the ... More
Magnetization Transfer in Magnetic Resonance FingerprintingJul 30 2019Purpose: To study the effects of magnetization transfer (MT, in which a semisolid spin pool interacts with the free pool), in the context of magnetic resonance fingerprinting (MRF). Methods: Simulations and phantom experiments were performed to study ... More
Investigation of the Peeling and Pull-off Behavior of Adhesive Elastic Fibers via a Novel Computational Beam Interaction ModelJul 30 2019Jul 31 2019This article studies the fundamental problem of separating two adhesive elastic fibers based on numerical simulation employing a recently developed finite element model for molecular interactions between curved slender fibers. Specifically, it covers ... More
Investigation of the Peeling and Pull-off Behavior of Adhesive Elastic Fibers via a Novel Computational Beam Interaction ModelJul 30 2019This article studies the fundamental problem of separating two adhesive elastic fibers based on numerical simulation employing a recently developed finite element model for molecular interactions between curved slender fibers. Specifically, it covers ... More
Non-Markovian barrier crossing with two-time-scale memory is dominated by the faster memory componentJul 30 2019We investigate non-Markovian barrier-crossing kinetics of a massive particle in one dimension in the presence of a memory function that is the sum of two exponentials with different memory times $\tau_1$ and $\tau_2$. Our Langevin simulations for the ... More
Investigating the Role of Non-Covalent Interactions in Conformation and Assembly of Triazine-Based Sequence-Defined PolymersJul 30 2019Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality by having various ... More
Probing axonal swelling with time dependent diffusion MRIJul 29 2019Development of therapies for neurological disorders depends on our ability to non-invasively diagnose and monitor the progression of underlying pathologies at the cellular level. Physics and physiology limit the resolution of human MRI to millimeters, ... More
Development of a Fragment-Based Machine Learning Algorithm for Designing Hybrid Drugs Optimized for Permeating Gram-Negative BacteriaJul 29 2019Gram-negative bacteria are a serious health concern due to the strong multidrug resistance that they display, partly due to the presence of a permeability barrier comprising two membranes with active efflux. New approaches are urgently needed to design ... More
Uniform intensity in multifocal microscopy using a spatial light modulatorJul 29 2019Multifocal microscopy (MFM) offers high-speed three-dimensional imaging through the simultaneous image capture from multiple focal planes. Conventional MFM systems use a fabricated grating in the emission path for a single emission wavelength band and ... More
The Effect of Social Information in the Dictator Game with a Taking OptionJul 29 2019We experimentally study how redistribution choices are affected by positive and negative information regarding the behaviour of a previous participant in a dictator game with a taking option. We use the strategy method to identify behavioural "types", ... More
Trait-space patterning and the role of feedback in antigen-immunity coevolutionJul 29 2019Coevolutionary arms races form between interacting populations that constitute each other's environment and respond to mutual changes. This inherently far-from-equilibrium process finds striking manifestations in the adaptive immune system, where highly ... More
The physics of Erythrocyte Sedimentation RateJul 28 2019An erythrocytes sedimentation rate (ESR) measures how fast a blood sample sediments along a test tube in one hour in a clinical laboratory. Since elevated level of ESR is associated with inflammatory diseases, ESR is one of the routine hematology test ... More
Emergence of cooperative bistability and robustness of gene regulatory networksJul 28 2019Gene regulatory networks (GRNs) are complex systems in which many genes mutually regulate their expressions for changing the cell state adaptively to the environmental conditions. Besides the functions, the GRNs utilized by living systems possess several ... More
Deep learning-based prediction of kinetic parameters from myocardial perfusion MRIJul 27 2019The quantification of myocardial perfusion MRI has the potential to provide a fast, automated and user-independent assessment of myocardial ischaemia. However, due to the relatively high noise level and low temporal resolution of the acquired data and ... More
Translational and Rotational Dynamics of Colloidal Particles Interacting through Reacting LinkersJul 26 2019Much work has studied effective interactions between micron-sized particles carrying linkers forming reversible, inter-particle linkages. These studies allowed understanding the equilibrium properties of colloids interacting through ligand-receptor interactions. ... More
Flocking in complex environments -- attention trade-offs in collective information processingJul 26 2019The ability of biological and artificial collectives to outperform solitary individuals in a wide variety of tasks depends crucially on the efficient processing of social and environmental information at the level of the collective. Here, we model collective ... More
Numerical modelling of phase separation on dynamic surfacesJul 25 2019The paper presents a model of lateral phase separation in a two component material surface. The resulting fourth order nonlinear PDE can be seen as a Cahn-Hilliard equation posed on a time-dependent surface. Only elementary tangential calculus and the ... More
Predominance of the weakest species in Lotka-Volterra and May-Leonard implementations of the rock-paper-scissors modelJul 25 2019We revisit the problem of the predominance of the 'weakest' species in the context of Lotka-Volterra and May-Leonard implementations of a spatial stochastic rock-paper-scissors model in which one of the species has its predation probability reduced by ... More
Optical study of laser biospeckle activity in leaves of Jatropha curcas L. A noninvasive analysis of foliar endophyte colonizationJul 25 2019Currently, the detection of endophytic fungi is determined mostly by invasive methods, including direct isolation of fungal organismsfrom plant tissue in growth media, molecular detection of endophyticfungi DNA from plant material by PCR, or evaluation ... More
Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics SimulationsJul 25 2019We here report on non-equilibrium targeted Molecular Dynamics simulations as tool for the estimation of protein-ligand unbinding kinetics. With this method, we furthermore investigate the molecular basis determining unbinding rates, correlating simulations ... More
Richardson diffusion in neuronsJul 25 2019The dynamics of an initial wave packed affected by random noise is considered in the framework of a comb model. The model is relevant to a diffusion problem in neurons where the transport of ions can be accelerated by an external random field due to synapse ... More
The effects of coating culture dishes with collagen on fibroblast cell shape and swirling pattern formationJul 25 2019Motile human-skin fibroblasts form macroscopic swirling patterns when grown to confluence on a culture dish. In this paper, we investigate the effect of coating the culture-dish surface with collagen on the resulting pattern, using human-skin fibroblast ... More
Persistent exclusion processes: inertia, drift, mixing and correlationJul 25 2019In many biological systems, motile agents exhibit random motion with short-term directional persistence, together with crowding effects arising from spatial exclusion. We formulate and study a class of lattice-based models for multiple walkers with motion ... More
Cell Motion Alignment as Polarity Memory EffectJul 25 2019The clarification of the motion alignment mechanism in collective cell migration is an important issue commonly in physics and biology. In analogy with the self-propelled disk, the polarity memory effect of eukaryotic cell is a fundamental candidate for ... More
A nonconvex optimization approach to IMRT planning with dose-volume constraintsJul 24 2019Fluence map optimization for intensity-modulated radiation therapy planning can be formulated as a large-scale inverse problem with multi-objectives on the tumors and organs-at-risk. Unfortunately, clinically relevant dose-volume constraints are nonconvex, ... More
Centering and symmetry breaking in confined contracting actomyosin networksJul 24 2019Centering and decentering of cellular components is essential for internal organization of cells and their ability to perform basic cellular functions such as division and motility. How cells achieve proper localization of their components is still not ... More
Chromatin state switching in a polymer model with mark-conformation couplingJul 24 2019We investigate the phase transition properties of the polymer-Potts model, a chain composed of monomers with magnetic degrees of freedom, with the motivation to study the conformation and mark switching dynamics of chromatin. By the mean-field approximation, ... More
Stay hydrated: Basolateral fluids shaping tissuesJul 24 2019During development, embryos perform a mesmerizing choreography, which is crucial for the correct shaping, positioning and function of all organs. The cellular properties powering animal morphogenesis have been the focus of much attention. On the other ... More
Mass-conservation sets excitable pulse collisions to be spatiotemporal organizing centersJul 24 2019Outcomes of propagating pulse collisions are of fundamental importance in many fields, ranging from physiology to industrial devices. Pulses are traditionally classified as solitons if upon collision they behave as particles, or excitable-pulses if they ... More
Sequence design-based control of DNA droplets formed from phase separation of DNA nanostructuresJul 24 2019DNA has the potential to realize a controllable liquid-liquid phase separation (LLPS) system, because the design of its base sequences results in programmable interactions. Here, we have developed a novel DNA-based LLPS system which enables us to create ... More
Complete inclusion of bioactive molecules and particles in polydime-thylsiloxane: a straightforward process under mild conditionsJul 23 2019By applying a slow curing process, we show that biomolecules can be incorporated via a simple process as liquid stable phases inside a polydimethylsiloxane (PDMS) matrix. The process is carried out under mild conditions with regards to temperature, pH ... More
An equilibrium model for ribosome competitionJul 22 2019The amount of ribosomes in a cell is considered as limiting, and gene expression is thus largely determined by their cellular concentration. In this work we develop a toy-model to study the trade-off between the ribosomal supply and the demand of the ... More
Extremophiles: a special or general case in the search for extra-terrestrial life?Jul 21 2019Since time immemorial, life has been viewed as being fragile, yet over the past few decades it has been found that many extreme environments are inhabited by organisms known as extremophiles.Knowledge of their emergence, adaptability, and limitations ... More
Extremophiles: a special or general case in the search for extra-terrestrial life?Jul 21 2019Aug 08 2019Since time immemorial, life has been viewed as being fragile, yet over the past few decades it has been found that many extreme environments are inhabited by organisms known as extremophiles.Knowledge of their emergence, adaptability, and limitations ... More
Current Distribution on Capacitive Electrode-Electrolyte InterfacesJul 21 2019The distribution of electric current on an electrode surface in electrolyte varies with time due to charge accumulation at a capacitive interface, as well as due to electrode kinetics and concentration polarization in the medium. Initially, the potential ... More
Current Distribution on Capacitive Electrode-Electrolyte InterfacesJul 21 2019Aug 11 2019The distribution of electric current on an electrode surface in electrolyte varies with time due to charge accumulation at a capacitive interface, as well as due to electrode kinetics and concentration polarization in the medium. Initially, the potential ... More
Enhanced Diffusion and Chemotaxis of EnzymesJul 21 2019Jul 23 2019Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, ... More
Enhanced Diffusion and Chemotaxis of EnzymesJul 21 2019Jul 27 2019Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, ... More
Spatial patterns emerging from a stochastic process near criticalityJul 20 2019There is mounting empirical evidence that many communities of living organisms display key features which closely resemble those of physical systems at criticality. We here introduce a minimal model framework for the dynamics of a community of individuals ... More
Learning spatiotemporal signals using a recurrent spiking network that discretizes timeJul 20 2019Learning to produce spatiotemporal sequences is a common task the brain has to solve. While many sequential behaviours differ superficially, the underlying organization of the computation might be similar. The way the brain learns these tasks remains ... More