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Yitzhak Rabin

Publications and source records attributed to Yitzhak Rabin.

At least 19 recordsLinked to original sources

Shape Transitions in Network Model of Active Elastic Shells

Morphogenesis involves the transformation of initially simple shapes, such as multicellular spheroids, into more complex $3D$ shapes. These shape changes are governed by mechanical forces including molecular motor-generated forces as well as hydrostatic fluid pressure, both of which are actively regulated in living matter through mechano-chemical feedback. Inspired by autonomous, biophysical shape change, such as occurring in the model organism hydra, we introduce a minimal, active, elastic model featuring a network of springs in a globe-like spherical shell geometry. In this model there is coupling between activity and the shape of the shell: if the local curvature of a filament represented by a spring falls below a critical value, its elastic constant is actively changed. This results in deformation of the springs that changes the shape of the shell. By combining excitation of springs and pressure regulation, we show that the shell undergoes a transition from spheroidal to either elongated ellipsoidal or a different spheroidal shape, depending on pressure. There exists a critical pressure at which there is an abrupt change from ellipsoids to spheroids, showing that pressure is potentially a sensitive switch for material shape. More complex shapes, involving loss of cylindrical symmetry, can arise when springs are excited both above (spring constants increase) and below (spring constants decrease) the curvature threshold. We thus offer biologically inspired design principles for autonomous shape transitions in active elastic shells.

cond-mat.soft

Network Model of Active Fluctuations of Thin Elastic Shells Swollen by Hydrostatic Pressure

Many organisms have an elastic skeleton that consists of a closed shell of epithelial cells that is filled with fluid, and can actively regulate both elastic forces in the shell and hydrostatic pressure inside it. In this work we introduce a simple network model of such pressure-stabilized active elastic shells in which cross-links are represented by material points connected by non-linear springs of some given equilibrium lengths and spring constants. We mimic active contractile forces in the system by changing the parameters of randomly chosen springs and use computer simulations to study the resulting local and global deformation dynamics of the network. We elucidate the statistical properties of these deformations by computing the corresponding distributions and correlation functions. We show that pressure-induced stretching of the network introduces coupling between its local and global behavior: while the network opposes the contraction of each excited spring and affects the amplitude and relaxation time of its deformation, random local excitations give rise to contraction of the network and to fluctuations of its surface area.

cond-mat.soft

Reentrant Transitions in a Mixture of Small and Big Particles Interacting via Soft Repulsive Potential

We report the first observation of temperature-controlled reentrant transition in simulations of mixtures of small and big particles interacting via soft repulsive potential in 2D. As temperature increases, the system passes from a fluid mixture, to a crystal of big particles in a fluid of small particles and back to a fluid mixture. Solidification is driven by entropy gain of small particles which overcomes the free energy cost of confining big ones. Melting results from enhanced interpenetration of particles at high temperature which reduces the entropic forces that stabilize the crystal.

cond-mat.soft

Non-Equilibrium Interaction Between Catalytic Colloids: Boundary Conditions and Penetration Depth

Spherical colloids that catalyze the interconversion reaction $A \leftrightharpoons B$ between solute molecules $A$ and $B$ whose concentration at infinity is maintained away from equilibrium effectively interact due to the non-uniform fields of solute concentrations. We show that this long range $1/r$ interaction is suppressed via a mechanism that is superficially reminiscent but qualitatively very different from electrostatic screening: catalytic activity drives the concentrations of solute molecules towards their equilibrium values and reduces the chemical imbalance that drives the interaction between the colloids. The imposed non-equilibrium boundary conditions give rise to a variety of geometry-dependent scenarios; while long-range interactions are suppressed (except for a finite penetration depth) in the bulk of the colloid solution in 3D, they can persist in quasi-2D geometry in which the colloids but not the solutes are confined to a surface, resulting in the formation of clusters or Wigner crystals, depending on the sign of the interaction between colloids.

cond-mat.soft

Sequence Effects on Internal Structure of Droplets of Associative Polymers

We used Langevin dynamics simulations of short associative polymers with two stickers placed symmetrically along their contour to study the effect of the primary sequence of these polymers on their organization inside condensed droplets. We observed that the shape, size and number of sticker clusters inside the condensed droplet change from a single cylindrical fiber to many compact clusters, as one varies the location of stickers along the chain contour. Aging due to conversion of intramoleclular to intermolecular associations was observed in droplets of telechelic polymers, but not for other sequences of associating polymers. The relevance of our results to condensates of intrinsically disordered proteins is discussed.

cond-mat.soft

Systems with size and energy polydispersity: from glasses to mosaic crystals

We use Langevin dynamics simulations to study dense 2d systems of particles with both size and energy polydispersity. We compare two types of bidisperse systems which differ in the correlation between particle size and interaction parameters: in one system big particles have high interaction parameters and small particles have low interaction parameters, while in the other system the situation is reversed. We study the different phases of the two systems and compare them to those of a system with size but not energy bidispersity. We show that, depending on the strength of interaction between big and small particles, cooling to low temperatures yields either homogeneous glasses or mosaic crystals.

cond-mat.soft

Aging of Thermoreversible Gel of Associating Polymers

We performed Langevin dynamics simulations of amphiphilic polymers that contain strongly associating stickers connected by long soluble chain segments. We explored the aging of a thermoreversible gel which is crosslinked by aggregates (clusters) of the stickers and observed a dramatic increase of their lifetime with aging. We find that the observed aging is the result of structural reorganization of the network: the number of crosslinks decreases with time as small clusters disintegrate and their stickers are reabsorbed by large clusters that grow and become more stable by forming additional intramolecular associations between their stickers.

cond-mat.soft

Assembly along lines in boundary-driven dynamical system

We introduce a simple dynamical rule in which each particle locates a particle that is farthest from it and moves towards it. Repeated application of this algorithm results in the formation of unusual dynamical patterns: during the process of assembly the system self-organizes into slices of low particle density separated by lines of increasingly high particle density along which most particles move. As the process proceeds, pairs of lines meet and merge with each other until a single line remains and particles move along it towards the zone of assembly. We show that this pattern is governed by particles (attractors) situated on the instantaneous outer boundary of the system and that both in two and in three dimensions the lines are formed by zigzag motion of a particle towards a pair of nearly equidistant attractors. This novel line-dominated assembly is very different from the local assembly in which particles that move towards their nearest neighbors produce point-like clusters that coalesce into new point-like clusters, etc.

math.DS

Chemically Active Nanodroplets in a Multi-Component Fluid

We introduce a model of chemically active particles of a multi-component fluid that can change their interactions with other particles depending on their state. Since such switching of interactions can only be maintained by the input of chemical energy, the system is inherently non-equilibrium. Focusing on a scenario where the equilibrium interactions would lead to condensation into a liquid droplet, and despite the relative simplicity of the interaction rules, these systems display a wealth of interesting and novel behaviors such as oscillations of droplet size and molecular sorting, and raise the possibility of spatio-temporal control of chemical reactions on the nanoscale

cond-mat.soft

Effect of liquid state organization on microstructure and strength of model multicomponent solids

When a multicomponent liquid composed of particles with random interactions is slowly cooled below the freezing temperature, the fluid reorganises in order to increase (decrease) the number of strong (weak) attractive interactions and solidifies into a microphase-separated structure composed of domains of strongly and of weakly interacting particles. Using Langevin dynamics simulations of a model system we find that the limiting tensile strength of such solids can exceed that of one-component solids.

cond-mat.soft

Identity Ordering and Metastable Clusters in Fluids with Random Interactions

We use Langevin dynamics simulations to study dense two-dimensional systems of particles where all binary interactions are different (AID) in the sense that each interaction parameter is characterized by a randomly chosen number. We compare two systems that differ by the probability distributions from which the interaction parameters are drawn: uniform (U) and exponential (E). Both systems undergo neighborhood identity ordering (NIO) and form metastable clusters in the fluid phase near the liquid-solid transition but the effects are much stronger in E than in U systems. Possible implications of our results for the control of the structure of multicomponent alloys are discussed.

cond-mat.soft

Effect of Grafting on Aggregation of Intrinsically Disordered Proteins

A significant part of the proteome is composed of intrinsically-disordered proteins (IDPs). These proteins do not fold into a well-defined structure and behave like ordinary polymers. In this work we consider IDPs which have the tendency to aggregate, model them as heteropolymers that contain a small number of associating monomers and use computer simulations in order to compare the aggregation of such IDPs that are grafted to a surface or free in solution. We then discuss how such grafting may affect the analysis of in-vitro experiments and could also be used to suppress harmful aggregation.

physics.bio-ph

Molecular dynamics simulations of shear-induced thermophoresis and non-Newtonian flow in compressible fluids

We use molecular dynamics simulations to study the behavior of a compressible Lennard-Jones fluid in simple shear flow in a two-dimensional nanochannel. The system is equilibrated in the fluid phase close to the triple point at which gas, liquid and solid phases coexist and is subjected to steady shear in Couette geometry. It is observed that at higher shear rates, the system develops a density gradient perpendicular to the direction of flow and exhibits solid-like layering near the boundaries. Both the number of solid-like layers and the number of layers that move with the velocity of the neighboring wall, increase with the shear rate. We argue that the inhomogeneous density profile develops as the consequence of thermophoresis due to the non-uniform temperature profile produced by shear-induced viscous heating in the simulated flow cell. The above phenomena are accompanied by non-Newtonian effects such as nonlinear velocity profiles, inhomogeneous stress distributions and shear rate dependent viscosity which exhibits shear thinning followed by shear thickening as the shear rate is increased. The connection between these phenomena is discussed.

cond-mat.soft

Darwinian Selection Induces Lamarckian Adaptation in a Holobiont Model

Current models of animal evolution focus on selection of individuals, ignoring the much faster selection of symbiotic bacteria. Here we take host-symbiont interactions into account by introducing a Population Genetics-like model of holobionts exposed to toxic stress. The stress can be alleviated by selection of resistant individuals (host and bacteria) and by secretion of a detoxification agent ("detox"). By defining a new measure, termed the Lamarckian, we show that selection of resistant bacteria over one generation of hosts leads to stress-dependent increase in the tolerance of the host's offspring. This benefit is mediated by co-alleviation of toxic and physiologic stress. Prolonged exposure leads to further adaptation by 'group selection' of bacterial communities with higher detox per bacterium. These findings show that Lamarckian adaptation can arise via interactions between two levels of Darwinian selection within a holobiont system. The conclusions and modelling framework are applicable to diverse types of holobiont systems.

q-bio.PE

Dynamics of Active Rouse Chains

We consider how active forces modeled as non-thermal random noise affect the average dynamical properties of a Rouse polymer. As the power spectrum of the noise is not known we keep the analytical treatment as generic as possible and then present results for a few examples of active noise. We discuss the connection between our results and recent experimental studies of dynamics of labeled DNA telomeres in living cells, and propose new chromatin tracking experiments that will allow one to determine the statistical properties of the active forces associated with chromatin remodeling processes.

cond-mat.stat-mech

Effect of non-specific interactions on formation and stability of specific complexes

We introduce a simple model to describe the interplay between specific and non-specific interactions. We study the influence of various physical factors on the static and dynamic properties of the specific interactions of our model and show that contrary to intuitive expectations, non-specific interactions can assist in the formation of specific complexes and increase their stability. We then discuss the relevance of these results for biological systems.

cond-mat.soft

Universal Protein Distributions in a Model of Cell Growth and Division

Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal measurements of protein content, showing accumulation and division across generations. Here we present a stochastic growth-and-division model with feedback which captures these observed properties. The limiting copy number distribution is calculated exactly, and a single parameter is found to determine the distribution shape and the variance-to-mean relation. Estimating this parameter from bacterial temporal data reproduces the measured distribution shape with high accuracy, and leads to predictions for future experiments.

physics.bio-ph

Particle dynamics in fluids with random interactions

We study the dynamics of particles in a multi-component 2d Lennard-Jones (LJ) fluid in the limiting case where {\it all the particles are different} (APD). The equilibrium properties of this APD system were studied in our earlier work [J.~Chem.~Phys.~142, 051104]. We use molecular dynamics simulations to investigate the statistical properties of particle trajectories in a temperature range covering both normal and supercooled fluid states. We calculate the mean-square displacement as well as angle, displacement and waiting time distributions, and compare the results with those for one-component LJ fluid. As temperature is lowered, the dynamics of the APD system becomes increasingly complex, as the intrinsic difference between the particles is amplified by neighborhood identity ordering and by the heterogeneous structure of the supercooled state.

cond-mat.soft