arXiv subjects

Eial Teomy

Publications and source records attributed to Eial Teomy.

15 recordsLinked to original sources

arXiv2020

Target finding in fibrous biological environments

We use a lattice model to study first-passage time distributions of target finding events through complex environments with elongated fibers distributed with different anisotropies and volume occupation fractions. For isotropic systems and for low densities of aligned fibers, the three-dimensional search is a Poisson process with the first-passage time exponentially distributed with the most probable finding time at zero. At high enough densities of aligned fibers, elongated channels emerge, reducing the dynamics dimensionality to one dimension. We show how the shape and size of the channels modify the behavior of the first-passage time distribution and its short, intermediate, and long time scales. We develop an exactly solvable model for synthetic rectangular channels, which captures the effects of the tortuous local structure of the elongated channels that naturally emerge in our system. For arbitrary values of the nematic order parameter of fiber orientations, we develop a mapping to the simpler situation of fully aligned fibers at some other effective volume occupation fraction. Our results shed light on the molecular transport of biomolecules between biological cells in complex fibrous environments.

cond-mat.stat-mech↗

arXiv2020

Constraint relaxation leads to jamming

Adding transitions to an equilibrium system increases the activity. Naively, one would expect this to hold also in out of equilibrium systems. This surprising effect is caused by adding heretofore forbidden transitions into less and less active states. We demonstrate, using relatively simple models, how adding transitions to an out of equilibrium system may in fact reduce the activity and even cause it to vanish. We investigate six related kinetically-constrained lattice gas models, some of which behave as naively expected while others exhibit this non-intuitive behavior. We introduce a semi-mean-field approximation describing the models, which agrees qualitatively with our numerical simulation.

cond-mat.stat-mech↗

arXiv2020

Ordered Hexagonal Patterns via Notch-Delta Signaling

Many developmental processes in biology utilize Notch-Delta signaling to construct an ordered pattern of cellular differentiation. This signaling modality is based on nearest-neighbor contact, as opposed to the more familiar mechanism driven by the release of diffusible ligands. Here, exploiting this "juxtacrine" property, we present an exact treatment of the pattern formation problem via a system of nine coupled ordinary differential equations. The possible patterns that are realized for realistic parameters can be analyzed by considering a co-dimension 2 pitchfork bifurcation of this system. This analysis explains the observed prevalence of hexagonal patterns with high Delta at their center, as opposed to those with central high Notch levels. We show that outside this range of parameters, in particular for low cis-coupling, a novel kind of pattern is produced, where high Delta cells have high Notch as well. It also suggests that the biological system is only weakly first order, so that an additional mechanism is required to generate the observed defect-free patterns. We construct a simple strategy for producing such defect-free patterns.

q-bio.MN↗

arXiv2019

Non-monotonic displacement distribution of active random walkers

We consider a simple model for active random walk with general temporal correlations, and investigate the shape of the probability distribution function of the displacement during a short time interval. We find that under certain conditions the distribution is non-monotonic and we show analytically and numerically that the existence of the non-monotonicity is governed by the walker's tendency to move forward, while the correlations between the timing of its active motion control the magnitude and shape of the non-monotonicity. In particular, we find that in a homogeneous system such non-monotonicity can occur only if the persistence is strong enough.

cond-mat.stat-mech↗

arXiv2019

Correlations and transport in exclusion processes with general finite memory

We consider the correlations and the hydrodynamic description of random walkers with a general finite memory moving on a $d$ dimensional hypercubic lattice. We derive a drift-diffusion equation and identify a memory-dependent critical density. Above the critical density, the effective diffusion coefficient decreases with the particles' propensity to move forward and below the critical density it increases with their propensity to move forward. If the correlations are neglected the critical density is exactly $1/2$. We also derive a low-density approximation for the same time correlations between different sites. We perform simulations on a one-dimensional system with one-step memory and find good agreement between our analytical derivation and the numerical results. We also consider the previously unexplored special case of totally anti-persistent particles. Generally, the correlation length converges to a finite value. However in the special case of totally anti-persistent particles and density $1/2$, the correlation length diverges with time. Furthermore, connecting a system of totally anti-persistent particles to external particle reservoirs creates a new phenomenon: In almost all systems, regardless of the precise details of the microscopic dynamics, when a system is connected to a reservoir, the mean density of particle at the edge is the same as the reservoir following the zeroth law of thermodynamics. In a totally anti-persistent system, however, the density at the edge is always higher than in the reservoir. We find a qualitative description of this phenomenon which agrees reasonably well with the numerics.

cond-mat.stat-mech↗

arXiv2019

Transport in exclusion processes with one-step memory: density dependence and optimal acceleration

We study a lattice gas of persistent walkers, in which each site is occupied by at most one particle and the direction each particle attempts to move to depends on its last step. We analyse the mean squared displacement (MSD) of the particles as a function of the particle density and their persistence (the tendency to continue moving in the same direction). For positive persistence the MSD behaves as expected: it increases with the persistence and decreases with the density. However, for strong anti-persistence we find two different regimes, in which the dependence of the MSD on the density is non-monotonic. For very strong anti-persistence there is an optimal density at which the MSD reaches a maximum. In an intermediate regime, the MSD as a function of the density exhibits both a minimum and a maximum, a phenomenon which has not been observed before. We derive a mean-field theory which qualitatively explains this behaviour.

cond-mat.stat-mech↗

arXiv2018

Confluent and non-confluent phases in a model of cell tissue

The Voronoi-based cellular model is highly successful in describing the motion of two-dimensional confluent cell tissues. In the homogeneous version of this model, the energy of each cell is determined solely by its geometric shape and size, and the interaction between adjacent cells is a byproduct of this additive energy. We generalize this model so as to allow zero or partial contact between cells. We identify several phases, two of which (solid confluent and liquid confluent) were found in previous studies that imposed confluency but others that are novel. Transitions in this model may be relevant for understanding both normal development as well as cancer metastasis.

q-bio.CB↗

arXiv2016

Hydrodynamics in kinetically-constrained lattice-gas models

Kinetically-constrained models are lattice-gas models that are used for describing glassy systems. By construction, their equilibrium state is trivial and there are no equal-time correlations between the occupancy of different sites. We drive such models out of equilibrium by connecting them to two reservoirs of different densities, and measure the response of the system to this perturbation. We find that under the proper coarse-graining, the behavior of these models may be expressed by a nonlinear diffusion equation, with a model- and density-dependent diffusion coefficient. We find a simple approximation for the diffusion coefficient, and show that the relatively mild discrepancy between the approximation and our numerical results arises due to non-negligible correlations that appear as the system is driven out of equilibrium, even when the density gradient is infinitesimally small. Similar correlations appear when such kinetically-constrained models are driven out of equilibrium by applying a uniform external force. We suggest that these correlations are the reason for the same discrepancy between the approximate diffusion coefficient and the numerical results for a broader group of models, non-gradient lattice-gas models, for which kinetically-constrained models are arguably the simplest example thereof.

cond-mat.stat-mech↗

arXiv2016

Combinatorial Design of Textured Mechanical Metamaterials

The structural complexity of metamaterials is limitless, although in practice, most designs comprise periodic architectures which lead to materials with spatially homogeneous features. More advanced tasks, arising in e.g. soft robotics, prosthetics and wearable tech, involve spatially textured mechanical functionality which require aperiodic architectures. However, a naïve implementation of such structural complexity invariably leads to frustration, which prevents coherent operation and impedes functionality. Here we introduce a combinatorial strategy for the design of aperiodic yet frustration-free mechanical metamaterials, whom we show to exhibit spatially textured functionalities. We implement this strategy using cubic building blocks - voxels - which deform anisotropically, a local stacking rule which allows cooperative shape changes by guaranteeing that deformed building blocks fit as in a 3D jigsaw puzzle, and 3D printing. We show that, first, these aperiodic metamaterials exhibit long-range holographic order, where the 2D pixelated surface texture dictates the 3D interior voxel arrangement. Second, they act as programmable shape shifters, morphing into spatially complex but predictable and designable shapes when uniaxially compressed. Third, their mechanical response to compression by a textured surface reveals their ability to perform sensing and pattern analysis. Combinatorial design thus opens a new avenue towards mechanical metamaterials with unusual order and machine-like functionalities.

cond-mat.soft↗

arXiv2016

Jamming vs. Caging in Three Dimensional Jamming Percolation

We investigate a three-dimensional kinetically-constrained model that exhibits two types of phase transitions at different densities. At the jamming density $ ρ_J $ there is a mixed-order phase transition in which a finite fraction of the particles become frozen, but the other particles may still diffuse throughout the system. At the caging density $ ρ_C > ρ_J $, the mobile particles are trapped in finite cages and no longer diffuse. The caging transition occurs due to a percolation transition of the unfrozen sites, and we numerically find that it is a continuous transition with the same critical exponents as random percolation.

cond-mat.stat-mech↗

arXiv2015

The relation between the structure of blocked clusters and the relaxation dynamics in kinetically-constrained models

We investigate the relation between the cooperative length and the relaxation time, represented respectively by the culling time and the persistence time, in the Fredrickson-Andersen, Kob-Andersen and spiral kinetically-constrained models. By mapping the dynamics to diffusion of defects, we find a relation between the persistence time, $τ_{p}$, which is the time until a particle moves for the first time, and the culling time, $τ_{c}$, which is the minimal number of particles that need to move before a specific particle can move, $τ_{p}=τ^γ_{c}$, where $γ$ is model- and dimension dependent. We also show that the persistence function in the Kob-Andersen and Fredrickson-Andersen models decays subexponentially in time, $P(t)=exp[-(t/τ)^β]$, but unlike previous works we find that the exponent $β$ appears to decay to 0 as the particle density approaches 1.

cond-mat.stat-mech↗

arXiv2014

Finite-density effects in the Fredrickson-Andersen and Kob-Andersen kinetically-constrained models

We calculate the corrections to the thermodynamic limit of the critical density for jamming in the Kob-Andersen and Fredrickson-Andersen kinetically-constrained models, and find them to be finite-density corrections, and not finite-size corrections. We do this by introducing a new numerical algorithm, which requires negligible computer memory since contrary to alternative approaches, it generates at each point only the necessary data. The algorithm starts from a single unfrozen site and at each step randomly generates the neighbors of the unfrozen region and checks whether they are frozen or not. Our results correspond to systems of size greater than 10^7x10^7, much larger than any simulated before, and are consistent with the rigorous bounds on the asymptotic corrections. We also find that the average number of sites that seed a critical droplet is greater than 1.

cond-mat.stat-mech↗

arXiv2014

Jamming Percolation in Three Dimensions

We introduce a three-dimensional model for jamming and glasses, and prove that the fraction of frozen particles is discontinuous at the directed-percolation critical density. In agreement with the accepted scenario for jamming- and glass-transitions, this is a mixed-order transition; the discontinuity is accompanied by diverging length- and time-scales. Because one-dimensional directed-percolation paths comprise the backbone of frozen particles, the unfrozen rattlers may use the third dimension to travel between their cages. Thus the dynamics are diffusive on long-times even above the critical density for jamming.

cond-mat.stat-mech↗

arXiv2014

Jamming by Shape in Kinetically-Constrained Models

We derive expressions for the critical density for jamming in a hyper-rhomboid system of arbitrary shape in any dimension for the Kob-Andersen and Fredrickson-Andersen kinetically-constrained models. We find that changing the system's shape without altering its total volume or particle density may induce jamming. We also find a transition between shapes in which the correlation length between jammed particles is infinite, and shapes that have a finite correlation length.

cond-mat.stat-mech↗

arXiv2012

Jamming transition of kinetically-constrained models in rectangular systems

We theoretically calculate the average fraction of frozen particles in rectangular systems of arbitrary dimensions for the Kob-Andersen and Fredrickson-Andersen kinetically-constrained models. We find the aspect ratio of the rectangle's length to width, which distinguishes short, square-like rectangles from long, tunnel-like rectangles, and show how changing it can effect the jamming transition. We find how the critical vacancy density converges to zero in infinite systems for different aspect ratios: for long and wide channels it decreases algebraically $v_{c}\sim W^{-1/2}$ with the system's width W, while in square systems it decreases logarithmically $v_{c}\sim1/\ln L$ with length L. Although derived for asymptotically wide rectangles, our analytical results agree with numerical data for systems as small as $W\approx10$.

cond-mat.stat-mech↗