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Lev S. Tsimring

Publications and source records attributed to Lev S. Tsimring.

At least 19 recordsLinked to original sources
arXiv2023

Statistical Theory of Asymmetric Damage Segregation in Clonal Cell Populations

Asymmetric damage segregation (ADS) is ubiquitous among unicellular organisms: After a mother cell divides, its two daughter cells receive sometimes slightly, sometimes strongly different fractions of damaged proteins accumulated in the mother cell. Previous studies demonstrated that ADS provides a selective advantage over symmetrically dividing cells by rejuvenating and perpetuating the population as a whole. 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. We show that for a large class of deterministic ADS rules the trajectories of damage along the lineages are chaotic, and the distributions of damage in cells born at a given time asymptotically becomes fractal. By exploiting the analogy of linear ADS models with the Iterated Function Systems known in chaos theory, we derive the Frobenius-Perron equation for the stationary damage density distribution and analytically compute the damage distribution moments and fractal dimensions. We also investigate nonlinear and stochastic variants of ADS models and show the robustness of the salient features of the damage distributions.

q-bio.PE↗
arXiv2007

Swarming and swirling in self-propelled polar granular rods

Using experiments with anisotropic vibrated rods and quasi-2D numerical simulations, we show that shape plays an important role in the collective dynamics of self-propelled (SP) particles. We demonstrate that SP rods exhibit local ordering, aggregation at the side walls, and clustering absent in round SP particles. Furthermore, we find that at sufficiently strong excitation SP rods engage in a persistent swirling motion in which the velocity is strongly correlated with particle orientation.

cond-mat.other↗
arXiv2007

Effects of crosslinks on motor-mediated filament organization

Crosslinks and molecular motors play an important role in the organization of cytoskeletal filament networks. Here we incorporate the effect of crosslinks into our model of polar motor-filament organization [Phys. Rev. E {\bf 71}, 050901 (2005)], through suppressing the relative sliding of filaments in the course of motor-mediated alignment. We show that this modification leads to a nontrivial macroscopic behavior, namely the oriented state exhibits a transverse instability in contrast to the isotropic instability that occurs without crosslinks. This transverse instability leads to the formation of dense extended bundles of oriented filaments, similar to recently observed structures in actomyosin. This model also can be applied to situations with two oppositely directed motor species or motors with different processing speeds.

cond-mat.soft↗
arXiv2006

Thermal collapse of a granular gas under gravity

Free cooling of a gas of inelastically colliding hard spheres represents a central paradigm of kinetic theory of granular gases. At zero gravity the temperature of a freely cooling homogeneous granular gas follows a power law in time. How does gravity, which brings inhomogeneity, affect the cooling? We combine molecular dynamics simulations, a numerical solution of hydrodynamic equations and an analytic theory to show that a granular gas cooling under gravity undergoes thermal collapse: it cools down to zero temperature and condenses on the bottom of the container in a finite time.

cond-mat.soft↗
arXiv2005

Theory of self-assembly of microtubules and motors

We derive a model describing spatio-temporal organization of an array of microtubules interacting via molecular motors. Starting from a stochastic model of inelastic polar rods with a generic anisotropic interaction kernel we obtain a set of equations for the local rods concentration and orientation. At large enough mean density of rods and concentration of motors, the model describes an orientational instability. We demonstrate that the orientational instability leads to the formation of vortices and (for large density and/or kernel anisotropy) asters seen in recent experiments. We derive the specific form of the interaction kernel from the detailed analysis of microscopic interaction of two filaments mediated by a moving molecular motor, and extend our results to include variable motor density and motor attachment to the substrate.

cond-mat.soft↗
arXiv2005

Patterns and Collective Behavior in Granular Media: Theoretical Concepts

Granular materials are ubiquitous in our daily lives. While they have been a subject of intensive engineering research for centuries, in the last decade granular matter attracted significant attention of physicists. Yet despite a major efforts by many groups, the theoretical description of granular systems remains largely a plethora of different, often contradicting concepts and approaches. Authors give an overview of various theoretical models emerged in the physics of granular matter, with the focus on the onset of collective behavior and pattern formation. Their aim is two-fold: to identify general principles common for granular systems and other complex non-equilibrium systems, and to elucidate important distinctions between collective behavior in granular and continuum pattern-forming systems.

cond-mat.soft↗
arXiv2005

Pattern formation of microtubules and motors: inelastic interaction of polar rods

We derive a model describing spatio-temporal organization of an array of microtubules interacting via molecular motors. Starting from a stochastic model of inelastic polar rods with a generic anisotropic interaction kernel we obtain a set of equations for the local rods concentration and orientation. At large enough mean density of rods and concentration of motors, the model describes orientational instability. We demonstrate that the orientational instability leads to the formation of vortices and (for large density and/or kernel anisotropy) asters seen in recent experiments.

cond-mat.soft↗
arXiv2003

Dynamics in a Bistable-Element-Network with Delayed Coupling and Local Noise

The dynamics of an ensemble of bistable elements under the influence of noise and with global time-delayed coupling is studied numerically by using a Langevin description and analytically by using 1) a Gaussian approximation and 2) a dichotomous model. We find that for a strong enough positive feedback the system undergoes a phase transition and adopts a non-zero stationary mean field. A variety of coexisting oscillatory mean field states are found for positive and negative couplings. The magnitude of the oscillatory states is maximal for a certain noise temperature, i.e., the system demonstrates the phenomenon of coherence resonance. While away form the transition points the system dynamics is well described by the Gaussian approximation, near the bifurcations it is more adequately described by the dichotomous model.

cond-mat.stat-mech↗
arXiv2002

MD simulations and continuum theory of partially fluidized shear granular flows

We carry out a detailed comparison of soft particle molecular dynamics simulations with the theory of partially fluidized shear granular flows. We verify by direct simulations a constitutive relation based on the separation of the shear stress tensor into a fluid part proportional to the strain rate tensor, and a remaining solid part. The ratio of these two components is determined by the order parameter. Based on results of the simulations we construct the ``free energy'' function for the order parameter. We also present the simulations of the stationary deep 2D granular flows driven by an upper wall and compare it with the continuum theory.

cond-mat.soft↗
arXiv2002

Dynamical model of sequential spatial memory: winnerless competition of patterns

We introduce a new biologically-motivated model of sequential spatial memory which is based on the principle of winnerless competition (WLC). We implement this mechanism in a two-layer neural network structure and present the learning dynamics which leads to the formation of a WLC network. After learning, the system is capable of associative retrieval of pre-recorded sequences of spatial patterns.

nlin.AO↗
arXiv2002

Contact tracing and epidemics control in social networks

A generalization of the standard susceptible-infectious-removed (SIR) stochastic model for epidemics in sparse random networks is introduced which incorporates contact tracing in addition to random screening. We propose a deterministic mean-field description which yields quantitative agreement with stochastic simulations on random graphs. We also analyze the role of contact tracing in epidemics control in small-world networks and show that its effectiveness grows as the rewiring probability is reduced.

nlin.AO↗
arXiv2002

Model of coarsening and vortex formation in vibrated granular rods

Neicu and Kudrolli observed experimentally spontaneous formation of the long-range orientational order and large-scale vortices in a system of vibrated macroscopic rods. We propose a phenomenological theory of this phenomenon, based on a coupled system of equations for local rods density and tilt. The density evolution is described by modified Cahn-Hilliard equation, while the tilt is described by the Ginzburg-Landau type equation. Our analysis shows that, in accordance to the Cahn-Hilliard dynamics, the islands of the ordered phase appear spontaneously and grow due to coarsening. The generic vortex solutions of the Ginzburg-Landau equation for the tilt correspond to the vortical motion of the rods around the cores which are located near the centers of the islands.

cond-mat.soft↗
arXiv2002

Formation of longitudinal structures in granular flows

In the framework of the theory of partially fluidized granular flows we study the formation of longitudinal structures observed experimentally by Forterre and Pouliquen in a flow down a rough inclined plane. We show that the formation of longitudinal structures is related to the positive feedback between the fluidization rate and the lateral stress (side pressure), which leads to a convective instability. Our theory explains main experimental features, such as appearance and amplification of the structure at some distance from the outlet and non-stationary behavior of the structures.

cond-mat.mtrl-sci↗
arXiv2001

Plasticity and learning in a network of coupled phase oscillators

A generalized Kuramoto model of coupled phase oscillators with slowly varying coupling matrix is studied. The dynamics of the coupling coefficients is driven by the phase difference of pairs of oscillators in such a way that the coupling strengthens for synchronized oscillators and weakens for non-synchronized pairs. The system possesses a family of stable solutions corresponding to synchronized clusters of different sizes. A particular cluster can be formed by applying external driving at a given frequency to a group of oscillators. Once established, the synchronized state is robust against noise and small variations in natural frequencies. The phase differences between oscillators within the synchronized cluster can be used for information storage and retrieval.

nlin.AO↗
arXiv2001

Continuum theory of partially fluidized granular flows

A continuum theory of partially fluidized granular flows is developed. The theory is based on a combination of the equations for the flow velocity and shear stresses coupled with the order parameter equation which describes the transition between flowing and static components of the granular system. We apply this theory to several important granular problems: avalanche flow in deep and shallow inclined layers, rotating drums and shear granular flows between two plates. We carry out quantitative comparisons between the theory and experiment.

cond-mat.stat-mech↗
arXiv2000

Continuum description of avalanches in granular media

We develop a continuum description of partially fluidized granular flows. Our theory is based on the hydrodynamic equation for the flow coupled with the order parameter equation which describes the transition between flowing and static components of the granular system. This theory captures important phenomenology recently observed in experiments with granular flows on rough inclined planes (Daerr and Douady, Nature (London) v. 399, 241 (1999)): layer bistability, and transition from triangular avalanches propagating downhill at small inclination angles to balloon-shaped avalanches also propagating uphill for larger angles.

cond-mat.soft↗
arXiv1999

Discrete stochastic modeling of calcium channel dynamics

We propose a simple discrete stochastic model for calcium dynamics in living cells. Specifically, the calcium concentration distribution is assumed to give rise to a set of probabilities for the opening/closing of channels which release calcium thereby changing those probabilities. We study this model in one dimension, analytically in the mean-field limit of large number of channels per site N, and numerically for small N. As the number of channels per site is increased, the transition from a non-propagating region of activity to a propagating one changes in nature from one described by directed percolation to that of deterministic depinning in a spatially discrete system. Also, for a small number of channels a propagating calcium wave can leave behind a novel fluctuation-driven state, in a parameter range where the limiting deterministic model exhibits only single pulse propagation.

patt-sol↗
arXiv1999

Crystallization Kinetics in the Swift--Hohenberg Model

It is shown numerically and analytically that the front propagation process in the framework of the Swift-Hohenberg model is determined by periodic nucleation events triggered by the explosive growth of the localized zero-eigenvalue mode of the corresponding linear problem. We derive the evolution equation for this mode using asymptotic analysis, and evaluate the time interval between nucleation events, and hence the front speed. In the presence of noise, we derive the velocity exponent of ``thermally activated'' front propagation (creep) beyond the pinning threshold.

patt-sol↗