Related papers: The sub-diffusive behavior of chromatin in changin…
We study the rate of activated motion over multiple barriers, in particular the correlated double-jump of an adatom diffusing on a missing-row reconstructed Platinum (110) surface. We develop a Transition Path Theory, showing that the…
Low-dimensional periodic arrays of scatterers with a moving point particle are ideal models for studying deterministic diffusion. For such systems the diffusion coefficient is typically an irregular function under variation of a control…
We propose a formalism for describing two-strand systems of a DNA type by means of soliton von Neumann equations, and illustrate how it works on a simple example exactly solvably by a Darboux transformation. The main idea behind the…
We 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…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
In this article we review classical and recent results in anomalous diffusion and provide mechanisms useful for the study of the fundamentals of certain processes, mainly in condensed matter physics, chemistry and biology. Emphasis will be…
A model for anomalous transport of tracer particles diffusing in complex media in two dimensions is proposed. The model takes into account the characteristics of persistent motion that active bath transfer to the tracer, thus the model…
Diffusion of a tagged particle near a constraining biological surface is examined numerically by modeling the surface-water interaction by an effective potential. The effective potential is assumed to be given by an asymmetric double well…
The two-dimensional cage model for polymer motion is discussed with an emphasis on the effect of sideways motions, which cross the barriers imposed by the lattice. Using the Density Matrix Method as a solver of the Master Equation, the…
Detailed experimental and theoretical studies of the temperature dependence of the effect of different scattering mechanisms on electrical transport properties of graphene devices are presented. We find that for high mobility devices the…
In this paper we detail the mechanisms that drive substitutional binary diffusion and derive appropriate governing equations. We focus on the one-dimensional case with insulated boundary conditions. Asymptotic expansions are used in order…
The problem of eliminating fast-relaxing variables to obtain an effective drift-diffusion process in position is solved in a uniform and straightforward way for models with velocity a function jointly of position and fast variables. A more…
We show that the Turing patterns in reaction systems with subdiffusion can be replicated in an effective system with Markovian cross-diffusion. The effective system has the same Turing instability as the original system, and the same…
We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous…
Run-and-tumble particles, frequently considered today for modeling bacterial locomotion, naturally appear outside a biological context as well, e.g. for producing waves in the telegraph process. Here, we use a wave function to drive their…
The concept of random walk, in which particles or waves undergo multiple collisions with the microscopic constituents of a surrounding medium, is central to understanding diffusive transport across many research areas. However, this…
Living cells exhibit multi-mode transport that switches between an active, self-propelled motion and a seemingly passive, random motion. Cellular decision-making over transport mode switching is a stochastic process that depends on the…
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…
Transport properties of a single-mode waveguide with rough boundary are studied by discrimination between two mechanisms of surface scattering, the amplitude and square-gradient ones. Although these mechanisms are generically mixed, we show…
A one-dimensional driven diffusive system with two types of particles and nearest neighbors interactions has been considered on a finite lattice with open boundaries. The particles can enter and leave the system from both ends of the…