Related papers: Markov Chain Modeling of Polymer Translocation Thr…
In forced polymer translocation, the average translocation time, $\tau$, scales with respect to pore force, $f$, and polymer length, $N$, as $\tau \sim f^{-1} N^{\beta}$. We demonstrate that an artifact in Metropolis Monte Carlo method…
Polymer translocation in crowded environments is a ubiquitous phenomenon in biological systems. We studied polymer translocation through a pore in free, one-sided (asymmetric), and two-sided (symmetric) crowded environments. Extensive…
The purpose of this comment is to correct mistaken assumptions and claims made in the paper Stochastic feedback, nonlinear families of Markov processes, and nonlinear Fokker-Planck equations by T. D. Frank. Our comment centers on the claims…
We investigate the problem of quantifying contraction coefficients of Markov transition kernels in Kantorovich ($L^1$ Wasserstein) distances. For diffusion processes, relatively precise quantitative bounds on contraction rates have recently…
We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the…
We use large scale Monte Carlo simulations to test scaling theories for the electrostatic persistence length $l_e$ of isolated, uniformly charged polymers with \DH intrachain interactions in the limit where the screening length…
We describe a general scheme of derivation of the Vlasov-type equations for Markov evolutions of particle systems in continuum. This scheme is based on a proper scaling of corresponding Markov generators and has an algorithmic realization…
A general theory is developed to study individual based models which are discrete in time. We begin by constructing a Markov chain model that converges to a one-dimensional map in the infinite population limit. Stochastic fluctuations are…
The local dynamical features of a PEO melt studied by MD simulations are compared to two model chain systems, namely the well-known Rouse model as well as the semiflexible chain model (SFCM) that additionally incorporates chain stiffness.…
In the framework of the problem of finding proper reaction coordinates (RCs) for complex systems and their effective evolution equations, we consider the case study of a polymer chain in an external double-well potential, experiencing…
Experimental data from a turbulent jet flow is analysed in terms of an additive, continuous stochastic process where the usual time variable is replaced by the scale. We show that the energy transfer through scales is well described by a…
We study a novel large dimensional approximate factor model with regime changes in the loadings driven by a latent first order Markov process. By exploiting the equivalent linear representation of the model, we first recover the latent…
The aim of this paper is to approximate a finite-state Markov process by another process with fewer states, called herein the approximating process. The approximation problem is formulated using two different methods. The first method,…
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces.…
Random walks are a fundamental model in applied mathematics and are a common example of a Markov chain. The limiting stationary distribution of the Markov chain represents the fraction of the time spent in each state during the stochastic…
At high levels, the asymptotic distribution of a stationary, regularly varying Markov chain is conveniently given by its tail process. The latter takes the form of a geometric random walk, the increment distribution depending on the sign of…
Multiplex networks are a common modeling framework for interconnected systems and multimodal data, yet we still lack fundamental insights for how multiplexity affects stochastic processes. We introduce a novel ``Markov chains of Markov…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
This article focuses on a preaveraging description of polymer nonequilibrium stretching, where a single polymer undergoes a transient process from equilibrium to nonequilibrium steady state by pulling one chain end. The preaveraging method…
This work investigates the effects of tangent polar activity on the conformational and dynamic properties of entangled polymer melts through Langevin molecular dynamics simulations. We examine systems composed of all self-propelled,…