Related papers: Polymer dynamics under tension: mean first passage…
Most of the theoretical models describing the translocation of a polymer chain through a nanopore use the hypothesis that the polymer is always relaxed during the complete process. In other words, models generally assume that the…
Modeling of polymer chains has received a lot of attention in mathematics. In fact, probabilistic models that naturally arise in statistical mechanics have been widely studied by mathematicians for the very challenging and novel problems…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were…
The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible…
How much time does it take for a fluctuating system, such as a polymer chain, to reach a target configuration that is rarely visited -- typically because of a high energy cost ? This question generally amounts to the determination of the…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but…
Polymer translocation across a corrugated channel is a paradigmatic stochastic process encountered in diverse systems. The instance of time when a polymer first arrives to some prescribed location defines an important characteristic time…
The purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multi-dimensional…
We theoretically investigate the looping dynamics of a linear polymer immersed in a viscoelastic fluid. The dynamics of the chain is governed by a Rouse model with a fractional memory kernel recently proposed by Weber et al. (S. C. Weber,…
The rate of escape of an ideal bead-spring polymer in a symmetric double-well potential is calculated using transition state theory (TST) and the results compared with direct dynamical simulations. The minimum energy path of the transitions…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different. Here we study the dynamics of polymers in a viscous medium containing…
We study the dynamics of the passage of a polymer through a membrane pore (translocation), focusing on the scaling properties with the number of monomers $N$. The natural coordinate for translocation is the number of monomers on one side of…
Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static, or temporally fluctuating far…
We consider the escape of a flexible, self-avoiding polymer chain out of a confined geometry. By means of simulations, we demonstrate that the translocation time can be described by a simple scaling law that exhibits a nonlinear dependence…
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance…
We study the translocation process of a polymer in the absence of external fields for various pore diameters $b$ and membrane thickness $L$. The polymer performs Rouse and reptation dynamics. The mean translocation time $<\tau_t>$ that the…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…