Related papers: Thermally activated processes in polymer dynamics
The dynamics of active particles is of interest at many levels and is the focus of theoretical and experimental research. There have been many attempts to describe the dynamics of particles affected by random active forces in terms of an…
The problem of thermally activated escape over a potential barrier is solved by means of path integrals for one-dimensional reaction dynamics with very general time dependences. For a suitably chosen but still quite simple static potential…
The thermal activation process by which a system passes from one local energy minimum to another is a recurring motif in physics, chemistry, and biology. For instance, biopolymer chains are typically modeled in terms of energy landscapes,…
Spontaneous persistent motions driven by active processes play a central role to maintain the living cells far from equilibrium. In the majority of the research works, the steady state dynamics of an active system has been described in…
We present a simple mathematical framework for the description of the dynamics of glassy systems in terms of a random walk in a complex energy landscape pictured as a network of minima. We show how to use the tools developed for the study…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…
The process of activation out a one-dimensional potential is investigated systematically in zero and nonzero temperature conditions. The features of the potential are traced through statistical escape out of its wells whose depths are tuned…
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…
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…
We consider the thermally activated fragmentation of a homopolymer chain. In our simple model the dynamics of the intact chain is a Rouse one until a bond breaks and bond breakdown is considered as a first passage problem over a barrier to…
This study deals with polymer looping, an important process in many chemical and biological systems. We investigate basic questions on the looping dynamics of a polymer under tension using the freely-jointed chain (FJC) model. Previous…
A quantum system in contact with a heat bath undergoes quantum transitions between energy levels upon absorption or emission of energy quanta by the bath. These transitions remain virtual unless the energy of the system is measured…
Thermal activation is mediated by field configurations that correspond to saddle points of the energy functional. The rate of probability flow along the unstable functional directions, i.e the activation rate, is usually obtained from the…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
Thermally-driven atmospheric escape evolves from an organized outflow (hydrodynamic escape) to escape on a molecule by molecules basis (Jeans escape) with increasing Jeans parameter, the ratio of the gravitational to thermal energy of…
We propose a new mathematical tool for the study of transport properties of models for lattice vibrations in crystalline solids. By replication of dynamical degrees of freedom, we aim at a new dynamical system where the "local" dynamics can…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
Understanding the thermally activated escape from a metastable state is at the heart of important phenomena such as the folding dynamics of proteins, the kinetics of chemical reactions or the stability of mechanical systems. In 1940 Kramers…
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…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…