Related papers: Non-Markovian polymer reaction kinetics
The theory of the dynamics of polymers in solution is developed coming from the hydrodynamic theory of the Brownian motion (BM) and the Rouse-Zimm (RZ) model. It is shown that the time correlation functions describing the polymer motion…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
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…
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 discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…
A Markov state model of the dynamics of a protein-like chain immersed in an implicit hard sphere solvent is derived from first principles for a system of monomers that interact via discontinuous potentials designed to account for local…
We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially…
We investigate the kinetics of a polymer collapse due to the formation of irreversible crosslinks between its monomers. Using the contact probability $P(s)$ as a scale-dependent order parameter depending on the chemical distance $s$, our…
The Langevin Equation for cooperative dynamics represents the dynamics of polymer melts with chains of increasing degree of polymerization, covering the full range of behavior from the unentangled to the entangled regime. This equation…
Using a simple exactly solvable model, we show that event-dependent time delays may lead to significant non-Poisson effects in the statistics of polymer chain growth. The results are confirmed by stochastic simulation of various growth…
Chemically-responsive polymers are macromolecules that respond to local variations of the chemical composition of the solution by changing their conformation, with notable examples including polyelectrolytes, proteins and DNA. The polymer…
In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. Based on a discrete kinetic network model, we use the integrated probability flux balance method to derive the…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
In simulation studies of crystallisation, the size of the largest crystalline nucleus is often used as a reaction coordinate to monitor the progress of the nucleation process. Here, we investigate, for the case of homogeneous ice…
The mean first-passage time (MFPT) is one standard measure for the reaction time in thermally activated barrier-crossing processes. While the relationship between MFPTs and phenomenological rate coefficients is known for systems that…
We report a theoretical study of stochastic processes modeling the growth of first-order Markov copolymers, as well as the reversed reaction of depolymerization. These processes are ruled by kinetic equations describing both the attachment…
Molecular dynamics simulations were conducted to investigate the dynamic properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N=1600 monomers per chain which…
Kinetic Monte Carlo methods such as the Gillespie algorithm model chemical reactions as random walks in particle number space. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. We…
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 non-Newtonian flow of a polymer melt is discussed. The description of the exponential decrease of the apparent viscosity by the well-known Eyring formula with an activation energy reduction proportional to the shear stress does not take…