Related papers: Non-Markovian polymer reaction kinetics
A link between memory effects in quantum kinetic equations and nonequilibrium correlations associated with the energy conservation is investigated. In order that the energy be conserved by an approximate collision integral, the one-particle…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
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 ring polymer molecular dynamics (RPMD) rate theory is an efficient and accurate method for estimating rate coefficients of chemical reactions affected by nuclear quantum effects. The commonly used RPMD treatment of gas-phase bimolecular…
Beyond the conventional quantum regression theorem, a general formula for non-Markovian correlation functions of arbitrary system operators both in the time- and frequency-domain is given. We approach the problem by transforming the…
We study theoretically the dynamics of living polymers which can add and subtract monomer units at their live chain ends. The classic example is ionic living polymerization. In equilibrium, a delicate balance is maintained in which each…
We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated…
The conformational and dynamical properties of isolated semiflexible active polar ring polymers are investigated analytically. A ring is modeled as continuous Gaussian polymer exposed to tangential active forces. The analytical solution of…
Dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an…
We introduce a new method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. Such reduced dynamics play an essential role in the study of a broad class of processes, ranging from…
The nonlinear response of molecular systems undergoing Markovian stochastic reorientations is calculated up to fifth order in the amplitude of the external field. Time-dependent perturbation theory is used to compute the relevant response…
We present a numerical method to compute non-equilibrium memory kernels based on experimental data or molecular dynamics simulations. The procedure uses a recasting of the non-stationary generalized Langevin equation, in which we expand the…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
The precise details of how myosin-V coordinates the biochemical reactions and mechanical motions of its two head elements to engineer effective processive molecular motion along actin filaments remain unresolved. We compare a quantitative…
Using molecular dynamics simulations, we determine the linear and nonlinear viscoelastic properties of a model polymer melt in the unentangled regime. Several approaches are compared for the computation of linear moduli, including…
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in…
We present an in-depth multi-scale analysis of the conformations and dynamics of polar active polymers, comparing very dilute and very dense conditions. We unveil characteristic length and time scales, common to both dilute and dense…
Polymer melts with chains undergoing reversible crosslinking have distinctively favorable dynamic properties, e.g., self healing and reprocessability. In these situations there are two relevant elementary time scales: the segmental and the…
Directed transport is a characteristic feature of numerous biological systems in response to signals such as nutrient and chemical gradients. These signals often depend on time owing to the high complexity of interactions in these systems.…