相关论文: Reactive conformations and non-Markovian cyclizati…
Spatially-distributed, nonequilibrium chemical systems described by a Markov chain model are considered. The evolution of such systems arises from a combination of local birth-death reactive events and random walks executed by the particles…
The presence of a viscoelastic mechanism distinctly different from the segmental a-relaxation and the Rouse modes within the glass-rubber transition zone of polymers had been justified by theoretical considerations, and subsequently…
We study the one-dimensional motion of a Brownian particle inside a confinement described by two reactive boundaries which can partially reflect or absorb the particle. Understanding the effects of such boundaries is important in physics,…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
The dynamics of flexible polymers in dilute solutions is studied taking into account the hydrodynamic memory, as a consequence of fluid inertia. As distinct from the Rouse-Zimm (RZ) theory, the Boussinesq friction force acts on the monomers…
We study an instantaneous bimolecular chemical reaction in a two-dimensional chaotic, incompressible and closed Navier-Stokes flow. Areas of well mixed reactants are initially separated by infinite gradients. We focus on the initial regime,…
Phase transitions ruled by nucleation and growth can occur by nonrandom arrangement of nuclei. This is verified, for instance, in thin film growth at solid surfaces by vapor condensation or by electrodeposition where, around each nucleus, a…
The theory of nonlinear response for Markov processes obeying a master equation is formulated in terms of time-dependent perturbation theory for the Green's functions and general expressions for the response functions up to third order in…
We study energy relaxation in a phenomenological model for polymer built from rheological considerations: a one dimensional nonlinear lattice with dissipative couplings. These couplings are well known in polymer's community to be possibly…
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…
Reaction-diffusion systems with reversible reactions generically display power-law relaxation towards chemical equilibrium. In this work we investigate through numerical simulations aging processes that characterize the non-equilibrium…
The process of polymer condensation, i.e. the formation of bonds between reactive end-groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing polymer condensation in competition with cyclisation. Using a…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
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…
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…
Using a lattice-based Monte Carlo code for simulating self-avoiding flexible polymers in three dimensions in the absence of explicit hydrodynamics, we study their Rouse modes. For self-avoiding polymers, the Rouse modes are not expected to…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
We present a simple reaction kinetics model to describe the polymer synthesis used by Lusignan et al. (PRE, 60, 5657, 1999) to produce randomly branched polymers in the vulcanization class. Numerical solution of the rate equations gives…
Dynamical properties of vulcanized polymer networks are addressed via a Rouse-type model that incorporates the effect of permanent random crosslinks. The incoherent intermediate scattering function is computed in the sol and gel phases, and…
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…