Related papers: Non-Markovian polymer reaction kinetics
We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral…
We study a Markov random process describing a muscle molecular motor behavior. Every motor is either bound up with a thin filament or unbound. In the bound state the motor creates a force proportional to its displacement from the neutral…
We continue our study of the linear response of a nonequilibrium system. This Part II concentrates on models of open and driven inertial dynamics but the structure and the interpretation of the result remain unchanged: the response can be…
Recent theoretical modeling offers a unified picture for the description of stochastic processes characterized by a crossover from anomalous to normal behavior. This is particularly welcome, as a growing number of experiments suggest the…
Any first course on polymer physics teaches that the dynamics of a tagged monomer of a polymer is anomalously subdiffusive, i.e., the mean-square displacement of a tagged monomer increases as $t^\alpha$ for some $\alpha<1$ until the…
Complex chemical reaction networks, which underlie many industrial and biological processes, often exhibit non-monotonic changes in chemical species concentrations, typically described using nonlinear models. Such non-monotonic dynamics are…
A co-polycondensation reaction is discussed analytically and by Monte-Carlo simulations where two reactive units compete for reactions with an alternating third reactive unit, whereby irreversible reactions replace bonds which are able to…
Structure and dynamics of an active polymer on a smooth cylindrical surface are studied by Brownian dynamics simulations. The effect of active force on the polymer adsorption behavior and the combined effect of chain mobility, length N,…
A polymer model given in terms of beads, interacting through Hookean springs and hydrodynamic forces, is studied. Brownian dynamics description of this bead-spring polymer model is extended to multiple resolutions. Using this multiscale…
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…
It is well known that path probabilities of Brownian motion correspond to the equilibrium configurational probabilities of flexible Gaussian polymers, while those of active Brownian motion correspond to in-extensible semiflexible polymers.…
Significant progress was made in recent years in the understanding of the proton spin kinetics in polymer melts. Generally, the proton spin kinetics is determined by intramolecular and intermolecular magnetic dipole-dipole contributions of…
When a flexible polymer is sucked into a localized small hole, the chain can initially respond only locally and the sequential nonequilibrium processes follow in line with the propagation of the tensile force along the chain backbone. We…
Much work has studied effective interactions between micron-sized particles carrying linkers forming reversible, inter-particle linkages. These studies allowed understanding the equilibrium properties of colloids interacting through…
We propose a theory based on non-equilibrium thermodynamics to describe the mechanical behavior of an active polymer gel created by the inclusion of molecular motors in its solvent. When activated, these motors attach to the chains of the…
Nonlinear behavior of electro-osmosis in dilute non-adsorbing polymer solutions with low salinity is investigated with Brownian dynamics simulations and a kinetic theory. In the Brownian simulations, the hydrodynamic interaction between the…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
We propose a simple dynamic model of polymers under shear with an anisotropic mobility tensor. We calculate the shear viscosity, the rheo-dielectric response function, and the parallel relaxation modulus under shear flow deduced from our…
The structural properties of a linear polymer and its evolution in time have a strong bearing on its anisotropic stress response. The mean-square bond length and mean bond angle are the critical parameters that influence the time-varying…
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…