Related papers: Non-Markovian polymer reaction kinetics
Predicting monomer reactivity ratios is crucial for controlling monomer sequence distribution in copolymers and their properties. Traditional experimental methods of determining reactivity ratios are time-consuming and resource-intensive,…
Movements of molecular motors on cytoskeletal filaments are described by directed walks on a line. Detachment from this line is allowed to occur with a small probability. Motion in the surrounding fluid is described by symmetric random…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
Ring polymers remain a major challenge to our current understanding of polymer dynamics. Experimental results are difficult to interpret because of the uncertainty in the purity and dispersity of the sample. Using both equilibrium and…
We study the diffusion of a linear polymer in the presence of permeable membranes without excluded volume interactions, using scaling theory and Monte Carlo simulations. We find that the average time it takes for a chain with polymerization…
In this paper, we investigate a stochastic model describing the time evolution of a polymerization process. A polymer is a macro-molecule resulting from the aggregation of several elementary sub-units called monomers. Polymers can grow by…
The identification of meaningful reaction coordinates plays a key role in the study of complex molecular systems whose essential dynamics is characterized by rare or slow transition events. In a recent publication, precise defining…
A rigorous and most general covariant kinetic formalism is developed to study the nonlinear waves interaction in relativistic Vlasov plasmas. The typical nonlinear plasma reaction is a nonlinear current measured by the nonlinear plasma…
To understand the role of collective motion in the often large changes in interfacial molecular mobility observed in polymer films, we investigate the extent of collective motion in the interfacial regions of a thin supported polymer film…
A new method based on quasi-independent parallel simulations approach, replica-averaging, has been developed to study the influence of flow on mechanical force-mediated polymer processes such as denaturation and breaking of bonds. This…
Memory effects arise in many complex systems, from protein folding, to the spreading of epidemics and financial decisions. While so-called non-Markovian dynamics is common in larger systems with interacting components, observations in…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…
Active polymers are ubiquitous in nature, and often kicked by persistent noises that break detailed balance. In order to capture the out-of-equilibrium dynamics of such active polymers, we propose a simple yet reliable analytical framework…
In this paper, we address the problem of fitting multivariate Hawkes processes to potentially large-scale data in a setting where series of events are not only mutually-exciting but can also exhibit inhibitive patterns. We focus on…
In this paper, we employ Molecular Dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
We introduce a unified operator-theoretic framework for analyzing mixing times of finite-state ergodic Markov chains that applies to both reversible and non-reversible dynamics. The central object in our analysis is the projected transition…
The conformational and dynamical properties of active polymers in solution are determined by the nature of the activity, and the behavior of polymers with self-propelled, active Brownian particle-type monomers differs qualitatively from…