Related papers: Non-Markovian polymer reaction kinetics
We propose and theoretically study an experiment designed to measure short time polymer reaction kinetics in melts or dilute solutions. The photolysis of groups centrally located along chain backbones, one group per chain, creates pairs of…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
We investigate the kinetics of loop formation in flexible ideal polymer chains (Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the…
The reversible kinetics of copolymerization is solved analytically for the multistate mechanism proposed by B. D. Coleman and T. G. Fox [J. Chem. Phys. 38, 1065 (1963)] under low conversion conditions where the concentrations of monomeric…
We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary…
Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…
The screening of hydrodynamic interactions (HI) essentially affects macroscopic properties of polymeric solutions. This screening depends not only on the polymer concentration but has a dynamic nature. In the present work, a bead-spring…
Defining low-dimensional reaction coordinates is crucial for analyzing the dynamics of complex systems and for comparison with experiments. The maximal value of the transition-path probability along the reaction coordinate $x$,…
The behavior of a particle in a solvent has been framed using stochastic dynamics since the early theory of Kramers. A particle in a chemical reaction reacts slower in a diluted solvent because of the lack of energy transfer via collisions.…
We present a general formalism able to derive the kinetic equations of polymer dynamics. It is based on the application of nonequilibrium thermodynamics to analyze the irreversible processes taking place in the conformational space of the…
Thermodynamic behavior of polymer chains out of equilibrium is a fundamental problem in both polymer physics and biological physics. By using molecular dynamics simulation, we discover a general non-equilibrium mechanism that controls the…
The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible…
We investigate the conformational and dynamical properties of a partially active Rouse chain, where activity is localized within a specific segment, positioned at various locations along the chain and spanning any given length. Through…
Chemical reactions generically require that particles come into contact. In practice, reaction is often imperfect and can necessitate multiple random encounters between reactants. In confined geometries, despite notable recent advances,…
In biochemistry, heteropolymers encoding biological information are assembled out of equilibrium by sequentially incorporating available monomers found in the environment. Current models of polymerization treat monomer incorporation as a…
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological,…
Some recent results on the rotational dynamics of polymers are reviewed and extended. We focus here on the relaxation of a polymer, either flexible or semiflexible, initially wrapped around a rigid rod. We also study the steady polymer…
We propose a theory of the dynamics of polymers in dilute solution, in which the popular Zimm and Rouse models are limiting cases of infinitely large and small draining parameter. The equation of motion for the polymer segments beads) is…
How much time does it take for a fluctuating system, such as a polymer chain, to reach a target configuration that is rarely visited -- typically because of a high energy cost ? This question generally amounts to the determination of the…
The longitudinal response of single semiflexible polymers to sudden changes in externally applied forces is known to be controlled by the propagation and relaxation of backbone tension. Under many experimental circumstances, realized, e.g.,…