Related papers: Non-Markovian polymer reaction kinetics
In this paper, the looping kinetics of a long polymer chain in solution has been investigated by using two state model, where one state represents open chain polymer molecule and the other represents closed chain polymer molecule. The…
Polydispersity is inevitable in industrially produced polymers. Established theories of polymer dynamics and rheology, however, were mostly built on monodisperse linear polymers. Dynamics of polydisperse polymers is yet to be fully explored…
We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high…
The competition between reptation and Rouse Dynamics is incorporated in the Rubinstein-Duke model for polymer motion by extending it with sideways motions, which cross barriers and create or annihilate hernias. Using the Density-Matrix…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with $N$ species, $M$ reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical…
The dynamics of polymer-nanoparticle (NP) mixtures, which involves multiple scales and system-specific variables, has posed a long-standing challenge on its theoretical description. In this paper, we construct a microscopic theory for…
High molecular weight polymer solutions have a powerful tendency to deposit adsorbed layers when exposed to even mildly attractive surfaces. The equilibrium properties of these dense interfacial layers have been extensively studied…
A great variety of models can describe the non-linear response of rubber to uni-axial tension. Yet an in-depth understanding of the successive stages of large extension is still lacking. We show that the response can be broken down in three…
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
We extend in two directions our previous results about the sampling and the empirical measures of immortal branching Markov processes. Direct applications to molecular biology are rigorous estimates of the mutation rates of polymerase chain…
Modeling of polymer chains has received a lot of attention in mathematics. In fact, probabilistic models that naturally arise in statistical mechanics have been widely studied by mathematicians for the very challenging and novel problems…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two dimensional system. Specifically, we analyse the polymer looping properties versus the SPP activity and…
We study the relaxation dynamics of a coarse-grained polymer chain at different degrees of stretching by both analytical means and numerical simulations. The macromolecule is modelled as a string of beads, connected by anharmonic springs,…
We study the motion of dispersed nanoprobes in entangled active-passive polymer mixtures. By comparing the two architectures of linear vs. unconcatenated and unknotted circular polymers, we demonstrate that novel, rich physics emerge. For…
We study the conformational properties of complex polymer macromolecules, consisting in general of $n$ subsequently connected chains (blocks) of different lengths and distinct chemical structure. Depending on the solvent conditions, the…
We study the dynamics of driven polymer translocation using both molecular dynamics (MD) simulations and a theoretical model based on the non-equilibrium tension propagation on the {\it cis} side subchain. We present theoretical and…