Related papers: Multistate reversible copolymerization of nonMarko…
In a preceding work [M. Lang, K. Kumar, A simple and general approach for reversible condensation polymerization with cyclization, Macromolecules 54 (2021) 7021], we have introduced a simple recursive scheme that allows to treat stepwise…
We describe the kinetics and thermodynamics of copolymers undergoing recombination reactions, which are important for prebiotic chemistry. We use two approaches: the first one, based on chemical rate equations and the mass-action law…
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 consider a stochastic model, called the replicator coalescent, describing a system of blocks of $k$ different types which undergo pairwise mergers at rates depending on the block types: with rate $C_{i,j}$ blocks of type $i$ and $j$…
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 a reversible polymerization process in which individual polymers aggregate and fragment at a rate proportional to their molecular weight. We find a nonequilibrium phase transition despite the fact that the dynamics are…
We refer the appearance of three-dimensional (3D) multiheaded chimera states that display cascades of self-organized spatiotemporal patterns of coexisting coherence and incoherence. We demonstrate that number of the incoherent chimera's…
Understanding the behaviour of a quantum system coupled to its environment is of fundamental interest in the general field of quantum technologies. It also has important repercussions on foundational problems in physics, such as the process…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
The Michaelis-Menten enzymatic reaction is sufficient to perceive many subtleties of network modeling, including the concentration and time scales separations, the formal equivalence between bulk phase and single-molecule approaches, or the…
Chemotaxis describes the movement of an organism, such as single or multi-cellular organisms and bacteria, in response to a chemical stimulus. Two widely used models to describe the phenomenon are the celebrated Keller-Segel equation and a…
We investigate the copolymerization behavior of a two-component system into quasi-linear self-assemblies under conditions that interspecies binding is favored over identical species binding. The theoretical framework is based on a…
We discuss a problem of cyclization of a polymer molecule, which is an important example of reaction in a system showing strongly non-Markovian behavior on the timescales of interest. We show that the knowledge of the joint three-time…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…
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…
Kinetics of steady-state copolymerization has been investigated since 1940s. Irreversible terminal and penultimate models were successfully applied to a number of comonomer systems, but failed for systems where depropagation is significant.…
We investigate theoretically a diffusion-limited reaction between a reactant attached to a Rouse polymer and an external fixed reactive site in confinement. The present work completes and goes beyond a previous study [T. Gu\'erin, O.…
There are some positively divisible non-Markovian processes whose transition matrices satisfy the Chapman-Kolmogorov equation. These processes should also satisfy the Kolmogorov consistency conditions, an essential requirement for a process…
We analyze a stochastic process resulting from the normalization of states in the zeroth-order optimization method CMA-ES. On a specific class of minimization problems where the objective function is scaling-invariant, this process defines…
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…