Related papers: A Universal Method for Analysing Copolymer Growth
The polymerization dynamics of double-stranded polymers, such as actin filaments, is investigated theoretically using simple chemical kinetic models that explicitly take into account some microscopic details of the polymer structure and the…
The irreversible adsorption of polymers to a two-dimensional solid surface is studied. An operator formalism is introduced for chemisorption from a polydisperse solution of polymers which transforms the analysis of the adsorption process to…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
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…
Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of…
The process of dimerization, in which two monomers bind to each other and form a dimer, is common in nature. This process can be modeled using rate equations, from which the average copy numbers of the reacting monomers and of the product…
Sintering, as a thermal process at elevated temperature below the melting point, is widely used to bond contacting particles into engineering products such as ceramics, metals, polymers, and cemented carbides. Modelling and simulation as…
We report a theoretical study of stochastic processes modeling the growth of first-order Markov copolymers, as well as the reversed reaction of depolymerization. These processes are ruled by kinetic equations describing both the attachment…
In this paper we review some recent results, obtained jointly with Stu Whittington, for a mathematical model describing a copolymer in an emulsion. The copolymer consists of hydrophobic and hydrophilic monomers, concatenated randomly with…
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…
The dynamics of polymer decompression, i.e., a process from compressed, compact state to the relaxed swoll en conformation, can be formally described as a {\it nonlinear diffusion}. We discuss here two basic examples: (i) the expansion, or…
Polymers, macromolecules formed from covalently bonded monomers, underpin countless technologies and are indispensable to modern life. While deep learning is advancing polymer science, existing methods typically represent the whole polymer…
Given the wide range of length scales, the analysis of polymer systems often requires coarse-graining, for which various levels of description may be possible depending on the phenomenon under consideration. Here, we provide a super-coarse…
Polymerization is a fundamental chemical process enabling large-scale production of material components across modern industries. By transforming a monomer mixture into a cross-linked polymer network, polymerization induces changes in…
This document presents a combinatorial framework for analyzing assembly systems using generating functions. We explore the theory through concrete examples, such as linear polymers, and develop recursive equations to characterize valid…
The production of sequence-specific copolymers using copolymer templates is fundamental to the synthesis of complex biological molecules and is a promising framework for the synthesis of synthetic chemical complexes. Unlike the…
Polymer composite materials require softening to reduce their glass transition temperature and improve processability. To this end, plasticizers, which are small organic molecules, are added to the polymer matrix. The miscibility of these…
Molecular dynamics simulations are used to study the phase behavior of a single linear multiblock copolymer with blocks of A- and B-type monomers under poor solvent conditions, varying the block length $N$, number of blocks $n$, and the…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…