Related papers: Folding Kinetics of a Polymer
We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, polymer undergoes a transition from the globule state to the folded like state. The conformation…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
Molecular dynamic (MD) simulations are applied to investigate the dependency of the kinetic friction coefficient on the temperature at the nano-scale. The system is comprised of an aluminum spherical particle consisting of 32000 atoms in an…
The adhesion between a polymer melt and substrate is studied in the presence of chemically attached chains on the substrate surface. Extensive molecular dynamics simulations have been carried out to study the effect of temperature, tethered…
We report Monte Carlo simulations of the self-assembly of supramolecular polymers based on a model of patchy particles. We find a first-order phase transition, characterized by hysteresis and nucleation, toward a solid bundle of polymers,…
Two coarse-grained models for polymer chains in dense glass-forming polymer melts are studied by computer simulation: the bond-fluctuation model on a simple cubic lattice, where a bond-length potential favors long bonds, is treated by…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
We solve a two dimensional model for polymer chain folding in the presence of mechanical pulling force ($f$) exactly using equilibrium statistical mechanics. Using analytically derived expression for the partition function we determine the…
Folding and unfolding of biopolymers are often manipulated in experiment by tuning pH, temperature, single-molecule force or shear field. Here we carry out Brownian dynamics simulations to explore the behavior of a single self-attracting…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
We present a modified version of our "sliding model", where chain arcs, between two contacts at the surface, may move if all the barriers along the arc are weaker than a certain threshold.An important advance of the revised model is that…
We investigate the behavior of entanglement entropy in the holographic QCD model proposed by Gubser et al. By choosing suitable parameters of the scalar self-interaction potential, this model can exhibit various types of phase structures:…
We investigate the crystallization mechanism of a single, flexible homopolymer chain with short range attractions. For a sufficiently narrow attractive well, the system undergoes a first-order like freezing transition from an expanded…
Bridging algorithms are global Monte Carlo moves which allow for an efficient sampling of single polymer chains. In this manuscript we discuss the adaptation of three bridging algorithms from lattice to continuum models, and give details on…
Pressure-induced phase transitions of spin-crossover materials were simulated by a Monte Carlo simulation in the constant pressure ensemble for the first time. Here, as the origin of the cooperative interaction, we adopt elastic interaction…
In this paper we complete the study of the phase diagram and conformational states of a stiff homopolymer. It is known that folding of a sufficiently stiff chain results in formation of a torus. We find that the phase diagram obtained from…
We investigate the cooperative effects of a single finite chain of monomers near an attractive substrate by first constructing a conformational pseudo-phase diagram based on the thermal fluctuations of energetic and structural quantities.…
The equilibrium thermodynamic properties of a linear polymer chain confined to a space between two impenetrable walls (lines) at a distance $D$ under various solvent conditions have been studied using series analysis and exact enumeration…
In earlier work we provided the first evidence that the collapse, or coil-globule, transition of an isolated polymer in solution can be seen in a four-dimensional model. Here we investigate, via Monte Carlo simulations, the canonical…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…