Related papers: Non-Gaussian dynamics from a simulation of a short…
Inhomogeneous polymers play an important role in various cellular processes, both in nature and in biotechnological applications. At finite temperatures, inhomogeneous polymers exhibit non-trivial thermal fluctuations. In a broader context,…
We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The…
Polymer chains with hard-core interaction on a two-dimensional lattice are modeled by directed random walks. Two models, one with intersecting walks (IW) and another with non-intersecting walks (NIW) are presented, solved and compared. The…
Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influence the…
Self-diffusion of a polymer chain in a melt is studied by Monte Carlo simulations of the bond fluctuation model, where only the excluded volume interaction is taken into account. Polymer chains, each of which consists of $N$ segments, are…
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials in a membrane-less fashion. Traditionally, these condensates…
We adopt the GW approximation and random phase approximation to study finite temperature effects on the inelastic mean free path and quasiparticle lifetime by directly calculating the imaginary part of the finite temperature self-energy…
A new first-principles statistical mechanics formulation is proposed to describe slow and dilated granular fluids, where prolonged intergranular contacts vitiate collision theory. The contacts, where all the important physics takes place,…
Constant temperature molecular dynamics simulations were used to study solutions of flexible polyelectrolyte chains at nonzero concentrations with explicit counterions and unscreened coulombic interactions. Counterion condensation, measured…
Some nearly-symmetric fusion reactions are systematically investigated with the improved quantum molecular dynamics (ImQMD) model. By introducing two-body inelastic scattering in the Fermi constraint procedure, the stability of an…
We perform a study of the interfacial properties of a model suspension of hard sphere colloids with diameter $\sigma_c$ and non-adsorbing ideal polymer coils with diameter $\sigma_p$. For the mixture in contact with a planar hard wall, we…
We present simulation data for the motion of a polymer chain through a regular lattice of impenetrable obstacles (Evans-Edwards model). Chain lengths range from N=20 to N=640, and time up to $10^{7}$ Monte Carlo steps. For $N \geq 160$ we…
Recent studies have established a connection between the macroscopic mechanical response of polymeric materials and the statistics of the shortest path (SP) length between distant nodes in the polymer network. Since these statistics can be…
We investigate Fickian diffusion in two-dimensional (2D) Yukawa liquids using molecular dynamics simulations. We compute the self-van Hove correlation function $G_s(r,t)$, and the self-intermediate scattering function $F_s(k,t)$ and compare…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
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 theoretically investigate the looping dynamics of a linear polymer immersed in a viscoelastic fluid. The dynamics of the chain is governed by a Rouse model with a fractional memory kernel recently proposed by Weber et al. (S. C. Weber,…
The endpoint distribution and dynamics of semiflexible fibers is studied by numerical simulation. A brief overview is given over the analytical theory of flexible and semiflexible polymers. In particular, a closed expression is given for…
Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…
We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the Mean First Contact Time (MFCT) for various…