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The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but…
Divertor plasma detachment is likely needed for the function of magnetically confined nuclear fusion. It greatly reduces the particle and heat flux incident on a target, and thus reduces the sputtering and heat loading on the target. It is…
The long-time behavior of a reaction-diffusion front between one static (e.g. porous solid) reactant A and one initially separated diffusing reactant B is analyzed for the mean-field reaction-rate density R(\rho_A,\rho_B) =…
Semi-analytical expressions are suggested for the temperature dependence of those combinations of transport coefficients which govern the fission process. This is based on experience with numerical calculations within the linear response…
Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ)…
The critical behavior of a dimer model with an interaction favoring parallel dimers in each plaquette of the square lattice is studied numerically by means of the Corner Transfer Matrix Renormalization Group algorithm. The critical…
The consistency across scales of a recently developed mathematical thermodynamic structure, between a continuous stochastic nonlinear dynamical system (diffusion process with Langevin or Fokker-Planck equations) and its emergent discrete,…
The dynamical evolution of a Brownian particle in an inhomogeneous medium with spatially varying friction and temperature field is important to understand conceptually. It requires to address the basic problem of relative stability of…
Within the Langevin framework, we investigate the dynamics of the fusion process for production of transfermium elements in reactions of $^{48}$Ca, $^{50}$Ti, $^{54}$Cr, and $^{58}$Fe with $^{208}$Pb. After the reacting nuclei have made…
This study deals with polymer looping, an important process in many chemical and biological systems. We investigate basic questions on the looping dynamics of a polymer under tension using the freely-jointed chain (FJC) model. Previous…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
Thermal activation of dislocations is critical for predicting the mechanical response of materials under common experimental conditions. According to transition state theory (TST), the rate for the system to overcome free energy barriers…
We consider a run-and-tumble particle on a half-line with an absorbing target at the origin. The particle has an internal velocity state that switches between two opposite values at Poisson-distributed times. The position of the particle…
We present a Generalized Langevin Equation for the dynamics of interacting semiflexible polymer chains, undergoing slow cooperative dynamics. The calculated Gaussian intermolecular center-of-mass and monomer potentials, wich enter the GLE,…
The efficiency of an encounter-controlled two-channel reaction between two independently-mobile reactants on a lattice is characterized by the mean number $\rt$ of steps to reaction. The two reactants are distinguished by their mass with…
We analyse the motion of a system of particles subjected a random force fluctuating in both space and time, and experiencing viscous damping. When the damping exceeds a certain threshold, the system undergoes a phase transition: the…
The length-scale dependence of the dynamic entropy is studied in a molecular dynamics simulation of a binary Lennard-Jones liquid above the mode-coupling critical temperature $T_c$. A number of methods exist for estimating the entropy of…
We study the effect of a gradient of solvent quality on the coil-globule transition for a polymer in a narrow pore. A simple self-attracting self-avoiding walk model of a polymer in solution shows that the variation in the strength of…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…