The formation and dynamics of long living metastable structures, the pressure tensor and diffusion properties of a simple particle system confined by a (infinite) nanopore with rectangular cross section is investigated using molecular dynamics simulation. The system is characterized by a short...

We study, by means of molecular dynamics (MD) simulations with explicit water, the structure and stability of β-sheet tapes, ribbons and double ribbons formed by rationally designed oligopeptides P11-I and P11-II in aqueous solutions. Two different methods for the treatment of the electrostatic...

We investigate the influence of long-range interactions on the energy localization in a one-dimensional Morse chain with an impurity by molecular dynamics simulations. The energy distribution around the impurity is studied. It shows that in the high temperature limit there is no difference upon...

A gas of particles which collide inelastically if their impact velocity exceeds a certain value is investigated. In difference to common granular gases, cluster formation occurs only as a transient phenomenon. We calculate the decay of temperature due to inelastic collisions. In spite of the...

The study of properties of water in the vicinity of surfaces poses a fascinating challenge. In this article we studied the behavior of water molecules in the neighborhood of membranes. We addressed the question of how these water molecules are influenced by the membranes’ hydrophilicity. Three...

Using molecular dynamics (MD) simulation and evolutionary game theory, we incorporate the spacial structure of individuals into the study of the behaviors of cooperation, by adopting the prisoner's dilemma and snowdrift game as metaphors of cooperation between unrelated individuals. The results...

Massively-parallel classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) model and single-particle model of Molinero <i>et al.</i> applied to simulation of methane hydrates, using systems consisting of...

We examine a simple non-equilibrium molecular dynamics (NEMD) technique for studying hard-spheroid fluids under shear flow. The method involves applying a thermostat which uses an analytical formula for the streaming angular velocity as a function of molecular orientation. Preliminary results...

Benford’s law is investigated for the simulation results generated from non-equilibrium molecular dynamics. A statistic to measure how closely a set of the numbers follows Benford’s law is defined. The simulation data are from the collisions of two nano droplets with different impact...

Panic during emergency building evacuation can cause crowd stampede, resulting in serious injuries and casualties. Agent-based methods have been successfully employed to investigate the collective human behavior during emergency evacuation in cases where the configurational space is extremely...