Support for Multiscale Simulations with Molecular Dynamics

Dynamics of Macro–Nano Mechanical Systems; Fixed Interfacial Multiscale Method

The continuum based approaches don’t provide the correct physics in atomic scales. On the other hand, the molecular based approaches are limited by the length and simulated process time. As an attractive alternative, this paper proposes the Fixed Interfacial Multiscale Method (FIMM) for computationally and mathematically efficient modeling of solid structures. The approach is applicable to mult...

Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations

Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...

Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations

The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...

Long Range Corrections to the Vapor-Liquid Equilibrium and Surface Tension of Methane with NVT Molecular Dynamics Simulations

Influences of Small-Scale Effect and Boundary Conditions on the Free Vibration of Nano-Plates: A Molecular Dynamics Simulation

This paper addresses the influence of boundary conditions and small-scale effect on the free vibration of nano-plates using molecular dynamics (MD) and nonlocal elasticity theory. Based on the MD simulations, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used to obtain fundamental frequencies of single layered graphene sheets (SLGSs) which modeled in this paper as the mo...

Molecular dynamics studies of straight-chain alkanes diffusion in SiO2 ceramic versus Bosanquet formula

Molecular Dynamics (MD) simulations were applied to calculate self-diffusion coefficients (Di ) and heats of adsorption for ethane, propane and n-butane. The simulations were done in temperature range of 300-525 K for various concentrations inside the pores of silicalite type zeolite. The calculated values of self-diffusion coefficients and heats of adsorption resulted from the current wo...