The shear viscosity coefficient of the one-component plasma is calculated with unprecedented accuracy using equilibrium molecular dynamics simulations and the Green-Kubo relation. Numerical and statistical uncertainties and their mitigation for improving accuracy are analyzed. In the weakly coupled regime, our results agree with the Landau-Spitzer prediction. In the moderately and strongly coup...

The use of coarse-grained (CG) models can significantly increase the time and length scales accessible to computational molecular dynamics (MD) simulations. To address very large-scale phenomena, however, requires a careful consideration of memory requirements and parallel MD load balancing in order to make efficient use of current supercomputers. In this work, a CG-MD code is introduced which ...

The MacArthur-Wilson equilibrium theory of island biogeography has been one of the more influential concepts in modern biogeography and ecology. In this paper, we synthesize the theory and examine effects of different immigration/extinction rate-species diversity curves on original predictions from the theory by using the System Dynamics simulation modeling approach. Moreover, we develop a comp...

Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate experimentally. We describe a multiscale method for the simulation of such systems in which the energetically active region is modelled using a robust tight-binding...

In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are...

Non-Newtonian fluids are widely used in microfluidic systems and biomedical fields. In this paper, based on molecular dynamics simulation, taking the system composed of sodium carboxymethyl cellulose molecules water as research object, configuration evolutions solution simulated under different shear rates. Change viscosity is characterized by mean square displacement relative velocity between ...

the internal structure of a molecule can be presented in terms of intra-molecular (i.e., inter atomic)and inter-molecular energies such as van der waals, bond and bending, torsion, and inversion energy.in this study, changes in molecular energies of individual asphalt components are evaluated as afunction of physical aging factors. the factors for physical aging such as temperature and pressure...

The distortion of structure of a simple, inverse-12, soft-disk fluid undergoing two-dimensional plane Couette flow was studied by nonequilibrium molecular dynamics (NEMD) simulation and by equilibrium Monte Carlo (MC) simulation with a nonequilibrium potential, under which the equilibrium structure of the fluid is that of the nonequilibrium fluid. Extension of the iterative predictor-corrector ...