Related papers: ms2: A molecular simulation tool for thermodynamic…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
A hybrid scheme that utilizes MPI for distributed memory parallelism and OpenMP for shared memory parallelism is presented. The work is motivated by the desire to achieve exceptionally high Reynolds numbers in pseudospectral computations of…
Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator.…
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…
In this article, we propose a novel conservative diffuse-interface method for the simulation of immiscible compressible two-phase flows. The proposed method discretely conserves the mass of each phase, momentum and total energy of the…
A recently proposed molecular model is discussed as a non-trivial extension of the Ising model. For d=2 the two models are shown to be equivalent, while for d>2 the molecular model describes a peculiar second order transition from an…
We have developed a fully parallel C++/MPI based simulation code for variable-density particle-laden turbulent flows. The fluid is represented through a uniform Eulerian staggered grid, while particles are modeled using a Lagrangian…
Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations, for example…
Thermodynamics and dynamics of a classical two-dimensional system with dipole-like isotropic repulsive interactions are studied systematically using extensive molecular dynamics (MD) simulations supplemented by appropriate theoretical…
Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…
We compare the mass functions obtained analytically, in the framework of an extended Press & Schechter (PS) formalism, in a previous paper to the numerical mass functions obtained in N -- body simulations, using different algorithms to…
A numerical model and parallel software for 3D simulations of granular flows have been developed based on the Lagrangian particle (LP) method [R.Samulyak, X. Wang, H.-C. Chen, Lagrangian particle method for compressible fluid dynamics, J.…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
An effective computer program for three dimensional relativistic hydrodynamical model has been developed. It implements a new approach to the early hot phase of relativistic heavy-ion collisions. The computer program simulates time-space…
The need to use a short time step is a key limit on the speed of molecular dynamics (MD) simulations. Simulations governed by classical potentials are often accelerated by using a multiple-time-step (MTS) integrator that evaluates certain…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…