Related papers: ls1 mardyn: The massively parallel molecular dynam…
This paper describes `Ludwig', a versatile code for the simulation of Lattice-Boltzmann (LB) models in 3-D on cubic lattices. In fact `Ludwig' is not a single code, but a set of codes that share certain common routines, such as I/O and…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
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…
Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…
For computational fluid dynamics (CFD) applications with a large number of grid points/cells, parallel computing is a common efficient strategy to reduce the computational time. How to achieve the best performance in the modern…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
Electrolyte solutions play critical role in a vast range of important applications, yet an accurate and scalable method of predicting their properties without fitting to experiment has remained out of reach, despite over a century of…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
Recent developments dedicated to the building of multiscale mechanical and chemical constitutive laws for energetic molecular crystals are presented and discussed. In particular, various tools have been specifically incorporated in…
Based on a plausible requirement for the ground state density, we introduce a novel one-dimensional (1D) atomic model potential for the 1D simulation of the quantum dynamics of a single active electron atom driven by a strong, linearly…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
Multidimensional nucleosynthesis studies with hundreds of nuclei linked through thousands of nuclear processes are still computationally prohibitive. To date, most nucleosynthesis studies rely either on hydrostatic/hydrodynamic simulations…
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…
Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular…
Large-scale first principles molecular dynamics are crucial for simulating complex processes in chemical, biomedical, and materials sciences. However, the unfavorable time complexity with respect to system sizes leads to prohibitive…
A massively parallel simulation code, called \textit{dHybrid}, has been developed to perform global scale studies of space plasma interactions. This code is based on an explicit hybrid model; the numerical stability and parallel scalability…