相关论文: Coupling a reactive potential with a harmonic appr…
All-atom dynamics simulations are an indispensable quantitative tool in physics, chemistry, and materials science, but large systems and long simulation times remain challenging due to the trade-off between computational efficiency and…
The goal of this paper is to demonstrate the general modeling and practical simulation of random equations with mixture model parameter random variables. Random equations, understood as stationary (non-dynamical) equations with parameters…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…
Molecules with versatile functionalities and well-defined structures, can serve as building blocks for extreme nanoscale devices. This requires their precise integration into functional heterojunctions, most commonly in the form of…
We present a GPU-friendly framework for real-time implicit simulation of elastic material in the presence of frictional contacts. The integration of hyperelasticity, non-interpenetration contact, and friction in real-time simulations…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious…
The development of interatomic potentials that can accurately capture a wide range of physical phenomena and diverse environments is of significant interest, but it presents a formidable challenge. This challenge arises from the numerous…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Dimensionality reduction of decision variables is a practical and classic method to reduce the computational burden in linear and Nonlinear Model Predictive Control (NMPC). Available results range from early move-blocking ideas to…
We present simulations of magnetized astrophysical shocks taking into account the interplay between the thermal plasma of the shock and supra-thermal particles. Such interaction is depicted by combining a grid-based magneto-hydrodynamics…
Non-ideal MHD effects are thought to be a crucial component of the star-formation process. Numerically, several complications render the study of non-ideal MHD effects in 3D simulations extremely challenging and hinder our efforts of…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
We describe a method for coupling an embedded domain in a magnetohydrodynamic (MHD) simulation with a particle-in-cell (PIC) method. In this two-way coupling we follow the work of Daldorff et al. in which the PIC domain receives its initial…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
Ring-polymer molecular dynamics (RPMD) has become a popular method for describing chemical reactions due to its ability to simultaneously capture tunneling, zero-point energy, anharmonicity and recrossing. Here we highlight that despite its…
A robust method to handle vacuum and near vacuum regions in hybrid simulations for space and astrophysical plasmas is presented. The conventional hybrid simulation model dealing with kinetic ions and a massless charge-neutralizing electron…
The particle contact model is important for powder simulations. Although several contact models have been proposed, their validity has not yet been well established. Therefore, we perform molecular dynamics (MD) simulations to clarify the…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…