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New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…
Numerical simulations of the propagation of charged particles through magnetic fields solving the equation of motion often leads to the usage of an interpolation in case of discretely defined magnetic fields, typically given on a…
Accurate representation of the molecular electrostatic potential, which is often expanded in distributed multipole moments, is crucial for an efficient evaluation of intermolecular interactions. Here we introduce a machine learning model…
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established quantitative descriptors (features). Graph neural networks…
Fast Multipole Methods (FMM) are a fundamental operation for the simulation of many physical problems. The high performance design of such methods usually requires to carefully tune the algorithm for both the targeted physics and the…
Imaginary-time path integral (PI) is a rigorous tool to compute static properties at finite temperatures. However, the stiff PI internal modes poses a sampling challenge. This is commonly tackled using staging coordinates, in which the free…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…
We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
Polymerization of C60 molecular crystal under high pressure and high temperature is simulated by using linear scaling tight binding molecular dynamics (TBMD) with Graphic Processing Unit (GPU) as a computational accelerator for…
Smoothed particle hydrodynamics (SPH) discretization techniques are generalized to develop a method, smoothed particle interpolation (SPI), for solving initial value problems of systems of non-hydrodynamical nature. Under this approach, SPH…
In recent years, machine learning interatomic potentials (MLIPs) have attracted significant attention as a method that enables large-scale, long-time atomistic simulations while maintaining accuracy comparable to electronic structure…
Our understanding of magnetic reconnection (MR) under chromospheric conditions remains limited. Recent observations have demonstrated the important role of ion-neutral interactions in the dynamics of the chromosphere. Furthermore, the…
Heliospheric plasmas require multi-scale and multi-physics considerations. On one hand, MHD codes are widely used for global simulations of the solar-terrestrial environments, but do not provide the most elaborate physical description of…
In this paper a simple, robust, and general purpose approach to implement the Incompressible Smoothed Particle Hydrodynamics (ISPH) method is proposed. This approach is well suited for implementation on CPUs and GPUs. The method is…
The distribution of Helium in the intracluster medium (ICM) permeating galaxy clusters is not well constrained due to the very high plasma temperature. Therefore, the plasma is often assumed to be homogeneous. A non-uniform Helium…
We investigate a hybrid numerical algorithm aimed at the large-scale cosmological N-body simulation for the on-going and the future high precious sky surveys. It makes use of a truncated Fast Multiple Method (FMM) for short-range gravity,…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…