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Machine-learned interatomic potentials have revolutionized molecular dynamics simulations by providing quantum-mechanical accuracy at empirical-potential speeds. The graphics processing unit molecular dynamics (GPUMD) package, featuring the…
Particle tracking simulations with space charge effects are very important for high-intensity proton rings. Since they include not only Hamilton mechanics of a single particle but constructing charge densities and solving Poisson equations…
The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size…
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…
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…
We equip dynamic geometry software (DGS) with a user-friendly method that enables massively parallel calculations on the graphics processing unit (GPU). This interplay of DGS and GPU opens up various applications in education and…
Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…
Recent progress in artificial intelligence (AI) and high-performance computing (HPC) have brought potentially game-changing opportunities in accelerating reactive flow simulations. In this study, we introduce an open-source computational…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
We describe the use of Graphics Processing Units (GPUs) for speeding up the code NBODY6 which is widely used for direct $N$-body simulations. Over the years, the $N^2$ nature of the direct force calculation has proved a barrier for…
A micromagnetic simulator running on graphics processing unit (GPU) is presented. It achieves significant performance boost as compared to previous central processing unit (CPU) simulators, up to two orders of magnitude for large input…
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…
Molecular dynamics (MD) simulations are a central tool in science and engineering enabling the study of dynamical behavior and the link between microscopic structure and macroscopic function. Their high computational cost, however, has…
We present implementations of a fourth-order symplectic integrator on graphic processing units for three $N$-body models with long-range interactions of general interest: the Hamiltonian Mean Field, Ring and two-dimensional self-gravitating…
With large-scale Integral Field Spectroscopy (IFS) surveys of thousands of galaxies currently under-way or planned, the astronomical community is in need of methods, techniques and tools that will allow the analysis of huge amounts of data.…
Hybrid computational architectures based on the joint power of Central Processing Units and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering,…
Graphics Processing Units (GPUs) are now powerful and flexible systems adapted and used for other purposes than graphics calculations (General Purpose computation on GPU -- GPGPU). We present here a prototype to be integrated into…
We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the atomic dynamics in structural…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…