Related papers: Long-range interactions & parallel scalability in …
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
As compute power increases with time, more involved and larger simulations become possible. However, it gets increasingly difficult to efficiently use the provided computational resources. Especially in particle-based simulations with a…
We present a parallel implementation of the particle-particle/particle-mesh (P3M) algorithm for distributed memory clusters. The GRACOS (GRAvitational COSmology) code uses a hybrid method for both computation and domain decomposition.…
The fast Ewald methods are widely used to compute the point-charge electrostatic interactions in molecular simulations. The key step that introduces errors in the computation is the particle-mesh interpolation. In this work, the optimal…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
Quantum computing is moving beyond its early stage and seeking for commercial applications in chemical and biomedical sciences. In the current noisy intermediate-scale quantum computing era, quantum resource is too scarce to support these…
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…
Molecular dynamics simulations are essential tools in computational biophysics, but their performance depend heavily on hardware choices and configuration. In this work, we presents a comprehensive performance analysis of four NVIDIA GPU…
Variational quantum algorithms (VQAs) are increasingly being applied in simulations of strongly-bound (covalently bonded) systems using full molecular orbital basis representations. The application of quantum computers to the weakly-bound…
A new parallel algorithm utilizing partitioned global address space (PGAS) programming model to achieve high scalability is reported for particle tracking in direct numerical simulations of turbulent flow. The work is motivated by the…
Particle-in-Cell (PIC) simulations are fundamental to plasma physics but often suffer from limited scalability due to particle-grid interaction bottlenecks and particle redistribution costs. Specifically, the particle-grid interaction…
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
Particle-in-cell (PIC) simulations with Monte-Carlo collisions are used in plasma science to explore a variety of kinetic effects. One major problem is the long run-time of such simulations. Even on modern computer systems, PIC codes take a…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
This paper presents a recently developed particle simulation code package PIFE-PIC, which is a novel three-dimensional (3-D) Parallel Immersed-Finite-Element (IFE) Particle-in-Cell (PIC) simulation model for particle simulations of…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
Ab initio wavefunction methods provide accurate molecular simulations but their computational scaling restricts applications to small systems. We develop a workflow combining quantum embedding to decompose a molecule into fragments with a…