Related papers: Parallel computing for 4-atomic molecular dynamics…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
To prepare images for better segmentation, we need preprocessing applications, such as smoothing, to reduce noise. In this paper, we present an enhanced computation method for smoothing 2D object in binary case. Unlike existing approaches,…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing…
In this work, a new partition-collocation strategy for the parallel execution of CFD--DEM couplings is investigated. Having a good parallel performance is a key issue for an Eulerian-Lagrangian software that aims to be applied to solve…
We describe source code level parallelization for the {\tt kira} direct gravitational $N$-body integrator, the workhorse of the {\tt starlab} production environment for simulating dense stellar systems. The parallelization strategy, called…
The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject,…
This paper presents implementation details and empirical results for a hybrid message passing and shared memory paralleliziation of the adaptive integral method (AIM). AIM is implemented on a (near) petaflop supercomputing cluster of…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of…
Parallel multiphysics simulations often suffer from load imbalances originating from the applied coupling of algorithms with spatially and temporally varying workloads. It is thus desirable to minimize these imbalances to reduce the time to…
Parallel computing is a standard approach to achieving high-performance computing (HPC). Three commonly used methods to implement parallel computing include: 1) applying multithreading technology on single-core or multi-core CPUs; 2)…
We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
We construct the velocity map images of the proton transfer reaction between helium and molecular hydrogen ions H2+. We perform simulations of imaging experiments at one representative total collision energy taking into account the inherent…
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…
We present a novel class of methods to compute functions of matrices or their action on vectors that are suitable for parallel programming. Solving appropriate simple linear systems of equations in parallel (or computing the inverse of…
This paper describes the parallel implementation of the TRANSIMS traffic micro-simulation. The parallelization method is domain decomposition, which means that each CPU of the parallel computer is responsible for a different geographical…
Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik et al., Science 309, 1704 (2005)] that they, if available, would be able to perform the full…
We provide algorithms for efficiently addressing quantum memory in parallel. These imply that the standard circuit model can be simulated with low overhead by the more realistic model of a distributed quantum computer. As a result, the…