相关论文: Message-Passing Multi-Cell Molecular Dynamics on t…

We describe an efficient Particle-Mesh algorithm for the Connection Machine CM-5. Our particular method parallelizes well and the computation time per time step decreases as the particles become more clustered. We achieve floating-point…

We present an algorithm for cluster dynamics to efficiently simulate large systems on MIMD parallel computers with large numbers of processors. The method divides physical space into rectangular cells which are assigned to processors and…

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…

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…

This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…

In diffusion-based molecular communication, information particles locomote via a diffusion process, characterized by random movement and heavy tail distribution for the random arrival time. As a result, the molecular communication shows…

We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…

This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…

The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…

In this demonstration, we will present the world's first molecular multiple-input multiple-output (MIMO) communication link to deliver two data streams in a spatial domain. We show that chemical signals such as concentration gradients could…

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…

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…

Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…

The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…

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…

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…

Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…

We present a simple hierarchical communication scheme for distributed Fast Multipole Methods (FMMs) based on MPI neighborhood collectives and uniform trees. The method targets the common case of extending an existing high-performance…

We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…