Related papers: Message-Passing Multi-Cell Molecular Dynamics on t…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
In the quest for highest performance in scientific computing, we present a novel framework that relies on high-bandwidth communication between GPUs in a compute cluster. The framework offers linear scaling of performance for explicit…
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…
A second-order accurate divergence-conserving hybrid particle-in-cell code Maximus has been developed for microscopic modeling of collisionless plasmas. The main specifics of the code include a constrained transport algorithm for exact…
Data transmission rate in molecular communication systems can be improved by using multiple transmitters and receivers. In molecular multiple-input multiple-output (MIMO) systems which use only single type of molecules, the performance at…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
Distributed MIMO and integrated sensing and communication are expected to be key technologies in future wireless systems, enabling reliable, low-latency communication and accurate localization. Dedicated localization solutions must support…
We report a model to evaluate the performance of multiple quantum key distribution (QKD) channel transmission using spatial division multiplexing (SDM) in multicore (MCF) and few-mode fibers (FMF). The model is then used to analyze the…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…
State-of-the-art numerical simulations of laser plasma by means of the Particle-in-Cell method are often extremely computationally intensive. Therefore there is a growing need for development of approaches for efficient utilization of…
We investigate the minimal number of failures that can partition a system where processes communicate both through shared memory and by message passing. We prove that this number precisely captures the resilience that can be achieved by…
This paper presents a distributed memory method for anisotropic mesh adaptation that is designed to avoid the use of collective communication and global synchronization techniques. In the presented method, meshing functionality is separated…
We study the feasibility of a PC-based parallel computer for medium to large scale lattice QCD simulations. The E\"otv\"os Univ., Inst. Theor. Phys. cluster consists of 137 Intel P4-1.7GHz nodes with 512 MB RDRAM. The 32-bit, single…
The Particle-In-Cell (PIC) method for plasma simulation tracks particle phase space information using particle and grid data structures. High computational costs in 2D and 3D device-scale PIC simulations necessitate parallelization, with…
In this paper we study from a numerical analysis perspective the Fractional Step Kinetic Monte Carlo (FS-KMC) algorithms proposed in [1] for the parallel simulation of spatially distributed particle systems on a lattice. FS-KMC are…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple…
Computational models have become one of the prevalent methods to model complex phenomena. To accurately model complex interactions, such as detailed biomolecular interactions, scientists often rely on multiscale models comprised of several…
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…