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

We present results of the implementation of one MILC lattice QCD application-simulation with dynamical clover fermions using the hybrid-molecular dynamics R algorithm-on the Cell Broadband Engine processor. Fifty-four individual…

The fifth generation (5G) of the wireless communication networks supports wide diversity of service classes, leading to a highly dynamic uplink (UL) and downlink (DL) traffic asymmetry. Thus, dynamic time division duplexing (TDD) technology…

We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…

Increasing AI computing demands and slowing transistor scaling have led to the advent of Multi-Chip-Module (MCMs) based accelerators. MCMs enable cost-effective scalability, higher yield, and modular reuse by partitioning large chips into…

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…

We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…

Using a realistic molecular catalyst system, we conduct scaling studies of ab initio molecular dynamics simulations using the CP2K code on both Intel Xeon CPU and NVIDIA V100 GPU architectures. We explore using process placement and…

MDMP is a new parallel programming approach that aims to provide users with an easy way to add parallelism to programs, optimise the message passing costs of traditional scientific simulation algorithms, and enable existing MPI-based…

We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that…

In this paper, we propose a novel distributed alternating direction method of multipliers (ADMM) algorithm with synergetic communication and computation, called SCCD-ADMM, to reduce the total communication and computation cost of the…

We provide a mathematically proven parallelization scheme for particle methods on distributed-memory computer systems. Particle methods are a versatile and widely used class of algorithms for computer simulations and numerical predictions…

We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…

Molecular communication (MC) enables information exchange at the nano- and microscale, with applications in areas like drug delivery and health monitoring. These event-driven scenarios often require alternatives to traditional transmission.…

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…

Diffusive molecular communications (DiMC) have recently gained attention as a candidate for nano- to micro- and macro-scale communications due to its simplicity and energy efficiency. As signal propagation is solely enabled by Brownian…

Modern compute nodes in high-performance computing provide a tremendous level of parallelism and processing power. However, as arithmetic performance has been observed to increase at a faster rate relative to memory and network bandwidths,…

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…

In this paper, we present a fluid-based experimental molecular communication (MC) testbed that, similar to the human cardiovascular system, operates in a closed circuit tube system. The proposed system is designed to be biocompatible,…

This paper presents the Parallel Coupler for Multimodel Simulations (PCMS), a new GPU accelerated generalized coupling framework for coupling simulation codes on leadership class supercomputers. PCMS includes distributed control and field…