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

We present the basic idea, implementation, measured performance and performance model of FDPS (Framework for developing particle simulators). FDPS is an application-development framework which helps the researchers to develop particle-based…

Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…

We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…

The design and engineering of molecular communication (MC) components capable of processing chemical concentration signals is the key to unleashing the potential of MC for interdisciplinary applications. By controlling the signaling pathway…

Molecular Dynamics (MD) simulations play a central role in physics-driven drug discovery. MD applications often use the Particle Mesh Ewald (PME) algorithm to accelerate electrostatic force computations, but efficient parallelization has…

Cell-free massive multiple-input multiple-output (MIMO) is a promising technology for next-generation communication systems. This work proposes a novel partially coherent (PC) transmission framework to cope with the challenge of phase…

Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this,…

Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…

Heterogeneous memory technologies are increasingly important instruments in addressing the memory wall in HPC systems. While most are deployed in single node setups, CXL.mem is a technology that implements memories that can be attached to…

Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…

Mass spectrometry (MS) based omics data analysis require significant time and resources. To date, few parallel algorithms have been proposed for deducing peptides from mass spectrometry-based data. However, these parallel algorithms were…

Molecular communication (MC) can enable the transfer of information between nanomachines using molecules as the information carrier. In MC systems, multiple receiver nanomachines often co-exist in the same communication channel to serve…

The shape that stem cells reach at the end of adhesion process influences their differentiation. Rearrangement of cytoskeleton and modification of intracellular tension may activate mechanotransduction pathways controlling cell commitment.…

This paper concerns development of a high-performance implementation of the Particle-in-Cell method for plasma simulation on Intel Xeon Phi coprocessors. We discuss suitability of the method for Xeon Phi architecture and present our…

Distributed computing frameworks such as MapReduce and Spark are often used to process large-scale data computing jobs. In wireless scenarios, exchanging data among distributed nodes would seriously suffer from the communication bottleneck…

Accurate representation of the molecular electrostatic potential, which is often expanded in distributed multipole moments, is crucial for an efficient evaluation of intermolecular interactions. Here we introduce a machine learning model…

We introduce a memory- and compute-efficient method for low-communication distributed training. Existing methods reduce communication by performing multiple local updates between infrequent global synchronizations. We demonstrate that their…

The small cells in millimeter wave (mmWave) have been utilized extensively for the fifth generation (5G) mobile networks. And full-duplex (FD) communications become possible with the development of self-interference (SI) cancellation…

Quantum-mechanical methods are widely used for understanding molecular interactions throughout biology, chemistry, and materials science. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple…

The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…