Related papers: Tinker-HP : Accelerating Molecular Dynamics Simula…
Recently, task-based programming models have emerged as a prominent alternative among shared-memory parallel programming paradigms. Inherently asynchronous, these models provide native support for dynamic load balancing and incorporate data…
High-performance computing, together with a neural network model trained from data generated with first-principles methods, has greatly boosted applications of \textit{ab initio} molecular dynamics in terms of spatial and temporal scales on…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
The JOREK extended magneto-hydrodynamic (MHD) code is a widely used simulation code for studying the non-linear dynamics of large-scale instabilities in divertor tokamak plasmas. Due to the large scale-separation intrinsic to these…
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Finite element simulations play a critical role in a wide range of applications, from automotive design to tsunami modeling and computational electromagnetics. Performing these simulations efficiently at the high resolutions needed for…
The increasing energy footprint of artificial intelligence systems urges alternative computational models that are both efficient and scalable. Neuromorphic Computing (NC) addresses this challenge by empowering event-driven algorithms that…
Tensor Processing Units (TPUs) were developed by Google exclusively to support large-scale machine learning tasks. TPUs can, however, also be used to accelerate and scale up other computationally demanding tasks. In this paper we repurpose…
Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware…
Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. However, software-based cellular network simulation has…
The Liquid Argon Time Projection Chamber (LArTPC) technology plays an essential role in many current and future neutrino experiments. Accurate and fast simulation is critical to developing efficient analysis algorithms and precise physics…
Today's computing systems require moving data back-and-forth between computing resources (e.g., CPUs, GPUs, accelerators) and off-chip main memory so that computation can take place on the data. Unfortunately, this data movement is a major…
Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements,…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
TurboGAP is a software package designed for efficient molecular dynamics simulations using Gaussian Approximation Potential (GAP) machine-learning interatomic potentials (MLIP). In this work, we enhance the capabilities of TurboGAP for…
Tensor Cores have been an important unit to accelerate Fused Matrix Multiplication Accumulation (MMA) in all NVIDIA GPUs since Volta Architecture. To program Tensor Cores, users have to use either legacy wmma APIs or current mma APIs.…
We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous…