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Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging…
We develop a novel parallel resampling algorithm for fully parallelized particle filters, which is designed with GPUs (graphics processing units) or similar parallel computing devices in mind. With our new algorithm, a full cycle of…
The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD,…
GPUs have significantly accelerated first-order methods for large-scale optimization, especially in continuous optimization. However, this success has not transferred cleanly to problems with discrete variables, combinatorial structure, and…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
We created an efficient algorithm suitable for graphics processing units (GPUs) to perform Monte Carlo simulations of a subset of reaction-diffusion models. The algorithm uses techniques that are specific to GPU programming, and combines…
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…
We employ the Partially Saturated Cells Method (PSM) to model the interaction between the fluid flow and solid moving objects as an extension to the conventional lattice Boltzmann method. We introduce an efficient and accurate method for…
Obtaining a thermodynamically accurate phase diagram through numerical calculations is a computationally expensive problem that is crucially important to understanding the complex phenomena of solid state physics, such as superconductivity.…
We provide a preliminary study on utilizing GPU (Graphics Processing Unit) to accelerate computation for three simulation optimization tasks with either first-order or second-order algorithms. Compared to the implementation using only CPU…
Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent, widely used to access the microscopic transitions in biomolecules, require a reliable source of random numbers. Here we present the two main…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
We present an implementation of phaseless Auxiliary-Field Quantum Monte Carlo (ph-AFQMC) utilizing graphical processing units (GPUs). The AFQMC method is recast in terms of matrix operations which are spread across thousands of processing…
We propose a CPU-GPU heterogeneous computing method for solving time-evolution partial differential equation problems many times with guaranteed accuracy, in short time-to-solution and low energy-to-solution. On a single-GH200 node, the…
Efficient simulation of quantum circuits has become indispensable with the rapid development of quantum hardware. The primary simulation methods are based on state vectors and tensor networks. As the number of qubits and quantum gates grows…
Highly-parallel graphics processing units (GPUs) can improve the speed of micromagnetic simulations significantly as compared to conventional computing using central processing units (CPUs). We present a strategy for performing…
Probabilistic breadth-first traversals (BPTs) are used in many network science and graph machine learning applications. In this paper, we are motivated by the application of BPTs in stochastic diffusion-based graph problems such as…
We present an efficient implementation for running three-dimensional numerical simulations of fluid-structure interaction problems on single GPUs, based on Nvidia CUDA through Numba and Python. The incompressible flow around moving bodies…
There has been significant recent interest in parallel graph processing due to the need to quickly analyze the large graphs available today. Many graph codes have been designed for distributed memory or external memory. However, today even…
Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute…