Related papers: Langevin dynamics simulations of biomolecules on g…
We present the results of gravitational direct $N$-body simulations using the Graphics Processing Unit (GPU) on a commercial NVIDIA GeForce 8800GTX designed for gaming computers. The force evaluation of the $N$-body problem is implemented…
Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and…
Heterogeneity in the cell population of cancer tissues poses many challenges in cancer diagnosis and treatment. Studying the heterogeneity in cell populations from gene expression measurement data in the context of cancer research is a…
Computational fluid dynamics and fluid-structure interaction simulations involving moving and deforming bodies is extremely hard. In this work, we present a graphical processing unit (GPU) optimized implementation of the sharp-interface…
Real-time trajectory optimization for nonlinear constrained autonomous systems is critical and typically performed by CPU-based sequential solvers. Specifically, reliance on global sparse linear algebra or the serial nature of dynamic…
In the next decade, the demands for computing in large scientific experiments are expected to grow tremendously. During the same time period, CPU performance increases will be limited. At the CERN Large Hadron Collider (LHC), these two…
General purpose computing on graphic processing units (GPU) is a potential method of speeding up scientific computation with low cost and high energy efficiency. We experimented with the particle physics simulation toolkit Geant4 used at…
The Graphics Processing Unit (GPU) is a powerful tool for parallel computing. In the past years the performance and capabilities of GPUs have increased, and the Compute Unified Device Architecture (CUDA) - a parallel computing architecture…
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…
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…
Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is…
This paper presents a Graphics Processing Units (GPUs) acceleration method of an iterative scheme for gas-kinetic model equations. Unlike the previous GPU parallelization of explicit kinetic schemes, this work features a fast converging…
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…
Current trends in the computer graphics community propose leveraging the massive parallel computational power of GPUs to accelerate physically based simulations. Collision detection and solving is a fundamental part of this process. It is…
Graphics Processing Unit, or GPUs, have been successfully adopted both for graphic computation in 3D applications, and for general purpose application (GP-GPUs), thank to their tremendous performance-per-watt. Recently, there is a big…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
Gaussian Processes have become an indispensable part of the spatial statistician's toolbox but are unsuitable for analyzing large dataset because of the significant time and memory needed to fit the associated model exactly. Vecchia…
This paper focuses on the parallel implementation of a direct $N$-body method~(particle-particle algorithm) and the application of multiple GPUs for galactic dynamics simulations. Application of a hybrid OpenMP-CUDA technology is considered…
Graphics processing units (GPU) had evolved from a specialized hardware capable to render high quality graphics in games to a commodity hardware for effective processing blocks of data in a parallel schema. This evolution is particularly…
In this work we present an efficient implementation of Canonical Monte Carlo simulation for Coulomb many body systems on graphics processing units (GPU). Our method takes advantage of the GPU Single Instruction, Multiple Data (SIMD)…