Related papers: Molecular Dynamics Simulation of Macromolecules Us…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
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)…
The recent trend of using Graphics Processing Units (GPU's) for high performance computations is driven by the high ratio of price performance for these units, complemented by their cost effectiveness. At first glance, computational fluid…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
It is shown micromagnetic and atomistic spin dynamics simulations can use multiple GPUs in order to reduce computation time, but also to allow for a larger simulation size than is possible on a single GPU. Whilst interactions which depend…
Over the last couple of years it has been realized that the vast computational power of graphics processing units (GPUs) could be harvested for purposes other than the video game industry. This power, which at least nominally exceeds that…
For many years, systems running Nvidia-based GPU architectures have dominated the heterogeneous supercomputer landscape. However, recently GPU chipsets manufactured by Intel and AMD have cut into this market and can now be found in some of…
Simulations of standard 1D and 2D quantum walks have been performed within Quantum Computer Simulator (QCS system) environment and with the use of GPU supported by CUDA technology. In particular, simulations of quantum walks may be seen as…
We explore how the big-three computing paradigms -- symmetric multi-processor (SMC), graphical processing units (GPUs), and cluster computing -- can together be brought to bare on large-data Gaussian processes (GP) regression problems via a…
A finite-difference Micromagnetic solver is presented utilizing the C++ Accelerated Massive Parallelism (C++ AMP). The high speed performance of a single Graphics Processing Unit (GPU) is demonstrated compared to a typical CPU-based solver.…
In this paper we describe and demonstrate a C++ code written to determine the trajectory of particles traversing oriented single crystals and a CUDA code written to evaluate the radiation spectra from charged particles with arbitrary…
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…
This paper introduces open-source computational fluid dynamics software named open computational fluid dynamic code for scientific computation with graphics processing unit (GPU) system (OpenCFD-SCU), developed by the authors for direct…
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…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at specified potential difference,…
As high energy physics experiments reach higher luminosities and intensities, the computing burden for real time data processing and reduction grows. Following the developments in the computing landscape, multi-core processors such as…
The future of computation is the Graphical Processing Unit, i.e. the GPU. The promise that the graphics cards have shown in the field of image processing and accelerated rendering of 3D scenes, and the computational capability that these…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…