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Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units

Ruxi Qi, Wesley M. Botello-Smith, Ray Luo

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Tags: Biomolecules, Biophysics, Boltzmann equation, Computational Physics, CUBLAS, CUDA, Electrostatics, Molecular simulation, nVidia, nVidia GeForce GTX 980 Ti, Physics, Poisson Boltzmann

April 11, 2017 by hgpu

An efficient numerical method for solving the Boltzmann equation in multidimensions

Giacomo Dimarco, Raphael Loubere, Jacek Narski, Thomas Rey

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Tags: Algorithms, Boltzmann equation, cfd, CUDA, Fluid dynamics, Mathematics, MPI, Numerical Analysis, nVidia, OpenMP, Physics

September 13, 2016 by hgpu

Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

Christopher D. Cooper, Lorena A. Barba

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Tags: Biomolecules, Boltzmann equation, Computational Physics, CUDA, Electrostatics, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

June 14, 2015 by hgpu

Optimization of solver for gas flow modeling

D. Savichkin, O. Dodulad, Yu. Kloss

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Tags: Boltzmann equation, Fluid dynamics, Intel Xeon Phi

May 29, 2014 by hgpu

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia

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Tags: Algorithms, Biology, Boltzmann equation, CUDA, Electrostatic potential, Electrostatics, Heterogeneous systems, Macromolecule, MPI, nVidia, nVidia GeForce GTX 580, Poisson Boltzmann, Tesla C2075

May 21, 2014 by hgpu

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba

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Tags: Biomolecules, Boltzmann equation, Computational Physics, CUDA, Electrostatics, Intel Phi, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

September 17, 2013 by hgpu

The Lattice Boltzmann Equation Method for Complex Flows

Laura Schaefer, Michael Ikeda, Jie Bao

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Tags: Boltzmann equation, Fluid dynamics, Lattice Boltzmann model, nVidia, nVidia GeForce GTX 280, Physics

May 15, 2013 by hgpu

Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

Christopher Cooper, Lorena A. Barba

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Tags: Bioinformatics, Biophysics, Boltzmann equation, Computational Physics, Computer science, CUDA, Electrostatics, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

January 31, 2013 by hgpu

High Performance Lattice Boltzmann Solvers on Massively Parallel Architectures with Applications to Building Aeraulics

Christian Obrecht

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Tags: Boltzmann equation, CUDA, Fluid dynamics, Lattice Boltzmann model, Navier-Stokes equations, NSEs, Numerical Analysis, nVidia, nVidia GeForce GTX 295, Thesis

January 24, 2013 by hgpu

Lattice Group Models: GPU Acceleration and Numerics

Stefan Brechtken

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Tags: Boltzmann equation, CUDA, Fluid dynamics, Numerical simulation, nVidia, nVidia GeForce GTX 580, Optimization

October 14, 2012 by hgpu

Solving the Boltzmann equation on GPUs

Aldo Frezzotti, Gian Pietro Ghiroldi, Livio Gibelli

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Tags: Boltzmann equation, CUDA, Finite difference, Fluid dynamics, nVidia, nVidia GeForce GTX 260, Particle simulation

January 18, 2012 by hgpu

Direct solution of the Boltzmann equation for a binary mixture on GPUs

Aldo Frezzotti, Gian Pietro Ghiroldi, Livio Gibelli

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Tags: Boltzmann equation, CUDA, Finite difference, nVidia, nVidia GeForce GTX 260, Physics

January 8, 2012 by hgpu

Over-synchronization in GPU Programs

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Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

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Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

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high performance computing on graphics processing units: hgpu.org

Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units

An efficient numerical method for solving the Boltzmann equation in multidimensions

Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

Optimization of solver for gas flow modeling

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

The Lattice Boltzmann Equation Method for Complex Flows

Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

High Performance Lattice Boltzmann Solvers on Massively Parallel Architectures with Applications to Building Aeraulics

Lattice Group Models: GPU Acceleration and Numerics

Solving the Boltzmann equation on GPUs

Direct solution of the Boltzmann equation for a binary mixture on GPUs

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Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

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Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

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