2.6k citations · 2.7k across the 10 of their papers we have counts for
11 papers
Convolution Based Self Attraction and Loading
Anthony Chen, He Wang, Brian Arbic +1
Self Attraction and Loading (SAL), which includes the deformation of the solid Earth under the load of the ocean tide and the self-gravitation of the so-deformed Earth as well as o…
A Cubed Sphere Fast Multipole Method
Anthony Chen, Robert Krasny
This work describes a new version of the Fast Multipole Method for summing pairwise particle interactions that arise from discretizing integral transforms and convolutions on the s…
Integral equation method for the 1D steady-state Poisson-Nernst-Planck equations
Zhen Chao, Weihua Geng, Robert Krasny
An integral equation method is presented for the 1D steady-state Poisson-Nernst-Planck equations modeling ion transport through membrane channels. The differential equations are re…
Accelerating the 3D-RISM theory of molecular solvation with treecode summation and cut-offs
Leighton Wilson, Robert Krasny, Tyler Luchko
The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such…
A GPU-Accelerated Fast Summation Method Based on Barycentric Lagrange Interpolation and Dual Tree Traversal
Leighton Wilson, Nathan Vaughn, Robert Krasny
We present the barycentric Lagrange dual tree traversal (BLDTT) fast summation method for particle interactions. The scheme replaces well-separated particle-particle interactions b…
Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson--Boltzmann solver
Leighton Wilson, Robert Krasny
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the di…
A GPU-Accelerated Barycentric Lagrange Treecode
Nathan Vaughn, Leighton Wilson, Robert Krasny
We present an MPI + OpenACC implementation of the kernel-independent barycentric Lagrange treecode (BLTC) for fast summation of particle interactions on GPUs. The distributed memor…
Treecode-accelerated Green Iteration for Kohn-Sham Density Functional Theory
Nathan Vaughn, Vikram Gavini, Robert Krasny
We present a real-space computational method called treecode-accelerated Green Iteration (TAGI) for all-electron Kohn-Sham Density Functional Theory. TAGI is based on a reformulati…
A kernel-independent treecode based on barycentric Lagrange interpolation
Lei Wang, Robert Krasny, Svetlana Tlupova
A kernel-independent treecode (KITC) is presented for fast summation of particle interactions. The method employs barycentric Lagrange interpolation at Chebyshev points to approxim…
A Treecode Algorithm for 3D Stokeslets and Stresslets
Lei Wang, Svetlana Tlupova, Robert Krasny
The Stokeslet and stresslet kernels are commonly used in boundary element simulations and singularity methods for slow viscous flow. Evaluating the velocity induced by a collection…
Improvements to the APBS biomolecular solvation software suite
Elizabeth Jurrus, Dave Engel, Keith Star +21
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact i…