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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…
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…