2.6k citations · 2.6k across the 8 of their papers we have counts for
8 papers
Optimized Parallelization of Boundary Integral Poisson-Boltzmann Solvers
Xin Yang, Elyssa Sliheet, Reece Iriye +2
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information abo…
Poisson-Boltzmann based machine learning (PBML) model for electrostatic analysis
Jiahui Chen, Yongjia Xu, Xin Yang +3
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it…
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…
A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
Jiahui Chen, Johannes Tausch, Weihua Geng
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our r…
MLIMC: Machine learning-based implicit-solvent Monte Carlo
Jiahui Chen, Weihua Geng, Guo-Wei Wei
Monte Carlo (MC) methods are important computational tools for molecular structure optimizations and predictions. When solvent effects are explicitly considered, MC methods become…
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…
Parallel Higher-order Boundary Integral Electrostatics Computation on Molecular Surfaces with Curved Triangulation
Weihua Geng
In this paper, we present a parallel higher-order boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formul…
A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver
Weihua Geng, Ferosh Jacob
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral f…