TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver.

This work describes TABI-PB 2.0, an improved version of the treecode-accelerated boundary integral Poisson-Boltzmann solver. The code computes the electrostatic potential on the molecular surface of a solvated biomolecule, and further processing yields the electrostatic solvation energy.

Accelerating the 3D reference interaction site model theory of molecular solvation with treecode summation and cut-offs.

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 as water and co-ions, around solute molecules. However, 3D-RISM solutions can be expensive to calculate, especially for proteins and other large molecules where calculating the potential energy between solute and solvent requires more than half the computation time. To address this problem, we have developed and implemented treecode summation for long-range interactions and analytically corrected cut-offs for short-range interactions to accelerate the potential energy and long-range asymptotics calculations in non-periodic 3D-RISM in the AmberTools molecular modeling suite.

Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson-Boltzmann solver.

The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of solvated biomolecules. In this model the dielectric interface between the biomolecule and solvent is often taken to be the molecular surface or solvent-excluded surface (SES), and the quality of the SES triangulation is critical in boundary element simulations of the model. This work compares the performance of the MSMS and NanoShaper surface triangulation codes for a set of 38 biomolecules.

Improvements to the APBS biomolecular solvation software suite.

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001.

Comparison of treecodes for computing electrostatic potentials in charged particle systems with disjoint targets and sources.

In molecular simulations, it is sometimes necessary to compute the electrostatic potential at M target sites due to a disjoint set of N charged source particles. Direct summation requires O(MN) operations, which is prohibitively expensive when M and N are large. Here, we consider two alternative tree-based methods that reduce the cost.