Fast Methods for accurate implicit solvent models
Steve D. Bond and Robert D. Skeel

Solvent interactions play a critical role in determining the structure and function of biomolecular systems. However, accurate modeling is a challenging task due to long-range correlations and vast numbers of solvent atoms and ions. For very large systems, one method for reducing this expense is the application of an implicit solvent model which replaces the explicit atoms and ions with a dielectric continuum. One of the more accurate implicit solvent models is described by a generalized Poisson equation or Poisson-Boltzmann equation with point charge source terms. Although the generalized Poisson approach is considered in very many cases to be sufficiently accurate, most current methods for approximating its solution have been deemed prohibitively expensive for very large systems and for applications requiring rapid repetitive evaluation.

This project centers on the creation and analysis of algorithms of unsurpassed effectiveness for approximating the solution to the generalized Poisson equation (GPE) and its extensions. The approach involves solving for an "effective charge distribution," whose electrostatic potential can be recovered using a fast N-body solver.

  Last updated 2014-6-22