A Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver for Electrostatics of Solvated Biomolecules

摘要: Abstract We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson–Boltzmann equation. The method employs well-conditioned formulation electrostatic potential and its normal derivative on molecular surface. surface is triangulated equations are discretized centroid collocation. system solved GMRES iteration matrix–vector product carried out Cartesian treecode which reduces cost from O ( N 2 ) to log , where number faces in triangulation. TABI applied compute solvation energy two cases, Kirkwood sphere protein. error, CPU time, memory usage, compare results Poisson equations. show that approximation error can be made smaller than discretization we versions treecode, one with uniform clusters non-uniform adapted For protein test case, those obtained using grid-based APBS code, also parallel simulations up eight processors. find exhibits good serial performance combined relatively simple implementation, efficient geometric adaptability.