title: A fast alternating direction implicit algorithm for geometric flow equations in biomolecular surface generation.
abstract: In this paper, a new alternating direction implicit (ADI) method is introduced to solve potential driven geometric flow PDEs for biomolecular surface generation. For such PDEs, an extra factor is usually added to stabilize the explicit time integration. However, two existing implicit ADI schemes are also based on the scaled form, which involves nonlinear cross derivative terms that have to be evaluated explicitly. This affects the stability and accuracy of these ADI schemes. To overcome these difficulties, we propose a new ADI algorithm based on the unscaled form so that cross derivatives are not involved. Central finite differences are employed to discretize the nonhomogenous diffusion process of the geometric flow. The proposed ADI algorithm is validated through benchmark examples with analytical solutions, reference solutions, or literature results. Moreover, quantitative indicators of a biomolecular surface, including surface area, surface-enclosed volume, and solvation free energy, are analyzed for various proteins. The proposed ADI method is found to be unconditionally stable and more accurate than the existing ADI schemes in all tests. This enables the use of a large time increment in the steady state simulation so that the proposed ADI algorithm is very efficient for biomolecular surface generation.
authors.affiliation: Department of Mathematics, University of Alabama, Tuscaloosa, AL 35487, USA.
authors.forename: Wufeng
authors.initials: W
authors.lastname: Tian
authors.forename: Shan
authors.initials: S
authors.lastname: Zhao
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004058:Diffusion; D008958:Models, Molecular; D013499:Surface Properties; D013816:Thermodynamics
keywords: alternating direction implicit (ADI) scheme; biomolecular surface generation; geometric flow equation; multiscale nonlinear solvation model; solvation free energy