title: Finite element solution of the steady-state Smoluchowski equation for rate constant calculations.
abstract: This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been developed to solve the steady-state Smoluchowski equation to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to mouse acetylcholinesterase. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different reaction criteria. The calculated rates were compared with experimental data and show very good agreement when the correct reaction criterion is used. Additionally, these finite element methods require significantly less computational resources than existing particle-based Brownian dynamics methods.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, St. Louis, Missouri 63110, USA.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Song
authors.forename: Yongjie
authors.initials: Y
authors.lastname: Zhang
authors.forename: Tongye
authors.initials: T
authors.lastname: Shen
authors.forename: Chandrajit L
authors.initials: CL
authors.lastname: Bajaj
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Baker
mesh_terms: D000110:Acetylcholinesterase / Q000737:chemistry*; D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D051379:Mice; D008958:Models, Molecular; D012984:Software
chemical_list: D000110:Acetylcholinesterase