title: Two-dimensional reaction of biological molecules studied by Weighted-Ensemble Brownian dynamics.
abstract: Computer simulations offer critical insights into the reaction of biological macromolecules, especially when the molecular shapes are too complex to be amenable to analytical solution. In this work, the Weighted-Ensemble Brownian (WEB) Dynamics simulation algorithm is adapted to a reaction of two unlike biological molecules, with the interaction modeled by a two-parameter system: a spherical molecular depositing on a target region of an infinite cylinder with a periodic boundary conditions. The original algorithm of Huber and Kim is streamlined for this class of reactive models. The reaction rate constant is calculated as a function of relative sizes of the reactive to non-reactive regions of the cylindrical molecule. An analytical expression for the rate constant is also obtained from the solution of the diffusion equation for the special case of a constant-flux boundary condition. Good agreement between analytical and simulation results validates the applicability of WEB Dynamics to a reaction of molecules of complicated shape. On the other hand, the simple form of our analytical expression is useful as a testing case for other simulation and numerical techniques.
authors.affiliation: Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison 53706-1544, USA.
authors.forename: I A
authors.initials: IA
authors.lastname: Shkel
authors.forename: S
authors.initials: S
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011336:Probability; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA