title: Three-Dimensional Brownian Dynamics Simulator for the Study of Ion Permeation through Membrane Pores.
abstract: A three-dimensional numerical simulator based on Brownian dynamics (BD) for the study of ion transport through membrane pores is presented. Published BD implementations suffer from severe shortcomings in accuracy and efficiency. Such limitations arise largely from (i) the nonrigorous treatment of unphysical ion configurations; (ii) the assumption that ion motion occurs always in the high friction limit, (iii) the inefficient solution of the Poisson equation with dielectric interfaces, and (iv) the inaccurate treatment of boundary conditions for ion concentrations. Here, we introduce a new BD simulator in which these critical issues are addressed, implementing advanced techniques: (i) unphysical ion configurations are managed with a novel retracing technique; (ii) ion motion is evaluated integrating the Langevin equation with the algorithm of van Gunsteren and Berendsen (Mol. Phys. 1982, 45, 637-647); (iii) dielectric response in the Poisson equation is solved at run time with the Induced Charge Computation (ICC) method of Boda et al. (J. Chem. Phys. 2006, 125, 034901); and (iv) boundary conditions for ion concentrations are enforced by an accurate Grand Canonical Monte Carlo (GCMC) algorithm. Although some of these techniques have already been separately adopted for the simulation of membrane pores, our tool is the first BD implementation, to our knowledge, that fully retrace ions to avoid unphysical configurations and that computes dielectric interactions at each time step. Most other BD codes have been used on wide channels. Our BD simulator is specifically designed for narrow and crowded ion channels (e.g., L-type calcium channels) where all the aforementioned techniques are necessary for accurate results. In this paper, we introduce our tool, focusing on the implementation and testing of key features and we illustrate its capabilities through the analysis of test cases. The source code is available for download at www.phys.rush.edu/BROWNIES .
authors.affiliation: Department of Molecular Biophysics and Physiology, Rush University Medical Center , Chicago,Illinois, United States.|ARCES and DEI, University of Bologna and IUNET , Cesena, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Berti
authors.affiliation: Department of Medical Biotechnologies, University of Siena , Siena, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Furini
authors.affiliation: Department of Molecular Biophysics and Physiology, Rush University Medical Center , Chicago,Illinois, United States.
authors.forename: Dirk
authors.initials: D
authors.lastname: Gillespie
authors.affiliation: Department of Physical Chemistry, University of Pannonia , Veszprém, Hungary.
authors.forename: Dezső
authors.initials: D
authors.lastname: Boda
authors.affiliation: Department of Molecular Biophysics and Physiology, Rush University Medical Center , Chicago,Illinois, United States.
authors.forename: Robert S
authors.initials: RS
authors.lastname: Eisenberg
authors.affiliation: ARCES and DEI, University of Bologna and IUNET , Cesena, Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Sangiorgi
authors.affiliation: ARCES and DEI, University of Bologna and IUNET , Cesena, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Fiegna