title: PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations.
abstract: We present PACO, a computationally efficient method for concentration boundary conditions in nonequilibrium particle simulations. Because it requires only particle counting, its computational effort is significantly smaller than other methods. PACO enables Brownian dynamics simulations of micromolar electrolytes (3 orders of magnitude lower than previously simulated). PACO for Brownian dynamics is integrated in the BROWNIES package (www.phys.rush.edu/BROWNIES). We also introduce a molecular dynamics PACO implementation that allows for very accurate control of concentration gradients.
authors.affiliation: Department of Molecular Biophysics and Physiology, Rush University Medical Center , Chicago, Illinois 60612, United States.
authors.forename: Claudio
authors.initials: C
authors.lastname: Berti
authors.affiliation: Department of Medical Biotechnologies, University of Siena , viale Mario Bracci 16 , I-53100, 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 60612, United States.
authors.forename: Dirk
authors.initials: D
authors.lastname: Gillespie
mesh_terms: D000465:Algorithms; D002122:Calcium Chloride / Q000737:chemistry*; D004573:Electrolytes / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D012965:Sodium Chloride / Q000737:chemistry*
chemical_list: D004573:Electrolytes; D012965:Sodium Chloride; D002122:Calcium Chloride