title: BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials.
abstract: The transport of ions and solutes by biological pores is central for cellular processes and has a variety of applications in modern biotechnology. The time scale involved in the polymer transport across a nanopore is beyond the accessibility of conventional MD simulations. Moreover, experimental studies lack sufficient resolution to provide details on the molecular underpinning of the transport mechanisms. BROMOC, the code presented herein, performs Brownian dynamics simulations, both serial and parallel, up to several milliseconds long. BROMOC can be used to model large biological systems. IMC-MACRO software allows for the development of effective potentials for solute-ion interactions based on radial distribution function from all-atom MD. BROMOC Suite also provides a versatile set of tools to do a wide variety of preprocessing and postsimulation analysis. We illustrate a potential application with ion and ssDNA transport in MspA nanopore.
authors.affiliation: Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4.
authors.forename: Pablo M
authors.initials: PM
authors.lastname: De Biase
authors.forename: Suren
authors.initials: S
authors.lastname: Markosyan
authors.forename: Sergei
authors.initials: S
authors.lastname: Noskov
mesh_terms: D001692:Biological Transport; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D007477:Ions / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D012984:Software
chemical_list: D007477:Ions; D004247:DNA
keywords: Brownian dynamics; effective potential; grand canonical Monte Carlo; inverse Monte Carlo; ion and DNA transport; nanopore