title: Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores.
abstract: Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
authors.forename: David B
authors.initials: DB
authors.lastname: Wells
authors.forename: Swati
authors.initials: S
authors.lastname: Bhattacharya
authors.forename: Rogan
authors.initials: R
authors.lastname: Carr
authors.forename: Christopher
authors.initials: C
authors.lastname: Maffeo
authors.forename: Anthony
authors.initials: A
authors.lastname: Ho
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Comer
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
mesh_terms: D001692:Biological Transport; D004247:DNA / Q000737:chemistry*; D004553:Electric Conductivity; D053841:Electroosmosis; D006460:Hemolysin Proteins / Q000737:chemistry; D007477:Ions / Q000737:chemistry*; D008051:Lipid Bilayers / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D018272:Porins / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D006460:Hemolysin Proteins; D007477:Ions; D008051:Lipid Bilayers; D018272:Porins; D012997:Solvents; D004247:DNA