Optimization of the molecular dynamics method for simulations of DNA and Ion transport through biological nanopores

David B. Wells, Swati Bhattacharya, Rogan Carr, Christopher Maffeo, Anthony Ho, Jeffrey Comer, Aleksei Aksimentiev

Research output: Chapter in Book/Report/Conference proceedingChapter

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.

Original languageEnglish (US)
Title of host publicationNanopore-Based Technology
EditorsMaria E. Gracheva
Pages165-186
Number of pages22
DOIs
StatePublished - May 8 2012

Publication series

NameMethods in Molecular Biology
Volume870
ISSN (Print)1064-3745

Fingerprint

Nanopores
Ion Transport
Molecular Dynamics Simulation
Ions
DNA
Research Design
Temperature

Keywords

  • Bionanotechnology
  • Computer simulations
  • Membrane proteins
  • Molecular dynamics
  • Nucleic acids
  • Transmembrane transport

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Wells, D. B., Bhattacharya, S., Carr, R., Maffeo, C., Ho, A., Comer, J., & Aksimentiev, A. (2012). Optimization of the molecular dynamics method for simulations of DNA and Ion transport through biological nanopores. In M. E. Gracheva (Ed.), Nanopore-Based Technology (pp. 165-186). (Methods in Molecular Biology; Vol. 870). https://doi.org/10.1007/978-1-61779-773-6_10

Optimization of the molecular dynamics method for simulations of DNA and Ion transport through biological nanopores. / Wells, David B.; Bhattacharya, Swati; Carr, Rogan; Maffeo, Christopher; Ho, Anthony; Comer, Jeffrey; Aksimentiev, Aleksei.

Nanopore-Based Technology. ed. / Maria E. Gracheva. 2012. p. 165-186 (Methods in Molecular Biology; Vol. 870).

Research output: Chapter in Book/Report/Conference proceedingChapter

Wells, DB, Bhattacharya, S, Carr, R, Maffeo, C, Ho, A, Comer, J & Aksimentiev, A 2012, Optimization of the molecular dynamics method for simulations of DNA and Ion transport through biological nanopores. in ME Gracheva (ed.), Nanopore-Based Technology. Methods in Molecular Biology, vol. 870, pp. 165-186. https://doi.org/10.1007/978-1-61779-773-6_10
Wells DB, Bhattacharya S, Carr R, Maffeo C, Ho A, Comer J et al. Optimization of the molecular dynamics method for simulations of DNA and Ion transport through biological nanopores. In Gracheva ME, editor, Nanopore-Based Technology. 2012. p. 165-186. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-773-6_10
Wells, David B. ; Bhattacharya, Swati ; Carr, Rogan ; Maffeo, Christopher ; Ho, Anthony ; Comer, Jeffrey ; Aksimentiev, Aleksei. / Optimization of the molecular dynamics method for simulations of DNA and Ion transport through biological nanopores. Nanopore-Based Technology. editor / Maria E. Gracheva. 2012. pp. 165-186 (Methods in Molecular Biology).
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