TY - CHAP
T1 - Optimization of the molecular dynamics method for simulations of DNA and Ion transport through biological nanopores
AU - Wells, David B.
AU - Bhattacharya, Swati
AU - Carr, Rogan
AU - Maffeo, Christopher
AU - Ho, Anthony
AU - Comer, Jeffrey
AU - Aksimentiev, Aleksei
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
KW - Bionanotechnology
KW - Computer simulations
KW - Membrane proteins
KW - Molecular dynamics
KW - Nucleic acids
KW - Transmembrane transport
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U2 - 10.1007/978-1-61779-773-6_10
DO - 10.1007/978-1-61779-773-6_10
M3 - Chapter
C2 - 22528264
AN - SCOPUS:84860510775
SN - 9781617797729
T3 - Methods in Molecular Biology
SP - 165
EP - 186
BT - Nanopore-Based Technology
A2 - Gracheva, Maria E.
ER -