Aleksei Aksimentiev, Robert K. Brunner, Eduardo Cruz-Chu, Jeffrey Comer, and
Klaus Schulten.
Modeling transport through synthetic nanopores.
IEEE Nanotechnology, 3:20-28, 2009.
(PMC: 3168529)
AKSI2009
Synthetic nanopores have proved to be useful tools
for studying the properties of biomolecules in confined environments
and under the influence of electric fields. However, a full
understanding of the behavior of biomolecule-nanopore systems
at the atomic level is beyond the limit of current experimental
methods. Molecular dynamics (MD) can provide a method for
modeling such systems, once several problems are addressed.
Our recent work has addressed some of these problems for some
popular nanopore materials. First, we describe a novel graphical
tool for setting up models incorporating inorganic materials
and biomolecules. Next, we illustrate MD simulations for silica,
silicon nitride, and polyethylene terephthalate nanopores. Then,
a method in which the pore surface is modeled by a potential
field, is presented. Finally, future directions for tool development
and nanopore modeling are described.
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