TCB Publications - Abstract

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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