TCB Publications - Abstract

Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. The role of molecular modeling in bionanotechnology. Physical Biology, 3:S40-S53, 2006. (PMC: 2430730)

LU2006 Molecular modeling is advocated here as a key methodology for research and development in bionanotechnology. Molecular modeling provides nanoscale images at atomic and even electronic resolution, predicts the nanoscale interaction of yet unfamiliar combinations of biological and inorganic materials, and can evaluate strategies for redesigning biopolymers for nanotechnological uses. The methodology is illustrated in this paper through three case studies. The first involves the use of single-walled carbon nanotubes as biomedical sensors where a computationally efficient, yet accurate description of the influence of biomolecules on nanotube electronic properties and a description of nanotube - biomolecule interactions were developed; this development furnishes the ability to test nanotube electronic properties in realistic biological environments. The second case study involves the use of nanopores manufactured into electronic nanodevices based on silicon compounds for single molecule electrical recording, in particular, for DNA sequencing. Here, modeling combining classical molecular dynamics, material science, and device physics, describes the interaction of biopolymers, e.g., DNA, with silicon nitrate and silicon oxide pores, furnishes accurate dynamic images of pore translocation processes, and predicts signals. The third case study involves the development of nanoscale lipid bilayers for the study of embedded membrane proteins and cholesterol. Molecular modeling tested scaffold proteins, redesigned lipoproteins found in mammalian plasma that hold the discoidal membranes in shape, and predicted the assembly as well as final structure of the nanodiscs. In entirely new technological areas like bionanotechnology qualitative concepts, pictures, and suggestions are sorely needed; these three case studies document that molecular modeling can serve a critical role in this respect, even though it may still fall short on quantitative precision.

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