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's value has been
reviewed for three uses in bionanotechnology. 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 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; the three
exemplary applications document that molecular modeling can serve a
critical role for the new bionanotechnology, even though it may still
fall short on quantitative precision.