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DNA Modeling within Ab Initio and Empirical Methods

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Abstract:

The realm of DNA-based nanotechnology has recently attracted an immense interest and became the research focus of a multi-disciplinary scientific community. Despite the wide range of ongoing experimental and theoretical efforts related to DNA, several controversial results exist and DNA-based device fabrication remains challenging. These challenges are related to the sequence dependent structural and dynamical properties of the complex polyelectrolyte DNA molecule and the difficulty in controlling ambient conditions and manipulating DNA. Accurate theoretical models should include, besides the DNA molecule, the effects of the surrounding environment and, if important, interactions with other system components. To give a better interpretation of the experimental results and to setup the path for rational design, phenomenological models should be extended to a hierarchical scheme, which includes quantum and atomistic descriptions. The present review summarizes major developments in the field of DNA modeling from ab initio to empirical. First principles based description of DNA addresses its electronic and transport characteristics within Hartree-Fock, Density Functional Theory, and Tight Binding approximations at different ambient conditions. The empirical description of DNA summarizes frequently employed classical potentials for atomic interactions extending to modern force fields, which include charge equilibration, polarization, and reactive potentials. Studies using full atom and coarse grain models under various environmental conditions using different force fields are also overviewed. DNA translocation through nanometersized pores is presently one of the most controversial and challenging problems and it is a major focus of this review article from a simulation standpoint.

Keywords: AB INITIO; ATOMISTIC SIMULATIONS; DESIGN; DNA; ELECTRONIC TRANSPORT; FORCE FIELD; NANOTECHNOLOGY; SEQUENCING; TRANSLOCATION

Document Type: Review Article

DOI: https://doi.org/10.1166/jctn.2007.2324

Publication date: 2007-05-01

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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