Large Scale Car-Parrinello Simulation of Fully Hydrated DNA

Francesco Luigi Gervasio, Paolo Carloni and Michele Parrinello
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Francesco Luigi Gervasio: Centro Svizzero di Calcolo Scientifico via Cantonale
Paolo Carloni: International School for Advanced Studies (SISSA/ISAS) and Istituto Nazionale di Fisica della Materia (INFM) via Beirut 4
Michele Parrinello: Centro Svizzero di Calcolo Scientifico via Cantonale

A chapter in High Performance Computing in Science and Engineering, Munich 2002, 2003, pp 207-216 from Springer

Abstract: Abstract Density functional (BLYP/plane wave) calculations have been used to investigate the structure and the frontier orbitals of a fully hydrated crystalline DNA. Due to the size of the system (1194 atoms, 3,960 valence electrons requiring a total of 408,238 plane waves) this is one of the largest scale ab-initio simulations ever made. We find that the structure of water molecules around the DNA as well as their dipole moments are rather different from those of bulk water. The lowest conduction band is, surprisingly, found to be localized between the Na+ counter-ions and the PO4- groups. This gives rise to a gap of only 1.28 eV. We have evaluated the anisotropic optical conductivity. At low frequency the conductivity along the DNA axis is dominated by the π — Na+ transitions, while the in-plane optical activity is mostly intrabase ( π — π and n — π*). Our calculation demonstrates that hydration effects are fundamental for a proper understanding of DNA electronic properties.

Keywords: DNA; electronic structure; plane waves; car-parrinello; ab initio (search for similar items in EconPapers)
Date: 2003
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-3-642-55526-8_17

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DOI: 10.1007/978-3-642-55526-8_17

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