Search

Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either from the solvent fluctuations or from base-pair vibrational modes can be taken into account in a straightforward way through time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the onsite energies along the DNA wire.

We present a hybrid method based on a combination of quantum/classical molecular dynamics (MD) simulations and a mod el Hamiltonian approach to describe charge transport through bio-molecular wires with variable lengths in presence o f a solvent. The core of our approach consists in a mapping of the bio-molecular electronic structure, as obtained f rom density-functional based tight-binding calculations of molecular structures along MD trajectories, onto a low di mensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuat ion effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the c ase of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

We have studied the influence of alloying copper with amorphous arsenic sulfide on the electronic properties of this material. In our computer-generated models, copper is found in two-fold near-linear and four-fold square-planar configurations, which apparently correspond to Cu(I) and Cu(II) oxidation states. The number of overcoordinated atoms, both arsenic and sulfur, grows with increasing concentration of copper. Overcoordinated sulfur is found in trigonal planar configuration, and overcoordinated (four-fold) arsenic is in tetrahedral configuration. Addition of copper suppresses the localization of lone-pair electrons on chalcogen atoms, and localized states at the top of the valence band are due to Cu 3d orbitals. Evidently, these additional Cu states, which are positioned at the same energies as the states due to ([As4]-)-([S_3]+) pairs, are responsible for masking photodarkening in Cu chalcogenides.

The electronic properties of squashed arm-chair carbon nanotubes are modeled using constraint free density functional tight binding molecular dynamics simulations. Independent from CNT diameter, squashing path can be divided into {\it three} regimes. In the first regime, the nanotube deforms with negligible force. In the second one, there is significantly more resistance to squashing with the force being $\sim 40-100$ nN/per CNT unit cell. In the last regime, the CNT looses its hexagonal structure resulting in force drop-off followed by substantial force enhancement upon squashing. We compute the change in band-gap as a function of squashing and our main results are: (i) A band-gap initially opens due to interaction between atoms at the top and bottom sides of CNT. The $\pi-$orbital approximation is successful in modeling the band-gap opening at this stage. (ii) In the second regime of squashing, large $\pi-\sigma$ interaction at the edges becomes important, which can lead to band-gap oscillation. (iii) Contrary to a common perception, nanotubes with broken mirror symmetry can have {\it zero} band-gap. (iv) All armchair nanotubes become metallic in the third regime of squashing. Finally, we discuss both differences and similarities obtained from the tight binding and density functional approaches., Comment: 16 pages and 6 figures, To appear in PRB