Quantum transport through a DNA wire in a dissipative environment

Electronic transport through DNA wires in the presence of a strong dissipative environment is investigated. We show that new bath-induced electronic states are formed within the bandgap. These states show up in the linear conductance spectrum as a temperature dependent background and lead to a crossover from tunneling to thermal activated behavior with increasing temperature. Depending on the strength of the electron-bath coupling, the conductance at the Fermi level can show a weak exponential or even an algebraic length dependence. Our results suggest a new environmental-induced transport mechanism. This might be relevant for the understanding of molecular conduction experiments in liquid solution, like those recently performed on poly(GC) oligomers in a water buffer (B. Xu et al., Nano Lett 4, 1105 (2004)).Comment: 5 pages, 3 figure

Optical emission spectroscopy of metal-halide lamps: Radially resolved atomic state distribution functions of Dy and Hg

Absolute line intensity measurements are performed on a metal-halide lamp. Several transitions of atomic and ionic Dy and atomic Hg are measured at different radial positions from which we obtain absolute atomic and ionic Dy intensity profiles. From these profiles we construct the radially resolved atomic state distribution function (ASDF) of the atomic and ionic Dy and the atomic Hg. From these ASDFs several quantities are determined as functions of radial position, such as the (excitation) temperature, the ion ratio Hg^+/Dy^+, the electron density, the ground state, and the totaldensity of Dy atoms and ions. Moreover, these ASDFs give us insight about the departure from equilibrium. The measurements show a hollow density profile for the atoms and the ionization of atoms in the center. In the outer parts of the lamp molecules dominate

Ab-initio study of model guanine assemblies: The role of pi-pi coupling and band transport

Several assemblies of guanine molecules are investigated by means of first-principle calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the pi orbitals in adjacent guanine molecules. pi-pi coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The bandstructure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible.Comment: 21 pages, 6 figures, 3 tables, to be published in Phys. Rev.

Green function techniques in the treatment of quantum transport at the molecular scale

The theoretical investigation of charge (and spin) transport at nanometer length scales requires the use of advanced and powerful techniques able to deal with the dynamical properties of the relevant physical systems, to explicitly include out-of-equilibrium situations typical for electrical/heat transport as well as to take into account interaction effects in a systematic way. Equilibrium Green function techniques and their extension to non-equilibrium situations via the Keldysh formalism build one of the pillars of current state-of-the-art approaches to quantum transport which have been implemented in both model Hamiltonian formulations and first-principle methodologies. We offer a tutorial overview of the applications of Green functions to deal with some fundamental aspects of charge transport at the nanoscale, mainly focusing on applications to model Hamiltonian formulations.Comment: Tutorial review, LaTeX, 129 pages, 41 figures, 300 references, submitted to Springer series "Lecture Notes in Physics

Tight-binding parameters for charge transfer along DNA

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wavefunctions and energies of DNA bases are discussed and then used for calculating the corresponding wavefunctions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the $\pi$ molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons, which probably indicates that hole transport along DNA is more favorable than electron transport. Our findings are also compared with existing calculations from first principles.Comment: 15 pages, 3 figures, 7 table

Pre-Columbian land use in the ring-ditch region of the Bolivian Amazon

The nature and extent of pre-Columbian (pre-1492 AD) human impact in Amazonia is a contentious issue. The Bolivian Amazon has yielded some of the most impressive evidence for large and complex pre-Columbian societies in the Amazon basin, yet there remains relatively little data concerning the land use of these societies over time. Palaeoecology, when integrated with archaeological data, has the potential to fill these gaps in our knowledge. We present a 6,000-year record of anthropogenic burning, agriculture and vegetation change, from an oxbow lake located adjacent to a pre-Columbian ring-ditch in north-east Bolivia (13°15’44” S, 63°42’37” W). Human occupation around the lake site is inferred from pollen and phytoliths of maize (Zea mays L.) and macroscopic charcoal evidence of anthropogenic burning. First occupation around the lake was radiocarbon dated to ~2500 years BP. The persistence of maize in the record from ~1850 BP suggests that it was an important crop grown in the ringditch region in pre-Columbian times, and abundant macroscopic charcoal suggests that pre-Columbian land management entailed more extensive burning of the landscape than the slash-and-burn agriculture practised around the site today. The site was occupied continuously until near-modern times, although there is evidence for a decline in agricultural intensity or change in land use strategy, and possible population decline, from ~600-500 BP. The long and continuous occupation, which predates the establishment of rainforest in the region, suggests that pre-Columbian land use may have had a significant influence on ecosystem development at this site over the last ~2000 years

Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent

We examined the ionization potential (IP) corresponding to the free energy of a hole on duplex DNA by semiempirical molecular orbital theory with a continuum solvent model. As for the contiguous guanines (a guanine run), we found that the IP in the gas phase significantly decreases with the increasing number of nucleotide pairs of the guanine run, whereas the IP in water (OP, oxidation potential) only slightly does. The latter result is consistent with the experimental result for DNA oligomers in water. This decrease in the IP is mainly due to the attractive electrostatic interaction between the hole and a nucleotide pair in the duplex DNA. This interaction is reduced in water, which results in the small decrease in the IP in water. This mechanism explains the discrepancy between the experimental result and the previous computational results obtained by neglecting the solvent. As for the chemically modified guanine, the previous work showed that the removal of some solvent (water) molecules due to the attachment of a neutral functional group to a guanine in a duplex DNA stabilizes the hole on the guanine. One might naively have expected the opposite case, since a polar solvent usually stabilizes ions. This mechanism also explains this unexpected stabilization of a hole as follows. When some water molecules are removed, the attractive electrostatic interaction stabilizing the hole increases, and thus, the hole is stabilized. In order to design the hole energetics by a chemical modification of DNA, this mechanism has to be taken into account and can be used. 1

A ruthenium polypyridyl intercalator stalls DNA replication forks, radiosensitizes human cancer cells and is enhanced by Chk1 inhibition

Ruthenium(II) polypyridyl complexes can intercalate DNA with high affinity and prevent cell proliferation; however, the direct impact of ruthenium-based intercalation on cellular DNA replication remains unknown. Here we show the multi-intercalator [Ru(dppz)2(PIP)]2+ (dppz = dipyridophenazine, PIP = 2-(phenyl)imidazo[4,5-f][1,10]phenanthroline) immediately stalls replication fork progression in HeLa human cervical cancer cells. In response to this replication blockade, the DNA damage response (DDR) cell signalling network is activated, with checkpoint kinase 1 (Chk1) activation indicating prolonged replication-associated DNA damage, and cell proliferation is inhibited by G1-S cell-cycle arrest. Co-incubation with a Chk1 inhibitor achieves synergistic apoptosis in cancer cells, with a significant increase in phospho(Ser139) histone H2AX (γ- H2AX) levels and foci indicating increased conversion of stalled replication forks to double-strand breaks (DSBs). Normal human epithelial cells remain unaffected by this concurrent treatment. Furthermore, pre-treatment of HeLa cells with [Ru(dppz)2(PIP)]2+ before external beam ionising radiation results in a supra-additive decrease in cell survival accompanied by increased γ-H2AX expression, indicating the compound functions as a radiosensitizer. Together, these results indicate ruthenium-based intercalation can block replication fork progression and demonstrate how these DNA-binding agents may be combined with DDR inhibitors or ionising radiation to achieve more efficient cancer cell killing