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

The mystery of the Marajoara: An ecological solution

For more than a century, the beautiful pottery from artificial mounds on the island of Marajó at the mouth of the Amazon has found its way into museums and private collections in Europe and North America, as well as Brazil. Since scientific investigations began in 1948, the discrepancy between the sophistication of the culture and the low agricultural potential of the environment has become increasingly apparent. Although claims that "Marajoara settlement pattern is urban in scale," that "the population could have been up to one million people," and that the ceramic art is "one of the most highly developed in the hemisphere" are extravagant, there is no doubt that the society maintained a relatively high level of complexity during nearly 1000 years in an environment that today supports only a sparse population dedicated mainly to cattle raising. Similar levels of cultural development elsewhere on the planet are sustained either by intensive agriculture or by unusually productive wild resources. Elimination of the former focuses attention on the latter and several new lines of evidence suggest that intensive exploitation of palm starch may be the solution to the mystery of the Marajoara

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

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

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

Reprogramming the assembly of unmodified DNA with a small molecule

The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA ‘alphabet’ by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials

Comparison of the environmental, energy, and thermal comfort performance of air and radiant cooling systems in a zero-energy office building in Singapore

In an experimental study set in Singapore's tropical climate, we evaluated the thermal environmental performance, energy consumption, and thermal comfort of air and radiant cooling systems, operating at an operative and air temperature of 26 °C. 78 participants across five groups answered thermal comfort surveys in a crossover study design. Environmental performance metrics indicated that both systems produced similar conditions, with a noticeable difference in air velocity. The mean radiant temperature to air temperature difference was less than 0.5 °C in both systems. The radiant system exhibited a 33 % higher heat flux extraction than the air system and required less electrical power for the transportation of the cooling medium and ventilation air. Overall, the radiant system used 4 % less energy than the air system when controlled at 26 °C and 34 % when operated at 23 °C. Results show that radiant and air systems provided equal thermal comfort in cooling, with over 60 % of participants expressing satisfaction and ∼ 20 % voted neutral thermal satisfaction. ∼ 40 % of participants preferred cooler conditions, and ∼ 30 % desired increased air movement