Mutual influence of structural distortion and superconductivity in systems with degenerate bands

The interplay between the band Jahn-Teller distortion and the superconductivity is studied for the system whose Fermi level lies in two-fold degenerate band. Assuming that the lattice distortion is coupled to the orbital electron density and the superconductivity arises due to BCS pairing mechanism between the electrons, the phase diagram is obtained for different doping with respect to half-filled band situation. The coexistence phase of superconductivity and distortion occurs within limited range of doping and the distortion lowers the superconducting transition temperature $T_c$. In presence of strong electron-lattice interaction the lattice strain is found to be maximum at half-filling and superconductivity does not appear for low doping. The maximum value of $T_c$ obtainable for an optimum doping is limited by the structural transition temperature $T_s$. The growth of distortion is arrested with the onset of superconductivity and the distortion is found to disappear at lower temperature for some hole density. Such arresting of the growth of distortion at $T_c$ produces discontinuous jump in thermal expansion coefficient. The variation of strain with temperature as well as with doping, thermal expansion coefficient, the $T_c$ vs $\delta$ behaviour are in qualitative agreement with recent experimental observations on interplay of distortion and superconductivity in cuprates.Comment: 15 pages Revtex style, 9 figures available on request to first Autho

Electronic transport and vibrational modes in the smallest molecular bridge: H2 in Pt nanocontacts

We present a state-of-the-art first-principles analysis of electronic transport in a Pt nanocontact in the presence of H2 which has been recently reported by Smit et al. in Nature 419, 906 (2002). Our results indicate that at the last stages of the breaking of the Pt nanocontact two basic forms of bridge involving H can appear. Our claim is, in contrast to Smit et al.'s, that the main conductance histogram peak at G approx 2e^2/h is not due to molecular H2, but to a complex Pt2H2 where the H2 molecule dissociates. A first-principles vibrational analysis that compares favorably with the experimental one also supports our claim .Comment: 5 pages, 3 figure

Electron transport in nanotube--molecular wire hybrids

We study contact effects on electron transport across a molecular wire sandwiched between two semi-infinite (carbon) nanotube leads as a model for nanoelectrodes. Employing the Landauer scattering matrix approach we find that the conductance is very sensitive to parameters such as the coupling strength and geometry of the contact. The conductance exhibits markedly different behavior in the two limiting scenarios of single contact and multiple contacts between the molecular wire and the nanotube interfacial atoms. In contrast to a single contact the multiple-contact configuration acts as a filter selecting single transport channels. It exhibits a scaling law for the conductance as a function of coupling strength and tube diameter. We also observe an unusual narrow-to-broad-to-narrow behavior of conductance resonances upon decreasing the coupling.Comment: 4 pages, figures include

Decision-making of the benthic diatom <i>Seminavis robusta</i> searching for inorganic nutrients and pheromones

Microorganisms encounter a diversity of chemical stimuli that trigger individual responses and influence population dynamics. However, microbial behavior under the influence of different incentives and microbial decision-making is poorly understood. Benthic marine diatoms that react to sexual attractants as well as to nutrient gradients face such multiple constraints. Here, we document and model behavioral complexity and context-sensitive responses of these motile unicellular algae to sex pheromones and the nutrient silicate. Throughout the life cycle of the model diatom Seminavis robusta nutrient-starved cells localize sources of silicate by combined chemokinetic and chemotactic motility. However, with an increasing need for sex to restore the initial cell size, a change in behavior favoring the attraction-pheromone-guided search for a mating partner takes place. When sex becomes inevitable to prevent cell death, safeguard mechanisms are abandoned, and cells prioritize the search for mating partners. Such selection processes help to explain biofilm organization and to understand species interactions in complex communities

Studying Kaon-pion S-wave scattering in K-matrix formalism

We generalize our previous work on \pi\pi scattering to K\pi scattering, and re-analyze the experiment data of K\pi scattering below 1.6 GeV. Without any free parameter, we explain K\pi I=3/2 S-wave phase shift very well by using t-channel rho and u-channel K^* meson exchange. With the t-channel and u-channel meson exchange fixed as the background term, we fit the K\pi I=1/2 S-wave data of the LASS experiment quite well by introducing one or two s-channel resonances. It is found that there is only one s-channel resonance between K\pi threshold and 1.6 GeV, i.e., K_0^*(1430) with a mass around 1438~1486 MeV and a width about 346 MeV, while the t-channel rho exchange gives a pole at (450-480i) MeV for the amplitude.Comment: REVTeX4 file, 11 pages and 3 figure

A first-principles approach to electrical transport in atomic-scale nanostructures

We present a first-principles numerical implementation of Landauer formalism for electrical transport in nanostructures characterized down to the atomic level. The novelty and interest of our method lies essentially on two facts. First of all, it makes use of the versatile Gaussian98 code, which is widely used within the quantum chemistry community. Secondly, it incorporates the semi-infinite electrodes in a very generic and efficient way by means of Bethe lattices. We name this method the Gaussian Embedded Cluster Method (GECM). In order to make contact with other proposed implementations, we illustrate our technique by calculating the conductance in some well-studied systems such as metallic (Al and Au) nanocontacts and C-atom chains connected to metallic (Al and Au) electrodes. In the case of Al nanocontacts the conductance turns out to be quite dependent on the detailed atomic arrangement. On the contrary, the conductance in Au nanocontacts presents quite universal features. In the case of C chains, where the self-consistency guarantees the local charge transfer and the correct alignment of the molecular and electrode levels, we find that the conductance oscillates with the number of atoms in the chain regardless of the type of electrode. However, for short chains and Al electrodes the even-odd periodicity is reversed at equilibrium bond distances.Comment: 14 pages, two-column format, submitted to PR

Fluid Models of Many-server Queues with Abandonment

We study many-server queues with abandonment in which customers have general service and patience time distributions. The dynamics of the system are modeled using measure- valued processes, to keep track of the residual service and patience times of each customer. Deterministic fluid models are established to provide first-order approximation for this model. The fluid model solution, which is proved to uniquely exists, serves as the fluid limit of the many-server queue, as the number of servers becomes large. Based on the fluid model solution, first-order approximations for various performance quantities are proposed

Density functional method for nonequilibrium electron transport

We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density functional theory (DFT) as implemented in the well tested Siesta approach (which uses non-local norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including selfconsistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme involving the scattering states. As an illustration, the method is applied to three systems where we are able to compare our results to earlier ab initio DFT calculations or experiments, and we point out differences between this method and existing schemes. The systems considered are: (1) single atom carbon wires connected to aluminum electrodes with extended or finite cross section, (2) single atom gold wires, and finally (3) large carbon nanotube systems with point defects.Comment: 18 pages, 23 figure

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Mutation of a single residue, β-glutamate-20, alters protein–lipid interactions of light harvesting complex II

It is well established that assembly of the peripheral antenna complex, LH2, is required for proper photosynthetic membrane biogenesis in the purple bacterium Rhodobacter sphaeroides. The underlying interactions are, as yet, not understood. Here we examined the relationship between the morphology of the photosynthetic membrane and the lipid–protein interactions at the LH2–lipid interface. The non-bilayer lipid, phosphatidylethanolamine, is shown to be highly enriched in the boundary lipid phase of LH2. Sequence alignments indicate a putative lipid binding site, which includes β-glutamate-20 and the adjacent carotenoid end group. Replacement of β-glutamate-20 with alanine results in significant reduction of phosphatidylethanolamine and concomitant raise in phosphatidylcholine in the boundary lipid phase of LH2 without altering the lipid composition of the bulk phase. The morphology of the LH2 housing membrane is, however, unaffected by the amino acid replacement. In contrast, simultaneous modification of glutamate-20 and exchange of the carotenoid sphaeroidenone with neurosporene results in significant enlargement of the vesicular membrane invaginations. These findings suggest that the LH2 complex, specifically β-glutamate-20 and the carotenoids' polar head group, contribute to the shaping of the photosynthetic membrane by specific interactions with surrounding lipid molecules