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

Non-local SFT Tachyon and Cosmology

Cosmological scenarios built upon the generalized non-local String Field Theory and $p$-adic tachyons are examined. A general kinetic operator involving an infinite number of derivatives is studied as well as arbitrary parameter $p$. The late time dynamics of just the tachyon around the non-perturbative vacuum is shown to leave the cosmology trivial. A late time behavior of the tachyon and the scale factor of the FRW metric in the presence of the cosmological constant or a perfect fluid with $w>-1$ is constructed explicitly and a possibility of non-vanishing oscillations of the total effective state parameter around the phantom divide is proven.Comment: 17 pages, LaTeX; v2: JHEP3 class is used, references adde

Darkness visible: reflections on underground ecology

1 Soil science and ecology have developed independently, making it difficult for ecologists to contribute to urgent current debates on the destruction of the global soil resource and its key role in the global carbon cycle. Soils are believed to be exceptionally biodiverse parts of ecosystems, a view confirmed by recent data from the UK Soil Biodiversity Programme at Sourhope, Scotland, where high diversity was a characteristic of small organisms, but not of larger ones. Explaining this difference requires knowledge that we currently lack about the basic biology and biogeography of micro-organisms. 2 It seems inherently plausible that the high levels of biological diversity in soil play some part in determining the ability of soils to undertake ecosystem-level processes, such as carbon and mineral cycling. However, we lack conceptual models to address this issue, and debate about the role of biodiversity in ecosystem processes has centred around the concept of functional redundancy, and has consequently been largely semantic. More precise construction of our experimental questions is needed to advance understanding. 3 These issues are well illustrated by the fungi that form arbuscular mycorrhizas, the Glomeromycota. This ancient symbiosis of plants and fungi is responsible for phosphate uptake in most land plants, and the phylum is generally held to be species-poor and non-specific, with most members readily colonizing any plant species. Molecular techniques have shown both those assumptions to be unsafe, raising questions about what factors have promoted diversification in these fungi. One source of this genetic diversity may be functional diversity. 4 Specificity of the mycorrhizal interaction between plants and fungi would have important ecosystem consequences. One example would be in the control of invasiveness in introduced plant species: surprisingly, naturalized plant species in Britain are disproportionately from mycorrhizal families, suggesting that these fungi may play a role in assisting invasion. 5 What emerges from an attempt to relate biodiversity and ecosystem processes in soil is our extraordinary ignorance about the organisms involved. There are fundamental questions that are now answerable with new techniques and sufficient will, such as how biodiverse are natural soils? Do microbes have biogeography? Are there rare or even endangered microbes

Kinetic Turbulence

The weak collisionality typical of turbulence in many diffuse astrophysical plasmas invalidates an MHD description of the turbulent dynamics, motivating the development of a more comprehensive theory of kinetic turbulence. In particular, a kinetic approach is essential for the investigation of the physical mechanisms responsible for the dissipation of astrophysical turbulence and the resulting heating of the plasma. This chapter reviews the limitations of MHD turbulence theory and explains how kinetic considerations may be incorporated to obtain a kinetic theory for astrophysical plasma turbulence. Key questions about the nature of kinetic turbulence that drive current research efforts are identified. A comprehensive model of the kinetic turbulent cascade is presented, with a detailed discussion of each component of the model and a review of supporting and conflicting theoretical, numerical, and observational evidence.Comment: 31 pages, 3 figures, 99 references, Chapter 6 in A. Lazarian et al. (eds.), Magnetic Fields in Diffuse Media, Astrophysics and Space Science Library 407, Springer-Verlag Berlin Heidelberg (2015

Integrating qualitative and quantitative data in the development of outcome measures: the case of the Recovering Quality of Life (ReQoL) measures in mental health populations

While it is important to treat symptoms, there is growing recognition that in order to help people with mental health problems lead meaningful and fulfilling lives, it is crucial to capture the impact of their conditions on wider aspects of their social lives. We constructed two versions of the Recovering Quality of Life (ReQoL) measure – ReQoL-10 ad ReQoL-20 – for use in routine settings and clinical trials from a larger pool of items by combining qualitative and quantitative evidence covering six domains. Qualitative evidence was gathered through interviews and focus groups with over 76 service users, clinicians, and a translatability assessment. Psychometric evidence generated from data from over 6200 service users was obtained from confirmatory factor models and item response theory analyses. An approach based on a traffic light pictorial format was developed to present qualitative and quantitative evidence to a group of service users, clinicians and researchers to help to make the final selection. This work provides a pragmatic yet rigorous approach to combining qualitative and quantitative evidence to ensure that ReQoL is psychometrically robust and has high relevance to service users and clinicians. This approach can be extended to the development of patient reported outcome measures in general

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

Incident Non-AIDS Comorbidity Burden among Women with or at Risk for Human Immunodeficiency Virus in the United States

Background: Human immunodeficiency virus (HIV) infection may accelerate development of aging-related non-AIDS comorbidities (NACMs). The incidence of NACMs is poorly characterized among women living with HIV (WLWH). Methods: WLWH and HIV-seronegative participants followed in the Women's Interagency HIV Study (WIHS) through 2009 (when >80% of WLWH used antiretroviral therapy) or onward were included, with outcomes measured through 31 March 2018. Sociodemographics, clinical covariates, and prevalent NACM were determined at enrollment. We used Poisson regression models to determine incident NACM burden (number of NACMs accrued through most recent WIHS visit out of 10 total NACMs assessed) by HIV serostatus and age. Results: There were 3129 participants (2239 WLWH, 890 HIV seronegative) with 36 589 person-years of follow-up. At enrollment, median age was 37 years, 65% were black, and 47% currently smoked. In fully adjusted analyses, WLWH had a higher incident NACM rate compared with HIV-seronegative women (incidence rate ratio, 1.36 [95% confidence interval (CI), 1.02-1.81]). Incident NACM burden was higher among WLWH vs HIV-seronegative women in most age strata (HIV × age interaction: P = .0438), and women <25 years old had the greatest incidence rate ratio by HIV serostatus at 1.48 (95% CI, 1.19-1.84) compared with those in older age groups. Incident NACM burden was associated with traditional comorbidity risk factors but not HIV-specific indices. Conclusions: Incident NACM burden was higher among WLWH than HIV-seronegative women. This difference was most dramatic among women aged <25 years, a group for whom routine comorbidity screening is not prioritized. Established non-HIV comorbidity risk factors were significantly associated with incident NACM burden. More data are needed to inform best practices for NACM screening, prevention, and management among WLWH, particularly young women

The Effect of Menopausal Status, Age, and Human Immunodeficiency Virus (HIV) on Non-AIDS Comorbidity Burden Among US Women

Menopause may impact the earlier onset of aging-related comorbidities among women with versus without human immunodeficiency virus (HIV). We found that menopausal status, age, and HIV were independently associated with higher comorbidity burden, and that HIV impacted burden most in the pre-/perimenopausal phases