MetExploreViz: web component for interactive metabolic network visualization

Summary: MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyse omics data in a biochemical context. Availability and implementation: Documentation and link to GIT code repository (GPL 3.0 license) are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc

Magnetic-field dependence of electron spin relaxation in n-type semiconductors

We present a theoretical investigation of the magnetic field dependence of the longitudinal ($T_1$) and transverse ($T_2$) spin relaxation times of conduction band electrons in n-type III-V semiconductors. In particular, we find that the interplay between the Dyakonov-Perel process and an additional spin relaxation channel, which originates from the electron wave vector dependence of the electron $g$-factor, yields a maximal $T_2$ at a finite magnetic field. We compare our results with existing experimental data on n-type GaAs and make specific additional predictions for the magnetic field dependence of electron spin lifetimes.Comment: accepted for publication in PRB, minor changes to previous manuscrip

Pure spin photocurrents in low-dimensional structures

As is well known the absorption of circularly polarized light in semiconductors results in optical orientation of electron spins and helicity-dependent electric photocurrent, and the absorption of linearly polarized light is accompanied by optical alignment of electron momenta. Here we show that the absorption of unpolarized light leads to generation of a pure spin current, although both the average electron spin and electric current vanish. We demonstrate this for direct interband and intersubband as well as indirect intraband (Drude-like) optical transitions in semiconductor quantum wells (QWs).Comment: 4 pages, 3 figure

A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks

This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities

Multiparticle Biased DLA with surface diffusion: a comprehensive model of electrodeposition

We present a complete study of the Multiparticle Biased Diffusion-Limited Aggregation (MBDLA) model supplemented with surface difussion (SD), focusing on the relevance and effects of the latter transport mechanism. By comparing different algorithms, we show that MBDLA+SD is a very good qualitative model for electrodeposition in practically all the range of current intensities {\em provided} one introduces SD in the model in the proper fashion: We have found that the correct procedure involves simultaneous bulk diffusion and SD, introducing a time scale arising from the ratio of the rates of both processes. We discuss in detail the different morphologies obtained and compare them to the available experimental data with very satisfactory results. We also characterize the aggregates thus obtained by means of the dynamic scaling exponents of the interface height, allowing us to distinguish several regimes in the mentioned interface growth. Our asymptotic scaling exponents are again in good agreement with recent experiments. We conclude by discussing a global picture of the influence and consequences of SD in electrodeposition.Comment: 15 pages, 20 figures, accepted for publication in Physical Review

Відображення розвитку науки України та Євросоюзу в реферативній базі даних SCOPUS

Досліджено публікаційну активність України та Євросоюзу за галузями науки. Розглянуто динаміку кількості публікацій, що припадають на одного дослідника впродовж 1996-2010 рр. Виконано порівняння відображення кількості публікацій БД Scopus у ВВП та витратах на НДДКР країн в розрахунку на кожен 1 млн. дол. США.Исследована публикационная активность Украины и Евросоюза по отраслям науки. Рассмотрена динамика количества публикаций, которые приходятся на одного исследователя на протяжении 1996–2010 гг. Сделано сравнение отображения количества публикаций БД Scopus в ВВП и затратах на НДДКР стран в расчете на каждый 1 млн. дол. США.The publication activity by fields of science of Ukraine and the European Union was investigated. The dynamics of the number of publications per 1 researcher was considered during 1996–2010 years. Countries comparison by the number of publications reflecting in GDP and R&D expenditures per 1 million U.S. dollars measurements in the abstract database Scopus was done

Weak localization in InSb thin films heavily doped with lead

The paper reports on the investigations of the weak localization (WL) effects in 3D polycrystalline thin films of InSb. The films are closely compensated showing the electron concentration n>10^{16} cm^{-3} at the total concentration of the donor and acceptor type structural defects >10^{18} cm^{-3}. Unless Pb-doped, the InSb films do not show any measurable or show very small WL effect at 4.2 K. The Pb-doping to the concentration of the order of 10^{18} cm^{-3} leads to pronounced WL effects below 7 K. In particular, a clearly manifested SO scattering is observed. From the comparison of the experimental data on temperature dependence of the magnetoresistivity and sample resistance with the WL theory, the temperature dependence of the phase destroying time is determined. The determination is performed by fitting theoretical terms obtained from Kawabata's theory to experimental data on magnetoresistance. It is concluded that the dephasing process is connected to three separate interaction processes. The first is due to the SO scatterings and is characterized by temperature-independent relaxation time. The second is associated with the electron-phonon interaction. The third dephasing process is characterized by independent on temperature relaxation time tau_c. This relaxation time is tentatively ascribed to inelastic scattering at extended structural defects, like grain boundaries. The resulting time dephasing time shows saturation in its temperature dependence. The temperature dependence of the resistance of the InSb films can be explained by the electron-electron interaction for T2 K.Comment: 15 pages with 5 figure

Early stages of ramified growth in quasi-two-dimensional electrochemical deposition

I have measured the early stages of the growth of branched metal aggregates formed by electrochemical deposition in very thin layers. The growth rate of spatial Fourier modes is described qualitatively by the results of a linear stability analysis [D.P. Barkey, R.H. Muller, and C.W. Tobias, J. Electrochem. Soc. {\bf 136}, 2207 (1989)]. The maximum growth rate is proportional to $(I/c)^\delta$ where $I$ is the current through the electrochemical cell, $c$ the electrolyte concentration, and $\delta = 1.37 \pm 0.08$. Differences between my results and the theoretical predictions suggest that electroconvection in the electrolyte has a large influence on the instability leading to ramified growth.Comment: REVTeX, four ps figure