Genome Network Project: An Integrated Genomic Platform

With the objective of elucidating the structure of gene interactions in the human genome, the Genome Network Project has generated a vast quantity of experimental data, mainly focusing on transcriptional control and transcription-factor related protein-protein interactions (PPI). This data has been collected and organized into the Genome Network Platform ("http://genomenetwork.nig.ac.jp/":http://genomenetwork.nig.ac.jp/) at the National Institute of Genetics. Expression data was obtained through CAGE (Cap Analysis Gene Expression), qRT-PCR, tiling array, microarray and short RNA analysis, while PPI information was gathered through yeast two hybrid (Y2H), mammalian two hybrid (M2H) and _in vitro_ virus (IVV) methods. The Genome Network Platform Viewer provides an integrated user interface to the complete database, including services of gene search, whole genome browsing, PPI network viewer, and expression profile analysis. Our platform represents an extremely useful resource for researchers in the field of genomics, and provides access to high quality data through the combination of intuitive browsing and visualization capabilities

Wannier representation of Floquet topological states

A universal feature of topological insulators is that they cannot be adiabatically connected to an atomic limit, where individual lattice sites are completely decoupled. This property is intimately related to a topological obstruction to constructing a localized Wannier function from Bloch states of an insulator. Here we generalize this characterization of topological phases toward periodically driven systems. We show that nontrivial connectivity of hybrid Wannier centers in momentum space and time can characterize various types of topology in periodically driven systems, which include Floquet topological insulators, anomalous Floquet topological insulators with micromotion-induced boundary states, and gapless Floquet states realized with topological Floquet operators. In particular, nontrivial time dependence of hybrid Wannier centers indicates impossibility of continuous deformation of a driven system into an undriven insulator, and a topological Floquet operator implies an obstruction to constructing a generalized Wannier function which is localized in real and frequency spaces. Our results pave a way to a unified understanding of topological states in periodically driven systems as a topological obstruction in Floquet states.Comment: 17 pages, 5 figure

Temperature and heat flux scalings for isoviscous thermal convection in spherical geometry

Parametrized convection, which has long been used to reconstruct the thermal history of planetary mantles, is based on scaling relationships between observables (including heat flux) and controlling parameters (the most important being the Rayleigh number, Ra). To explore the influence of spherical geometry on heat transfer, we have conducted two series of numerical experiments of thermal convection (one with bottom heating and the other with mixed heating) in an isoviscous spherical shell with various curvatures. Using these calculations and a generalized non-linear inversion, we then derive scaling laws for the average temperature and for the surface heat flux. In the case of bottom heating, we found that the non-dimensional average temperature is given by θm=f2/(1 +f2), where f is the ratio between the core and total radii. The non-dimensional surface heat flux is fitted well by Nutop= 0.36f0.32 Ra(0.273+0.05f)θ0.6m. This scaling indicates that the available heating power decreases with increasing curvature (decreasing f). There exist strong trade-offs between the inverted parameters, that is, different sets of parameters explain our calculations well within error bars. For mixed heating, the non-dimensional average temperature and surface heat flux are well explained by θH=θm+ (1.68 − 0.8f)[(1 +f+f2)/3]0.79 h0.79/Ra0.234, where h is the non-dimensional rate of internal heating, and Nutop= 0.59f0.05 Ra(0.300−0.003f)θ1.23H. Due to a competition between the radiogenic and convective powers, and for given values of h and Ra, there is a curvature for which the Urey ratio reaches a minimum. Applied to the Earth's mantle, the mixed heating scaling predicts a Urey ratio between 0.4 and 0.6, depending on the Rayleigh number. Additional parameters, including the thermal viscosity ratio, phase transitions, the presence of dense material in the deep mantle, and variability of the flow pattern in time, may enter an appropriate modelling of the Earth's mantle thermal histor

On the Mechanism of BaSi2 Thin Film Formation on Si Substrate by Vacuum Evaporation

AbstractWe report on the formation mechanism of BaSi2 thin film on Si substrate grown by vacuum evaporation using BaSi2 granules as source materials. Since the vapor flux at the initial stage of evaporation is known to be Ba-rich, Si supply from the substrate is of crucial importance to obtain homogeneous BaSi2 thin film. In fact, low substrate temperature and/or thick film deposition led to formation of rough film with voids, and the oxidation proceeded upon exposure to air. We revealed that appropriate choice of substrate temperature, film thickness, and post-growth in-situ annealing can provide enough diffusion of Si and Ba, leading to realization of homogeneous BaSi2 thin film