A biophysical approach to large-scale protein-DNA binding data

About this book * Cutting-edge genome analysis methods from leading bioinformaticians An accurate description of current scientific developments in the field of bioinformatics and computational implementation is presented by research of the BioSapiens Network of Excellence. Bioinformatics is essential for annotating the structure and function of genes, proteins and the analysis of complete genomes and to molecular biology and biochemistry. Included is an overview of bioinformatics, the full spectrum of genome annotation approaches including; genome analysis and gene prediction, gene regulation analysis and expression, genome variation and QTL analysis, large scale protein annotation of function and structure, annotation and prediction of protein interactions, and the organization and annotation of molecular networks and biochemical pathways. Also covered is a technical framework to organize and represent genome data using the DAS technology and work in the annotation of two large genomic sets: HIV/HCV viral genomes and splicing alternatives potentially encoded in 1% of the human genome

Unquenched Charmonium with NRQCD - Lattice 2000

We present results from a series of NRQCD simulations of the charmonium system, both in the quenched approximation and with n_f = 2 dynamical quarks. The spectra show evidence for quenching effects of ~10% in the S- and P-hyperfine splittings. We compare this with other systematic effects. Improving the NRQCD evolution equation altered the S-hyperfine by as much as 20 MeV, and we estimate radiative corrections may be as large as 40%.Comment: Lattice 2000 (Heavy Quark Physics

Mean link versus average plaquette tadpoles in lattice NRQCD

We compare mean-link and average plaquette tadpole renormalization schemes in the context of the quarkonium hyperfine splittings in lattice NRQCD. Simulations are done for the three quarkonium systems $c\bar c$, $b\bar c$, and $b\bar b$. The hyperfine splittings are computed both at leading and at next-to-leading order in the relativistic expansion. Results are obtained at a large number of lattice spacings. A number of features emerge, all of which favor tadpole renormalization using mean links. This includes much better scaling of the hyperfine splittings in the three quarkonium systems. We also find that relativistic corrections to the spin splittings are smaller with mean-link tadpoles, particularly for the $c\bar c$ and $b\bar c$ systems. We also see signs of a breakdown in the NRQCD expansion when the bare quark mass falls below about one in lattice units (with the bare quark masses turning out to be much larger with mean-link tadpoles).Comment: LATTICE(heavyqk) 3 pages, 2 figure

In situ radiographic investigation of de lithiation mechanisms in a tin electrode lithium ion battery.

The lithiation and delithiation mechanisms of multiple Sn particles in a customized flat radiography cell were investigated by in amp; 8197;situ synchrotron radiography. For the first time, four de lithiation phenomena in a Sn electrode battery system are highlighted 1 amp; 8197;the de lithiation behavior varies between different Sn particles, 2 amp; 8197;the time required to lithiate individual Sn particles is markedly different from the time needed to discharge the complete battery, 3 amp; 8197;electrochemical deactivation of originally electrochemically active particles is reported, and 4 amp; 8197;a change of electrochemical behavior of individual particles during cycling is found and explained by dynamic changes of de lithiation pathways amongst particles within the electrode. These unexpected findings fundamentaly expand the understanding of the underlying de lithiation mechanisms inside commercial lithium ion batteries LIBs and would open new design principles for high performance next generation LIB

Impact of catalyst layer morphology on the operation of high temperature PEM fuel cells

Electrochemical impedance spectroscopy (EIS) is a well-established method to analyze a polymer electrolyte membrane fuel cell (PEMFC). However, without further data processing, the impedance spectrum yields only qualitative insight into the mechanism and individual contribution of transport, kinetics, and ohmic losses to the overall fuel cell limitations. The distribution of relaxation times (DRT) method allows quantifying each of these polarization losses and evaluates their contribution to a given electrocatalyst\u27s depreciated performances. We coupled this method with a detailed morphology study to investigate the impact of the 3D-structure on the processes occurring inside a high-temperature polymer electrolyte membrane fuel cell (HT-PEMFC). We tested a platinum catalyst (Pt/C), a platinum-cobalt alloy catalyst (Pt$_{3}$Co/C), and a platinum group metal-free iron-nitrogen-carbon (Fe–N–C) catalyst. We found that the hampered mass transport in the latter is mainly responsible for its low performance in the MEA (along with its decreased intrinsic performances for the ORR reaction). The better performance of the alloy catalyst can be explained by both improved mass transport and a lower ORR resistance. Furthermore, single-cell tests show that the catalyst layer morphology influences the distribution of phosphoric acid during conditioning

Measuring the aspect ratio renormalization of anisotropic-lattice gluons

Using tadpole inproved actions we investigate the consistency between different methods of measuring the aspect ratio renormalization of anisotropic-lattice gluons for bare aspect ratios \chi_0=4,6,10 and inverse lattice spacing in the range a_s^{-1}=660-840 MeV. The tadpole corrections to the action, which are established self-consistently, are defined for two cases, mean link tadpoles in Landau gauge and gauge invariant mean plaquette tadpoles. Parameters in the latter case exhibited no dependence on the spatial lattice size, L, while in the former, parameters showed only a weak dependence on L easily extrapolated to L=\infty. The renormalized anisotropy \chi_R was measured using both the torelon dispersion relation and the sideways potential method. We found good agreement between these different approaches. Any discrepancy was at worst 3-4% which is consistent with the effect of lattice artifacts that for the torelon we estimate as O(\a_Sa_s^2/R^2) where R is the flux-tube radius. We also present some new data that suggests that rotational invariance is established more accurately for the mean-link action than the plaquette action.Comment: LaTeX 18 pages including 7 figure

X ray Compton Tomography

The potentials of incoherent X ray scattering Compton tomography are investigated. Imaging materials of very different density or atomic number at once is a perpetual challenge for X ray tomography or radiography, in general. In a basic laboratory set up for simultaneous perpendicular Compton scattering and direct beam attenuation tomographic scans are conducted by single channel photon counting. This results in asymmetric distortions of the projection profiles of the scattering CT data set. In a first approach corrections of Compton scattering data by taking advantage of rotational symmetry yield tomograms without major geometric artefacts. A cylindrical sample composed of PE, PA, PVC, glass and wood demonstrates similar Compton contrast for all the substances, while the conventional absorption tomogram only reveals the two high order materials. Comparison to neutron tomography reveals astonishing similarities except for the glass component without hydrogen . Therefore, Compton CT bears the potential to replace neutron tomography, which requires much more efforts