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

Exotic Quarkonia from Anisotropic Lattices

We study in detail the spectrum of heavy quarkonia with different orbital angular momentum along with their radial and gluonic excitations. Using an anisotropic formulation of Lattice QCD we achieved an unprecedented control over statistical errors and were able to study systematic errors such as lattice spacing artefacts, finite volume effects and relativistic corrections. First results on the spin structure in heavy hybrids are also presented.Comment: 4 pages, 4 figure

Heavy Quarkonia from Anisotropic and Isotropic Lattices

We report on recent results for the spectrum of heavy quarkonia. Using coarse and anisotropic lattices we achieved an unprecedented control over statistical and systematic errors for higher excited states such as exotic hybrid states. In a parallel study on isotropic lattices we also investigate the effect of two dynamical flavours on the spin structure of charmonium and bottomonium for several symmetric lattices.Comment: LATTICE'99 (heavy quarks), 3 pages, 3 figure

Correction, improvement and model verification of CARE 3, version 3

An independent verification of the CARE 3 mathematical model and computer code was conducted and reported in NASA Contractor Report 166096, Review and Verification of CARE 3 Mathematical Model and Code: Interim Report. The study uncovered some implementation errors that were corrected and are reported in this document. The corrected CARE 3 program is called version 4. Thus the document, correction. improvement, and model verification of CARE 3, version 3 was written in April 1984. It is being published now as it has been determined to contain a more accurate representation of CARE 3 than the preceding document of April 1983. This edition supercedes NASA-CR-166122 entitled, 'Correction and Improvement of CARE 3,' version 3, April 1983

Lethality and entropy of protein interaction networks

We characterize protein interaction networks in terms of network entropy. This approach suggests a ranking principle, which strongly correlates with elements of functional importance, such as lethal proteins. Our combined analysis of protein interaction networks and functional profiles in single cellular yeast and multi-cellular worm shows that proteins with large contribution to network entropy are preferentially lethal. While entropy is inherently a dynamical concept, the present analysis incorporates only structural information. Our result therefore highlights the importance of topological features, which appear as correlates of an underlying dynamical property, and which in turn determine functional traits. We argue that network entropy is a natural extension of previously studied observables, such as pathway multiplicity and centrality. It is also applicable to networks in which the processes can be quantified and therefore serves as a link to study questions of structural and dynamical robustness in a unified way

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

Charmonium Spectrum from Quenched Anisotropic Lattice QCD

We present a detailed study of the charmonium spectrum using anisotropic lattice QCD. We first derive a tree-level improved clover quark action on the anisotropic lattice for arbitrary quark mass. The heavy quark mass dependences of the improvement coefficients, i.e. the ratio of the hopping parameters $\zeta=K_t/K_s$ and the clover coefficients $c_{s,t}$, are examined at the tree level. We then compute the charmonium spectrum in the quenched approximation employing $\xi = a_s/a_t = 3$ anisotropic lattices. Simulations are made with the standard anisotropic gauge action and the anisotropic clover quark action at four lattice spacings in the range $a_s$=0.07-0.2 fm. The clover coefficients $c_{s,t}$ are estimated from tree-level tadpole improvement. On the other hand, for the ratio of the hopping parameters $\zeta$, we adopt both the tree-level tadpole-improved value and a non-perturbative one. We calculate the spectrum of S- and P-states and their excitations. The results largely depend on the scale input even in the continuum limit, showing a quenching effect. When the lattice spacing is determined from the $1P-1S$ splitting, the deviation from the experimental value is estimated to be $\sim$30% for the S-state hyperfine splitting and $\sim$20% for the P-state fine structure. Our results are consistent with previous results at $\xi = 2$ obtained by Chen when the lattice spacing is determined from the Sommer scale $r_0$. We also address the problem with the hyperfine splitting that different choices of the clover coefficients lead to disagreeing results in the continuum limit.Comment: 43 pages, 49 eps figures, revtex; minor changes, version to appear in Physical Review

Ab Initio Study of Hybrid b-bar-gb Mesons

Hybrid b-bar-gb molecules in which the heavy b-bar-b pair is bound together by the excited gluon field g are studied using the Born-Oppenheimer expansion and numerical simulations. The consistency of results from the two approaches reveals a simple and compelling physical picture for heavy hybrid states.Comment: 4 pages, 3 figures, uses REVTeX and epsf, final published versio

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