Thermodynamics of SU(3) gauge theory on anisotropic lattices

Finite temperature SU(3) gauge theory is studied on anisotropic lattices using the standard plaquette gauge action. The equation of state is calculated on $16^{3} \times 8$, $20^{3} \times 10$ and $24^{3} \times 12$ lattices with the anisotropy $\xi \equiv a_s / a_t = 2$, where $a_s$ and $a_t$ are the spatial and temporal lattice spacings. Unlike the case of the isotropic lattice on which $N_t=4$ data deviate significantly from the leading scaling behavior, the pressure and energy density on an anisotropic lattice are found to satisfy well the leading $1/N_t^2$ scaling from our coarsest lattice, $N_t/\xi=4$. With three data points at $N_t/\xi=4$, 5 and 6, we perform a well controlled continuum extrapolation of the equation of state. Our results in the continuum limit agree with a previous result from isotropic lattices using the same action, but have smaller and more reliable errors.Comment: RevTeX, 21 pages, 17 PS figures. A quantitative test about the benefit of anisotropic lattices added, minor errors corrected. Final version for PR

Graph Transformation in Molecular Biology

In the beginning, one of the main fields of application of graph transformation was biology, and more specifically morphology. Later, however, it was like if the biological applications had been left aside by the graph transformation community, just to be moved back into the mainstream these very last years with a new interest in molecular biology. In this paper, we review several fields of application of graph grammars in molecular biology, including: the modeling higherdimensional structures of biomolecules, the description of biochemical reactions, the analysis of metabolic pathways, and their potential use in computational systems biology

Haemoglobin: The surface buried between the α1β1 and α2β2 dimers in the deoxy and oxy structures

Using the newly available refined co-ordinates of deoxy and oxyhaemoglobin, we have reexamined and compared the interfaces between the dimers α1β1 and α2β2. The most extensive monomer-monomer contacts are between α1 and β2, and, symmetrically, α2 and β1. In oxyhaemoglobin these interfaces bury 700 Å2less protein surface than in deoxyhaemoglobin. The α1α2 interface involves similar salt bridges in both forms, but in oxyhaemoglobin buries 240 Å2more surface than in deoxyhaemoglobin. There is a loosely packed β1β2 interface burying 320 Å2 of surface in oxyhaemoglobin; there is no β1β2 interface in deoxyhaemoglobin. The greater stability of the deoxy form, in the absence of ligands, can be attributed to a combination of hydrophobic, van der Waals' and electrostatic interactions. © 1985.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

A method for multiple superposition of structures

The study of families of protein structures is important in analysing the results of NMR structure determinations and in investigating mechanisms of molecular evolution at the level of conformation. A method is discussed for finding the transformations that mutually superpose an arbitrary number of structures in the least-squares sense given specified atom-to-atom correspondence

Structural alignment and analysis of two distantly related proteins: Aplysia limacina myoglobin and sea lamprey globin

Two new globin structures have recently been determined at high resolution: the globin from the mollusc Aplysia limacina at 1.6 A resolution and a new refinement of the structure from sea lamprey. Two amino acid sequences of these homologous molecules have only 30% residue identity in an optimal alignment. We discuss some of the problems arising in the alignment of Aplysia globin with other globins of known structure, a challenging problem because of the distant relationship. Four independent approaches were applied to the alignment of the Aplysia and lamprey globins, including those based on individual sequence comparisons, structural analysis, and the relatively new method of templates or fingerprints derived for an entire family of proteins. We also compare these two new structures with what is already known about the globin family. A detailed description of the two structures shows that the two molecules contain the main structural features common to all the globins so far studied, with several minor but interesting hitherto unobserved variations

Hardware Designs for Local Alignment of Protein Sequences

IEEE Turkey Section;Int. Federation for Information Processing,IFIP;Sabanci University;The Scientific and Technological Research Council of TurkeyISCIS 2006: 21th International Symposium on Computer and Information Sciences --1 November 2006 through 3 November 2006 -- Istanbul --Local alignment of two protein sequences shows the similar regions between these proteins. Usually, a query protein sequence is aligned with several hundred thousands of protein sequences stored in databases. Since this procedure is computationally demanding, various hardware units are designed to get high quality results in a practically useful time. This paper presents efficient hardware designs that compute the local alignment scores of protein sequences. The presented designs are compared with the reference designs. All designs are implemented using ASIC and FPGA technologies. Syntheses results show that compared to the reference designs the proposed ASIC implementations achieve frequency improvements up to 250 % and hardware gains up to 40 %, and the proposed FPGA implementations achieve frequency improvements up to 29 % and hardware gains up to 48 %. © Springer-Verlag Berlin Heidelberg 2006

Probing Protein Structure by Solvent Perturbation of NMR Spectra: II. Determination of Surface and Buried Residues in Homologous Proteins

The experimental assignment of most residues in a protein to the surface or interior is in principle possible without prior solution of a complete three-dimensional structure. The method described is based on nmr measurements that determine the amino acid composition of the surface of a protein [A. Petros, L. Mueller, and K.D. Kopple (1990) Biochemistry, Vol. 29, pp. 10041-10048; G. Esposito, A. M. Lesk, H. Molinari, A. Motta, N. Niccolai, and A. Pastore (1992) Journal of Molecular Biology, Vol. 224, pp. 659-670]. If these measurements are carried out on several homologous proteins of known sequence, it is possible to combine the results to determine, in most cases, which positions in the sequence contain exposed residues

Probing Protein Structure by Solvent Perturbation of NMR Spectra: the Surface Accessibility of BPTI.

In the absence of specific interactions, the relative attenuation of protein NMR signals due to added stable free radicals such as TEMPOL should reflect the solvent accessibility of the molecular surface. The quantitative correlation between observed attenuation and surface accessibility was investigated with a model system, i.e., the small protein bovine pancreatic trypsin inhibitor. A detailed discussion is presented on the reliability and limits of the approach, and guidelines are provided for data acquisition, treatment, and interpretation. The NMR-derived accessibilities are compared with those obtained from x-ray diffraction and molecular dynamics data. Although the time-averaged accessibilities from molecular dynamics are ideally suited to fit the NMR data, better agreement was observed between the paramagnetic attenuations of the fingerprint cross-peaks of homonuclear proton spectra and the total NH and H alpha accessibilities calculated from x-ray coordinates, than from time-averaged molecular dynamics simulations. In addition, the solvent perturbation response appears to be a promising approach for detecting the thermal conformational evolution of secondary structure elements in proteins