Distributed BLAST in a grid computing context

The Basic Local Alignment Search Tool (BLAST) is one of the best known sequence comparison programs available in bioinformatics. It is used to compare query sequences to a set of target sequences, with the intention of finding similar sequences in the target set. Here, we present a distributed BLAST service which operates over a set of heterogeneous Grid resources and is made available through a Globus toolkit v.3 Grid service. This work has been carried out in the context of the BRIDGES project, a UK e-Science project aimed at providing a Grid based environment for biomedical research. Input consisting of multiple query sequences is partitioned into sub-jobs on the basis of the number of idle compute nodes available and then processed on these in batches. To achieve this, we have implemented our own Java-based scheduler which distributes sub-jobs across an array of resources utilizing a variety of local job scheduling systems

Magnetic Ordering and Superconductivity in the RE2_2Ir3_3Ge5_5 (RE = Y, La-Tm, Lu) System

We find that the compounds for RE = Y, La-Dy, crystallize in the tetragonal Ibam (U$_2$Co$_3$Si$_5$ type) structure whereas the compounds for RE = Er-Lu, crystallize in a new orthorhombic structure with a space group Pmmn. Samples of Ho$_2$Ir$_3$Ge$_5$ were always found to be multiphase. The compounds for RE = Y to Dy which adopt the Ibam type structure show a metallic resistivity whereas the compounds with RE = Er, Tm and Lu show an anomalous behavior in the resistivity with a semiconducting increase in $\rho$ as we go down in temperature from 300K. Interestingly we had earlier found a positive temperature coefficient of resistivity for the Yb sample in the same temperature range. We will compare this behavior with similar observations in the compounds RE$_3$Ru$_4$Ge$_{13}$ and REBiPt. La$_2$Ir$_3$Ge$_5$ and Y$_2$Ir$_3$Ge$_5$ show bulk superconductivity below 1.8K and 2.5K respectively. Our results confirm that Ce$_2$Ir$_3$Ge$_5$ shows a Kondo lattice behavior and undergoes antiferromagnetic ordering below 8.5K. Most of the other compounds containing magnetic rare-earth elements undergo a single antiferromagnetic transition at low temperatures (T$\leq$12K) while Gd$_2$Ir$_3$Ge$_5$, Dy$_2$Ir$_3$Ge$_5$ and Nd$_2$Ir$_3$Ge$_5$ show multiple transitions. The T$_N$'s for most of the compounds roughly scale with the de Gennes factor. which suggests that the chief mechanism of interaction leading to the magnetic ordering of the magnetic moments may be the RKKY interaction.Comment: 25 pages, 16 figure

Quadrupole deformation of deuterons and final state interaction in 2H⃗(e,e′p)^2 \vec H (e,e'p) scattering on tensor polarized deuterons at CEBAF energies

The strength of final state interaction (FSI) between struck proton and spectator neutron in $^2\vec{H}(e,e'p)$ scattering depends on the alignment of the deuteron. We study the resulting FSI effects in the tensor analyzing power in detail and find substantial FSI effects starting at still low missing momentum p_m \gsim 0.9 fm^{-1}. At larger p_m \gsim 1.5 fm^{-1}, FSI completely dominates both missing momentum distribution and tensor analyzing power. We find that to a large extent FSI masks the sensitivity of the tensor analyzing power to models of the deuteron wave function. For the transversely polarized deuterons the FSI induced forward-backward asymmetry of the missing momentum distribution is shown to have a node at precisely the same value of $p_m$ as the PWIA missing momentum distribution. The position of this node is not affected by FSI and can be a tool to distinguish experimentally between different models for the deuteron wave function.Comment: 24 pages, figures available from the authors on reques

Dynamics of the Hubbard model: a general approach by time dependent variational principle

We describe the quantum dynamics of the Hubbard model at semi-classical level, by implementing the Time-Dependent Variational Principle (TDVP) procedure on appropriate macroscopic wavefunctions constructed in terms of su(2)-coherent states. Within the TDVP procedure, such states turn out to include a time-dependent quantum phase, part of which can be recognized as Berry's phase. We derive two new semi-classical model Hamiltonians for describing the dynamics in the paramagnetic, superconducting, antiferromagnetic and charge density wave phases and solve the corresponding canonical equations of motion in various cases. Noticeably, a vortex-like ground state phase dynamics is found to take place for U>0 away from half filling. Moreover, it appears that an oscillatory-like ground state dynamics survives at the Fermi surface at half-filling for any U. The low-energy dynamics is also exactly solved by separating fast and slow variables. The role of the time-dependent phase is shown to be particularly interesting in the ordered phases.Comment: ReVTeX file, 38 pages, to appear on Phys. Rev.

Exceptional Collections and del Pezzo Gauge Theories

Stacks of D3-branes placed at the tip of a cone over a del Pezzo surface provide a way of geometrically engineering a small but rich class of gauge/gravity dualities. We develop tools for understanding the resulting quiver gauge theories using exceptional collections. We prove two important results for a general quiver gauge theory: 1) we show the ordering of the nodes can be determined up to cyclic permutation and 2) we derive a simple formula for the ranks of the gauge groups (at the conformal point) in terms of the numbers of bifundamentals. We also provide a detailed analysis of four node quivers, examining when precisely mutations of the exceptional collection are related to Seiberg duality.Comment: 26 pages, 1 figure; v2 footnote 2 amended; v3 ref adde

Dibaryons from Exceptional Collections

We discuss aspects of the dictionary between brane configurations in del Pezzo geometries and dibaryons in the dual superconformal quiver gauge theories. The basis of fractional branes defining the quiver theory at the singularity has a K-theoretic dual exceptional collection of bundles which can be used to read off the spectrum of dibaryons in the weakly curved dual geometry. Our prescription identifies the R-charge R and all baryonic U(1) charges Q_I with divisors in the del Pezzo surface without any Weyl group ambiguity. As one application of the correspondence, we identify the cubic anomaly tr R Q_I Q_J as an intersection product for dibaryon charges in large-N superconformal gauge theories. Examples can be given for all del Pezzo surfaces using three- and four-block exceptional collections. Markov-type equations enforce consistency among anomaly equations for three-block collections.Comment: 47 pages, 11 figures, corrected ref

High Energy QCD: Stringy Picture from Hidden Integrability

We discuss the stringy properties of high-energy QCD using its hidden integrability in the Regge limit and on the light-cone. It is shown that multi-colour QCD in the Regge limit belongs to the same universality class as superconformal $\cal{N}$=2 SUSY YM with $N_f=2N_c$ at the strong coupling orbifold point. The analogy with integrable structure governing the low energy sector of $\cal{N}$=2 SUSY gauge theories is used to develop the brane picture for the Regge limit. In this picture the scattering process is described by a single M2 brane wrapped around the spectral curve of the integrable spin chain and unifying hadrons and reggeized gluons involved in the process. New quasiclassical quantization conditions for the complex higher integrals of motion are suggested which are consistent with the $S-$duality of the multi-reggeon spectrum. The derivation of the anomalous dimensions of the lowest twist operators is formulated in terms of the Riemann surfacesComment: 37 pages, 3 figure

Strangeness Enhancement in p+Ap+A and S+AS+A Interactions at SPS Energies

The systematics of strangeness enhancement is calculated using the HIJING and VENUS models and compared to recent data on $\,pp\,$, $\,pA\,$ and $\,AA\,$ collisions at CERN/SPS energies ($200A\,\, GeV\,$). The HIJING model is used to perform a {\em linear} extrapolation from $pp$ to $AA$. VENUS is used to estimate the effects of final state cascading and possible non-conventional production mechanisms. This comparison shows that the large enhancement of strangeness observed in $S+Au$ collisions, interpreted previously as possible evidence for quark-gluon plasma formation, has its origins in non-equilibrium dynamics of few nucleon systems. % Strangeness enhancement %is therefore traced back to the change in the production dynamics %from $pp$ to minimum bias $pS$ and central $SS$ collisions. A factor of two enhancement of $\Lambda^{0}$ at mid-rapidity is indicated by recent $pS$ data, where on the average {\em one} projectile nucleon interacts with only {\em two} target nucleons. There appears to be another factor of two enhancement in the light ion reaction $SS$ relative to $pS$, when on the average only two projectile nucleons interact with two target ones.Comment: 29 pages, 8 figures in uuencoded postscript fil

A simple conceptual model of abrupt glacial climate events

Here we use a very simple conceptual model in an attempt to reduce essential parts of the complex nonlinearity of abrupt glacial climate changes (the so-called Dansgaard-Oeschger events) to a few simple principles, namely (i) the existence of two different climate states, (ii) a threshold process and (iii) an overshooting in the stability of the system at the start and the end of the events, which is followed by a millennial-scale relaxation. By comparison with a so-called Earth system model of intermediate complexity (CLIMBER-2), in which the events represent oscillations between two climate states corresponding to two fundamentally different modes of deep-water formation in the North Atlantic, we demonstrate that the conceptual model captures fundamental aspects of the nonlinearity of the events in that model. We use the conceptual model in order to reproduce and reanalyse nonlinear resonance mechanisms that were already suggested in order to explain the characteristic time scale of Dansgaard-Oeschger events. In doing so we identify a new form of stochastic resonance (i.e. an overshooting stochastic resonance) and provide the first explicitly reported manifestation of ghost resonance in a geosystem, i.e. of a mechanism which could be relevant for other systems with thresholds and with multiple states of operation. Our work enables us to explicitly simulate realistic probability measures of Dansgaard-Oeschger events (e.g. waiting time distributions, which are a prerequisite for statistical analyses on the regularity of the events by means of Monte-Carlo simulations). We thus think that our study is an important advance in order to develop more adequate methods to test the statistical significance and the origin of the proposed glacial 1470-year climate cycle

Dynamical mean-field approach to materials with strong electronic correlations

We review recent results on the properties of materials with correlated electrons obtained within the LDA+DMFT approach, a combination of a conventional band structure approach based on the local density approximation (LDA) and the dynamical mean-field theory (DMFT). The application to four outstanding problems in this field is discussed: (i) we compute the full valence band structure of the charge-transfer insulator NiO by explicitly including the p-d hybridization, (ii) we explain the origin for the simultaneously occuring metal-insulator transition and collapse of the magnetic moment in MnO and Fe2O3, (iii) we describe a novel GGA+DMFT scheme in terms of plane-wave pseudopotentials which allows us to compute the orbital order and cooperative Jahn-Teller distortion in KCuF3 and LaMnO3, and (iv) we provide a general explanation for the appearance of kinks in the effective dispersion of correlated electrons in systems with a pronounced three-peak spectral function without having to resort to the coupling of electrons to bosonic excitations. These results provide a considerable progress in the fully microscopic investigations of correlated electron materials.Comment: 24 pages, 14 figures, final version, submitted to Eur. Phys. J. for publication in the Special Topics volume "Cooperative Phenomena in Solids: Metal-Insulator Transitions and Ordering of Microscopic Degrees of Freedom