ViCTree: an automated framework for taxonomic classification from protein sequences

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/

Impurity Effect on Spin Ladder System

Effects of nonmagnetic impurity doping in a spin ladder system with a spin gap are investigated by the exact diagonalization as well as by the variational Monte Carlo calculations. Substantial changes in macroscopic properties such as enhancements in spin correlations and magnetic susceptibilities are observed in the low impurity concentration region, which are caused by the increase of low-energy states. These results suggest that small but finite amount of nonmagnetic impurity doping relevantly causes the reduction or the vanishment of the spin gap. This qualitatively explains the experimental result of Zn-doped SrCu$_{2}$O$_{3}$ where small doping induces gapless nature. We propose a possible scenario for this drastic change as a quantum phase transition in a spin gapped ladder system due to spinon doping effects.Comment: 14 pages LaTeX including 5 PS figure

Contraction of cross-linked actomyosin bundles

Cross-linked actomyosin bundles retract when severed in vivo by laser ablation, or when isolated from the cell and micromanipulated in vitro in the presence of ATP. We identify the time scale for contraction as a viscoelastic time tau, where the viscosity is due to (internal) protein friction. We obtain an estimate of the order of magnitude of the contraction time tau ~ 10-100 s, consistent with available experimental data for circumferential microfilament bundles and stress fibers. Our results are supported by an exactly solvable, hydrodynamic model of a retracting bundle as a cylinder of isotropic, active matter, from which the order of magnitude of the active stress is estimated.Comment: To be published in Physical Biolog

Scaling Properties of Antiferromagnetic Transition in Coupled Spin Ladder Systems Doped with Nonmagnetic Impurities

We study effects of interladder coupling on critical magnetic properties of spin ladder systems doped with small concentrations of nonmagnetic impurities, using the scaling theory together with quantum Monte Carlo (QMC) calculations. Scaling properties in a wide region in the parameter space of the impurity concentration x and the interladder coupling are governed by the quantum critical point (QCP) of the undoped system for the transition between antiferromagnetically ordered and spin-gapped phases. This multi-dimensional and strong-coupling region has characteristic power-law dependences on x for magnetic properties such as the N\'eel temperature. The relevance of this criticality for understanding experimental results of ladder compounds is stressed.Comment: 4 pages LaTeX including 3 PS figure

Mechanisms for Non-Trivial Magnetization Plateaux of an S=1 Frustrated Spin Ladder

We investigate the non-trivial magnetization plateau at 1/4 of the saturation magnetization of S=1 spin ladder, especially with reference to recent experimental results on a new organic tetraradical 3,3',5,5'-tetrakis(N-tert-butylaminoxyl)biphenyl, abbreviated as BIP-TENO. We propose three mechanisms for the formation of the plateau; the Neel mechanism, the dimer mechanism and the spin-Peierls mechanism. We also discuss the effect of four-spin exchange interactions.Comment: 3 pages, 5 figures, Orbital2001 (International Conference on Strongly Correlated Electrons with Orbital Degrees of Freedom) (September 11-14, 2001. Sendai

Magnetization Plateau of an S=1 Frustrated Spin Ladder

We study the magnetization plateau at 1/4 of the saturation magnetization of the S=1 antiferromagnetic spin ladder both analytically and numerically, with the aim of explaining recent experimental results on BIP-TENO by Goto et al. We propose two mechanisms for the plateau formation and clarify the plateau phase diagram on the plane of the coupling constants between spins

Critical exponents of the quantum phase transition in a planar antiferromagnet

We have performed a large scale quantum Monte Carlo study of the quantum phase transition in a planar spin-1/2 Heisenberg antiferromagnet with CaV4O9 structure. We obtain a dynamical exponent z=1.018+/-0.02. The critical exponents beta, nu and eta agree within our errors with the classical 3D O(3) exponents, expected from a mapping to the nonlinear sigma model. This confirms the conjecture of Chubukov, Sachdev and Ye [Phys. Rev. B 49, 11919 (1994)] that the Berry phase terms in the planar Heisenberg antiferromagnet are dangerously irrelevant.Comment: 5 pages including 4 figures; revised version: some minor changes and added reference

Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum

Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental program are often studied in cells starved in suspension while cAMP is provided exogenously. Previous studies revealed massive shifts in the transcriptome under both developmental conditions and a close relationship between gene expression and morphogenesis, but were limited by the sampling frequency and the resolution of the methods. Here, we combine the superior depth and specificity of RNA-seq-based analysis of mRNA abundance with high frequency sampling during filter development and cAMP pulsing in suspension. We found that the developmental transcriptome exhibits mostly gradual changes interspersed by a few instances of large shifts. For each time point we treated the entire transcriptome as single phenotype, and were able to characterize development as groups of similar time points separated by gaps. The grouped time points represented gradual changes in mRNA abundance, or molecular phenotype, and the gaps represented times during which many genes are differentially expressed rapidly, and thus the phenotype changes dramatically. Comparing developmental experiments revealed that gene expression in filter developed cells lagged behind those treated with exogenous cAMP in suspension. The high sampling frequency revealed many genes whose regulation is reproducibly more complex than indicated by previous studies. Gene Ontology enrichment analysis suggested that the transition to multicellularity coincided with rapid accumulation of transcripts associated with DNA processes and mitosis. Later development included the up-regulation of organic signaling molecules and co-factor biosynthesis. Our analysis also demonstrated a high level of synchrony among the developing structures throughout development. Our data describe D. discoideum development as a series of coordinated cellular and multicellular activities. Coordination occurred within fields of aggregating cells and among multicellular bodies, such as mounds or migratory slugs that experience both cell-cell contact and various soluble signaling regimes. These time courses, sampled at the highest temporal resolution to date in this system, provide a comprehensive resource for studies of developmental gene expression

Origin of spin-gap in CaV4_4O9_9: effect of frustration and lattice distortion

We study the origin of spin-gap in recently discovered material CaV$_4$O$_9$. We analyze the spin-$1/2$ Heisenberg model on the $1/5$ depleted square lattice with nearest neighbor (nn) and next nearest neighbor (nnn) interactions, in terms of the singlet and triplet states of the 4-spin plaquettes and 2-spin dimers. Phase diagram of the model is obtained within a linear ``spin-wave"-like approximation, and is shown to agree well with the earlier results of QMC simulations for nn interactions. We further propose that the special lattice structure of CaV$_4$O$_9$ naturally leads to lattice distortions, which enhances the spin-gap via a spin-Peierls mechanism.Comment: 4 pages, RevTex, 2 postscript figures. Latex file and figures have been uuencode

Plaquette-singlet solid state and topological hidden order in spin-1 antiferromagnetic Heisenberg ladder

Ground-state properties of the spin-1 two-leg antiferromagnetic ladder are investigated precisely by means of the quantum Monte Carlo method. It is found that the correlation length along the chains and the spin gap both remain finite regardless of the strength of interchain coupling, i.e., the Haldane state and the spin-1 dimer state are connected smoothly without any quantum phase transitions between them. We propose a plaquette-singlet solid state, which qualitatively describes the ground state of the spin-1 ladder quite well, and also a corresponding topological hidden order parameter. It is shown numerically that the new hidden order parameter remains finite up to the dimer limit, though the conventional string order defined on each chain vanishes immediately when infinitesimal interchain coupling is introduced.Comment: RevTeX, 10 pages, 9 figure