358,396 research outputs found

    Transmission and Spectral Aspects of Tight Binding Hamiltonians for the Counting Quantum Turing Machine

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    It was recently shown that a generalization of quantum Turing machines (QTMs), in which potentials are associated with elementary steps or transitions of the computation, generates potential distributions along computation paths of states in some basis B. The distributions are computable and are thus periodic or have deterministic disorder. These generalized machines (GQTMs) can be used to investigate the effect of potentials in causing reflections and reducing the completion probability of computations. This work is extended here by determination of the spectral and transmission properties of an example GQTM which enumerates the integers as binary strings. A potential is associated with just one type of step. For many computation paths the potential distributions are initial segments of a quasiperiodic distribution that corresponds to a substitution sequence. The energy band spectra and Landauer Resistance (LR) are calculated for energies below the barrier height by use of transfer matrices. The LR fluctuates rapidly with momentum with minima close to or at band-gap edges. For several values of the parameters, there is good transmission over some momentum regions.Comment: 22 pages Latex, 13 postscript figures, Submitted to Phys. Rev.

    Red star-forming and blue passive galaxies in clusters

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    We explore the relation between colour and specific star formation rate (derived from optical spectra obtained by SDSS DR4) of over 6,000 galaxies (M_r<=-20.5) in and around low redshift (z<0.12) clusters. Even though most red galaxies have little or no ongoing star formation, and most blue galaxies are currently forming stars, there are significant populations of red star-forming (SF) and blue passive galaxies. This paper examines various properties of galaxies belonging to the latter two categories. These properties include morphological parameters, internal extinction, spectral features such as EW(H_delta) and the 4000 ang break, and metallicity. Our analysis shows that the blue passive galaxies have properties very similar to their SF counterparts, except that their large range in EW(H_delta) indicates recent truncation of star formation. The red SF galaxies fall into two broad categories, one of them being massive galaxies in cluster cores dominated by an old stellar population, but with evidence of current star formation in the core. For the remaining red SF galaxies it is evident from various metallicity measures and mean stellar ages, that their colours result from the predominance of a metal-rich stellar population. The implication of the properties of these SF galaxies on environmental studies, like that of the Butcher-Oemler effect, is discussed.Comment: 13 pages, 11 figures, accepted for publication in MNRA

    Angular momentum transport by internal gravity waves. IV - Wave generation by surface convection zone, from the pre-main sequence to the early-AGB in intermediate mass stars

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    This is the fourth in a series of papers that deal with angular momentum transport by internal gravity waves in stellar interiors. Here, we want to examine the potential role of waves in other evolutionary phases than the main sequence. We study the evolution of a 3Msun Population I model from the pre-main sequence to the early-AGB phase and examine whether waves can lead to angular momentum redistribution and/or element diffusion at the external convection zone boundary. We find that, although waves produced by the surface convection zone can be ignored safely for such a star during the main sequence, it is not the case for later evolutionary stages. In particular, angular momentum transport by internal waves could be quite important at the end of the sub-giant branch and during the early-AGB phase. Wave-induced mixing of chemicals is expected during the early-AGB phase.Comment: A&A in press; 11 figure

    Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

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    The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

    Intrinsically Disordered C-Terminal Tails of \u3cem\u3eE. coli\u3c/em\u3e Single-Stranded DNA Binding Protein Regulate Cooperative Binding to Single-Stranded DNA

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    The homotetrameric Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA replication, repair and recombination. E. coli SSB can bind to long single-stranded DNA (ssDNA) in multiple binding modes using all four subunits [(SSB)65 mode] or only two subunits [(SSB)35 binding mode], with the binding mode preference regulated by salt concentration and SSB binding density. These binding modes display very different ssDNA binding properties with the (SSB)35 mode displaying highly cooperative binding to ssDNA. SSB tetramers also bind an array of partner proteins, recruiting them to their sites of action. This is achieved through interactions with the last 9 amino acids (acidic tip) of the intrinsically disordered linkers (IDLs) within the four C-terminal tails connected to the ssDNA binding domains. Here, we show that the amino acid composition and length of the IDL affects the ssDNA binding mode preferences of SSB protein. Surprisingly, the number of IDLs and the lengths of individual IDLs together with the acidic tip contribute to highly cooperative binding in the (SSB)35 binding mode. Hydrodynamic studies and atomistic simulations suggest that the E. coli SSB IDLs show a preference for forming an ensemble of globular conformations, whereas the IDL from Plasmodium falciparum SSB forms an ensemble of more extended random coils. The more globular conformations correlate with cooperative binding

    Field reconnaissance geologic mapping of the Columbia Hills, Mars, based on Mars Exploration Rover Spirit and MRO HiRISE observations

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    Chemical, mineralogic, and lithologic ground truth was acquired for the first time on Mars in terrain units mapped using orbital Mars Reconnaissance Orbiter's High Resolution Imaging Science Experiment (MRO HiRISE) image data. Examination of several dozen outcrops shows that Mars is geologically complex at meter length scales, the record of its geologic history is well exposed, stratigraphic units may be identified and correlated across significant areas on the ground, and outcrops and geologic relationships between materials may be analyzed with techniques commonly employed in terrestrial field geology. Despite their burial during the course of Martian geologic time by widespread epiclastic materials, mobile fines, and fall deposits, the selective exhumation of deep and well-preserved geologic units has exposed undisturbed outcrops, stratigraphic sections, and structural information much as they are preserved and exposed on Earth. A rich geologic record awaits skilled future field investigators on Mars. The correlation of ground observations and orbital images enables construction of a corresponding geologic reconnaissance map. Most of the outcrops visited are interpreted to be pyroclastic, impactite, and epiclastic deposits overlying an unexposed substrate, probably related to a modified Gusev crater central peak. Fluids have altered chemistry and mineralogy of these protoliths in degrees that vary substantially within the same map unit. Examination of the rocks exposed above and below the major unconformity between the plains lavas and the Columbia Hills directly confirms the general conclusion from remote sensing in previous studies over past years that the early history of Mars was a time of more intense deposition and modification of the surface. Although the availability of fluids and the chemical and mineral activity declined from this early period, significant later volcanism and fluid convection enabled additional, if localized, chemical activity

    Substrate Induced Structural and Dynamics Changes in Human Phosphomevalonate Iinase and Implications for Mechanism

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    Phosphomevalonate kinase (PMK) catalyzes an essential step in the mevalonate pathway, which is the only pathway for synthesis of isoprenoids and steroids in humans. PMK catalyzes transfer of the γ-phosphate of ATP to mevalonate 5-phosphate (M5P) to form mevalonate 5-diphosphate. Bringing these phosphate groups in proximity to react is especially challenging, given the high negative charge density on the four phosphate groups in the active site. As such, conformational and dynamics changes needed to form the Michaelis complex are of mechanistic interest. Herein, we report the characterization of substrate induced changes (Mg-ADP, M5P, and the ternary complex) in PMK using NMR-based dynamics and chemical shift perturbation measurements. Mg-ADP and M5P Kd\u27s were 6–60 μM in all complexes, consistent with there being little binding synergy. Binding of M5P causes the PMK structure to compress (τc = 13.5 nsec), whereas subsequent binding of Mg-ADP opens the structure up (τc = 15.6 nsec). The overall complex seems to stay very rigid on the psec-nsec timescale with an average NMR order parameter of S2 ∼0.88. Data are consistent with addition of M5P causing movement around a hinge region to permit domain closure, which would bring the M5P domain close to ATP to permit catalysis. Dynamics data identify potential hinge residues as H55 and R93, based on their low order parameters and their location in extended regions that connect the M5P and ATP domains in the PMK homology model. Likewise, D163 may be a hinge residue for the lid region that is homologous to the adenylate kinase lid, covering the “Walker-A” catalytic loop. Binding of ATP or ADP appears to cause similar conformational changes; however, these observations do not indicate an obvious role for γ-phosphate binding interactions. Indeed, the role of γ-phosphate interactions may be more subtle than suggested by ATP/ADP comparisons, because the conservative O to NH substitution in the β-γ bridge of ATP causes a dramatic decrease in affinity and induces few chemical shift perturbations. In terms of positioning of catalytic residues, binding of M5P induces a rigidification of Gly21 (adjacent to the catalytically important Lys22), although exchange broadening in the ternary complex suggests some motion on a slower timescale does still occur. Finally, the first nine residues of the N-terminus are highly disordered, suggesting that they may be part of a cleavable signal or regulatory peptide sequence. Proteins 2009. © 2008 Wiley-Liss, Inc
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