4,164 research outputs found

    Exploring the energy landscapes of cyclic tetrapeptides with discrete path sampling

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    [Image: see text] Cyclic tetrapeptides are an important class of biologically active molecules that exhibit interesting conformational dynamics, with slow interconversion of several different structures. We present calculations on their energy landscapes using discrete path sampling. In acyclic peptides and large cyclic peptides, isomers containing cis-peptide groups are much less stable than the all-trans isomers and separated from them by large barriers. Strain in small cyclic peptides causes the cis and trans isomers to be closer in energy and separated by much lower barriers. If d-amino acids or proline residues are introduced, isomers containing cis-peptides become more stable than the all-trans structures. We also show that changing the polarity of the solvent has a significant effect on the energy landscapes of cyclic tetrapeptides, causing changes in the orientations of the peptide groups and in the degree of intramolecular hydrogen bonding

    Vibration Isolation Design for the Micro-X Rocket Payload

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    Micro-X is a NASA-funded, sounding rocket-borne X-ray imaging spectrometer that will allow high precision measurements of velocity structure, ionization state and elemental composition of extended astrophysical systems. One of the biggest challenges in payload design is to maintain the temperature of the detectors during launch. There are several vibration damping stages to prevent energy transmission from the rocket skin to the detector stage, which causes heating during launch. Each stage should be more rigid than the outer stages to achieve vibrational isolation. We describe a major design effort to tune the resonance frequencies of these vibration isolation stages to reduce heating problems prior to the projected launch in the summer of 2014.Comment: 6 pages, 7 figures, LTD15 Conference Proceeding

    HypTrails: A Bayesian Approach for Comparing Hypotheses About Human Trails on the Web

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    When users interact with the Web today, they leave sequential digital trails on a massive scale. Examples of such human trails include Web navigation, sequences of online restaurant reviews, or online music play lists. Understanding the factors that drive the production of these trails can be useful for e.g., improving underlying network structures, predicting user clicks or enhancing recommendations. In this work, we present a general approach called HypTrails for comparing a set of hypotheses about human trails on the Web, where hypotheses represent beliefs about transitions between states. Our approach utilizes Markov chain models with Bayesian inference. The main idea is to incorporate hypotheses as informative Dirichlet priors and to leverage the sensitivity of Bayes factors on the prior for comparing hypotheses with each other. For eliciting Dirichlet priors from hypotheses, we present an adaption of the so-called (trial) roulette method. We demonstrate the general mechanics and applicability of HypTrails by performing experiments with (i) synthetic trails for which we control the mechanisms that have produced them and (ii) empirical trails stemming from different domains including website navigation, business reviews and online music played. Our work expands the repertoire of methods available for studying human trails on the Web.Comment: Published in the proceedings of WWW'1

    ISO/IEC 15504 measurement applied to COBIT process maturity

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    Purpose: The assessment of COBIT process maturity levels is fraught with a number of problems regarding the objectivity of the assessment results. Unlike ISO/IEC 15504, COBIT does not define an assessment model. The purpose of this paper is to align the behavioural aspects of the six COBIT process attributes with achievement results defined for the nine process attributes associated with the ISO/IEC 15504-2 measurement scale. The authors believe that this alignment permits a translation of the ISO/IEC 15504 assessment data into an objective COBIT process maturity rating. Design/methodology/approach: The tables presented in the paper identify the COBIT process attributes, the applicable ISO/IEC 15504 process attribute achievement results and the aggregated rating that pertains to the selected achievement results. A final table lists the derived COBIT process maturity level in terms of the ratings for the ISO/IEC 15504 process attribute achievement results for an assessed process. Findings: The objectivity of the aggregated result (COBIT process maturity level) appeals strongly to end-users of this measurement result, particularly where contractual obligations must be satisfied. Practical implications: The method is useful where measurement rigour must be demonstrated in the computation of the COBIT process maturity levels. Originality/value: This assessment and computational method was developed and trialled in the second half of 2010 in the context of the assessment of 13 information technology (IT) service management processes at two different customer sites. The material is of special value to service managers in companies that have outsourced IT service management processes to external IT service providers. © Emerald Group Publishing Limited

    Structure of an eight-membered CN 4

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    Visualizing energy landscapes with metric disconnectivity graphs

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    The visualization of multidimensional energy landscapes is important, providing insight into the kinetics and thermodynamics of a system, as well the range of structures a system can adopt. It is, however, highly nontrivial, with the number of dimensions required for a faithful reproduction of the landscape far higher than can be represented in two or three dimensions. Metric disconnectivity graphs provide a possible solution, incorporating the landscape connectivity information present in disconnectivity graphs with structural information in the form of a metric. In this study, we present a new software package, PyConnect, which is capable of producing both disconnectivity graphs and metric disconnectivity graphs in two or three dimensions. We present as a test case the analysis of the 69-bead BLN coarse-grained model protein and show that, by choosing appropriate order parameters, metric disconnectivity graphs can resolve correlations between structural features on the energy landscape with the landscapes energetic and kinetic properties

    A Suborbital Payload for Soft X-ray Spectroscopy of Extended Sources

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    We present a suborbital rocket payload capable of performing soft X-ray spectroscopy on extended sources. The payload can reach resolutions of ~100(lambda/dlambda) over sources as large as 3.25 degrees in diameter in the 17-107 angstrom bandpass. This permits analysis of the overall energy balance of nearby supernova remnants and the detailed nature of the diffuse soft X-ray background. The main components of the instrument are: wire grid collimators, off-plane grating arrays and gaseous electron multiplier detectors. This payload is adaptable to longer duration orbital rockets given its comparatively simple pointing and telemetry requirements and an abundance of potential science targets.Comment: Accepted to Experimental Astronomy, 12 pages plus 1 table and 17 figure

    Metabolic flexibility as a major predictor of spatial distribution in microbial communities

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    A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology

    Keratins as markers of differentiated taste cells of the rat

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    Cytokeratins in taste buds were immunocytochemically evaluated with monoclonal antibodies. In each of six different epithelial sites in the rat oral cavity, intragemmal cells of taste buds were immunoreactive for keratin polypeptides 8, 18, and 19, as well as for keratin 7, which has not been previously reported in taste buds. Keratin-18-like immunoreactivity was present in fewer than half of the intragemmal cells, whereas all intragemmal cells were immunopositive for keratins 7, 8, and 19. Apart from some salivary duct cells, no other cells in the tongue were immunoreactive for any of these four keratins. Morphological and immunocytochemical profiles indicate that taste buds are islets of simple epithelium embedded in an expanse of stratified squamous epithelium. These simple epithelial cells and their keratins are nerve-dependent, since denervation eliminated all four keratins and replaced elongated taste cells of the vallate papilla with stratified squamous epithelium. We conclude that antibodies against keratins 7, 8, or 19 are useful markers for intragemmal cells in studies of taste bud development, degeneration, regeneration, turnover and tissue culture.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75334/1/j.1432-0436.1995.5850341.x.pd
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