5,204 research outputs found

    Maximum likelihood estimates of pairwise rearrangement distances

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    Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. In the case of sequence evolution models (such as the Jukes-Cantor model and associated metric) have been used to correct pairwise distances. Similar correction methods for genome rearrangement processes are required to improve inference. Current attempts at correction fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has obvious implications for the use of minimal distance in phylogeny reconstruction. The work also tackles the above problem allowing free rotation of the genome. Generally a frame of reference is locked, and all computation made accordingly. This work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference.Comment: 21 pages, 7 figures. To appear in the Journal of Theoretical Biolog

    Ideas on DC-DC Converters for Delivery of Low Voltage and High Currents for the SLHC / ILC Detector Electronics in Magnetic field and Radiation environments

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    For more efficient power transport to the electronics embedded inside large colliding beam detectors, we explore the feasibility of supplying 48 Volts DC and using local DCDC conversion to 2 V (or lower, depending upon on the lithography of the embedded electronics) using switch mode regulators located very close to the front end electronics. These devices will be exposed to high radiation and high magnetic fields, 10 – 100 Mrads and 2 - 4 Tesla at the SLHC, and 20 Krads and 6 Tesla at the ILC

    Exhaustive generation of kk-critical H\mathcal H-free graphs

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    We describe an algorithm for generating all kk-critical H\mathcal H-free graphs, based on a method of Ho\`{a}ng et al. Using this algorithm, we prove that there are only finitely many 44-critical (P7,Ck)(P_7,C_k)-free graphs, for both k=4k=4 and k=5k=5. We also show that there are only finitely many 44-critical graphs (P8,C4)(P_8,C_4)-free graphs. For each case of these cases we also give the complete lists of critical graphs and vertex-critical graphs. These results generalize previous work by Hell and Huang, and yield certifying algorithms for the 33-colorability problem in the respective classes. Moreover, we prove that for every tt, the class of 4-critical planar PtP_t-free graphs is finite. We also determine all 27 4-critical planar (P7,C6)(P_7,C_6)-free graphs. We also prove that every P10P_{10}-free graph of girth at least five is 3-colorable, and determine the smallest 4-chromatic P12P_{12}-free graph of girth five. Moreover, we show that every P13P_{13}-free graph of girth at least six and every P16P_{16}-free graph of girth at least seven is 3-colorable. This strengthens results of Golovach et al.Comment: 17 pages, improved girth results. arXiv admin note: text overlap with arXiv:1504.0697

    Improved Simulation of the Mass Charging for ASTROD I

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    The electrostatic charging of the test mass in ASTROD I (Astrodynamical Space Test of Relativity using Optical Devices I) mission can affect the quality of the science data as a result of spurious Coulomb and Lorentz forces. To estimate the size of the resultant disturbances, credible predictions of charging rates and the charging noise are required. Using the GEANT4 software toolkit, we present a detailed Monte Carlo simulation of the ASTROD I test mass charging due to exposure of the spacecraft to galactic cosmic-ray (GCR) protons and alpha particles (3He, 4He) in the space environment. A positive charging rate of 33.3 e+/s at solar minimum is obtained. This figure reduces by 50% at solar maximum. Based on this charging rate and factoring in the contribution of minor cosmic-ray components, we calculate the acceleration noise and stiffness associated with charging. We conclude that the acceleration noise arising from Coulomb and Lorentz effects are well below the ASTROD I acceleration noise limit at 0.1 mHz both at solar minimum and maximum. The coherent Fourier components due to charging are investigated, it needs to be studied carefully in order to ensure that these do not compromise the quality of science data in the ASTROD I mission.Comment: 20 pages, 14 figures, submitted to International Journal of Modern Physics

    Measuring random force noise for LISA aboard the LISA Pathfinder mission

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    The LTP (LISA Testflight Package), to be flown aboard the ESA / NASA LISA Pathfinder mission, aims to demonstrate drag-free control for LISA test masses with acceleration noise below 30 fm/s^2/Hz^1/2 from 1-30 mHz. This paper describes the LTP measurement of random, position independent forces acting on the test masses. In addition to putting an overall upper limit for all source of random force noise, LTP will measure the conversion of several key disturbances into acceleration noise and thus allow a more detailed characterization of the drag-free performance to be expected for LISA.Comment: 7 pages, 3 figures. To be published in Classical and Quantum Gravity with the proceedings of the 2003 Amaldi Meetin

    Subaqueous shrinkage cracks in the Sheepbed mudstone: Implications for early fluid diagenesis, Gale crater, Mars

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    The Sheepbed mudstone, Yellowknife Bay formation, Gale crater, represents an ancient lakebed now exhumed and exposed on the Martian surface. The mudstone has four diagenetic textures, including a suite of early diagenetic nodules, hollow nodules, and raised ridges and later diagenetic light-toned veins that crosscut those features. In this study, we describe the distribution and characteristics of the raised ridges, a network of short spindle-shaped cracks that crosscut bedding, do not form polygonal networks, and contain two to four layers of isopachous, erosion-resistant cement. The cracks have a clustered distribution within the Sheepbed member and transition laterally into concentrations of nodules and hollow nodules, suggesting that these features formed penecontemporaneously. Because of the erosion-resistant nature of the crack fills, their three-dimensional structure can be observed. Cracks that transition from subvertical to subhorizontal orientations suggest that the cracks formed within the sediment rather than at the surface. This observation and comparison to terrestrial analogs indicate that these are syneresis cracks—cracks that formed subaqueously. Syneresis cracks form by salinity changes that cause sediment contraction, mechanical shaking of sediment, or gas production within the sediment. Examination of diagenetic features within the Sheepbed mudstone favors a gas production mechanism, which has been shown to create a variety of diagenetic morphologies comparable to the raised ridges and hollow nodules. The crack morphology and the isopachous, layered cement fill show that the cracks were filled in the phreatic zone and that the Sheepbed mudstone remained fluid saturated after deposition and through early burial and lithification

    Automatic 3D facial model and texture reconstruction from range scans

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    This paper presents a fully automatic approach to fitting a generic facial model to detailed range scans of human faces to reconstruct 3D facial models and textures with no manual intervention (such as specifying landmarks). A Scaling Iterative Closest Points (SICP) algorithm is introduced to compute the optimal rigid registrations between the generic model and the range scans with different sizes. And then a new template-fitting method, formulated in an optmization framework of minimizing the physically based elastic energy derived from thin shells, faithfully reconstructs the surfaces and the textures from the range scans and yields dense point correspondences across the reconstructed facial models. Finally, we demonstrate a facial expression transfer method to clone facial expressions from the generic model onto the reconstructed facial models by using the deformation transfer technique

    Parallel Mapper

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    The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint trees. In this paper, we study the parallel analysis of the construction of Mapper. We give a provably correct parallel algorithm to execute Mapper on multiple processors and discuss the performance results that compare our approach to a reference sequential Mapper implementation. We report the performance experiments that demonstrate the efficiency of our method

    Observations of the Hubble Deep Field with the Infrared Space Observatory V. Spectral energy distributions starburst models and star formation history

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    We have modelled the spectral energy distributions of the 13 Hubble Deep Field (HDF) galaxies reliably detected by the Infrared Space Observatoiy (ISO). For two galaxies the emission detected by ISO is consistent with being starlight or the infrared 'cirrus' in the galaxies. For the remaining 11 galaxies there is a clear mid-infrared excess, which we interpret as emission from dust associated with a strong starburst. 10 of these galaxies are spirals or interacting pairs, while the remaining one is an elliptical with a prominent nucleus and broad emission lines. We give a new discussion of how the star formation rate can be deduced from the far-infrared luminosity, and derive star formation rates for these galaxies of 8-1000ø M¿ yr-1, where ø takes account of the uncertainty in the initial mass function. The HDF galaxies detected by ISO are clearly forming stars at a prodigious rate compared with nearby normal galaxies. We discuss the implications of our detections for the history of star and heavy element formation in the Universe. Although uncertainties in the calibration, reliability of source detection, associations and starburst models remain, it is clear that dust plays an important role in star formation out to redshift 1 at least
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