Maximum likelihood estimates of pairwise rearrangement distances

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

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

FeH Absorption in the Near-Infrared Spectra of Late M and L Dwarfs

We present medium-resolution z-, J-, and H-band spectra of four late-type dwarfs with spectral types ranging from M8 to L7.5. In an attempt to determine the origin of numerous weak absorption features throughout their near-infrared spectra, and motivated by the recent tentative identification of the E 4\Pi- A ^4\Pi system of FeH near 1.6 microns in umbral and cool star spectra, we have compared the dwarf spectra to a laboratory FeH emission spectrum. We have identified nearly 100 FeH absorption features in the z-, J-, and H-band spectra of the dwarfs. In particular, we have identified 34 features which dominate the appearance of the H-band spectra of the dwarfs and which appear in the laboratory FeH spectrum. Finally, all of the features are either weaker or absent in the spectrum of the L7.5 dwarf which is consistent with the weakening of the known FeH bandheads in the spectra of the latest L dwarfs.Comment: accepted by Ap

Measuring random force noise for LISA aboard the LISA Pathfinder mission

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

Flow dynamics and mixing processes in hydraulic jump arrays: Implications for channel-lobe transition zones

A detailed field investigation of a saline gravity current in the southwest Black Sea has enabled the first complete analysis of three-dimensional flow structure and dynamics of a series of linked hydraulic jumps in stratified, density-driven, flows. These field observations were collected using an acoustic Doppler current profiler mounted on an autonomous underwater vehicle, and reveal that internal mixing processes in hydraulic jumps, including flow expansion and recirculation, provide a previously unrecognised mechanism for grain-size sorting and segregation in stratified density-driven flows. Field observations suggest a newly identified type of hydraulic jump, that is a stratified low Froude number (< 1.5–2) subaqueous hydraulic jump, with an enhanced ability to transport sediment downstream of the jump, in comparison to hydraulic jumps in other subaerial and submarine flows. These novel field data underpin a new process-based conceptual model of channel lobe transition zones (CLTZs) that explains the scattered offset nature of scours within such settings, the temporal variations in infill and erosion between adjacent scours, how bed shear stresses are maintained across the CLTZ, and why the locus of deposition is so far downstream of the scour zone

Passive magnetic shielding in static gradient fields

The effect of passive magnetic shielding on dc magnetic field gradients imposed by both external and internal sources is studied for two idealized shield models: concentric spherical and infinitely-long cylindrical shells of linear material. It is found that higher-order multipoles of an externally applied magnetic field are always shielded progressively better for either geometry by a factor related to the order of the multipole. In regard to the design of internal coil systems, we determine reaction factors for the general multipole field and provide examples of how one can take advantage of the coupling of the coils to the innermost shell to optimize the uniformity of the field. Furthermore, we provide formulae relevant to active magnetic compensation systems which attempt to stabilize the interior fields by sensing and cancelling the exterior fields close to the outermost shell. Overall this work provides a comprehensive framework that is useful for the analysis and optimization of dc magnetic shields, serving as a theoretical and conceptual design guide as well as a starting point and benchmark for finite-element analysis."We gratefully acknowledge the support of the Natural Sciences and Engineering Research Council of Canada."https://aip.scitation.org/doi/10.1063/1.487371

Parallel Mapper

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