Simulation of phosphorus implantation into silicon with a single-parameter electronic stopping power model

We simulate dopant profiles for phosphorus implantation into silicon using a new model for electronic stopping power. In this model, the electronic stopping power is factorized into a globally averaged effective charge Z1*, and a local charge density dependent electronic stopping power for a proton. There is only a single adjustable parameter in the model, namely the one electron radius rs0 which controls Z1*. By fine tuning this parameter, we obtain excellent agreement between simulated dopant profiles and the SIMS data over a wide range of energies for the channeling case. Our work provides a further example of implant species, in addition to boron and arsenic, to verify the validity of the electronic stopping power model and to illustrate its generality for studies of physical processes involving electronic stopping.Comment: 11 pages, 7 figures. See http://bifrost.lanl.gov/~reed

Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

Phylogenetic search through partial tree mixing.

BACKGROUND: Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. RESULTS: When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda CONCLUSIONS: The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution

The feasibility of associate EU citizenship for UK citizens post-Brexit

Modern code-conforming buildings have a high probability of surviving major seismic events without collapse, hence minimizing the number of casualties. Nevertheless, the risk of substantial post-earthquake economic losses remains high, as a consequence of inadequate damage prevention guidelines in current earthquake design codes. Rocking post-tensioned moment-resisting frames present a viable damage-free structural solution, with a nominal increase in building costs compared with conventional buildings. This structural system comprises of: (i) unbonded post-tensioned strands to provide overturning resistance and self-centering capability, and (ii) opening joints at the column-foundation and beam-column interfaces designed to rock during a seismic event. Rocking frames with various forms of supplemental damping have been previously examined numerically, adopting different finite element frameworks. However, there is a shortage of numerical studies studying the non-linear dynamic response of pure rocking multi-story post-tensioned moment frames, exclusive of supplementary energy-dissipation elements and devices. Hence, it is critical to develop modelling procedures for multiple stories which adequately capture the full range of their nonlinear dynamic behavior due to the joint rocking mechanism, and investigate the resulting response. Numerical studies are presented herein, including static and dynamic analyses of three- to nine-story building models. The proposed modelling methods are shown to effectively predict the non-linear response of multi-story rocking frames over a wide range of forcing frequencies and amplitudes. It is further concluded that the structural response is influenced by both sub-harmonic resonances and beam-column interactions.</p

Structural Basis for the Autoinhibition and STI-571 Inhibition of c-Kit Tyrosine Kinase

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On the use of cartographic projections in visualizing phylo-genetic tree space

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger data sets

AMI-LA radio continuum observations of Spitzer c2d small clouds and cores: Serpens region

We present deep radio continuum observations of the cores identified as deeply embedded young stellar objects in the Serpens molecular cloud by the Spitzer c2d programme at a wavelength of 1.8cm with the Arcminute Microkelvin Imager Large Array (AMI-LA). These observations have a resolution of ~30arcsec and an average sensitivity of 19microJy/beam. The targets are predominantly Class I sources, and we find the detection rate for Class I objects in this sample to be low (18%) compared to that of Class 0 objects (67%), consistent with previous works. For detected objects we examine correlations of radio luminosity with bolometric luminosity and envelope mass and find that these data support correlations found by previous samples, but do not show any indiction of the evolutionary divide hinted at by similar data from the Perseus molecular cloud when comparing radio luminosity with envelope mass. We conclude that envelope mass provides a better indicator for radio luminosity than bolometric luminosity, based on the distribution of deviations from the two correlations. Combining these new data with archival 3.6cm flux densities we also examine the spectral indices of these objects and find an average spectral index of 0.53+/-1.14, consistent with the canonical value for a partially optically thick spherical or collimated stellar wind. However, we caution that possible inter-epoch variability limits the usefulness of this value, and such variability is supported by our identification of a possible flare in the radio history of Serpens SMM 1.Comment: accepted MNRA

AMI radio continuum observations of young stellar objects with known outflows

We present 16 GHz (1.9 cm) deep radio continuum observations made with the Arcminute Microkelvin Imager (AMI) of a sample of low-mass young stars driving jets. We combine these new data with archival information from an extensive literature search to examine spectral energy distributions (SEDs) for each source and calculate both the radio and sub-mm spectral indices in two different scenarios: (1) fixing the dust temperature (Td) according to evolutionary class; and (2) allowing Td to vary. We use the results of this analysis to place constraints on the physical mechanisms responsible for the radio emission. From AMI data alone, as well as from model fitting to the full SED in both scenarios, we find that 80 per cent of the objects in this sample have spectral indices consistent with freefree emission. We find an average spectral index in both Td scenarios, consistent with freefree emission. We examine correlations of the radio luminosity with bolometric luminosity, envelope mass and outflow force, and find that these data are consistent with the strong correlation with envelope mass seen in lower luminosity samples. We examine the errors associated with determining the radio luminosity and find that the dominant source of error is the uncertainty on the opacity index, beta. We examine the SEDs for variability in these young objects, and find evidence for possible radio flare events in the histories of L1551 IRS 5 and Serpens SMM 1