Statistical analysis of crystallographic data

The Cambridge structural database (CSD) is a vast resource for crystallographic information. As of 1st January 2009 there are more than 469,611 crystal structures available in the CSD. This work is centred on a program dSNAP which has been developed at the University of Glasgow. dSNAP is a program that uses statistical methods to group fragments of molecules into groups that have a similar conformation. This work is aimed at applying methods to reduce the number of variables required to describe the geometry of the fragments mined from the CSD. To this end, the geometric definition employed by dSNAP was investigated. The default definition is total geometries which are made up of all angles and all distances, including all non-bonded distances and angles. This geometric definition was investigated in a comparative manner with four other definitions. There were all angles, all distances, bonded angles and distances and bonded angles, distances and torsion angles. These comparisons show that non-bonded information is critical to the formation of groups of fragments with similar conformations. The remainder of this work was focused in reducing the number of variables required to group fragments having similar conformations into distinct groups. Initially a method was developed to calculate the area of triangles between three atoms making up the fragment. This was employed systematically as a means of reducing the total number of variables required to describe the geometry of the fragments. Multivariate statistical methods were also applied with the aim of reducing the number of variables required to describe the geometry of the fragment in a systematic manner. The methods employed were factor analysis and sparse principal components analysis. Both of these methods were used to extract important variables from the original default geometric definition, total geometries. The extracted variables were then used as input for dSNAP and were compared with the original output. Biplots were used to visualise the variables describing the fragments. Biplots are multivariate analogues to scatter plots and are used to visualise how the fragments are related to the variables describing them. Owing to the large number of variables that make up the definition factor analysis was applied to extract the important variables before the biplot was calculated. The biplots give an overview of the correlation matrix and using these plots it is possible to select variables that are influencing the formation of clusters in dSNAP

Mus musculus populations in Western Australia lack VKORC1 mutations conferring resistance to first generation anticoagulant rodenticides: Implications for conservation and biosecurity

Background Humans routinely attempt to manage pest rodent populations with anticoagulant rodenticides (ARs). We require information on resistance to ARs within rodent populations to have effective eradication programs that minimise exposure in non-target species. Mutations to the VKORC1 gene have been shown to confer resistance in rodents with high proportions of resistance in mice found in all European populations tested. We screened mutations in Mus musculus within Western Australia, by sampling populations from the capital city (Perth) and a remote island (Browse Island). These are the first Australian mouse populations screened for resistance using this method. Additionally, the mitochondrial D-loop of house mice was sequenced to explore population genetic structure, identify the origin of Western Australian mice, and to elucidate whether resistance was linked to certain haplotypes. Results No resistance-related VKORC1 mutations were detected in either house mouse population. A genetic introgression in the intronic sequence of the VKORC1 gene of Browse Island house mouse was detected which is thought to have originated through hybridisation with the Algerian mouse (Mus spretus). Analysis of the mitochondrial D-loop reported two haplotypes in the house mouse population of Perth, and two haplotypes in the population of Browse Island. Conclusions Both house mouse populations exhibited no genetic resistance to ARs, in spite of free use of ARs in Western Australia. Therefore weaker anticoagulant rodenticides can be employed in pest control and eradication attempts, which will result in reduced negative impacts on non-target species. Biosecurity measures must be in place to avoid introduction of resistant house mice, and new house mouse subspecies to Western Australia

A Simple Model of Epidemics with Pathogen Mutation

We study how the interplay between the memory immune response and pathogen mutation affects epidemic dynamics in two related models. The first explicitly models pathogen mutation and individual memory immune responses, with contacted individuals becoming infected only if they are exposed to strains that are significantly different from other strains in their memory repertoire. The second model is a reduction of the first to a system of difference equations. In this case, individuals spend a fixed amount of time in a generalized immune class. In both models, we observe four fundamentally different types of behavior, depending on parameters: (1) pathogen extinction due to lack of contact between individuals, (2) endemic infection (3) periodic epidemic outbreaks, and (4) one or more outbreaks followed by extinction of the epidemic due to extremely low minima in the oscillations. We analyze both models to determine the location of each transition. Our main result is that pathogens in highly connected populations must mutate rapidly in order to remain viable.Comment: 9 pages, 11 figure

Numerical analysis of piled embankments on soft soils

The construction of embankments on soft soils is a common problem. Soft soil cannot sustain external loads without having large deformations. Piled embankments system provides a possible solution for the construction of roads and railways over soft soils. Until now, the system behaviour could only be described by analytical models such as those included in British or German codes. This paper describes research undertaken to investigate the effects of pile embankment construction in soft soils. Experimental results are used to help investigate arching effect developed due to differential settlement between pile and surrounding soft soil. A numerical parametric study was carried out to examine the impact of various soil parameters on the pile-embankment system behaviour. The outcome of the parametric study implemented using numerical analysis has been investigated and discussed throughout this paper. Based on the numerical analysis carried out in this research, it was found that the earth pressure coefficient normalized by the passive earth pressure Kp plotted on a vertical profile at the midpoint between piles can give a good illustration of arching behaviour. The findings presented in this paper can be considered as guides for numerical analysis and design criteria of soil arching for embankments constructed over piles

SUSY-QCD Effect on Top-Charm Associated Production at Linear Collider

We evaluate the contribution of SUSY-QCD to top-charm associated production at next generation linear colliders. Our results show that the production cross section of the process $e^+e^-\to t\bar c{or}\bar t c$ could be as large as 0.1 fb, which is larger than the prediction of the SM by a factor of $10^8$.Comment: version to appear in PR

Fractional plateaus in the Coulomb blockade of coupled quantum dots

Ground-state properties of a double-large-dot sample connected to a reservoir via a single-mode point contact are investigated. When the interdot transmission is perfect and the dots controlled by the same dimensionless gate voltage, we find that for any finite backscattering from the barrier between the lead and the left dot, the average dot charge exhibits a Coulomb-staircase behavior with steps of size e/2 and the capacitance peak period is halved. The interdot electrostatic coupling here is weak. For strong tunneling between the left dot and the lead, we report a conspicuous intermediate phase in which the fractional plateaus get substantially altered by an increasing slope.Comment: 6 pages, 4 figures, final versio

The shape of the CMB lensing bispectrum

Lensing of the CMB generates a significant bispectrum, which should be detected by the Planck satellite at the 5-sigma level and is potentially a non-negligible source of bias for f_NL estimators of local non-Gaussianity. We extend current understanding of the lensing bispectrum in several directions: (1) we perform a non-perturbative calculation of the lensing bispectrum which is ~10% more accurate than previous, first-order calculations; (2) we demonstrate how to incorporate the signal variance of the lensing bispectrum into estimates of its amplitude, providing a good analytical explanation for previous Monte-Carlo results; and (3) we discover the existence of a significant lensing bispectrum in polarization, due to a previously-unnoticed correlation between the lensing potential and E-polarization as large as 30% at low multipoles. We use this improved understanding of the lensing bispectra to re-evaluate Fisher-matrix predictions, both for Planck and cosmic variance limited data. We confirm that the non-negligible lensing-induced bias for estimation of local non-Gaussianity should be robustly treatable, and will only inflate f_NL error bars by a few percent over predictions where lensing effects are completely ignored (but note that lensing must still be accounted for to obtain unbiased constraints). We also show that the detection significance for the lensing bispectrum itself is ultimately limited to 9 sigma by cosmic variance. The tools that we develop for non-perturbative calculation of the lensing bispectrum are directly relevant to other calculations, and we give an explicit construction of a simple non-perturbative quadratic estimator for the lensing potential and relate its cross-correlation power spectrum to the bispectrum. Our numerical codes are publicly available as part of CAMB and LensPix.Comment: 32 pages, 10 figures; minor changes to match JCAP-accepted version. CMB lensing and primordial local bispectrum codes available as part of CAMB (http://camb.info/

Coulomb blockade of strongly coupled quantum dots studied via bosonization of a channel with a finite barrier

A pair of quantum dots, coupled through a point contact, can exhibit Coulomb blockade effects that reflect an oscillatory term in the dots' total energy whose value depends on whether the total number of electrons on the dots is even or odd. The effective energy associated with this even-odd alternation is reduced, relative to the bare Coulomb blockade energy for uncoupled dots, by a factor (1-f) that decreases as the interdot coupling is increased. When the transmission coefficient for interdot electronic motion is independent of energy and the same for all channels within the point contact (which are assumed uncoupled), the factor (1-f) takes on a universal value determined solely by the number of channels and the dimensionless conductance g of each individual channel. This paper studies corrections to the universal value of (1-f) that result when the transmission coefficent varies over energy scales of the size of the bare Coulomb blockade energy. We consider a model in which the point contact is described by a single orbital channel containing a parabolic barrier potential, and we calculate the leading correction to (1-f) for one-channel (spin-split) and two-channel (spin-degenerate) point contacts in the limit where the single orbital channel is almost completely open. By generalizing a previously used bosonization technique, we find that, for a given value of the dimensionless conductance g, the value of (1-f) is increased relative to its value for a zero-thickness barrier, but the absolute value of the increase is small in the region where our calculations apply.Comment: 13 pages, 3 Postscript figure

Le retour des grands mammifères sauvages dans la région méditerranéenne française.

Cet article consacré au retour des grands mammifères sauvages dans la région méditerranéenne française, parle du passé des extinctions, de la pénurie à l'abondance des grands mammifères, de l'historique de l'évolution des ongulés (sanglier, chevreuil, cerf, mouflon, chamois et bouquetin), des évolutions probables, et des connaissances prévisibles