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

Little String Theory from Double-Scaling Limits of Field Theories

We show that little string theory on S^5 can be obtained as double-scaling limits of the maximally supersymmetric Yang-Mills theories on RxS^2 and RxS^3/Z_k. By matching the gauge theory parameters with those in the gravity duals found by Lin and Maldacena, we determine the limits in the gauge theories that correspond to decoupling of NS5-brane degrees of freedom. We find that for the theory on RxS^2, the 't Hooft coupling must be scaled like ln^3(N), and on RxS^3/Z_k, like ln^2(N). Accordingly, taking these limits in these field theories gives Lagrangian definitions of little string theory on S^5.Comment: 16 pages, 5 figures. Minor change

Dynamic Ordering and Transverse Depinning of a Driven Elastic String in a Disordered Media

We examine the dynamics of an elastic string interacting with quenched disorder driven perpendicular and parallel to the string. We show that the string is the most disordered at the depinning transition but with increasing drive partial ordering is regained. For low drives the noise power is high and we observe a 1/f^2 noise signature crossing over to a white noise character with low power at higher drives. For the parallel driven moving string there is a finite transverse critical depinning force with the depinning transition occuring by the formation of running kinks.Comment: 4 pages, 4 postscript figure

Generalized Quantum Theory of Recollapsing Homogeneous Cosmologies

A sum-over-histories generalized quantum theory is developed for homogeneous minisuperspace type A Bianchi cosmological models, focussing on the particular example of the classically recollapsing Bianchi IX universe. The decoherence functional for such universes is exhibited. We show how the probabilities of decoherent sets of alternative, coarse-grained histories of these model universes can be calculated. We consider in particular the probabilities for classical evolution defined by a suitable coarse-graining. For a restricted class of initial conditions and coarse grainings we exhibit the approximate decoherence of alternative histories in which the universe behaves classically and those in which it does not. For these situations we show that the probability is near unity for the universe to recontract classically if it expands classically. We also determine the relative probabilities of quasi-classical trajectories for initial states of WKB form, recovering for such states a precise form of the familiar heuristic "J d\Sigma" rule of quantum cosmology, as well as a generalization of this rule to generic initial states.Comment: 41 pages, 4 eps figures, revtex 4. Modest revisions throughout. Physics unchanged. To appear in Phys. Rev.

Velocity-force characteristics of an interface driven through a periodic potential

We study the creep dynamics of a two-dimensional interface driven through a periodic potential using dynamical renormalization group methods. We find that the nature of weak-drive transport depends qualitatively on whether the temperature $T$ is above or below the equilibrium roughening transition temperature $T_c$. Above $T_c$, the velocity-force characteristics is Ohmic, with linear mobility exhibiting a jump discontinuity across the transition. For $T \le T_c$, the transport is highly nonlinear, exhibiting an interesting crossover in temperature and weak external force $F$. For intermediate drive, $F>F_*$, we find near $T_c^{-}$ a power-law velocity-force characteristics $v(F)\sim F^\sigma$, with $\sigma-1\propto \tilde{t}$, and well-below $T_c$, $v(F)\sim e^{-(F_*/F)^{2\tilde{t}}}$, with $\tilde{t}=(1-T/T_c)$. In the limit of vanishing drive ($F\ll F_*$) the velocity-force characteristics crosses over to $v(F)\sim e^{-(F_0/F)}$, and is controlled by soliton nucleation.Comment: 18 pages, submitted to Phys. Rev.

Determination of the mechanical properties of amorphous materials through instrumented nanoindentation

A novel methodology based on instrumented indentation is developed to determine the mechanical properties of amorphous materials which present cohesive-frictional behaviour. The approach is based on the concept of a universal hardness equation, which results from the assumption of a characteristic indentation pressure proportional to the hardness. The actual universal hardness equation is obtained from a detailed finite element analysis of the process of sharp indentation for a very wide range of material properties, and the inverse problem (i.e. how to extract the elastic modulus, the compressive yield strength and the friction angle) from instrumented indentation is solved. The applicability and limitations of the novel approach are highlighted. Finally, the model is validated against experimental data in metallic and ceramic glasses as well as polymers, covering a wide range of amorphous materials in terms of elastic modulus, yield strength and friction angle

Derivation of the human embryonic stem cell line RCe014-A (RC-10)

AbstractThe human embryonic stem cell line RCe014-A (RC-10) was derived from a fresh oocyte voluntarily donated as unsuitable and surplus to fertility requirements following ethics committee approved informed consent under licence from the UK Human Fertilisation and Embryology Authority. The cell line shows normal pluripotency marker expression and differentiation to the three germ layers in vitro. It has a mixed 46XY and 47XY +12 male karyotype and microsatellite PCR identity, HLA and blood group typing data is available

Using Facebook as a platform for self-regulated curriculum evaluation and feedback for medical students

No abstract available