A computer system to perform structure comparison using TOPS representations of protein structure

We describe the design and implementation of a fast topology–based method for protein structure comparison. The approach uses the TOPS topological representation of protein structure, aligning two structures using a common discovered pattern and generating measure of distance derived from an insert score. Heavy use is made of a constraint-based pattern matching algorithm for TOPS diagrams that we have designed and described elsewhere Gilbert et al. (1999). The comparison system is maintained at the European Bioinformatics Institute and is available over the Web via the at tops.ebi.ac.uk/tops. Users submit a structure description in Protein Data Bank (PDB) format and can compare it with structures in the entire PDB or a representative subset of protein domains, receiving the results by email

Land rights and the forest peoples of Africa: historical, legal and anthropological perspectives: legal rights under international law

International law, and more particularly international human rights law, has for some time been seen as a positive tool to support indigenous peoples’ rights; when it comes to land rights, however, such positivity is new. September 2007 marked the start of a new era for indigenous peoples, with the adoption of the United Nations Declaration on the Rights of Indigenous Peoples. Despite this recent development, international law has historically played a negative role regarding indigenous peoples’ rights, and more especially their rights to land. An important tool in the hands of the colonial powers, international law has been a central vehicle in the dispossession of indigenous peoples. Most of the rules regarding title to territory under international law were aimed at justifying the dispossession of indigenous peoples of their lands. While various legal systems applied, during colonisation, to land rights for indigenous peoples – depending on which state was the coloniser – international law played the role of common denominator, ensuring that all powers adhered to the same legal doctrine. The rules governing title to territory under international law became the basis of the ‘rules of the game’ between the colonial powers, and as such had a direct impact on indigenous peoples’ land rights. Because of this legacy, international law still plays a huge part in the contemporary situations faced by indigenous communities throughout the continent today. But this legacy is seriously challenged by recent development stemming from international human rights law. The first part of this chapter provides the historical background, setting out the complexity of contemporary indigenous land claims. Based on this analysis, the second part of the chapter examines the content of states’ obligations regarding land rights for indigenous peoples under international human rights law

Gilbert damping and spin Coulomb drag in a magnetized electron liquid with spin-orbit interaction

We present a microscopic calculation of the Gilbert damping constant for the magnetization of a two-dimensional spin-polarized electron liquid in the presence of intrinsic spin-orbit interaction. First we show that the Gilbert constant can be expressed in terms of the auto-correlation function of the spin-orbit induced torque. Then we specialize to the case of the Rashba spin-orbit interaction and we show that the Gilbert constant in this model is related to the spin-channel conductivity. This allows us to study the Gilbert damping constant in different physical regimes, characterized by different orderings of the relevant energy scales -- spin-orbit coupling, Zeeman coupling, momentum relaxation rate, spin-momentum relaxation rate, spin precession frequency -- and to discuss its behavior in various limits. Particular attention is paid to electron-electron interaction effects,which enter the spin conductivity and hence the Gilbert damping constant via the spin Coulomb drag coefficient.Comment: 18 pages, 8 figure

Ratio control in a cascade model of cell differentiation

We propose a kind of reaction-diffusion equations for cell differentiation, which exhibits the Turing instability. If the diffusivity of some variables is set to be infinity, we get coupled competitive reaction-diffusion equations with a global feedback term. The size ratio of each cell type is controlled by a system parameter in the model. Finally, we extend the model to a cascade model of cell differentiation. A hierarchical spatial structure appears as a result of the cell differentiation. The size ratio of each cell type is also controlled by the system parameter.Comment: 13 pages, 7 figure

Microscopic mechanisms of magnetization reversal

Two principal scenarios of magnetization reversal are considered. In the first scenario all spins perform coherent motion and an excess of magnetic energy directly goes to a nonmagnetic thermal bath. A general dynamic equation is derived which includes a tensor damping term similar to the Bloch-Bloembergen form but the magnetization magnitude remains constant for any deviation from equilibrium. In the second reversal scenario, the absolute value of the averaged sample magnetization is decreased by a rapid excitation of nonlinear spin-wave resonances by uniform magnetization precession. We have developed an analytic k-space micromagnetic approach that describes this entire reversal process in an ultra-thin soft ferromagnetic film for up to 90^{o} deviation from equilibrium. Conditions for the occurrence of the two scenarios are discussed

The application of active controls technology to a generic hypersonic aircraft configuration

Analytical methods are described for the prediction of aerothermoelastic stability of hypersonic aircraft including active control systems. Thermal loads due to aerodynamic heating were applied to the finite element model of the aircraft structure and the thermal effects on flutter were determined. An iterative static aeroelastic trim analysis procedure was developed including thermal effects. And active control technology was assessed for flutter suppression, ride quality improvement, and gust load alleviation to overcome any potential adverse aeroelastic stability or response problems due to aerodynamic heating. A generic hypersonic aircraft configuration was selected which incorporates wing flaps, ailerons, and all moveable fins to be used for active control purposes. The active control system would use onboard sensors in a feedback loop through the aircraft flight control computers to move the surfaces for improved structural dynamic response as the aircraft encounters atmospheric turbulence

Modelling the hepatitis B vaccination programme in prisons

A vaccination programme offering hepatitis B (HBV) vaccine at reception into prison has been introduced into selected prisons in England and Wales. Over the coming years it is anticipated this vaccination programme will be extended. A model has been developed to assess the potential impact of the programme on the vaccination coverage of prisoners, ex-prisoners, and injecting drug users (IDUs). Under a range of coverage scenarios, the model predicts the change over time in the vaccination status of new entrants to prison, current prisoners and IDUs in the community. The model predicts that at baseline in 2012 57% of the IDU population will be vaccinated with up to 72% being vaccinated depending on the vaccination scenario implemented. These results are sensitive to the size of the IDU population in England and Wales and the average time served by an IDU during each prison visit. IDUs that do not receive HBV vaccine in the community are at increased risk from HBV infection. The HBV vaccination programme in prisons is an effective way of vaccinating this hard-to-reach population although vaccination coverage on prison reception must be increased to achieve this

Learning with multiple representations: An example of a revision lesson in mechanics

We describe an example of learning with multiple representations in an A-level revision lesson on mechanics. The context of the problem involved the motion of a ball thrown vertically upwards in air and studying how the associated physical quantities changed during its flight. Different groups of students were assigned to look at the ball's motion using various representations: motion diagrams, vector diagrams, free-body diagrams, verbal description, equations and graphs, drawn against time as well as against displacement. Overall, feedback from students about the lesson was positive. We further discuss the benefits of using computer simulation to support and extend student learning.Comment: 10 pages, 5 figures, 2 tables http://iopscience.iop.org/0031-912

Modelling rotational failure in confined geometries using DLO

Discontinuity layout optimisation (DLO) is a generally applicable numerical limit analysis procedure that can be used to identify critical plastic collapse mechanisms in engineering problems. Considering the modelling of in-plane failure, the authors have previously presented a formulation capable of identifying rotational failure mechanisms in non-dilating media. However, the formulation presented did not explicitly address cases involving confined geometries, where curved slip lines could potentially intersect boundaries. In this paper, methods are outlined which permit efficient modelling of such cases. Details of the kinematic and equilibrium formulations are provided, which are then verified through application to various geotechnical and structural mechanics problems. It is shown that results of high accuracy can be obtained, both in terms of the predicted collapse load and the corresponding failure mechanism