A computational approach to unbiased districting

In the context of discrete districting problems with geographical constraints, we demonstrate that determining an (ex post) unbiased districting, which requires that the number of representatives of a party should be proportional to its share of votes, turns out to be a computationally intractable (NP-complete) problem. This raises doubts as to whether an independent jury will be able to come up with a “fair” redistricting plan in case of a large population, that is, there is no guarantee for finding an unbiased districting (even if such exists). We also show that, in the absence of geographical constraints, an unbiased districting can be implemented by a simple alternating-move game among the two parties.

Bone morphology of the femur and tibia captured by statistical shape modelling predicts rapid bone loss in acute spinal cord injury patients

We would like to thank the study participants and the clinical and research staff at the Queen Elizabeth National Spinal Injury Unit, as without them this study would not have been possible. We are grateful for the funding received from Glasgow Research Partnership in Engineering for the employment of SC during data collection for this study. We would like to thank the Royal Society of Edinburgh's Scottish Crucible scheme for providing the opportunity for this collaboration to occur. We are also indebted to Maria Dumitrascuta for her time and effort in producing inter-repeatability results for the shape models.

Bone morphology of the femur and tibia captured by statistical shape modelling predicts rapid bone loss in acute spinal cord injury patients

We would like to thank the study participants and the clinical and research staff at the Queen Elizabeth National Spinal Injury Unit, as without them this study would not have been possible. We are grateful for the funding received from Glasgow Research Partnership in Engineering for the employment of SC during data collection for this study. We would like to thank the Royal Society of Edinburgh's Scottish Crucible scheme for providing the opportunity for this collaboration to occur. We are also indebted to Maria Dumitrascuta for her time and effort in producing inter-repeatability results for the shape models.

Modelling of Stress-Corrosion Cracking by Using Peridynamics

Acknowledgement The authors are grateful to Prof. Siegfried Schmauder and Prof. Erdogan Madenci for the useful discussions that occurred throughout the realization of this study and acknowledge the Defence Science and Technology Laboratory (DSTL) for the financial support. A special thanks go to the anonymous reviewers, whose time and contribution have been highly appreciated. Results were obtained using the EPSRC funded ARCHIE-WeSt High Performance Computer (www.archie-west.ac.uk). EPSRC grant no. EP/K000586/1.

State-space modelling of geolocation data reveals sex differences in the use of management areas by breeding northern fulmars

We thank Orkney Islands Council for access to Eynhallow and Talisman Energy (UK) Ltd and Marine Scotland for fieldwork and equipment support. Handling and tagging of fulmars was conducted under licences from the British Trust for Ornithology and the UK Home Office. EE was funded by a Marine Alliance for Science and Technology for Scotland/University of Aberdeen College of Life Sciences and Medicine studentship and LQ was supported by a NERC Studentship. Thanks also to the many colleagues who assisted with fieldwork during the project, and to Helen Bailey and Arliss Winship for advice on implementing the state-space model.

State-space modelling of geolocation data reveals sex differences in the use of management areas by breeding northern fulmars

We thank Orkney Islands Council for access to Eynhallow and Talisman Energy (UK) Ltd and Marine Scotland for fieldwork and equipment support. Handling and tagging of fulmars was conducted under licences from the British Trust for Ornithology and the UK Home Office. EE was funded by a Marine Alliance for Science and Technology for Scotland/University of Aberdeen College of Life Sciences and Medicine studentship and LQ was supported by a NERC Studentship. Thanks also to the many colleagues who assisted with fieldwork during the project, and to Helen Bailey and Arliss Winship for advice on implementing the state-space model.

Physiologically based pharmacokinetic modelling in drug delivery

The application of pharmacokinetic modelling within the drug development field essentially allows one to develop a quantitative description of the temporal behaviour of a compound of interest at a tissue/organ level, by identifying and defining relationships between a dose of a drug and dependent variables. In order to understand and characterise the pharmacokinetics of a drug, it is often helpful to employ pharmacokinetic modelling using empirical or mechanistic approaches. Pharmacokinetic models can be developed within mathematical and statistical commercial software such as MATLAB using traditional mathematical and computation coding, or by using the Simbiology Toolbox available within MATLAB for a graphical user interface approach to developing pharmacokinetic (PBPK) models. For formulations dosed orally, a prerequisite for clinical activity is the entry of the drug into the systemic circulation.

A process-based Knowledge Management framework supported by ARIS Enterprise Modelling architecture

Knowledge and its management have been respectively accepted as a critical resource and a core business competency. Despite that literature proves the existence of a gap between the theoretical considerations of Knowledge Management (KM) and their efficient application. Such lacking, we argue, derives from the missing link between a framework of Knowledge Management and the particular methods and guidelines of its implementation. In an attempt to bridge this gap, an original, process- based holistic Knowledge Management framework is proposed, aiming to address the problem of knowledge management application and performance by utilising a set of well accepted Enterprise Modelling (EM) methods and tools.

Multilingualism and conceptual modelling

One of the leading motivations behind the multilingual semantic web is to make resources accessible digitally in an online global multilingual context. Consequently, it is fundamental for knowledge bases to find a way to manage multilingualism and thus be equipped with those procedures for its conceptual modelling. In this context, the goal of this paper is to discuss how common-sense knowledge and cultural knowledge are modelled in a multilingual framework. More particularly, multilingualism and conceptual modelling are dealt with from the perspective of FunGramKB, a lexico-conceptual knowledge base for natural language understanding. This project argues for a clear division between the lexical and the conceptual dimensions of knowledge. Moreover, the conceptual layer is organized into three modules, which result from a strong commitment towards capturing semantic knowledge (Ontology), procedural knowledge (Cognicon) and episodic knowledge (Onomasticon). Cultural mismatches are discussed and formally represented at the three conceptual levels of FunGramKB.

Application of GPCR Structures for Modelling of Free Fatty Acid Receptors

Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids, FFA2 (GPR43) and FFA3 (GPR41) bind short-chain fatty acids and GPR84 binds medium-chain fatty acids. Free fatty acid receptors have now emerged as potential targets for the treatment of diabetes, obesity and immune diseases. The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors. Analysis of the crystal structure and improved homology models, along with mutagenesis data and structure activity, highlighted an unusual arginine charge pairing interaction in FFA1-3 for receptor modulation, distinct structural features for ligand binding to FFA1 and FFA4 and an arginine of the second extracellular loop as a possible anchoring point for FFA at GPR84. Structural data will be helpful for searching novel small molecule modulators at the FFA receptors.

Principles and Practice of Fire Modelling: A Collection of Lecture Notes for a Short Course

Once the preserve of university academics and research laboratories with high-powered and expensive computers, the power of sophisticated mathematical fire models has now arrived on the desk top of the fire safety engineer. It is a revolution made possible by parallel advances in PC technology and fire modelling software. But while the tools have proliferated, there has not been a corresponding transfer of knowledge and understanding of the discipline from expert to general user. It is a serious shortfall of which the lack of suitable engineering courses dealing with the subject is symptomatic, if not the cause. The computational vehicles to run the models and an understanding of fire dynamics are not enough to exploit these sophisticated tools. Too often, they become 'black boxes' producing magic answers in exciting three-dimensional colour graphics and client-satisfying 'virtual reality' imagery. As well as a fundamental understanding of the physics and chemistry of fire, the fire safety engineer must have at least a rudimentary understanding of the theoretical basis supporting fire models to appreciate their limitations and capabilities. The five day short course, "Principles and Practice of Fire Modelling" run by the University of Greenwich attempt to bridge the divide between the expert and the general user, providing them with the expertise they need to understand the results of mathematical fire modelling. The course and associated text book, "Mathematical Modelling of Fire Phenomena" are aimed at students and professionals with a wide and varied background, they offer a friendly guide through the unfamiliar terrain of mathematical modelling. These concepts and techniques are introduced and demonstrated in seminars. Those attending also gain experience in using the methods during "hands-on" tutorial and workshop sessions. On completion of this short course, those participating should: - be familiar with the concept of zone and field modelling; - be familiar with zone and field model assumptions; - have an understanding of the capabilities and limitations of modelling software packages for zone and field modelling; - be able to select and use the most appropriate mathematical software and demonstrate their use in compartment fire applications; and - be able to interpret model predictions. The result is that the fire safety engineer is empowered to realise the full value of mathematical models to help in the prediction of fire development, and to determine the consequences of fire under a variety of conditions. This in turn enables him or her to design and implement safety measures which can potentially control, or at the very least reduce the impact of fire.

PHYSICA: A multiphysics computational framework and its application to casting simulations

Metal casting is a process governed by the interaction of a range of physical phenomena. Most computational models of this process address only what are conventionally regarded as the primary phenomena – heat conduction and solidification. However, to predict other phenomena, such as porosity formation, requires modelling the interaction of the fluid flow, heat transfer, solidification and the development of stressdeformation in the solidified part of the casting. This paper will describe a modelling framework called PHYSICA[1] which has the capability to stimulate such multiphysical phenomena.

A three dimensional finite volume approach to the thermo-mechanical modelling of the shape casting of metals

This paper presents a three dimensional, thermos-mechanical modelling approach to the cooling and solidification phases associated with the shape casting of metals ei. Die, sand and investment casting. Novel vortex-based Finite Volume (FV) methods are described and employed with regard to the small strain, non-linear Computational Solid Mechanics (CSM) capabilities required to model shape casting. The CSM capabilities include the non-linear material phenomena of creep and thermo-elasto-visco-plasticity at high temperatures and thermo-elasto-visco-plasticity at low temperatures and also multi body deformable contact with which can occur between the metal casting of the mould. The vortex-based FV methods, which can be readily applied to unstructured meshes, are included within a comprehensive FV modelling framework, PHYSICA. The additional heat transfer, by conduction and convection, filling, porosity and solidification algorithms existing within PHYSICA for the complete modelling of all shape casting process employ cell-centred FV methods. The termo-mechanical coupling is performed in a staggered incremental fashion, which addresses the possible gap formation between the component and the mould, and is ultimately validated against a variety of shape casting benchmarks.

In silico metabolic modelling of Saccharomyces cerevisiae for the overproduction of succinate using OptKnock and OptGene

Succinate is a naturally occurring metabolite in organism’s cell and is industrially important chemical with various applications in food and pharmaceutical industry. It is also widely used to produce bio-degradable plastics, surfactants, detergents etc. In last decades, emphasis has been given to bio-based chemical production using industrial biotechnology route rather than fossil-based production considering sustainability and environment friendly economy. In this thesis I am presenting a computational model for silico metabolic engineering of Saccharomyces cerevisiae for large scale production of succinate. For metabolic modelling, I have used OptKnock and OptGene optimization algorithms to identify the reactions to delete from the genome-scale metabolic model of S. cerevisiae to overproduce succinate by coupling with organism’s growth. Both OptKnock and OptGene proposed numerous straightforward and non-intuitive deletion strategies when number of constraints including growth constraint to the model were applied. The most interesting strategy identified by both algorithms was deletion combination of pyruvate decarboxylase and Ubiquinol:ferricytochrome c reductase(respiratory enzyme) reactions thereby also suggesting anaerobic fermentation of the organism in glucose medium. Such strategy was never reported earlier for growth-coupled succinate production in S.cerevisiae.

Evaluating conservation and fisheries management strategies by linking spatial prioritization software and ecosystem and fisheries modelling tools

Well-designed marine protected area (MPA) networks can deliver a range of ecological, economic and social benefits, and so a great deal of research has focused on developing spatial conservation prioritization tools to help identify important areas. However, whilst these software tools are designed to identify MPA networks that both represent biodiversity and minimize impacts on stakeholders, they do not consider complex ecological processes. Thus, it is difficult to determine the impacts that proposed MPAs could have on marine ecosystem health, fisheries and fisheries sustainability. Using the eastern English Channel as a case study, this paper explores an approach to address these issues by identifying a series of MPA networks using the Marxan and Marxan with Zones conservation planning software and linking them with a spatially explicit ecosystem model developed in Ecopath with Ecosim. We then use these to investigate potential trade-offs associated with adopting different MPA management strategies. Limited-take MPAs, which restrict the use of some fishing gears, could have positive benefits for conservation and fisheries in the eastern English Channel, even though they generally receive far less attention in research on MPA network design. Our findings, however, also clearly indicate that no-take MPAs should form an integral component of proposed MPA networks in the eastern English Channel, as they not only result in substantial increases in ecosystem biomass, fisheries catches and the biomass of commercially valuable target species, but are fundamental to maintaining the sustainability of the fisheries. Synthesis and applications. Using the existing software tools Marxan with Zones and Ecopath with Ecosim in combination provides a powerful policy-screening approach. This could help inform marine spatial planning by identifying potential conflicts and by designing new regulations that better balance conservation objectives and stakeholder interests. In addition, it highlights that appropriate combinations of no-take and limited-take marine protected areas might be the most effective when making trade-offs between long-term ecological benefits and short-term political acceptability.