Computational Modelling Group

A composite likelihood approach to genome-wide data analyses.

Andrew Collins (Investigator), Jane Gibson, Ioannis Politopoulos

We describe composite likelihood-based analysis of a genome-wide breast cancer case-control sample by determining genome regions of fixed size on a linkage disequilibrium map which delimit comparable levels of linkage disequilibrium. Analysis of findings suggests further validation in more samples from other cohorts as well as the exploitation of novel computationally-intensive methods such as next-generation sequencing.

A Fast Multipole Method for the Bessel potential

Marc Molinari, Simon Cox (Investigators), Neil O'Brien

The fast multipole method (FMM) proposed by Greengard and Rokhlin provides a method by which the O(N-squared) many-body problem can be reduced to O(N) complexity. In this project, a multipole method is developed to calculate the energy of a system of vortices in a high temperature superconductor, where the many-body interactions give rise to rich and complex physics. The method developed here is suitable for systems where the interactions are governed by a Bessel potential rather than the usual logarithmic potentials occurring in gravitational and electrostatic problems. We derive and apply vectorised forms of the Gegenbauer addition formulae in order to achieve the O(N) scaling associated with fast multipole methods.

A Fortran Based Mesh Viewer

Gabriel Amine-Eddine (Investigator)

During my final year as an undergraduate, I developed a fully functional software program for visualising geometry, grid and grid quality for a custom developed CFD software tool. It has and now in use in conjunction with the HARTREE CFD code by some of the other fellow postgrads working in my supervisors team.

A step toward establishing minimum requirement for CFD modelling of dispersion from floating roof tanks

Zheng-Tong Xie, Ian Castro (Investigators)

It is of great importance to estimate an emission flux (due to leaking from an oil tank) from near field wake, which requires a better understanding of vortex shedding from the tank, in particularly in how the low frequency motion behaves. Large-eddy simulation approaches embedded in up-to-date CFD package will be used for this purpose. This project has a strong link with Concawe and U Surrey.

Adding social ties to the Schelling model

Seth Bullock, Sally Brailsford (Investigators), Elisabeth zu-Erbach-Schoenberg

The Schelling model is an abstract model for segregation in
a spatially arranged population. We extended the traditional model by the addition of a dynamic social network. The social network influences the spatial dynamics of agents moving on the grid by changing the agents’ evaluation of their neighbourhood. In turn, the spatial arrangement influences the change of the social network.

Advanced modelling for two-phase reacting flow

Edward Richardson (Investigator)

Engine designers want computer programs to help them invent ways to use less fuel and produce less pollution. This research aims to provide an accurate and practical model for the injection and combustion of liquid fuel blends.

Aerofoil noise

Richard Sandberg (Investigator)

High-performance computing is used to identify noise sources on aerofoils.

An Investigation into the Cascade Effect of Mergers on the Global Financial Markets

Seth Bullock, Antonella Ianni (Investigators), Camillia Zedan

An investigation into the external effects that horizontal mergers have on the interconnected global markets.

Antimicrobial Peptide and E. coli Membrane Interactions

Syma Khalid (Investigator), Thomas Piggot, Nils Berglund

Antimicrobial peptides (AMPs) are known to disrupt the membranes of bacterial cells such as E. coli. I work on investigating the nature of these interactions using molecular dynamics (MD) simulations.

B-meson coupling with relativistic heavy quarks

Jonathan Flynn (Investigator), Patrick Fritzsch, Dirk Broemmel

We non-perturbatively compute the coupling between B* and B pi meson states relying on relativistic heavy quarks and domain wall light fermions. The coupling is of importance for an effective description of hadronic heavy meson decays.

Bioinformatic identification and physiological analysis of ethanol-related genes in C. elegans

Richard Edwards, Vincent O'Connor, Lindy Holden-Dye (Investigators), Ben Ient

Investigating the broad molecular, cellular and systems level impacts of acute and chronic ethanol in the nematode, Caenorhabditis elegans, as a model.

BioSimGrid

Jonathan Essex, Hans Fangohr (Investigators), Richard Boardman, Syma Khalid, Steven Johnston

The aim of the BioSimGrid project is to make the results of large-scale computer simulations of biomolecules more accessible to the biological community. Such simulations of the motions of proteins are a key component in understanding how the structure of a protein is related to its dynamic function.

Cavity-Mediated Cooling

Peter Horak, Timothy Freegarde (Investigators), Andre Xuereb

Optical resonators enhance the interaction of light with matter while simultaneously acting as a temporal buffer. Both effects can be exploited to generate light-induced friction, or cooling, forces on atoms, molecules, or micromirrors. We investigate various aspects of these effects through numerical simulations, assisted by approximate analytical models, in this EPSRC and ESF sponsored project.

Cellular Automata Modelling of Membrane Formation and Protocell Evolution

Seth Bullock (Investigator), Stuart Bartlett

We simulate the meso-level behaviour of lipid-like particles in a range of chemical and physical environments. Self-organised protocellular structures can be shown to emerge spontaneously in systems with random, homogeneous initial conditions. We aim to take the current model further and explore more complex chemical scenarios in which a broad range of evolutionary behaviours will be exhibited.

Cloud Computing for Planetary Defense

Hugh Lewis, Kenji Takeda (Investigators), Steven Johnston

We demonstrate how a cloud-based computing architecture can be used for planetary defense and space situational awareness (SSA). We show how utility compute can facilitate both a financially economical and highly scalable solution for space debris and near-earth object impact analysis. As we improve our ability to track smaller space objects, and satellite collisions occur, the volume of objects being tracked vastly increases, increasing computational demands. Propagating trajectories and calculating conjunctions becomes increasingly time critical, thus requiring an architecture which can scale with demand. The extension of this to tackle the problem of a future near-earth object impact is discussed, and how cloud computing can play a key role in this civilisation-threatening scenario.

Complex Systems Simulations Centre for Doctoral Training

Jonathan Essex, Seth Bullock, Hans Fangohr (Investigators)

The centre for doctoral training brings together students from a variety of backgrounds, ranging from mathematics, physics and chemistry to oceanography, geography, biology, computer science, and engineering. Students carry out a four-year programme combining taught courses with a PhD project.

Complexity in Modelling Electric Marine Propulsive Devices

Suleiman Sharkh, Neil Bressloff, Hans Fangohr (Investigators), Aleksander Dubas

This project involves the simulation of turbulent flow around a marine rim-driven thruster and the complex interaction of flow features involved through computational fluid dynamics.

Computational electromagnetic modelling of 3D photonic structures

Marc Molinari, Darren Bagnall, Simon Cox (Investigators), Asa Asadollahbaik, Elizabeth Hart

Nano-structured materials can provide very specific and often very special optical effects which can be exploited for a large range of optical applications including wavelength filters, LEDs, micro-lasers, HDTV, solar-cell coatings, optical high-Q fibres, diffraction gratings, polarisation devices, optical switches, etc. This research in “Computational Electromagnetic Modelling of 3D Photonic Structures” aims to address the need for accurate and fast three-dimensional modelling, simulation and analysis processes in the photonics industry. A FEM/FDTD software suite will be developed to simulate Maxwell’s field equations and thin-film quantum effects (plasmons) in the visible and near-infrared EM frequency spectrum. The results obtained from running the software on suitable compute clusters will then be compared to the analysis results of experimentally manufactured materials. We will investigate structures occurring in nature such as iridescent butterfly wings, white/black reflecting beetle shells, etc., and aim to optimise artificially designed structures with periodic, quasi-periodic and random configurations.

Control and Prediction of the Organic Solid State

Richard Boardman

This project aims to produce a computer technology for the prediction of the crystal structure(s) of an organic molecule, that could be used even prior to the synthesis of the compound.

Such a computational study could be done relatively quickly to predict the dangers and opportunities of the solid phases of a molecule under development. Our project will develop the methods of experimental screening for polymorphs and their characterisation, and hence the combination will provide a major new technology for aiding industrial formulation.

Cosmological evolution of supermassive black holes in the centres of galaxies

Anna Kapinska (Investigator)

Abstract to be added...

DePuy Technology Partnership

Mark Taylor (Investigator), Adam Briscoe

This initiative concerns the transfer of knowledge between three key institutions (University of Southampton, University of Leeds and University of Hamburg) and DePuy International limited. The project is concerned with the ongoing advancement of technology used in orthopaedic devices.

Designer 3D Magnetic Mesostructures

Hans Fangohr (Investigator), Matteo Franchin, Andreas Knittel

A new electrodeposition self-assembly method allows for the growth of well defined mesostructures. This project's aim is to use this method in order to fabricate supraconducting and ferromagnetic mesostructures. Numerical methods based on well-established models are used in order to characterise the grown structures.

Development of a novel Navier-Stokes solver (HiPSTAR)

Richard Sandberg (Investigator)

Development of a highly efficient Navier-Stokes solver for HPC.

Development of wide-ranging functionality in ONETEP

Chris-Kriton Skylaris (Investigator), Jacek Dziedzic

ONETEP is at the cutting edge of developments in first principles calculations. However, while the fundamental difficulties of performing accurate first-principles calculations with linear-scaling cost have been solved, only a small core of functionality is currently available in ONETEP which prevents its wide application. In this collaborative project between three Universities, the original developers of ONETEP will lead an ambitious workplan whereby the functionality of the code will be rapidly and significantly enriched.

Discrete ECogeomorphic Aeolian Landscape (DECAL) modelling

Joanna Nield (Investigator)

DECAL is a cellular automaton based model which incorporated mutual feedback processes between geomorphic forcing and ecological growth to investigate fundamental controls, self-organising and non-linear behaviour in semi-arid aeolian dune environments. This project explores landscape evolution and disturbance response, developing a phase-space in which dune fields can be quantified.

Dynamag: computational magnonics

Hans Fangohr, Atul Bhaskar (Investigators), Matteo Franchin, Andreas Knittel

Analytical treatment of long range magneto-dipole interactions is a bottle-neck of magnonics and more generally of the theory of spin waves in non-uniform media. This project develops a theoretical framework for analysis of magnonic phenomena in magnetic nano-structures, including isolated nano-elements, arrays of those, and extended magnonic crystals. The DYNAMAG project is funded by the EU FP7 and the DST of India.

Dynamics of interacting magnetic nanoparticles

Thomas Fischbacher (Investigator), Maximilian Albert

The project aims at extending the micromagnetic simulation framework 'nmag' developed at the University of Southampton to enable it to handle dynamic geometries. The extended framework will then be used to study systems such as interacting magnetic nanoparticles.

Electrostatic embedded energy calculations of proteins, using the ONETEP DFT code

Chris-Kriton Skylaris (Investigator), Stephen Fox, Chris Pittock

Calculating the energy of a biomolecule in solvent, using quantum mechanics (QM) is possible, but extremely challenging, even with linear-scaling QM methods like ONETEP. Using electrostatic embedding, a novel twist on the existing QM/MM method is used to calculate the binding energy of a small ligand to a solvated protein, increasing the accuracy and realism of our general project work.

Evaluation of Vortex Shedding of Slender Structures using LES Techniques

Zheng-Tong Xie, Ian Castro (Investigators), Steven Daniels

Vortex shedding is a critical design consideration for slender structures such as long-span bridges, high-rise buildings and tele-communication masts. It can create large responses at relatively low wind speeds, leading to serviceability and fatigue concerns.

Since vortex shedding is highly sensitive to the precise shape of the object, there are no established codes or standards that provide adequate evaluation of vortex shedding risks.

The aim of this project is to develop a novel computational approach (based on Large Eddy Simulation, implemented in OpenFoam) that will be available for use by Arup on relevant bridge and building projects. It is anticipated that this tool will be used in early stages of a project to assess vortex shedding risks, which may be confirmed through wind tunnel testing at later stages

Fluid Loads and Motions of Damaged Ships

Dominic Hudson, Ming-yi Tan (Investigators), Christian Wood, James Underwood, Adam Sobey

An area of research currently of interest in the marine industry is the effect of damage on ship structures. Research into the behaviour of damaged ships began in the mid nineties as a result of Ro-Ro disasters (e.g. Estonia in 1994). Due to the way the Estonia sank early research mainly focused on transient behaviour immediately after the damage takes place, the prediction of capsize, and of large lateral motions. Further research efforts, headed by the UK MoD, began following an incident where HMS Nottingham ran aground tearing a 50m hole from bow to bridge, flooding five compartments and almost causing the ship to sink just off Lord Howe Island in 2002. This project intends to answer the following questions:
“For a given amount of underwater damage (e.g. collision or torpedo/mine hit), what will be the progressive damage spread if the ship travels at ‘x’ knots? OR for a given amount of underwater damage, what is the maximum speed at which the ship can travel without causing additional damage?”

Fracturing of small social networks

Seth Bullock, Sally Brailsford (Investigators), Elisabeth zu-Erbach-Schoenberg

A connected social network is a very important factor for the success of groups and organisations. We investigate which factors make a group more resistant to the effects of disagreements which commonly happen in small social networks.

Generating Optimal Ensembles of Earth System Models

Simon Cox (Investigator), Elizabeth Hart, Andras Sobester

GENIE is an Earth system model of intermediate complexity. As with other climate models, the tuning of its parameters is essential for providing reliable long-term forecasts of Earth system behaviour. We apply a multi-objective optimization algorithm to the problem. The aim of the tuning exercise is to find the optimal values for the free parameters that produce and euqilibrium model end state with the closest fit to equivalent observational data.

Generic Operational Simulation of Civil Unmanned Air Vehicle Operations

Kenji Takeda, James Scanlan (Investigators)

This project creates a generic operational simulation of Unmanned Air Vehicle Operations. UAVs can be valued for their mission-suitability and compared against various configurations.

Graphical Simulation of Archaeological Environments

Graeme Earl (Investigator)

This project defines an emerging area of interest in physically accurate rendering within the Archaeological Computing Research Group. Sub-projects include analysis of Roman spaces at herculaneum, Neolithic buildings at Catalhoyuk and simulation of a range of artefacts.

Gravitational waves from neutron stars

Ian Hawke (Investigator)

Gravitational waves, once detected, will give information about the extremes of space and time. Compact objects such as neutron stars are perfect locations for generating such waves.

Hadronic structure on the computer

Jonathan Flynn (Investigator), Dirk Broemmel, Thomas Rae, Ben Samways

In experiments at the Large Hadron Collider (LHC) at CERN, Geneva, the interactions that occur between the colliding particles (protons in this case) can be factorised into a simple scattering between two constituent particles, called quarks, followed by a hadronisation process, which describes the dynamics of forming the bound proton states. Quarks are particles within the proton that bind to form composite particles (hadrons) such as a proton. The scattering process can be computed relatively easily, but hadronisation is intrinsically non-perturbative and hard to calculate. Lattice QCD (computer simulation of QCD on a discrete space-time lattice) provides our only known first-principles and systematically-improvable method to address problems like hadronisation. This project uses Iridis to extract parton distribution amplitudes which are experimentally inaccessible, but needed to describe the quark structure of hadrons.

How far can we stretch the MARTINI?

Syma Khalid (Investigator), Ric Gillams

To date, coarse-grained lipid models have generally been parameterised to ensure the correct prediction of structural properties of membranes, such as the area per lipid and the bilayer thickness. The work described here explores the extent to which coarse-grained models are able to predict correctly bulk properties of lipids (phase behaviour) as well as the mechanical properties, such as lateral pressure profiles and stored elastic stress in bilayers. Such an evaluation is crucial for understanding the predictive capabilities of coarse-grained models.

Hybrid quantum and classical free energy methods in computational drug optimisation

Jonathan Essex, Chris-Kriton Skylaris (Investigators), Christopher Cave-Ayland

This work is based around the application of thermodynamics and quantum mechanics to the field of computational drug design and optimisation. Through the application of these theories the calculation of the physical properties of drug-like molecules is possible and hence some predictive power for their pharmaceutical activity in vivo can be obtained.

Hybrid RANS/LES methods

Richard Sandberg (Investigator), Markus Weinmann

Novel hybrid RANS/LES methods are developed for more accurate and efficient simulation of flow over complex geometries.

Identification of novel Crustacean Pathogen Receptor Proteins

Richard Edwards, Chris Hauton, Timothy Elliott (Investigators), Oyindamola Lawal, Lloyd Mushambadzi

We are mining EST libraries (sequence fragments of expressed genes) for novel proteins that might play a role in the immune response of crustaceans.

Immunotherapy Research: Modelling MHC Class I Complex Assembly

Timothy Elliott, Jorn Werner (Investigators), Alistair Bailey

This project uses mathematical modelling and simulation to investigate mechanisms by which our cells process and present biological information that is used by our immune system to distinguish between healthy and diseased cells.

Integrated in silico prediction of protein-protein interaction motifs

Richard Edwards (Investigator), Kieren Lythgow

Many vital protein-protein interactions are mediated by Short Linear Motifs (SLiMs) which are short proteins typically 5-15 amino acids long containing only a few positions crucial to function. This project integrates a number of leading computational techniques to predict novel SLiMs and add crucial detail to protein-protein interaction networks.

Interactome-wide prediction of short linear protein interaction motifs in humans

Richard Edwards (Investigator)

Short Linear Motifs (SLiMs) are important in many protein-protein interactions. In previous work, we have developed a computational tool, SLiMFinder, which places the interpretation of evidence for motifs within a statistical framework with high specificity, and subsequently enhanced sensitivity through application of conservation-based sequence masking. We are now applying these tools to a comprehensive set of human protein-protein interactions in order to predict novel human SLiMs in silico.

Is fine-scale turbulence universal?

Richard Sandberg (Investigator)

Complementary numerical simulations and experiments of various canonical flows will try to answer the question whether fine-scale turbulence is universal.

Jet noise

Richard Sandberg (Investigator), Neil Sandham

Direct numerical simulations are used to investigate jet noise.

Kaon to two pion decays in lattice QCD

Jonathan Flynn (Investigator), Elaine Goode, Dirk Broemmel

We calculate kaon decay amplitudes on the lattice so we may compare the Standard Model to experiment.

Laminar to Turbulent Transition in Hypersonic Flows

Neil Sandham, Heinrich Luedeke

Understanding of laminar to turbulent transition in hypersonic boundary-layer flows is crucial for re-entry vehicle design and optimization. The boundary-layer state directly affects the temperatures on the vehicle surface and its viscous drag. Therefore transition has to be considered to correctly compensate for drag and to properly design the thermal protection system.
For the proposed study, in order to obtain a clear understanding of the transition process, the configuration is kept as simple as possible by varying only a minimum number of parameters affecting transition on a simple test geometry such as a swept ramp at different sweep angles. To investigate the influence of such sweep angles on the transition process in the hypersonic regime, Direct Numerical Simulations (DNS) of the turbulent flow field are carried out on the Iridis cluster.

Lyotropic phase transitions of lipids studied by CG MD simulation and experimental techniques

Syma Khalid (Investigator), Josephine Corsi

A study of the phase behaviour of cationic lipid - DNA complexes such as those used for transfection by coarse grained molecular dynamics simulation. Lipid systems studied include DOPE, DOPE/DNA and DOPE/DOTAP/DNA. Structural parameters and phase behaviour observed computationally have been compared with those gained using Small Angle X-ray Scattering (SAXS) and polarising light microscopy techniques.

Mathematical modelling of plant nutrient uptake

Tiina Roose (Investigator)

In this project I will describe a model of plant water and nutrient uptake and how to translate this model and experimental data from the single root scale to the root branching structure scale.

Measuring biomolecules - improvements to the spectroscopic ruler

Pavlos Lagoudakis, Tom Brown (Investigators), Jan Junis Rindermann, James Richardson

The spectroscopic ruler is a technique to measure the geometry of biomolecules on the nm scale by labeling them with pairs of fluorescent markers and measuring distance dependent non-radiative energy transfer between them. The remaining uncertainty in the application of the technique originates from the unknown orientation between the optical dipole moments of the fluorescent markers, especially when the molecule undergoes thermal fluctuations in physiological conditions. Recently we introduced a simulation based method for the interpretation of the fluorescence decay dynamics of the markers that allows us to retrieve both the average orientation and the extent of directional fluctuations of the involved dipole moments.

Meshless Methods for Photonic Crystal Modelling

Kamal Djidjeli, Marc Molinari, Simon Cox (Investigators), Neil O'Brien, Elizabeth Hart

We apply meshless methods to the problems of simulating photonic crystals. The meshless methods utilise compactly-supported radial basis functions (CSRBFs) and offer a promising alternative to the conventional plane-wave expansion method for calculating the band structure of photonic crystals.

Miscible multiphase systems with phase transition

Andrea Boghi

We aim to develop the computational model for the miscible displacement of liquid occupying a porous bulk, as, for instance, in the processes of vegetable solvent extraction, soil remediation or enhanced oil recovery. All these process includes the dissolution of solute and the displacement of solution from porous media. The focus of our current research work is, therefore, twofold: (i) to develop and verify a theoretical model for an evolving miscible displacement, by taking into account dynamic surface tension and mass diffusion through the interphase boundary, and (ii) to provide a model for the solute/solvent displacement from the porous volume.

Modelling Macro-Nutrient Release & Fate Resulting from Sediment Resuspension in Shelf Seas

Chris Wood

This study involves adapting a previously-published model to take into account the effect resuspension events (both natural and anthropogenic) may have on nutrient dynamics at the sediment-water interface, and hence produce better estimates for the total nutrient budgets for shelf seas.

Modelling micromagnetism at elevated temperature

Hans Fangohr (Investigator), Dmitri Chernyshenko

The project aim is to develop a multiscale multiphysics model of
micromagnetism at elevated temperatures combining finite
element/finite difference modelling with atomistic simulations for
material parameter. The tool will be used to guide the development of the next generation magnetic data storage technology: heat assisted magnetic recording.

Modelling power output and wake effects in tidal stream turbine arrays

William Batten (Investigator), Matthew Harrison, Luke Blunden

The PhD research is regards the investigation of modelling techniques for simplifying turbine simulation so that models of large arrays can be investigated.

Molecular Fragments in Inhibitor Design

Jonathan Essex (Investigator), Michael Bodnarchuk

Fragment-Based Drug Discovery (FBDD) has emerged as an important tool in the drug discovery process. Instead of screening entire drug molecules, FBDD screens molecular fragments; constituents which make up drug molecules. A computational approach to identifying fragment binding is currently being sought which also yield binding free energy estimation.

Multi-objective design optimisation of coronary stents

Neil Bressloff, Georges Limbert (Investigators), Sanjay Pant

Stents are tubular type scaffolds that are deployed (using an inflatable balloon on a catheter), most commonly to recover the shape of narrowed (diseased) arterial segments. Despite the widespread clinical use of stents in cardiovascular intervention, the presence of such devices can cause adverse responses leading to fatality or to the need for further treatment. The most common unwanted responses of inflammation are in-stent restenosis and thrombosis. Such adverse biological responses in a stented artery are influenced by many factors, including the design of the stent. This project aims at using multi-objective optimisation techniques to find an optimum family of coronary stents which are more resistant to the processes of in-stent restenosis (IR) and stent thrombosis (ST).

Multi-scale simulations of bacterial outer-membrane proteins

Syma Khalid (Investigator), Jamie Parkin

Using Iridis to run multiple simulations, I aim to simulate the outer membrane proteins of Pseudomonas aeruginosa, using X-ray crystal structures of proteins only recently resolved by Bert van den Berg, University of Massachusetts. By modelling the proteins in a realistic P. aeruginosa outer membrane, I am to gain insight into the binding of these proteins to specific substrates and their function.

Multiscale modelling of biological membranes

Jonathan Essex (Investigator), Mario Orsi

Biological membranes are complex and fascinating systems, characterised by proteins floating in a sea of lipids. Biomembranes, besides being the fundamental structures employed by nature to encapsulate cells, play crucial roles in many phenomena indispensable for life, such as growth, energy storage, and in general information transduction via neural activity. In this project, we develop and apply multiscale computational models to simulate biological membranes and obtain molecular-level insights into fundamental structures and phenomena.

Multiscale Simulation of Cellular Calcium Signalling

Hans Fangohr, Jonathan Essex (Investigators), Dan Mason

Calcium ions play a vitally important role in signal transduction and are key to many cellular processes including muscle contraction and cell apoptosis (cell death). This importance has made calcium an active area in biomedical science and mathematical modelling.

MXL Project

Mark Taylor, Junfen Shi (Investigators)

‘MXL’ is short for “Enhanced patient safety by computational Modelling from clinically available X-rays to minimise the risk of overload and instability for optimised function and Longevity”. This is an international EU-funded project which the Bioengineering Sciences Research Group at Southampton is involved in. For more information, visit http://www.m-x-l.eu

nano-CMOS

Mark Zwolinski (Investigator), Michael Merrett

Modelling random device variations within systems using nano-CMOS technologies.

Network Analysis of Roman Transport Routes in the Imperial Roman Mediterranean

David Potts

This research is designed to explore the nature of the relationships between Portus, Rome, and other selected ports in the Mediterranean and to establish patterns and the changing nature of trading networks derived from the distribution of known Roman artefacts.

Nmag - computational micromagnetics

Hans Fangohr, Thomas Fischbacher (Investigators), Matteo Franchin, Andreas Knittel, Maximilian Albert, Dmitri Chernyshenko, Massoud Najafi, Richard Boardman

Nmag is a micromagnetic simulation package based on the general purpose multi-physics library nsim. It is developed by the group of Hans Fangohr and Thomas Fischbacher in the School of Engineering Sciences at the University of Southampton and released under the GNU GPL.

Nmag finite difference

Hans Fangohr (Investigator), Dmitri Chernyshenko, Matteo Franchin, Massoud Najafi

The goal of this project is to extends the finite element based micromagnetic simulation tool Nmag by the finite difference based extension Nmagfd and so to get an simulation tool where the user can easily switch between the used discretization method.

Non-Perturbative Renormalisation on the Lattice

Jonathan Flynn (Investigator), Dirk Broemmel, Thomas Rae

In this project we compute renormalisation factors for various physical observables in a non-perturbative lattice framework. Renormalisation hereby arises due to a fundamental scale dependence of the physical processes.

Nonequilibrium Dynamics of Atomic Gases in Optical Lattices

Sophie Marika Reed

Many-body, quantum systems exhibit emergent properties which allows for quantum events to influence properties on macroscopic scales. Such emergent properties are studied using stochastic phase-space techniques.

Nonlinear Optical Pulse Propagation

Peter Horak, Francesco Poletti (Investigators)

The work is concerned with the propagation of high-power short-pulse propagation in microstructured fibres or waveguides. Dispersion properties and optical nonlinearities are exploited for pulse shaping techniques in space, time, and frequency. Investigated microstructures include silica or soft-glass templates, gas-filled capillaries, and semiconductor-filled fibres, and optical wavelengths range from the X-ray to the mid-infrared regime.

Nonlinear Optics in Structured Material

Peter Horak, Neil Broderick (Investigators)

Structured materials such as photonic crystals, optical fibres, Bragg gratings etc. are the ideal material for nonlinear optics. Properly engineered materials allows one to control which nonlinear interactions are observed and enhanced whilst other nonlinear interactions can be neglected. This work looks both at fundamental ideas as well as the fabrication of devices for advanced telecommunications.

Numerical Elastic Neutron Stars

Ian Hawke, Ian Jones (Investigators), Andrew Penner

We study the gravitational wave forms that radiate from an asymmetric neutron star using an elasto-hydrodynamic model.

Numerical investigation of the true sources of jet noise

Anurag Agarwal (Investigator), Samuel Sinayoko

Aircraft noise severely impacts the quality of life of people living close to airports. Noise generation by aircrafts is especially large during take-off. Jet noise is the dominant noise source during take-off. It is produced by the high speed flow generated by the engine. However, the actual source of sound remains unknown. A deeper understanding of the sources of jet noise is need to be able to reduce the noise. The aim of this project is to implement a innovative method that would allow to identify the sources of jet noise.

OCCASION: Overcoming Capacity Constraints - A Simulation Integrated with Optimisation for Nodes

OCCASION is a collaboration between TRG and the Schools of Mathematics and Management. The project's objective is to identify and investigate innovative methods of increasing the capacity of nodes (i.e. junctions and stations) on the railway network, without substantial investment in additional infrastructure. To this end, a state-of-the-art review of recent and ongoing work in this area will be conducted, followed by the development of tools to (i) assess existing levels of capacity utilisation at nodes, and (ii) investigate options for re-routeing and re-scheduling trains, with a view to reducing capacity utilisation levels. These tools will be used in combination to develop solutions delivering reduced levels of capacity utilisation, and thus increases in capacity and/or service reliability. Incremental changes to existing railway technologies (e.g. improved points) and operating practice (e.g. relaxations of the Rules of the Plan) will be investigated, as will concepts from other modes (e.g. road and air transport) and sectors (e.g. production scheduling).

OMSys Towards a system model of a bacterial outer membrane

Syma Khalid (Investigator)

Many bacteria have an outer membrane which is the interface between the cell and its environment. The components of this membrane are well studied at an individual level, but there is a need to model and understand the outer membrane as a whole. In this project we aim to develop such a model of a bacterial outer membrane, linking computer simulations of the component molecules through to a more "systems biology" approach to modelling the outer membrane as a whole. Such an approach to modelling an OM must be multi-scale i.e. it must embrace a number of levels ranging from atomistic level modelling of e.g. the component proteins through to higher level "agent-based" modelling of the interplay of multiple components within the outer membrane as a whole. The different levels of description will be integrated to enable predictive modelling in order to explore the roles of outer membrane changes in e.g. antibiotic resistance.

Operational Simulation of the Solent Search-and-Rescue environment

James Scanlan, Kenji Takeda, Hans Fangohr (Investigators), Ben Schumann

This project aims to identify useful metrics for a proposed Search-and-Rescue UAV and test it virtually in a realistic environment.

Performance improvement in kinetic energy converters though fluid separation

William Batten (Investigator), Tom Blackmore, Luke Blunden

The PhD research is regards the investigation of the effect of flow separators in confined tidal channels to improve performance of tidal stream turbines.

Population24/7: space-time specific population surface modelling

Samantha Cockings, David Martin, Samuel Leung (Investigators)

Project funded by Economic and Social Research Council to compute time-specific geographical representations of population distribution.

Prediction of orifice flow flooding rates through generic orifices

Dominic Hudson, Ming-yi Tan (Investigators), Christian Wood, Adam Sobey

This presearch concentrates on the modelling of compartment flooding rates following the occurrence of damage in a ship's side shell. Typical state of the art flooding models use Torricelli’s formula to calculate flooding rates using a constant co-efficient of discharge (Cd). Based on Bernoulli’s theorem, turbulence and viscosity effects are not included using a Cd independent of damage shape or size. Previous work indicates that this assumption over-simplifies the problem to an extent where the flooding rates used for calculation are in error. This project will use CFD validated by experiment to calculate flooding rates for a large number of cases from which a 'krigged' response surface will be generated. Validity of the subsequent response surface will be interrogated.

Probing the oligomeric state and interaction surface of Fukutin Transmembrane Domain in lipid bilayer via Molecular Dynamics simulations

Nils Berglund

Fukutin Transmembrane Domain (FK1TMD) is localised to the endoplasmic reticulum or Golgi Apparatus within the cell where it is believed to function as a glycosyltransferase. Its localisation within the cell is thought to be mediated by the interaction of its N-terminal transmembrane domain with the lipid bilayers surrounding these compartments, each of which possess a distinctive lipid composition. Studies have revealed that the N-terminal transmembrane domain of FK1TMD exists as dimer within dilauroylphosphatidylcholine bilayers and this interaction is driven by interactions between a characteristic TXXSS motif. Furthermore residues close to the N-terminus that have previously been shown to play a key role in the clustering of lipids are shown to play a key role in anchoring the protein in the membrane.

Real-time CFD for helicopter flight simulation

Kenji Takeda (Investigator), James Kenny

Project aims to show how real-time computational fluid dynamics (CFD) could be used to improve the realism of helicopter flight simulators.

Reconstructing past lake conditions using sediment cores

Lake sediments can be analysed for the reconstruction of past environmental conditions, and past abundances of different species. These data are the first step in the creation of a simulation model which will investigate the dramatic fluctuations in environmental conditions in the East African Rift Valley soda lakes.

Scalability of Energy Efficient Routing Algorithms in WSN

Davide Zilli

This project compares two broad classes of routing algorithms for Wireless Sensor Networks, message flooding and single path, by means of a simulation model. In particular, we want to understand how the two scale in terms of energy efficiency on large networks of sensors.

Self-Force and Black Hole Inspirals

Sam Dolan (Investigator)

We use IRIDIS to compute the self-force acting on a solar-mass black hole orbiting a supermassive black hole.

Separation of timescales in models of complex networks

Seth Bullock (Investigator), Elisabeth zu-Erbach-Schoenberg, Connor McCabe

In many real-world systems several processes act on the system state. The way these processes interact can have implications for the resulting system state. We investigate how separation of the timescales of two processes influences the system's equilibrium state.

Simulating Hydro-geomorphic Changes in European Climate Hotspots

John Dearing (Investigator), Ying Wang

This project will simulate the behaviour of hydro-geomorphological processes in a fluvial system over decadal timescales is an important basis for research on catchment environmental management, especially with regards climate changes and human impacts on fluvial system.

Simulation modelling of habitat permeability for mammalian wildlife

Patrick Doncaster, Jason Noble (Investigators), Angela Watkins

Using and integrating least-cost models and agent-based simulations to explore the way in which mammals interact with, and hence move, through fragmented landscapes.

Soft x-ray science on a tabletop

Peter Horak, Jeremy Frey, Bill Brocklesby (Investigators), Patrick Anderson

Complex numerical simulations are being performed to aid experimentalists at Southampton realize the next generation of high brightness tabletop sources of coherent soft x-rays.


Spatial Mobility in the Formation of Agent-Based Economic Networks

Antonella Ianni, Seth Bullock (Investigators), Camillia Zedan

An investigation into the effect of spatial mobility on endogenous economic network formation.

Statistical model of the knee

Mark Taylor (Investigator), Francis Galloway, Prasanth Nair

Development of methods for large scale computational testing of a tibial tray incorporating inter-patient variability.

Stochastic computational methods for aero-acoustics

Gwenael Gabard (Investigator), Martina Dieste

Stochastic methods are used to synthesize a turbulent flow which is then used to model the sound radiated by an airfoil interacting with this turbulence. This approach is faster than performing a complete simulation of the flow field.

Stratified combustion physics and modelling

Edward Richardson (Investigator)

Full-resolution simulation data for turbulent combustion are used to investigate the fundamental impact, and practical modelling, of fuel-air stratification.

Structured low-rank approximation

Ivan Markovsky

Today's state-of-the-art methods for data processing are model based. We propose a fundamentally new approach that does not depend on an explicit model representation and can be used for model-free data processing. From a theoretical point of view, the prime advantage of the newly proposed paradigm is conceptual unification of existing methods. From a practical point of view, the proposed paradigm opens new possibilities for development of computational methods for data processing.

Study of global instability in separated flows at high Mach number

Neil Sandham, Zhiwei Hu (Investigators), Kangping Zhang

Flow instability is observed when extending two-dimensional (2D) stable flow into three-dimensional (3D). Development of instability varies along different spanwise length. Thresholds are also discovered for the flow studied to become instable.

Supersonic axisymmetric wakes

Richard Sandberg (Investigator)

Direct numerical simulations are used to shed more light on structure formation and evolution in supersonic wakes.

Surface moisture-induced feedback in aeolian environments

Joanna Nield (Investigator)

This project explores the importance of surface moisture for aeolian processes, particularly feedback between surface moisture and bedform sedimentation and migration.

Sustainable domain-specific software generation tools for extremely parallel particle-based simulations

Chris-Kriton Skylaris (Investigator)

A range of particle based methods (PBM) are currently used to simulate materials in chemistry, engineering, physics and biophysics. The 4 types of PBM considered directly in the proposed are molecular dynamics (MD), the ONETEP quantum mechanics-based program, discrete element modelling (DEM), and smoothed particle hydrodynamics (SPH).
The overall research objective is to develop a sustainable tool that will deliver, in the future, cutting edge research applicable to applications ranging from dam engineering to atomistic drug design.

Tag based transcriptome analysis of gene expression in a promising green algae

Richard Edwards, Andreas Johansson

We use SuperSAGE in combination with next-generation sequencing to compare differences in gene expression between selected mutants and the wild type of a green algae. The data in the form of millions of 26 bp tags representing short stretches of expressed genes, will be analysed to find patterns of variation in gene expression under different conditions.

The application of automated pattern metrics to surface moisture influences on modelled dune field development

Robin Wilson, Joanna Nield (Investigators)

Areas of sand dunes (known as dunefields) develop complex patterns over time. These are influenced by both the past and present environmental conditions, including surface moisture, vegetation distribution and human impact. This project develops a method of automated pattern analysis which allow the patterns produced by a large number of sand dune evolution simulations (performed using the DECAL model) to be quantified over time.

The effect of roughness upon turbulent supersonic flows

Neil Sandham (Investigator), Christopher Tyson

Understanding the interaction between surface roughness and supersonic air flows are crucial in the design of re-entry vehicles such as the space shuttle. Numerical simulations of these flows has been conducted in order to examine the relationship in order to attempt to achieve a much clearer understanding of the behaviour.

The Endogenous Formation of Economic Networks

Antonella Ianni, Seth Bullock (Investigators), Camillia Zedan

An investigation into endogenous network formation using a simple agent-based approach.

The ONETEP project

Chris-Kriton Skylaris (Investigator), Stephen Fox, Chris Pittock, Alvaro Ruiz-Serrano, Jacek Dziedzic

Program for large-scale quantum mechanical simulations of matter from first principles quantum mechanics. Based on theory and algorithms we have developed for linear-scaling density functional theory calculations on parallel computers.

The Role of Information in Price Discovery

Antonella Ianni, Seth Bullock (Investigators), Camillia Zedan

The recent economic crisis has highlighted a continued vulnerability and lack of understanding in the financial markets. In order to overcome this, many believe that current market models must be improved. Recently, a trend towards agent-based modelling has emerged. Viewing the economy as a complex system is beginning to be seen as key to explaining certain market characteristics that were originally considered anomalies.

One of the fundamental assumptions in economics is that of information efficiency: that the price of a stock reflects its worth, that all possible information about a security is publicly known, and that any changes to price take place instantaneously. In reality, however, this is not the case.

This project considers the use of agents in modelling economic systems and demonstrates the effect of information levels on price discovery using a simple market simulation.

Transition to turbulence in high-speed boundary layers

Neil Sandham (Investigator), Nicola De Tullio

This work is focused on the numerical simulation of hypersonic transition to turbulence in boundary layers. We use direct numerical simulations of the Navier-Stokes equations to analyse the effects of different flow conditions and external disturbances on the transition process. The main objective is to gain insight into the different aspects of transition to turbulence at high speeds, which can lead to the design of new transition models and transition control techniques for high-speed flows.

Traveling and movement during European Late Prehistory

Patricia Murrieta Flores

This project has as main purpose to investigate through spatial analysis and computational modelling the variables and factors that influenced how humans traveled during prehistoric times.
One of the principal objectives will be to clarify the role that certain landscape elements (i.e megalithic monuments) played in terrestrial navigation and territorial definition.

This project is supported by CONACYT (Mexico) as a doctoral research by Patricia Murrieta-Flores under the supervision of Dr. David Wheatley (University of Southampton) and Dr. Leonardo Garcia Sanjuan (University of Seville, Spain). It also counts with the collaboration of Dr. Dimitrij Mlekuz (Gent University, Belgium).

Vortex Dynamics in High-Tc superconductors

Hans Fangohr (Investigator)

The dynamics of vortices in high temperature superconductors exhibits the complex and rich physics we expect from many body systems with competing interactions. Molecular Dynamics, Langevin Dynamics and Monte Carlo Computer simulations are carried out to understand this system in more detail.

Vortices in Spinor Bose-Einstein Condensates

Janne Ruostekoski (Investigator), Justin Lovegrove

We numerically study the effect of spin degrees of freedom on the structure of a vortex in a Bose-Einstein Condensate. Such objects are of interest as macroscopic examples of quantum phenomena, as well as for their analogies in other fields, such as cosmology and high energy physics.

Water Molecules in Protein Binding Sites

Jonathan Essex (Investigator), Michael Bodnarchuk

Water molecules are commonplace in protein binding sites, although the true location of them can often be hard to predict from crystallographic methods. We are developing tools which enable the location and affinity of water molecules to be found.

Wave-based discontinuous Galerkin methods

Gwenael Gabard (Investigator), Greg Kennedy

Wave-based computational methods are developed to model sound propagation in moving inhomogeneous media.

Whisky Code

Ian Hawke (Investigator)

A 3D finite volume code for simulating compact relativistic hydrodynamics.

Wind direction effects on urban flows

Zheng-Tong Xie, Ian Castro (Investigators), Jean Claus

Numerical simulations of turbulent air flow are conducted on Iridis to investigate the effects of different wind directions on the flow within and above an urban-like canopy.

Wind Turbine Blade Flow in Abnormal Environments

Zheng-Tong Xie (Investigator), Yusik Kim

Large wind turbines are being installed throughout UK and often in regions with complex meteorology and/or topography (e.g. involving wind gusts, turbulence, icing), which affect turbine performance (energy output, noise emission etc), life expectancy and safety. It is very expensive to conduct experiments to study such problems. This proposal suggests, firstly, an LES study of low-Re flows around an oscillating airfoil, to investigate the transition, separation, vortex shedding and dynamic stall behaviour. Secondly, a combined LES-RANS approach (with, e.g., a transitional RANS model in the near wall region) will be carefully designed (using our recently developed efficient turbulence generator at the interface between LES and RANS) and validated against low-Re results.

µ-VIS Computed Tomography Centre

Ian Sinclair, Richard Boardman, Dmitry Grinev, Philipp Thurner, Simon Cox, Jeremy Frey, Mark Spearing, Kenji Takeda (Investigators)

A dedicated centre for computed tomography (CT) at Southampton, providing complete support for 3D imaging science, serving Engineering, Biomedical, Environmental and Archaeological Sciences. The centre encompasses five complementary scanning systems supporting resolutions down to 200nm and imaging volumes in excess of one metre: from a matchstick to a tree trunk, from an ant's wing to a gas turbine blade.