Computational Modelling Group

Computational platforms

Categories within this topic include .NET (3), ARCHER (9), Cloud computing (4), Condor (1), Docker (1), Emerald (3), FPGA (2), GPU (13), HECToR (23), HPCx (8), Iridis (155), Jaguar (1), Linux (136), Lyceum (8), Mac OS X (50), Microsoft Azure (3), NGS (4), Raspberry Pi (1), Spitfire (2), Vagrant (2), VirtualBox (5), Windows (73), Xeon Phi (4)

All Projects

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

John Shrimpton (Investigator), Gabriel Amine-Eddine

During my final year as an undergraduate, I developed a fully functional software program for visualising geometries, grids and grid quality metrics, for and in-house CFD software tool (HARTREE CFD).

A novel approach to analysing fixed points in complex systems

James Dyke (Investigator), Iain Weaver

This work aims to contribute to our understanding of the relationship between complexity and stability. By describing an abstract coupled life-environment model, we are able to employ novel analytical, and computational techniques to shed light on the properties of such a system.

A novel method for monitoring air pollution from satellites at very high resolution

Joanna Nield, Jason Noble, Edward Milton (Investigators), Robin Wilson

Developing methods to monitor the clarity of the atmosphere from satellites at 100,000 times the resolution of previous methods. This can then be used to monitor air pollution, correct satellite images and provide data for climate studies. Simulation is used to model the effects of atmospheric pollution on light passing through the atmosphere, and to test the method under 'synthetic atmospheres'.

A spatially-explicit agent-based model of jaguar population dynamics

Jason Noble, Patrick Doncaster (Investigators), Angela Watkins

A single species spatially-explicit agent-based model has been developed that illustrates the role of simulation modelling, integrated with an adapted least-cost modelling approach and real-world geographical data, in exploring jaguar population dynamics.

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.

Ab initio simulations of chemical reactions on platinum nanoparticles

Chris-Kriton Skylaris (Investigator), Álvaro Ruiz-Serrano, Peter Cherry

•Use first principles calculations to study the relationship between shape and size of nanoparticle and the oxygen adsorption energy.

• Investigate the effect of high oxygen coverage on the catalytic activity of the nanoparticles.

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.

Advanced simulation tools for prediction of flash-back in hydrogen-rich gas turbine combustion

Edward Richardson (Investigator), James Bailey

The project involves the numerical simulation of hydrogen-rich flows using Direct Numerical Simulation (DNS) and Large Eddy simulations. Hydrogen rich fuels offer the opportunity to reduce the carbon intensity of energy supply. Hydrogen-rich fuels and other low-carbon energy sources are expect to become increasingly important in this regard. Hydrogen is more reactive and diffusive than conventional hydrocarbon fuels requiring advanced computational methods to optimise the use of these fuels in gas turbines.

Aerofoil noise

Richard Sandberg (Investigator)

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

An Evolutionary Economic Approach to the Household?

Jason Hilton

The household is a fundamental societal unit. In a huge array of contexts, our understanding of social behaviour relies on an interpretation of how decision are taken at the household level.This work aims to model individual decision-making and interactions between individuals explicitly within the framework of agent-based modelling, following the work of Potts (2000). Potts describes how economic problems can better be dealt with by considering how agents with incomplete, evolving preferences in the form of decision rules interact on a network, and how they cooperate and form ties to produce combinatorial technologies. Following the work of Gary Becker, he then considers how this ostensibly economic framework might hypothetically describe partnership search and household formation and dissolution.

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.

Application of RNA-Seq for gene fusion identification in blood cancers

William Tapper (Investigator), Marcin Knut

Gene fusions are often the cause of different blood cancers. As such, accurate identification of them provides information on the underlying cause of a cancer, ensuring appropriate choice of treatment. However, due to shortcomings of the currently applied methods for gene fusion identification, some of them escape undetected. We are employing RNA-Seq, a cutting-edge method for sequencing RNA, the messenger of genetic information, to investigate gene fusions.

Assessment of the performance of novel RANS and hybrid turbulence models on the flow around a cylinder

Manuel Diaz Brito

The turbulent flow around a circular cylinder is a widely studied problem in fluid dynamics. At a certain characteristic Reynolds numbers the development of a turbulent wake occurs simultaneously with separation of the laminar boundary layer. The mechanisms defining this critical flow state are very complex to predict computationally. In this project the suitability of novel non-linear eddy viscosity closures and a hybrid Flow Simulation Methodology formulation to face these massively separated flows is studied. The flow predicting capabilities of the baseline EASM, ?-?-EASM and FSM-?-?-EASM tested are contrasted with the industrial renowned k-?-SST turbulence model. In the visualisation of the results it is evident that the ?-?-EASM has greater flexibility estimating the components of the Reynolds stresses with respect to the baseline EASM and the k-?-SST. Although dome differences are observed, the prediction of the critical flow around a cylinder is not accurately achieved by any of these RANS models, but the FSM-?-?-EASM shows great resemblance with the validation data, demonstrating capabilities of resolving very complex flow phenomena with minimum user input if the computational grid is fine enough. In order to demonstrate even greater advantages of non-linear models it was postulated that the addition of a streamwise impinging vortex hitting the leading edge of the cylinder would make the flow field fully three-dimensional. First attempts were tried in this route but time constraints limited the ultimate scope of the present work.

Automatic Image Retrieval with Soft Biometrics for Surveillance

Mark Nixon, John Carter (Investigators), Daniel Martinho-Corbishley

We're investigating ways to automatically describe and identify pedestrians from surveillance footage using human understandable, soft biometric labels. Our goal is to enable surveillance operators to search for pedestrians in a video network using soft biometric descriptions, and to automatically retrieve these descriptions from CCTV images.

B-meson coupling with relativistic heavy quarks

Jonathan Flynn (Investigator), Ben Samways, Dirk Broemmel, Patrick Fritzsch

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.

Benchmarking the GOPHER orthologue prediction algorithm.

Richard Edwards, Shaun Maguire

Generation of Orthologous Proteins from High-throughput Evolutionary Relationships (GOPHER) is an orthologue prediction algorithm. This experiment aims to benchmark this algorithm.

Bioclimatic Architecture

Seth Bullock (Investigator), Nicholas Hill

This was a review report on bioclimatic architecture and how such architecture may be designed by agent-based models inspired by the building behaviour of insects.

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.


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.

Body Forces in Particle Suspensions in Turbulence

Gabriel Amine-Eddine (Investigator), John Shrimpton

The behaviour of multiphase flows is of primary importance in many engineering applications. In the past, experimental observations have provided many researchers with the ability to understand and probe the phenomena and physical processes occurring in such flows. With advancements in modern day computational power, we now have the ability to gain an even greater wealth of knowledge, from what used to be a physical experiment, is now a virtual simulation.

Amine-Eddine, G.H. (2015) Body forces in particle suspensions in turbulence. University of Southampton, Faculty of Engineering and the Environment, Doctoral Thesis , 283pp.

BRECcIA - Building REsearch Capacity for sustainable water and food security In sub-saharan Africa

The BRECcIA project is aimed at developing research and researchers to understand water and food security challenges in sub-Saharan Africa

Can we calculate the pKa of new drugs, based on their structure alone?

Chris-Kriton Skylaris (Investigator), Chris Pittock, Jacek Dziedzic

The pKa of an active compound in a pharmaceutical drug affects how it is absorbed and distributed around the human body. While there are various computational methods to predict pKa using only molecular structure data, these tend to be specialised to only one class of drug - we aim to generate a more generalised prediction method using quantum mechanics.

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 simulated 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. Introducing an additional 'toxic' particle species and an associated set of synthesis reactions produced a new set of ecological behaviours compared to the original model of Ono and Ikegami.

Centre for Doctoral Training in Next Generation Computational Modelling

Hans Fangohr, Ian Hawke, Peter Horak (Investigators), Susanne Ufermann Fangohr, Ryan Pepper, Hossam Ragheb, Emanuele Zappia, Ashley Setter, David Lusher, Alvaro Perez-Diaz, Kieran Selvon, Thorsten Wittemeier, Mihails Milehins, Stephen Gow, Ioannis Begleris, Jonathon Waters, James Harrison, Joshua Greenhalgh, Rory Brown, Robert Entwistle, Paul Chambers, Jan Kamenik, Craig Rafter

The £10million Centre for Doctoral Training was launched in November 2013 and is jointly funded by EPSRC, the University of Southampton, and its partners.

The NGCM brings together world-class simulation modelling research activities from across the University of Southampton and hosts a 4-year doctoral training programme that is the first of its kind in the UK.

Challenging Topological Prejudice - Automated Airframe Layout Design

Andras Sobester (Investigator), Paul Chambers

Aircraft preliminary design scopes are drastically narrowed by topological prejudice. Modern aircraft have settled on the same 'tube plus wing and cruciform tail' type topology that has been adopted through their ancestry, with no scientific evidence that this layout is optimal. This research project poses the question:

“Given a topologically flexible aircraft geometry that is free of prejudice or bias, would a sophisticated multi-disciplinary optimization process yield a conventional layout?”

Chaotic Analysis of Partial Discharge

Paul Lewin (Investigator), Lyuboslav Petrov

The deterministic character of PD pulses predicted by theory has been shown to be existent for certain PD events. Finding characteristic patterns in phase space enables field-data PD detection with high reliability.

Characterisation of the Genomic Landscape in Splenic Marginal Zone Lymphoma

Sarah Ennis, Jane Gibson, Jon Strefford (Investigators), Carolina Jaramillo Oquendo, Helen Parker

This project aims to expand the catalogue of mutated genes in splenic marginal zone lymphoma (SMZL) and construct a detailed characterisation of the genetic landscape of this disease. Using next generation sequencing, we aim to identify somatic mutations in over 100 samples, and enrich clinical data with this information to improve patient treatment and prognosis.

Chip Implementation of a Signal Detector for a Multiple-Input Multiple-Output (MIMO) Wireless System

Mark Zwolinski, Basel Halak, Mohammed El-Hajjar (Investigators), Ibrahim Bello

We implement an Application Specific Integrated Circuit (ASIC) for the signal detection of a MIMO receiver.

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.

Colonising Polynesia; Uncertain sailing craft route modelling

Thomas Dickson (Investigator), David Sear

Through developing a novel methodology of modelling sailing craft routing it is possible to investigate archaeological problems as well as applications to modern yacht racing and autonomous sailing technology. This research uses iridis to provide accurate and fast analysis of shortest path routes for sailing craft in order to provide insight and improve safety of operation.

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. Following this, the optimisation of design parameters using computational fluid dynamics to calculate the objective function is performed and surrogate modelling utilised to estimate optimum design configuration.

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.

Computational Fluid Dynamics of Compressor Blades Within a Gas Turbine Engine (HiPSTAR)

Richard Sandberg (Investigator), John Leggett

As modern engines become more and more efficient, the importance of understanding the finer details of the physics involved grows, if further gains are to be achieved. In such harsh enviroments, such as within a gas turbine engine, there are few means of studying them physicaly and we are left with little choice but to use super computers to model the flow.

Continuously Tunable Optical Buffer

Peter Horak (Investigator)

The project aims to design, fabricate and test a novel integrated all-optical buffer device that is based on MEMS technology and provides a continuously tunable delay for optical pulses over a broad wavelength region. Such a device could play a crucial role in future packet-switched optical networks, photonic integrated circuits and coherent light based applications such as optically steered phase array antennas, LIDAR and optical coherence tomography.

This EPSRC funded project is a collaboration between the Optoelectronics Research Centre, Southampton, and University College London.

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.

Controlling Ant-Based Construction

Seth Bullock (Investigator), Lenka Pitonakova

This paper investigates dynamics of ant nest building and shows that algorithms capable of generating ant-like structures can also be used to create nests, shapes of which are imposed from outside of the system.

Coronary Artery Stent Design for Challenging Disease

Neil Bressloff (Investigator), Georgios Ragkousis

In this work, a method has been setup to (i) reconstruct diseased patient specific coronary artery segments; (ii) use the new supercomputer to run many simulations of this complex problem and (iii) assess the degree of stent malapposition. The aim now is to devise a stent delivery system that can mitigate this problem

Cosmological evolution of supermassive black holes in the centres of galaxies

Anna Kapinska (Investigator)

Radio galaxies and quasars are among the largest and most powerful single objects known and are believed to have had a significant impact on the evolving Universe and its large-scale structure. Their jets inject a significant amount of energy into the surrounding medium, hence they can provide useful information in the study of the density and evolution of the intergalactic and intracluster medium. The jet activity is also believed to regulate the growth of massive galaxies via the AGN feedback. In this project, through the use of numerical simulations, I explore the intrinsic and extrinsic physical properties of the population of Fanaroff-Riley II (FR II) objects, i.e. their kinetic luminosities, lifetimes, and central densities of their environments. This allows one to investigate evolution of these radio sources across cosmic time, and to discuss the significance of the impact of these sources on the evolving Universe.

Coupled Fluid-Structure Interaction to model Three-Dimensional Dynamic Behaviour of Ships in Waves

Pandeli Temarel, Zhi-Min Chen (Investigators), Puram Lakshmynarayanana

In the present study we focus our attention on fluid-structure interactions (FSI) of flexible marine structures in waves by coupling a fluid solver using Computational Fluid Dynamics (CFD) and a structural solver using Finite Element Analysis (FEA) software.

Coupled multi-scale simulation of high Reynolds number airfoil flows

Neil Sandham, Nicola De Tullio (Investigators), David Lusher

Application of multi-scale nested direct numerical simulations to high Reynolds number aerofoil flows.

Deep Optimisation

Jamie Caldwell

The project will develop the implementation and application of a new optimisation technique. 'Deep optimisation' combines deep learning techniques in neural networks with distributed optimisation methods to create a dynamically re-scalable optimisation process. This project will develop this technique to better-understand its capabilities and limitations and develop GPU implementations. The protein structure prediction problem will be used as the main test application.

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.

Desiging Near-Capacity Quantum Error Correction Codes

Lajos Hanzo (Investigator), Zunaira Babar

Design efficient quantum error correction codes to correct the errors encountered in a quantum transmission; thus, increasing reliability and robustness of the future quantum systems.

Design of Unmanned Air Vehicles

James Scanlan (Investigator), Robert Entwistle

Using computational modelling of a 3D airspace simulation environment to meet the safety and collision-avoidance requirements of the certification authorities.

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.

Developing programming skills with Minecraft and Python

Hans Fangohr (Investigator), Alvaro Perez-Diaz

PythonTool is a Minecraft mod created for this project which allows interactive execution of Python scripts which interact with the game in real time. It intends to make teaching programming to children or non-expert users easier and more appealing.

Development and application of powerful methods for identifying selective sweeps

Andrew Collins, Reuben Pengelly, Timothy Sluckin, Sarah Ennis (Investigators), Clare Horscroft

This project is about detecting regions of the genome which have experienced selective pressure. To achieve this, mathematical models will be developed and applied to human genomic data sets, as well as to those of other species.

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.

Diffusion at solute/solvent interfaces

Anatoliy Vorobev (Investigator), Ruilin Xie

We aim to develop the theoretical model that would provide an accurate description for the mixing process of two miscible liquids, and, in particular, would reproduce our experimental optical observations. The model based on the phase-field (Cahn-Hilliard) approach is adopted for the mixture of two miscible liquids. The model takes into account the surface tension effects, the non-Fickian diffusion across the liquid/liquid interface, and hydrodynamic flows that might be generated near the interface by the concentration gradients.

DIPLOS - Dispersion of Localised Releases in a Street Network

Trevor Thomas, Ian Castro (Investigators)

The security threat level from international terrorism, introduced by the UK Security Service, has been classified as either "severe" or "critical" for much of its six-year history, and currently remains as "substantial" (source: MI5 website). Part of the risk posed by terrorist threats involves potential releases of air-borne chemical, biological, radiological or nuclear (CBRN) material into highly populated urbanised areas. Smoke from industrial accidents within or in the vicinity of urban areas also pose risks to health and can cause widespread disruption to businesses, public services and residents. The Buncefield depot fire of 2005 resulted in the evacuation of hundreds of homes and closure of more than 200 schools and public buildings for two days; consequences would have been much more severe if prevailing meteorological conditions had promoted mixing or entrainment of the smoke plume into the urban canopy. In both these scenarios it is crucial to be able to model, quickly and reliably, dispersion from localised sources through an urban street network in the short range, where the threat to human health is greatest. However, this is precisely where current operational models are least reliable because our understanding and ability to model short-range dispersion processes is limited. The contribution that DIPLOS will make is:

1. to fill in the gaps in fundamental knowledge and understanding of key dispersion processes,
2. to enable these processes to be parametrized for use in operational models,
3. to implement them into an operational model, evaluate the improvement and apply the model to a case study in central London

Most of the existing research on urban dispersion has focused on air quality aspects, with sources being extensive and distributed in space. Scientifically, this research is novel in focusing on localized releases within urban areas, and on dispersion processes at short range. Through a combination of fundamental studies using wind tunnel experiments and high resolution supercomputer simulations, extensive data analysis and development of theoretical and numerical models, DIPLOS will contribute to addressing this difficult and important problem from both a scientific research and a practical, operational perspective.

Direct Numerical Simulations of transsonic turbine tip gap flow

Richard Sandberg (Investigator)

Direct Numerical Simulations are conducted of the transsonic flow through the tip gap at real engine conditions.

Directing magnetic skyrmion traffic flow with nanoscale patterning.

Hans Fangohr, Ondrej Hovorka (Investigators), Mark Vousden

Skyrmions in magnetic nanostructures may lead to new data storage technologies. Appropriate simulation methodologies are developed and applied.

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.

Dispersion of Small Inertial Particles in Characteristic Atmospheric Boundary Layer Flows

John Shrimpton, Zheng-Tong Xie (Investigators), Thorsten Wittemeier

This project aims at improving the near-field accuracy of short term predictions of the dispersion of particulate matter in the atmospheric boundary layer. For this purpose a variety of LES and DNS modelling approaches is used.

Dual resolution simulations of lipid membrane systems

Jonathan Essex (Investigator), Kieran Selvon

This project aims to shed light on cell membrane mechanisms which are difficult to probe experimentally, in particular drug permiation across the cell membrane. If one had a full understanding of this mechanism, drugs could be designed to easily cross the membrane, or target particular embedded proteins to improve their efficacy. A reliable and robust computational method to asses a molecules permeability would be invaluable in the field of drug design, we seek to perfect such a method.

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.

Dynamics simulations for quantum feedback to steer a single-particle harmonic oscillator in non-classical states

Hendrik Ulbricht (Investigator), Ashley Setter

This PhD project is about using digital electronics to implement a parametric feedback loop to modulate the intensity of an optical trapping laser in order to stabilise/cool the centre of mass motion of a nanoparticle. It is then intended we use digital parametric feedback to drive the motion of the particle, which is essentially a quantum harmonic oscillator, into non-classical quantum states such as squeezed and number states.

E ffects of Sample Contamination on Alternate Allele Frequency

Jane Gibson (Investigator), Roshan Sood

Accurate calling of genetic variants is reliant on the purity of samples, contamination will reduce the accuracy of results. Currently there are few programs able to identify contamination in samples, potentially misinforming a researcher or clinician. To better understand the changes caused by sample contamination in
silico simulations were performed where a known percentage of DNA sequence reads from a contaminating
fi le were added. Understanding the changes will assist the development of a new method and program to
detect sample contamination.

Eddy-resol?ving Simulation?s for Turbomachi?nery Applicatio?ns

Richard Sandberg (Investigator), Li-Wei Chen

Traditionally, the design of turbomachinery components has been exclusively accomplished with steady CFD, with Reynolds Averaged Navier-Stokes (RANS) models being the predominant choice. With computing power continuously increasing, high-fidelity numerical simulations of turbomachinery components are now becoming a valuable research tool for validating the design process and continued development of design tool.
In the current project, Direct Numerical Simulations (DNS) and other eddy-resolving approaches will be performed of turbomachinery components to establish benchmark data for design tools, and to investigate physical mechanisms that cannot be captured by traditional CFD approaches.

Effects of trailing edge elasticity on trailing edge noise

Richard Sandberg (Investigator), Stefan C. Schlanderer

This work considers the effect of trailing edge elasticity on the acoustic and hydrodynamic field of a trailing edge flow. To that end direct numerical simulations that are fully coupled to a structural solver are conducted.

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 effects on Slender Structures using Large-Eddy Simulation

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

Wind-induced vortex shedding on buildings is a main concern for the engineer, as this can lead to severe structural failures, or at the very least fatigue concerns. Wind tunnel testing of this effect is somewhat limited with the generation of turbulent flow, making the use of numerical techniques more appealing. Using Iridis3&4, Computational Fluid Dynamics has been employed to simulate the turbulent wind flow around tall buildings and bridge decks. The research proposes novel numerical techniques for the analysis of vortex induced effects on these structures for an effective use in industry.

Exploring Higgs Boson Physics Beyond the Standard Model

Alexander Belyaev (Investigator), Marc Thomas

The Higgs Boson has recently been discovered at the Large Hadron Collider (LHC) at CERN. The purpose of this project is to look for signs of physics beyond the 'Standard Model' of particle physics by studying properties of this boson.

First Principles Simulation of Glycine Adsorption to Amorphous Silica

Chris-Kriton Skylaris (Investigator), Benjamin Lowe

Understanding the molecular interactions between silica and biomolecules is an important in the fields of Bionanotechnology, Biomimetic Material Science and Prebiotic Chemistry. DFT calculations were performed based on a literature study to better understand the interaction between silica and glycine.

Fluid Dynamics Optimisation of Rim-Drive Thrusters and Ducted Hydrokinetic Generators

Aleksander Dubas, Suleiman Sharkh (Investigators)

This is a Knowledge Transfer Partnership project is a collaboration between the University of Southampton and TSL Technology Ltd. to develop computational fluid dynamics software design tools for modelling and optimising the design of propeller thrusters and water turbine generators.

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


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

Hans Fangohr, James Scanlan (Investigators)


Genetic studies to characterise the role of genetic factors in early-onset breast cancer

Andrew Collins (Investigator), Rosanna Upstill-Goddard

Breast cancer is a highly heterogeneous disease, with many distinct subtypes. In the majority of breast cancer cases the causative genetic component is poorly characterised. This study aims to explore both rare and common mutations in early-onset breast cancer patients and the contribution of such variants to disease using a variety of analytic approaches.

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.

Holistic Transceiver Optimisation: The Iridis Approach

Conventional radio frequency (RF) transceiver optimisation, which only focuses on the optimisation of one specific part of the transceiver, has been widely used in the transceiver design, i.e. source coding optimisation and channel coding optimisation. However, this category of optimisation techniques ignores the inherent connection of the components of a RF transceiver. In this case, the concept of holistic optimisation, which jointly considers optimisation of all the components, may be adopted for RF transceiver optimisation. In this presentation, we will mainly discuss the pros and cons by adopting holistic transceiver optimisation and demonstrate the benefits of using parallel computing to circumvent the potentially high complexity.

Homogenisation of liquid crystal colloids

Giampaolo D'Alessandro, Keith Daly (Investigators), Thomas Bennett

We use homogenization thoery to obtain macroscopic governing equations for nematic liquid crystals that host arbitrarily shaped nano particles.

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.

How sensitive is ocean model utility to resolution?

Kevin Oliver (Investigator), Maike Sonnewald

One of the most intriguing problems in recent ocean modeling research is the impact of varying model resolution on model accuracy. Increasing model resolution one includes more of the important processes. However, the increase in accuracy with resolution is unlikely to be linear. Thus, as computational cost increases with resolution, a critical assessment of achieved benefits is prudent. Here we analyse a suite of realistic and compatible global ocean model runs from coarse (1o, ORCA1), eddy-permitting (1/4o, ORCA025) and eddy resolving (1/12o, ORCA12) resolutions. Comparisons of steric height variability (varSH) highlight changes in ocean density structure, revealing impacts on mechanisms such as downwelling and eddy energy dissipation. We assess vertical variability using the covariace of the deep and shallow varSH. Together with assessing isopycnal movements, we demonstrate the influence of deep baroclinic modes and regions where the barotropic flow sheds eddies. Significant changes in the deepwater formation and dispersion both in the Arctic and Antarctic are found between resolutions. The varSH increased from ORCA1 to ORCA025 and ORCA12, particularily in the Southern Ocean and Western Boundary Currents. However, there is no significant covariance between the surface and deep in ORCA1, while ORCA025 and ORCA12 show significant covariance, implying an important missing energy pathway in ORCA1. Comparing ORCA025 and ORCA12 we see significant differences in eddy energy dissipation. We assess the impact of varying model resolution on the mean flow, discussing implications to dissipation pathways on model accuracy, with reference to stochastic parameterisation schemes.

Hunting for Walking Technicolor at the LHC

Alexander Belyaev (Investigator), Azaria Coupe

Now that the LHC experiment at CERN has observed the Higgs boson, the final piece of the particle physics theory called the Standard Model, the focus of theoretical and experimental physicists shifts to what could possibly be discovered next. Phenomenologists, such as myself, straddle this line between theory and experiment, comparing the many theories of physics Beyond the Standard Model to whatever the LHC discovers, even drawing conclusions from what it doesn’t discover. I focus on a theory called Walking Technicolor (WTC), what the LHC would see if it were correct, and what the lack of discovery so far means for the fate of WTC.

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 Gene-Modules Associated to a Predisposition of Post-Traumatic Stress Disorder

Christopher Woelk (Investigator), Michael Breen

The predisposing genetic factors associated to Post-Traumatic Stress Disorder (PTSD) are altogether unknown. Since not all trauma-survivors later develop the PTSD, it has been hypothesized that transcript differentiation prior–to-trauma exposure could be associated to the risk and resilience of PTSD. We apply a systems-level approach to investigate changes in transcript abundance (gene expression profiles) in whole blood of U.S. Marines sampled prior-to-deployment to the battlefield and followed through-out a seven month deployment to obtain disorder related outcomes.

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.

Identifying variants in next generation sequencing data of 61 paediatric Inflammatory Bowel Disease patients

Sarah Ennis (Investigator), Gaia Andreoletti

This study aims to characterise the mutations of genes known to predispose Inflammatory bowel disease in 61 paediatric patients using next generation sequencing analysis. Our aim is to identify the relative impact of known genes in individual case presentations of disease and correlate matches with clinical manifestation.

Image Based Modelling of Fluid Flow through Lymph Nodes


In this project we are using images of mouse lymph nodes to investigate the fluid transport pathways through it. The images of the nodes are taken using selective plane illumination microscopy, and synchrotron micro computed tomography. The fluid flow is modelled using Darcy's law in COMSOL Multiphysics and the models are run on the Iridis cluster.

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), Nicolas Palopoli, 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.

Investigation into the Interfacial Physics of Field Effect Biosensors

Nicolas Green, Chris-Kriton Skylaris (Investigators), Benjamin Lowe

This interdisciplinary research aims to improve understanding of Field Effect Transistor Biosensors (Bio-FETs) and to work towards a multiscale model which can be used to better understand and predict device response.

Investigations of Lymphatic Fluid Flow



Is fine-scale turbulence universal?

Richard Sandberg (Investigator), Patrick Bechlars

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


Seth Bullock



Valerio Restocchi (Investigator), Frank McGroarty, Enrico Gerding


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.

Lagrangian modelling of ecosystem dynamics at the Bermuda Atlantic Time-series Study station

Tom Anderson, Seth Bullock (Investigators), Melissa Saeland

Focus in the marine ecosystem modelling community is starting to shift towards the use of Lagrangian, agent-based models as these are believed to produce more realistic results. The basic assumptions behind these models have not been thoroughly tested, and this project aims to undertake a detailed study of Lagrangian marine ecosystem models, before creating one to investigate the dynamics at the Bermuda Atlantic Time-series Study station (BATS).

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.

Lattice Holographic Cosmology

Andreas Juttner (Investigator), Matthew Mostert

This project will aim to develop new theoretical field methods and massively parallel computational algorithms to be utilised on both new computational architectures (e.g. Intel Xeon Phi) and existing high performance computers (HPCs).

The ultimate goal is to make predictions for the power spectrum and non-gaussianties of the CMB which would then be falsifiable by comparison to the Planck and WMAP data.

Life assessment methods for industrial steam turbine blade to disc interfaces

Katherine Soady (Investigator)

This is an EngD project sponsored by E.ON New Build and Technology Ltd. which aims to develop the methods currently implemented in life assessment of industrial steam turbine blade to disc interfaces to take account of the surface treatment process (shot peening) which is applied to component before service and after repair.

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.

Magnetic dynamics under the Landau-Lifshitz-Baryakhtar equation

Hans Fangohr (Investigator), Weiwei Wang

Magnetic dynamics using the Landau-Lifshitz-Baryakhtar (LLBar) equation that the nonlocal damping is included as well as the scalar Gilbert damping.

Magnon-Driven Domain-Wall Dynamics in the presence of Dzyaloshinskii-Moriya Interaction

Hans Fangohr (Investigator), Weiwei Wang

The domain wall motion induced by spin waves (magnons) in the presence of Dzyaloshinskii-Moriya Interaction is studied in this project.

Massively-Parallel Computational Fluid Dynamics

Simon Cox, Stephen Turnock, Alexander Phillips (Investigators), James Hawkes

Computational Fluid Dynamics (CFD) is a numerical method for modelling fluid flows and heat transfer - and is used in many industries. It can be used to model dynamics around aircraft, ships and land vehicles; and also has uses in engine design, architecture, weather forecasting, medicine, computer-generated imagery (CGI) and much more. To harness the full power of CFD, it is necessary to utilise the full power of modern supercomputers. This project aims to improve the scalabilty of existing CFD codes so that more complex problems can be tackled efficiently.

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.

Mathematical tools for analysis of genome function, linkage disequilibrium structure and disease gene prediction

Andrew Collins, Mahesan Niranjan, Reuben Pengelly (Investigators), Alejandra Vergara Lope

This iPhD project uses a Gaussian Bayesian Networks approaches framework through machine learning approach to predict which genes are involved in the development of different diseases.


Mahesan Niranjan, Andrew Collins, Reuben Pengelly (Investigators)

This iPhD project uses a Gaussian Bayesian Networks framework through Machine learning methods to predict which genes are involved in the development of different diseases.


Mahesan Niranjan, Andrew Collins, Reuben Pengelly (Investigators)

This PhD project uses a Monte Carlo molecular simulation processes approach to predict which genes are involved in the development of different diseases.

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.

Membrane-Protein Interactions: The Outer Membrane of Gram-Negative Bacteria

Syma Khalid (Investigator), Pin-Chia Hsu

The aim of the project is to looking for the interaction sites, which may responsible for turning on/off activity in outer membrane protein with gram-negative bacteria membrane using molecular dynamic (MD) approach.

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, Kees de Groot, Peter de_Groot (Investigators), Dmitri Chernyshenko

We aim to develop a multiscale multiphysics model of
micromagnetism at elevated temperatures 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.

Modelling the Easterlin Effect

Jason Hilton

This project is an attempt to formalise the Easterlin hypothesis in a simulation model and test its plausibility.
The Easterlin Hypothesis, developed by economist Richard Easterlin, purports to describe a mechanism whereby the fertility decisions of a particular cohort of individuals are linked to population level conditions that held sway when they were born The empirical support for the theory is quite strong for the certain periods in the history of the United States, but elsewhere it is circumstantial and patchy. A simulation model may allows us to test under what conditions it may hold and not hold, and also might help inform more general theory building.

Modelling the morphodynamic evolution of the Ganges-Brahmaputra-Meghna (GBM) Delta over centennial time scales

Stephen Darby (Investigator), Balaji Angamuthu

Around 0.5 Billion people live in deltaic environments where they are threatened by flooding and land loss frequently. Yet, our understanding of the threats posed by land dynamic process remains limited. In this work, we try to address this issue through a land dynamic simulation of the largest and most populated of all the deltas, the GBM Delta, using the CFD software Delft3D for a range of climate change and management scenarios. The results provide new insight into the factors controlling past morphodynamics that, in turn, are helpful when assessing the possible trajectories of future evolution.

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 aim to gain insight into the binding of these proteins to specific substrates and their function.

Multidecadal Sediment Fluxes to Deltas Under future Environmental Change Scenarios

Stephen Darby (Investigator), Frances Dunn


Multimode simulation of high power fibre lasers and amplifiers

Peter Horak (Investigator), Ioannis Begleris

This project aims to address the challenge of ever-increasing demand for higher powers from fibre lasers by developing theoretical and numerical methods to simulate laser pulse amplification in large-mode area fibres supporting multiple spatial modes.

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 Modelling 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.

Multiscale modelling of neutron star oceans

Ian Hawke (Investigator), Alice Harpole

Type I X-ray bursts are explosions which occur on the surface of some
neutron stars. It is believed that the burning begins in a localised spot in the ocean of the
star before spreading across the entire surface. By gaining a better understanding of X-ray
bursts, it is hoped that tighter limits can be determined for other neutron star properties
such as the radius and magnetic field strength.

Multiscale Relativistic Simulations

Ian Hawke (Investigator), Alex Wright

There has been recent success in experiments, such as LIGO, in detecting the mergers of celestial objects via the gravitational waves they emit. By implementing numerical methods, we aim to speed up the numerical simulations of these events but up to two orders of magnitudes, and study binary inspirals in greater detail and over much larger timespans.

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


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 astrophysical effects of the crust on a 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

Tolga Bektas (Investigator)

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.

On the applicability of nonlinear timeseries methods for partial discharge analysis

Paul Lewin (Investigator), Lyuboslav Petrov

The governing processes of Partial Discharge (PD)
phenomena trigger aperiodic chains of events resulting in ’ap-
parently’ stochastic data, for which the widely adopted analysis
methodology is of statistical nature. However, it can be shown,
that nonlinear analysis methods can prove more adequate in
detecting certain trends and patterns in complex PD timeseries.
In this work, the application of nonlinear invariants and phase
space methods for PD analysis are discussed and potential pitfalls
are identified. Unsupervised statistical inference techniques based
on the use of surrogate data sets are proposed and employed for
the purpose of testing the applicability of nonlinear algorithms
and methods. The Generalized Hurst Exponent and Lempel Ziv
Complexity are used for finding the location of the system under
test on the spectrum between determinism and stochasticity. The
algorithms are found to have strong classification abilities at
discerning between surrogates and original point series, giving
motivation for further investigations.


Hans Fangohr (Investigator), Marijan Beg

OpenDreamKit is a [Horizon 2020]( European Research Infrastructure project (#676541) provided substantial funding to the open source computational mathematics ecosystem, and in particular popular tools such as LinBox, MPIR, SageMath, GAP, Pari/GP, LMFDB, Singular, MathHub, and the IPython/Jupyter interactive computing environment.

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.

Optical Characterisation of Black Silicon for Photovoltaics Using the Finite Element Method

Jack Tyson (Investigator)

Here we present a novel method of simulating the reflectance spectra of black silicon solar cells using the finite element method. Designed in COMSOL Multiphysics is a new set of algorithm-controlled-geometries rendering a vast array of different structural permutations of silicon nanowires. Our model focused on the variation of this geometry within customisable predefined conditions in large output quantities, collated and averaged to reliably determine the reflectance of an entire black silicon solar cell.

Origins of Evolvability

Richard Watson, Markus Brede (Investigators), William Hurndall

This project examined the putative evolvability of a Lipid World model of fissioning micelles. It was demonstrated that the model lacked evlovability due to poor heritability. Explicit structure for micelles was introduced along with a spatially localised form of catalysis which increased the strength of selection as coupling between potential chemical units of heredity were reduced.

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.

Porcupine Basin Project

Louise Watremez

The Porcupine Basin is a narrow failed rift, offshore SW Ireland, featuring extreme crustal thinning. The M61/2 survey (May 2004, T. Reston and B. O'Reilly) allowed for the acquisition of seismic refraction data across and along the basin, along 5 transects. The processing of the data along these transects will give us information about the crustal structure across the basin, faulting due to the crustal extension, nature of the upper-mantle, etc. This project is funded by Petroleum Infrastructure Programme (PIP).

Porous Media and Hydrothermal Circulation in Weakened Ocean Crust



Precision study of critical slowing down in lattice simulations of the CP^{N-1} model

Jonathan Flynn, Andreas Juttner (Investigators), Andrew Lawson

This project involves the study of critical slowing down (CSD): a property that may arise when taking measurements in Monte Carlo simulations. In order to study and quantify this phenomenon we have performed extensive simulations of the CP^{N-1} model. By studying the properties of the Monte Carlo algorithms in this model, we hope to make algorithmic improvements that can then be employed in simulations of physical quantum field theories, such as in lattice quantum chromodynamics (lattice QCD).

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.

Preventing Alzheimer's Disease: A Multiphysics Simulation Approach

Neil Bressloff, Giles Richardson, Roxana-Octavia Carare (Investigators), Alexandra Diem

Experimental research has identified the causes of many diseases, such as Alzheimer's Disease. However, finding an effective treatment is very cost- and time-intensive and sacrifices many animals and does not guarantee success. In this PhD project, we investigate the driving force of solute drainage in the brain using multiphysics simulations in order to identify possible ways of preventing dementia.

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

Syma Khalid, Philip Williamson (Investigators), Daniel Holdbrook, Jamie Parkin, Nils Berglund, Yuk Leung

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.

Pushing the Envelope of Planetary Formation and Evolution Simulations

Peter Bartram

A full understanding of the formation and the early evolution of the Solar System and extrasolar planetary systems ranks among natural science's grand challenges, and at present, even the dominant processes responsible for generating the observed planetary architecture remain elusive.


Matthew Spraggs

A basic Python package to perform coarse lattice QCD simulations on desktop and workstation computers.

Quantifying Collective Construction

Seth Bullock (Investigator), Nicholas Hill

This was an initial investigation into how best to develop quantifying and discriminating measures of both the processes and results of collective construction.

Quantum Computation for Signal Detection in Multiple-Input Multiple-Output Communication Systems

Lajos Hanzo (Investigator), Panagiotis Botsinis

Optimal, classic optimization processes in communication systems, such as signal detection, introduce an extremely high computational complexity in the system. Quantum computation offers the optimal equivalent algorithms in the quantum domain, with at least a quadratic degradation in complexity. Since quantum computers have still not been physically realized though, the quantum algorithms' simulation's complexity is higher than that of the optimal classic equivalents. Use of Iridis is essential in facilitating their simulation.

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.

Reforging the Wedding Ring: Exploring a Semi-Artificial Model of Population for the United Kingdom with Gaussian process emulators

Jason Hilton

Note: Jakub Bijak from Social Science is the lead author on this project, which is forthcoming in Demographic Research (
Co-Authors: Eric Silverman, Viet Dung Cao

We extend the „Wedding Ring? agent-based model of marriage formation to include some empirical information on the natural population change for the United Kingdom together with behavioural explanations that drive the observed nuptiality trends.

Reversal of ferromagnetic nanotubes

Hans Fangohr (Investigator), David Cortes

We are analysing the feasibility of reversing a nano scaled magnetic tube by applying weak pulses of currents through the nano-tube inner core

Sample tracking in whole-exome sequencing projects

Andrew Collins, Sarah Ennis (Investigators), Reuben Pengelly

Whole-exome sequencing is entering clinical use for genetic investigations, and it is therefore essential that robust quality control is utilised. As such we designed and validated a tool to allow for unambiguous tying of patient data to a patient, to identify, and thus prevent errors such as the switching of samples during processing.

SAVE: Solent Achieving Value through Efficiency

Patrick James, Ben Anderson (Investigators), Luke Blunden


Scalability of Energy Efficient Routing Algorithms in Wireless Sensor Networks

Geoff Merrett (Investigator), 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.


Stephen Darby, Julian Leyland, Christopher Hackney (Investigators)


Self Organized Network Routing using Quantum Evolutionary Methods

Lajos Hanzo (Investigator), Dimitrios Alanis

Self Organized Networks (SON) may consist of a large number of nodes, which could be fully interconnected. Optimizing its performance satisfying various Quality of Service (QoS) requirements is a quite complex procedure and the optimization problem belongs to the family of the Travelling Salesman Problems (TSP) which has been proven to be NP-hard as the number of nodes increases. In this project, various suboptimal methods are used in order to tackle this multi-objective optimization problem; in particular, the Ant Colony Optimization (ACO) and its quantum inspired counterpart (QACO) are being employed in order to reduce complexity.

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.

Sensitivity of the critical depth to the choice of particle movement rules in Lagrangian models and the consequences for the predicted timing of the spring bloom

Tom Anderson (Investigator), Melissa Saeland

Individual-based (Lagrangian) models lend themselves to the study of the controls of the spring bloom in the ocean, due to their ability to represent both the turbulence and the phytoplankton motion. Here, we use a Lagrangian phytoplankton model to test some of the most prevalent hypotheses (e.g. critical depth and critical turbulence).

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 Household Decision Making in Rural Malawi

James Dyke, Kate Schreckenberg (Investigators), Samantha Dobbie

A scoping exercise to determine whether data collection tools of the social sciences can be used effectively in the construction of empirical ABM. Focus fell upon simulating drought coping strategies of Malawian smallholders. Model implementation enabled inferences to be made concerning the impact of drought and input subsidies upon smallholder food security.

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.

Simulating Sleeping Sickness: a two-host agent-based model

Jason Noble, Peter Atkinson (Investigators), Simon Alderton

Sleeping sickness is a vector-borne, parastic disease which affects millions of people across 36 sub-Saharan African countries. Using agent-based models, we aim to gain a greater understanding of the interactions between the tsetse fly vector and both animal and human hosts.

Building an accurate representation will allow the testing of local interventation scenarios including the closing of watering holes, and the selective spraying of cattle with insecticides.

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.

Simulation of biological systems at long length and distance scales

Jonathan Essex (Investigator), Kieran Selvon

This project aims to shed light on cell membrane mechanisms which are difficult to probe experimentally, in particular drug permiation across the cell membrane. If one had a full understanding of the mechanism, drugs could be designed to target particular embedded proteins to improve their efficacy, the viability of nano based medicines and materials could also be assessed, testing for toxicity etc.

Simulations investigating droplet diameter-charge models, for predicting electrostatically atomized dielectric liquid spray chracteristics

Gabriel Amine-Eddine (Investigator), John Shrimpton

Liquid sprays are atomized using electrostatic methods in many scienti fic, industrial and engineering applications. Due to jet and droplet breakup mechanisms, these spray plumes contain a range of drop diameters with differing droplet charge levels. Using an transient charged spray CFD code, simulations have been performed to investigate charge-diameter relationship models for predicting dynamics of poly-disperse and electrostatically atomized hydrocarbon sprays.

The methodology developed can be readily extended towards high-pressure spray applications, where secondary atomization plays a dominant role within the spray dynamics and subsequent performance of the spray itself.

Amine-Eddine, G. H. and Shrimpton, J. S. (2013), On simulations investigating droplet diameter–charge distributions in electrostatically atomized dielectric liquid sprays. Int. J. Numer. Meth. Fluids, 72: 1051–1075. doi:10.1002/fld.3776

Simulations of Magnetic Skyrmions

Hans Fangohr (Investigator), Ryan Pepper

The manipulation of magnetic skyrmions could prove to be a useful technique for storing data on an unprecedented density scale. In this project we seek to better understand their properties and ways to control them.

Skyrmionic states in confined nanostructures

Hans Fangohr (Investigator), Marijan Beg

An ever increasing need for data storage creates great challenges for the development of high-capacity storage devices that are cheap, fast, reliable, and robust. Because of the fundamental constraints of today's technologies, further progress requires radically different approaches. Magnetic skyrmions are very promising candidates for the development of future low-power, high-capacity, non-volatile data storage devices.

Soft x-ray science on a tabletop

Peter Horak, Jeremy Frey, Bill Brocklesby (Investigators), Patrick Anderson, Arthur Degen-Knifton

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.?

Software Sustainability Institute

Simon Hettrick (Investigator)

A national facility for cultivating world-class research through software

Software helps researchers to enhance their research, and improve the speed and accuracy of their results. The Software Sustainability Institute can help you introduce software into your research or improve the software you already use.


We help people build better software, and we work with researchers, developers, funders and infrastructure providers to identify key issues and best practice in scientific software.

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.

Spatial variability of the atmosphere in southern England


No-one really knows how variable key atmospheric parameters such as Aerosol Optical Thickness and Water Vapour content are over relatively small areas. This study aims to find out!

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.

Studying microevolution in clinical isolates of Neisseria lactamica

Robert Read (Investigator), Jay Laver, Anish Pandey

We intranasally infected and successfully colonised six volunteers with Neisseria lactamica, a commensal species genetically similar to Neisseria meningitidis. A bioinformatics approach was then used to understand the microevolution of this bacterium and its adaptations to the nasopharynx.

Supernova Rates in the Local Universe

Mark Sullivan (Investigator), Christopher Frohmaier

This project will calculate the frequency of exploding stars -- or supernovae -- in the nearby universe. We simulate a 'toy universe' by exploding billions of stars in a computer, and then artificially 'observing' these explosions by replicating a real astronomical sky survey, the Palomar Transient Factory (PTF). The results of this simulation allows us to discover the rate at which supernovae occur in the local universe each year.

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 (Investigator), 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 and critical assessment of protein-ligand binding affinities

Jonathan Essex (Investigator), Ioannis Haldoupis

A method that can accurately predict the binding affinity of small molecules to a protein target would be imperative to pharmaceutical development due to the time and resources that could be saved. A head-to-head comparison of such methodology, ranging from approximate methods to more rigorous methods, is performed in order to assess their accuracy and utility across a range of targets.

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 application of next-generation sequencing to unresolved familial disease

Andrew Collins, Sarah Ennis (Investigators), Jane Gibson, Reuben Pengelly

Next-generation sequencing (NGS) allows us to sequence individual patients cost-effectively, allowing us to enter a new era of genomic medicine. The level of genetic detail that we can access through these methods is unprecedented making it suitable for clinical molecular diagnostics.

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 high speed vehicles, including space re-entry vehicles. Numerical simulations of these flows has been conducted in order to examine and understand how the surface roughness interacts with high speed flows in terms of drag prediction and heat transfer to the wall surface.

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 Higgs Boson at Future Colliders - an Explorative Journey Beyond the Standard Model

Alexander Belyaev (Investigator), Patrick Schaefers

It has been three years since the discovery of a Higgs boson at the CERN LHC and many new insights in Higgs physics were gathered since then. However, its true nature remains unknown to this day. This project aims at exploring the Higgs properties at Future High Energy Colliders beyond the Standard Model to help unveiling its secret.

The hydrogen abstraction phase of the CYP-cyclohexene reaction, using large-scale DFT

Chris-Kriton Skylaris (Investigator), Chris Pittock, Karl Wilkinson

Studying the hydrogen-abstraction reaction between cyclohexene and the active site of cytochrome P450. This starts a series of reactions that eventually oxidise the small molecule to become either an epoxide or an alcohol.

Understanding the finer detail of this reaction can assist towards a model that will predict the breakdown of drugs in the human body.

The Maximum Entropy Production Principle and Natural Convection

Seth Bullock, James Dyke (Investigators), Stuart Bartlett

In this project I wanted to perform some tests of the so-called Maximum Entropy Production Principle (MEPP) in the context of buoyancy-driven convection in a system with negative feedback boundary conditions.


Syma Khalid (Investigator), Daniel Holdbrook, Thomas Piggot, Yuk Leung

The multidrug and toxic compound extrusion (MATE) transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane. Multiple atomistic simulation are performed on a MATE transporter, NorM from Neisseria gonorrheae (NorM_NG) and NorM from Vibrio cholera (NorM_VC). These simulations have allowed us to identify the nature of the drug-protein/ion-protein interactions, and secondly determine how these interactions contribute to the conformational rearrangements of the protein.

The ONETEP project

Chris-Kriton Skylaris (Investigator), Stephen Fox, Chris Pittock, Álvaro 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 Origin of Aeolian Dunes (TOAD)

Joanna Nield (Investigator)

The overall aim of this project is to understand the genesis and subsequent evolution of aeolian early stage bedforms by quantifying for the very first time the role and importance of flow, transport and surface feedbacks in the initiation and emergence of dunes. This project offers the genuine prospect of surmounting arguably the major enduring research question within aeolian geomorphology, leading to broader insights which will offer knowledge benefits for sedimentary landform studies as a whole.

The Perks of Complexity Reduction

Lajos Hanzo (Investigator), Chao Xu

Reliable high-speed modems facilitate ubiquitous communications in our daily lives amongst people and/or machines. The communication technologies we need for the future have to have a high reliability and a low cost. My research aims for reducing the complexity of state-of-the-art communication systems, so that they can communicate in real time at an increased throughput. Naturally having access to parallel computers such as Iridis gives my research a competitive advantage over other researchers, relying on slower simulations.

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.

The tarsal intersegmental reflex control system in the locust hind leg

David Simpson, Philip Newland (Investigators), Alicia Costalago Meruelo

Locomotion is vital for vertebrates and invertebrates to survive. Despite that feet are responsible for stability and agility in most animals, research on feet movements and their reflexes is scarce.
In this thesis, the tarsal reflex responses of locust will be studied and modelled with ANNs to achieve a deeper comprehension of how stability and agility is accomplished.
The choice of ANNs is linked to the applicability of the method into other fields, such as technological designs or medical treatment.

Today's Computation Enabling Tomorrow's Seamless Communication

Lajos Hanzo (Investigator), Varghese Thomas

Radio Over Fibre (ROF) is a communication technique that aims to gainfully amalgamate the benefits of optical and wireless communication, while keeping the system cost low. This technique would support the next generation of wireless services.


Richard Sandberg (Investigator), Sonia Serrano-Galiano

Despite a good knowledge of the physiology of bats and birds, engineering applications with active dynamic wing compliance capability are currently few and far between. Recent advances in development of electroactive materials together with high-fidelity numerical/experimental methods provide a foundation to develop biologically-inspired dynamically-active wings that can achieve "on-demand" aerodynamic performance. However this requires first to develop a thorough understanding of the dynamic coupling between the electro-mechanical structure of the membrane wing and its unsteady aerodynamics. In this collaborative initiative between the University of Southampton and Imperial College London, we are developing an integrated research programme that carries out high-fidelity experiments and computations to achieve a fundamental understanding of the dynamics of aero-electro-mechanical coupling in dynamically-actuated compliant wings. The goal is to utilise our understanding and devise control strategies that use integral actuation schemes to improve aerodynamic performance of membrane wings. The long-term goal of this project is to enable the use of soft robotics technology to build integrally-actuated wings for Micro Air Vehicles (MAV) that mimic the dynamic shape control capabilities of natural flyers.

Towards design patterns for robot swarms

Richard Crowder, Seth Bullock (Investigators), Lenka Pitonakova

Swarm robotics is an inter-disciplinary field that seeks to design the behaviour of robots that can cooperate effectively on tasks like search and retrieval, reconnaissance, construction, etc. In this project, we are aiming towards a theoretical understanding of swarm intelligence and the development of design patterns for effective robot swarms.

Towards Exascale computing in particle physics

Andreas Juttner, Jonathan Flynn (Investigators), James Harrison

Lattice QCD

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).

Turbulence and tidal turbines

William Batten (Investigator), Tom Blackmore, Luke Blunden

The PhD research is focused on understanding the effects of turbulence on tidal turbines. The problem has been simplified using grid generated turbulence and actuator disc representations of tidal turbines.

Understanding Stochastic Processes in Interacting Spin Models

Ondrej Hovorka (Investigator), Oliver Laslett

Applying efficient computational models to compute Langevin dynamics and master equation equilibrium solutions for interacting magnetic spin systems.

Understanding the Role of Recruitment in Robot Foraging

Seth Bullock, Richard Crowder (Investigators), Lenka Pitonakova

It is shown that recruitment among foraging robots is useful when resources are hard to find, but that the extra cost associated with such robots is not returned when there are many locations to gather from or simply when the relative gain from using communication is low.

Using computer intensive methods to produce small area estimates of poverty

Nikolaos Tzavidis (Investigator), Steve Donbavand

By using computer intensive methods this work compares, and suggests improvements, to existing methods for estimating poverty levels. These poverty estimates are used to produce maps which in turn help to target government policies.

Using MEP to determine parameter values of ocean and atmosphere diffusivity

Kevin Oliver, James Dyke (Investigators), Maike Sonnewald

Entropy budgets can potentially offer new and valuable insights into the dissipation of energy in the ocean system. Specifically, if one assumes the Earth system maximises the dissipation of energy, one can use this as a guiding principle maximising the internal entropy production. In this study, resultant temperature distributions from a four box ocean-atmosphere-ice model are used to assess to what extent such considerations could ameliorate the need for tuning parameter values associated with oceanic and atmospheric diffusivity. Results from a standard implementation with fixed, empirically determined, parameters were compared to one where the maximum entropy production principle is applied to determine the value of oceanic and atmospheric diffusivity parameters. These methods have been successfully applied to cloud fraction and convection in the atmosphere.

The MEP principle suggested using diffusivity values of 3.3×1014 W K ?1 and 3.2×1014 W K ?1
for the ocean and atmosphere respectively, where the empirical values were 2.0 × 1014 W K ?1
and 1.0 × 1014 W K ?1 . The oceanic temperatures of the MEP implementation were 3 and -1oC
away the high and low latitude observed ocean temperatures respectively, while the empirical
implementation was -5 and 3oC away, largely within the observational standard deviation of
8 and 2? C respectively. For the atmospheric values, MEP implementation was 3W m?2 away
from the high latitude observed value, while the empirical implementation was 6W m?2 away,
both within the standard deviation of 13.2W m?2 . However, in the low latitudes this reverses,
with the empirical implementation being only -16W m?2 off while the MEP implementation
is -21W m?2 off. However, both figures are outside the range of the standard deviation of
4.2W m?2 . Overall, both methods were found to be very close to oceanic observations. This
confirms that in the model used, the assumption of maximal dissipation of energy is reasonable.

Furthermore, the nature of the landscape of internal entropy production created by the
oceanic and atmospheric diffusivity was found to be fairly smooth, with non-linearities mainly
coming from ice albedo. Assuming the Earth system is in a state of maximal energy dissipa-
tion, applying the MEP principle successfully may depend on such a smooth, easily optimisable
landscape. Thus, the successful application of the MEP principle could be much more difficult
if attempting to aid parametrisation in more detailed ocean models, as these are likely to have
internal entropy production landscapes with local maxima. Nevertheless, results presented
are very promising, and encourage further exploration of to what extent this principle could
be applied to ameliorate the need for tuning parameters in light of lacking information.

Validation of a spatial-temporal soil water movement and plant water uptake model

Tiina Roose, Sevil Payvandi (Investigators), James Heppell

We develop a model that estimates the water saturation level within the soil at different depths, and the uptake of water by the root system. Data from Smethurst et al (2012) is used to validate our model and obtain a fully calibrated system for plant water uptake. When compared quantitatively to other models such as CROPWAT, our model achieves a better fit to the experimental data because of the simpler, first, second and third order terms present in the boundary condition, as opposed to complicated non-linear functions.

Validation of GPS-derived water vapour estimates


Measurements from GPS base stations can be processed to provide estimates of the water vapour content in the atmosphere. These are lots of these base stations across the world and they take measurements very frequently, making them perfect data sources for scientific use. However, we need to understand their accuracy - and this project aims to do this.

Vertical turbulence structures in the benthic boundary layer as related to suspended sediments

Hachem Kassem (Investigator), Charlie Thompson

There is a genuine need for better, more robust modelling of suspended sediment transport in the coastal zone, both to understand its morphological evolution and it's impact on biogeochemical cycling, ecosystems services and to guide engineering applications such as dredging and defence schemes against erosion and flooding.
The suspension of sediment in turbulent flows is a complex case of fluid-particle interaction, governed by shear stresses (momentum exchanges) at the bed and within the benthic boundary layer (BBL). The intermittent transfer of momentum is a manifestation of coherent turbulent vortex structures within the flow. The passage of such structures (or clusters of) is often related to perturbations of bottom sediment, which may be entrained and maintained in suspension if sufficient turbulent energy is provided. The first part of my PhD investigated the temporal and scale relationships between wave–generated boundary layer turbulence and event–driven sediment transport in oscillatory flow in the nearshore. This involved complex statistical, spectral, quadrant and wavelet analysis of high frequency nearshore measurements of turbulence and suspended sediments (medium sand), collected as part of the EU-funded Barrier Dynamics Experiment II (BARDEX II). The following step aims to develop a 3D numerical model in OpenFOAM which would reproduce the fine scale turbulence structures observed over a fixed rippled bed in oscillatory flow. The 3D velocity field, turbulent components, correlations (stresses) and quadrant structures will then be linked to observed sediment resuspension events. The model will be validated against a set of laboratory experiments undertaken at the Fast Flow Facility at HR Wallingford.

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 an atomic superfluid. 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 drug development: can we predict drug affinity when water molecules are involved?

Jonathan Essex (Investigator), Hannah Bruce Macdonald, Christopher Cave-Ayland

Water molecules are often found to be involved in drug-protein binding and can influence the effectiveness of a drug. We aim to aid drug design by calculating the energies involved with complexes of drugs, proteins and water molecules to predict the affinities of drug molecules.

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.

Whole exome sequencing identifies novel FLNA mutation in familial Ebstein's anomaly

Jane Gibson, Andrew Collins, Sarah Ennis (Investigators), Gaia Andreoletti

We describe the application of whole-exome sequencing in a family in which eight people in three generations presented Ebstein's anomaly.

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

