Computational Modelling Group

Adding social ties to the Schelling model

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

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

Advanced modelling for two-phase reacting flow

Edward Richardson (Investigator)

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

Aerofoil noise

Richard Sandberg (Investigator)

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

Amorphous Computation, Random Graphs and Complex Biological Networks

Seth Bullock (Investigator)

This interdisciplinary research collaboration arose within the Simple Models of Complex Networks research cluster funded by the EPSRC www.epsrca.ac.uk through the Novel Computation Initiative. Here, leading groups from the Universities of Leeds, Sheffield, Nottingham, Southampton, Royal Holloway and King’s College and industrial partners BT are brought together for the first time to develop novel amorphous computation methods based on the theory of random graphs.

An investigation in to the effects of information provision on driver learning

Ben Waterson, Hans Fangohr (Investigators), James Snowdon

This work aims to better understand and model the role of individual learning and experience on driver route choice. We intend to demonstrate that vehicle-driver agent based models stand alone in being able to capture the complex reciprocal interactions between drivers and their environment, and allow us to incorporate the effects of prior knowledge from previous trips and advice from official information sources and social networks.

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

Seth Bullock, Antonella Ianni (Investigators), Camillia Zedan

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

Antimicrobial Peptide and E. coli Membrane Interactions

Syma Khalid (Investigator), Thomas Piggot, Nils Berglund

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

B-meson coupling with relativistic heavy quarks

Jonathan Flynn (Investigator), Patrick Fritzsch, Dirk Broemmel

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

BioSimGrid

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

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

Cellular Automata Modelling of Membrane Formation and Protocell Evolution

Seth Bullock (Investigator), Stuart Bartlett

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

Chaotic Analysis of Partial Discharge

Paul Lewin

The deterministic character of PD pulses predicted by theory can experimentally (real and numerical) be shown to be existent. Finding characteristic patterns in phase space enables field-data PD detection with high reliability.

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.

Cosmological evolution of supermassive black holes in the centres of galaxies

Anna Kapinska (Investigator)

Abstract to be added...

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.

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.

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?”

Fluid Structure Interactions of Yacht Sails

Stephen Turnock (Investigator), Daniele Trimarchi

The research is the main subject of the PhD topic. It regards the application of fluid structure interaction techniques to the domain of yacht sails simulation

Fracturing of small social networks

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

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

Generic Operational Simulation of Civil Unmanned Air Vehicle Operations

Kenji Takeda, James Scanlan (Investigators)

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

Graphical Simulation of Archaeological Environments

Graeme Earl (Investigator)

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

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.

High-resolution shock-capturing (HRSC) methods for elastic matter in general relativity

Carsten Gundlach, Ian Hawke (Investigators)

We are designing HRSC methods for numerical simulation of elastic matter coupled to general relativity and later magnetic fields, with the ultimate aim of simulating old neutron stars, which have elastic crusts.

How far can we stretch the MARTINI?

Syma Khalid (Investigator), Ric Gillams

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

Hybrid quantum and classical free energy methods in computational drug optimisation

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

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

Hybrid RANS/LES methods

Richard Sandberg (Investigator), Markus Weinmann

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

Integrated in silico prediction of protein-protein interaction motifs

Richard Edwards (Investigator), Kieren Lythgow

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

Is fine-scale turbulence universal?

Richard Sandberg (Investigator)

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

Jet noise

Richard Sandberg (Investigator), Neil Sandham

Direct numerical simulations are used to investigate jet noise.

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.

Mathematical modelling of plant nutrient uptake

Tiina Roose (Investigator)

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

Measuring biomolecules - improvements to the spectroscopic ruler

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

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

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 mechanoreceptor reaction to tissue deformation

Mark Taylor (Investigator), Gwen Palmer

This project involved the modelling of a piece of knee joint capsule, which will produce an electrical output when mechanically stimulated. The model is based on expermental work carried out by P. Grigg and A.H. Hoffman (1982).

Modelling micromagnetism at elevated temperature

Hans Fangohr (Investigator), Dmitri Chernyshenko

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

Modelling neuronal activity at the knee joint

Mark Taylor, Tiina Roose (Investigators), Gwen Palmer

The function of the knee joint is reliant on proprioception, which involves the response of nerve endings in the tissues at the joint. This project will be concentrating on the neuronal activity, caused by mechanical stimuli, of the more common receptors found at the knee (Ruffini, Paciniform, Golgi and Nociceptor).

There are three stages to this project:
1. Modelling the behaviour of each individual receptor, with the use of the Hodgkin-Huxley model [1].
2. These models will then be applied to the soft tissues around a knee, where a global deformation of the tissue will result in local stimulation of receptors.
3. The soft tissue models will then be applied to structures in the knee.

[1] - Hodgkin, A.L. and A.F. Huxley, A quantitative description of membrane current and its application to conduction and excitation in nerve. Journal of Physiology, 1952. 117: p. 500-544.

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.

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).

Multiscale Modelling of Electrochemical Processes in Neurons

John Chad (Investigator), Stuart George

Using asymptotic expansions to determine how the signalling behaviour of neurons is related to their microstructure.

MXL Project

Mark Taylor, Junfen Shi (Investigators)

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

nano-CMOS

Mark Zwolinski (Investigator), Michael Merrett

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

Network Analysis of Roman Transport Routes in the Imperial Roman Mediterranean

David Potts

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

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 Optics in Structured Material

Peter Horak, Neil Broderick (Investigators)

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

Numerical Elastic Neutron Stars

Ian Hawke, Ian Jones (Investigators), Andrew Penner

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

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.

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.

Reconstructing past lake conditions using sediment cores

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

Scalability of Energy Efficient Routing Algorithms in WSN

Davide Zilli

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

Self-Force and Black Hole Inspirals

Sam Dolan (Investigator)

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

Separation of timescales in models of complex networks

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

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

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 Parking Choice Behaviour

Ben Waterson, Hans Fangohr (Investigators), James Snowdon

Exploring how psychological models of individual parking search behaviours can be combined into an accurate simulation of vehicle flows, allowing for assessment of the impact on searching traffic of different demand/ supply ratios, different driver population characteristics and different charging regimes.

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.

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.

Supersonic axisymmetric wakes

Richard Sandberg (Investigator)

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

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

Chris-Kriton Skylaris (Investigator)

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

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

Richard Edwards, Andreas Johansson

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

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

Robin Wilson, Joanna Nield (Investigators)

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

The 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 Origins of Communication Revisited

Jason Noble (Investigator), Jordi Arranz

Quinn (2001) sought to demonstrate that communication be- tween simulated agents could be evolved without pre-defined communication channels. Quinn’s work was exciting because it showed the potential for ALife models to look at the real origin of communication; however, the work has never been replicated. In order to test the generality of Quinn’s result we use a similar task but a completely different agent architecture. We find that qualitatively similar behaviours emerge, but it is not clear whether they are genuinely communicative. We extend Quinn’s work by adding perceptual noise and internal state to the agents in order to promote ritualization of the nascent signal. Results were inconclusive; philosophical implications are discussed.

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.

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).

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.