Computational Modelling Group

Emacs

Emacs is a family of text editors, characterized by their extensibility. One manual describes it as "the extensible, customizable, self-documenting, real-time display editor." Development began in the mid-1970s and continues actively as of 2012. Emacs has over 2,000 built-in commands and allows the user to combine these commands into macros to automate work, in particular with the use of Emacs Lisp, a variant of Lisp, providing a deep extension capability. (More from Wikipedia on Emacs )

Emacs has initially a steep learning curve but is a very powerful tool once the basics are mastered.

Commonly used implementations are Emacs and XEmacs on Linux-like systems, and additionally Aquamacs on Mac OS X.

For queries about this topic, contact Hans Fangohr.

View the calendar of events relating to this topic.

Projects

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.

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.

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.

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?”

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.

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.

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 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

Hadronic structure on the computer

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

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

How far can we stretch the MARTINI?

Syma Khalid (Investigator), Ric Gillams

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

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.

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.

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.

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.

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.

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.

OpenDreamKit

Hans Fangohr (Investigator), Marijan Beg

OpenDreamKit is a [Horizon 2020](https://ec.europa.eu/programmes/horizon2020/) European Research Infrastructure project (#676541) that will run for four years, starting from September 2015. It will provide 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.

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.

pyQCD

Matthew Spraggs

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

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.

Skyrmionic states in confined helimagnetic 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.

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.

The Institute is based at the universities of Edinburgh, Manchester, Oxford and Southampton, and draws on a team of experts with a breadth of experience in software development, project and programme management, research facilitation, publicity and community engagement.

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.

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.

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.

The Role of the Biota in the Carpenter Model on Lake Eutrophication

James Dyke (Investigator), Alexandra Diem

The Carpenter model is a useful and simple model to predict the eutrophication of shallow lakes via phosphorus input. This project aimed at resolving the function of the biota, which play a major role in the phosphorus dynamics, but are so far only implicitly modelled, and extending the model to explicitly represent them.

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.

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.

µ-VIS Computed Tomography Centre

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

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

People

Neil Bressloff
Professor, Engineering Sciences (FEE)
Seth Bullock
Professor, Electronics and Computer Science (FPAS)
Andrew Collins
Professor, Medicine (FM)
Simon Cox
Professor, Engineering Sciences (FEE)
Jonathan Essex
Professor, Chemistry (FNES)
Hans Fangohr
Professor, Engineering Sciences (FEE)
Jonathan Flynn
Professor, Physics & Astronomy (FPAS)
Jeremy Frey
Professor, Chemistry (FNES)
Carsten Gundlach
Professor, Mathematics (FSHS)
Suleiman Sharkh
Professor, Engineering Sciences (FEE)
Ian Sinclair
Professor, Engineering Sciences (FEE)
Mark Spearing
Professor, Engineering Sciences (FEE)
Stephen Turnock
Professor, Engineering Sciences (FEE)
Peter Horak
Reader, Optoelectronics Research Centre
Giles Richardson
Reader, Mathematics (FSHS)
Roxana-Octavia Carare
Senior Lecturer, Medicine (FM)
Prasanth Nair
Senior Lecturer, Engineering Sciences (FEE)
Zheng-Tong Xie
Senior Lecturer, Engineering Sciences (FEE)
Srinandan Dasmahapatra
Lecturer, Electronics and Computer Science (FPAS)
James Dyke
Lecturer, Electronics and Computer Science (FPAS)
Ian Hawke
Lecturer, Mathematics (FSHS)
Ondrej Hovorka
Lecturer, Engineering Sciences (FEE)
Ivan Markovsky
Lecturer, Electronics and Computer Science (FPAS)
Chris-Kriton Skylaris
Lecturer, Chemistry (FNES)
Andras Sobester
Lecturer, Engineering Sciences (FEE)
Philipp Thurner
Lecturer, Engineering Sciences (FEE)
Anatoliy Vorobev
Lecturer, Engineering Sciences (FEE)
Syma Khalid
Principal Research Fellow, Chemistry (FNES)
Richard Boardman
Senior Research Fellow, Engineering Sciences (FEE)
Edward Richardson
Senior Research Fellow, Engineering Sciences (FEE)
Charlie Thompson
Senior Research Fellow, Ocean & Earth Science (FNES)
Philip Williamson
Senior Research Fellow, Biological Sciences (FNES)
Marijan Beg
Research Fellow, Engineering Sciences (FEE)
Dirk Broemmel
Research Fellow, Physics & Astronomy (FPAS)
Sam Dolan
Research Fellow, Mathematics (FSHS)
Aleksander Dubas
Research Fellow, Engineering Sciences (FEE)
Patrick Fritzsch
Research Fellow, Physics & Astronomy (FPAS)
Dmitry Grinev
Research Fellow, Engineering Sciences (FEE)
Robin Wilson
Research Fellow, Geography (FSHS)
Maximilian Albert
Postgraduate Research Student, Engineering Sciences (FEE)
Stuart Bartlett
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Ioannis Begleris
Postgraduate Research Student, Engineering Sciences (FEE)
Rory Brown
Postgraduate Research Student, Civil Engineering & the Environment (FEE)
Paul Chambers
Postgraduate Research Student, Engineering Sciences (FEE)
Peter Cherry
Postgraduate Research Student, Chemistry (FNES)
Jean Claus
Postgraduate Research Student, Engineering Sciences (FEE)
Alexandra Diem
Postgraduate Research Student, Engineering Sciences (FEE)
Samuel Diserens
Postgraduate Research Student, Engineering Sciences (FEE)
Robert Entwistle
Postgraduate Research Student, Engineering Sciences (FEE)
Ric Gillams
Postgraduate Research Student, Chemistry (FNES)
Stephen Gow
Postgraduate Research Student, Engineering Sciences (FEE)
Joshua Greenhalgh
Postgraduate Research Student, Engineering Sciences (FEE)
James Harrison
Postgraduate Research Student, Engineering Sciences (FEE)
Joshua Jeeson Daniel
Postgraduate Research Student, Engineering Sciences (FEE)
Jan Kamenik
Postgraduate Research Student, Engineering Sciences (FEE)
Aditya Karnik
Postgraduate Research Student, Engineering Sciences (FEE)
Hachem Kassem
Postgraduate Research Student, Ocean & Earth Science (FNES)
David Lusher
Postgraduate Research Student, Engineering Sciences (FEE)
Alvaro Perez-Diaz
Postgraduate Research Student, Engineering Sciences (FEE)
Daniel Powell
Postgraduate Research Student, Engineering Sciences (FEE)
Thomas Rae
Postgraduate Research Student, Physics & Astronomy (FPAS)
Craig Rafter
Postgraduate Research Student, Engineering Sciences (FEE)
Hossam Ragheb
Postgraduate Research Student, Engineering Sciences (FEE)
Álvaro Ruiz-Serrano
Postgraduate Research Student, Chemistry (FNES)
Ben Samways
Postgraduate Research Student, Physics & Astronomy (FPAS)
Kieran Selvon
Postgraduate Research Student, Engineering Sciences (FEE)
Ashley Setter
Postgraduate Research Student, Engineering Sciences (FEE)
Matthew Spraggs
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Daniele Trimarchi
Postgraduate Research Student, Engineering Sciences (FEE)
Valerio Vitale
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Mark Vousden
Postgraduate Research Student, Engineering Sciences (FEE)
Jonathon Waters
Postgraduate Research Student, Engineering Sciences (FEE)
Iain Weaver
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Thorsten Wittemeier
Postgraduate Research Student, Engineering Sciences (FEE)
Emanuele Zappia
Postgraduate Research Student, Engineering Sciences (FEE)
Jess Jones
Technical Staff, iSolutions
Elena Vataga
Technical Staff, iSolutions
Petrina Butler
Administrative Staff, Research and Innovation Services
Susanne Ufermann Fangohr
Administrative Staff, Civil Engineering & the Environment (FEE)
Anurag Agarwal
Alumnus, Institute of Sound & Vibration Research (FEE)
Thomas Fischbacher
Alumnus, Engineering Sciences (FEE)
Matteo Franchin
Alumnus, Engineering Sciences (FEE)
Kondwani Kanjere
Alumnus, Engineering Sciences (FEE)
Anna Kapinska
Alumnus, ICG, University of Portsmouth
Andreas Knittel
Alumnus, Industry
Gunnar Mallon
Alumnus, Geography (FSHS)
Mihails Milehins
Alumnus, University of Southampton
John Muddle
Alumnus, Mathematics (FSHS)
Massoud Najafi
Alumnus, Arbeitsbereich Technische Informatik Systeme, University of Hamburg, Germany
Alkin Nasuf
Alumnus, Engineering Sciences (FEE)
Samuel Sinayoko
Alumnus, BMLL
Kenji Takeda
Alumnus, Engineering Sciences (FEE)
Weiwei Wang
Alumnus, Ningbo University
Ian Bush
External Member, NAG Ltd, Oxford
Mario Orsi
External Member, Queen Mary University of London
Ian Castro
None, None
Simon Hettrick
None, None
Pin-Chia Hsu
None, None