Computational Modelling Group

Vim

Vim is a text editor released by Bram Moolenaar in 1991 for the Amiga computer. The name "Vim" is an acronym for "Vi IMproved" because Vim was created as an extended version of the vi editor, with many additional features designed to be helpful in editing program source code.

Although Vim was originally released for the Amiga, Vim has since been developed to be cross-platform, supporting many other platforms. It is the most popular editor amongst Linux Journal readers.

Released under a software license compatible with the GNU General Public License, Vim is free and open source software.

Read more from Wikipedia. Image taken from same Wikipedia site.

For queries about this topic, contact Hans Fangohr.

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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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Stability of chiral structures in magnetic nanodisks

Hans Fangohr, Weiwei Wang (Investigators), David Cortes

This project is aimed to study the stability of skyrmionic and helical equilibrium states in magnetic nanodisks, using computational simulations.

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.

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.

People

Neil Bressloff
Professor, Engineering Sciences (FEE)
Jonathan Essex
Professor, Chemistry (FNES)
Hans Fangohr
Professor, Engineering Sciences (FEE)
Jonathan Flynn
Professor, Physics & Astronomy (FPAS)
Mark Nixon
Professor, Electronics and Computer Science (FPAS)
Mark Zwolinski
Professor, Electronics and Computer Science (FPAS)
Nicolas Green
Reader, Electronics and Computer Science (FPAS)
Peter Horak
Reader, Optoelectronics Research Centre
Giles Richardson
Reader, Mathematics (FSHS)
Roxana-Octavia Carare
Senior Lecturer, Medicine (FM)
John Carter
Senior Lecturer, Electronics and Computer Science (FPAS)
Zheng-Tong Xie
Senior Lecturer, Engineering Sciences (FEE)
Jane Gibson
Lecturer, Biological Sciences (FNES)
Basel Halak
Lecturer, Electronics and Computer Science (FPAS)
Ian Hawke
Lecturer, Mathematics (FSHS)
Kevin Oliver
Lecturer, National Oceanography Centre (FNES)
Chris-Kriton Skylaris
Lecturer, Chemistry (FNES)
Trevor Thomas
Lecturer, Engineering Sciences (FEE)
Anatoliy Vorobev
Lecturer, Engineering Sciences (FEE)
Edward Richardson
Senior Research Fellow, Engineering Sciences (FEE)
Dirk Broemmel
Research Fellow, Physics & Astronomy (FPAS)
David Arden
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Ioannis Begleris
Postgraduate Research Student, Engineering Sciences (FEE)
Gabriele Boschetto
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)
David Cortes
Postgraduate Research Student, Engineering Sciences (FEE)
Alexandra Diem
Postgraduate Research Student, Engineering Sciences (FEE)
Robert Entwistle
Postgraduate Research Student, Engineering Sciences (FEE)
Darius Pepe Falahat
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Elaine Goode
Postgraduate Research Student, Physics & Astronomy (FPAS)
Stephen Gow
Postgraduate Research Student, Engineering Sciences (FEE)
Joshua Greenhalgh
Postgraduate Research Student, Engineering Sciences (FEE)
Ioannis Haldoupis
Postgraduate Research Student, Chemistry (FNES)
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)
Benjamin Lowe
Postgraduate Research Student, Electronics and Computer Science (FPAS)
David Lusher
Postgraduate Research Student, Engineering Sciences (FEE)
Sanjay Pant
Postgraduate Research Student, Engineering Sciences (FEE)
Alvaro Perez-Diaz
Postgraduate Research Student, Engineering Sciences (FEE)
Richard Pichler
Postgraduate Research Student, Civil Engineering & the Environment (FEE)
David Potts
Postgraduate Research Student, Humanities (FH)
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)
Kieran Selvon
Postgraduate Research Student, Engineering Sciences (FEE)
Ashley Setter
Postgraduate Research Student, Engineering Sciences (FEE)
Maike Sonnewald
Postgraduate Research Student, National Oceanography Centre (FNES)
Johannes Van Der Horst
Postgraduate Research Student, Electronics and Computer Science (FPAS)
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)
Davide Zilli
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Elisabeth zu-Erbach-Schoenberg
Postgraduate Research Student, Management (FBL)
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)
Kondwani Kanjere
Alumnus, Engineering Sciences (FEE)
Arthur Lugtigheid
Alumnus, Psychology (FSHS)
Mihails Milehins
Alumnus, University of Southampton
Nicolas Palopoli
Alumnus, Biological Sciences (FNES)
Weiwei Wang
Alumnus, Ningbo University
Moresh Wankhede
Alumnus, Dacolt International B.V.
Daniel Pope
External Member, Mauve Internet Ltd.
Ibrahim Bello
None, None
Ian Castro
None, None
Simon Hettrick
None, None
Roshan Sood
None, None
Sheng Yang
None, None