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  • Peter Coveney, David Wright, Shunzhou Wan, and Hugh Martin have featured in a TV-report for German science-magazine "nano" about no-deal Brexit. The segment features sections of the CompBioMed "Virtual Humans" film.

 

  • The CCS is supporting a meeting on "HemeLB: cardiovascular modelling and simulation in UKCOMES", 29-30 May 2019 in London. Follow this link for more information and how to register.

 

  • Effective today, 1 March 2019, Prof Peter Coveney is professor by special appointment in the Informatics Institute at the University of Amsterdam (UvA). The chair, in Applied High Performance Computing, will run concurrently with his UCL appointment.

 

 

 

  • The CCS has been awarded an allocation of node hours on the world's most powerful supercomputer, Summit. Read more about this allocation and the research it will unlock.

 

 

  • Peter Coveney's group at UCL have had a paper accepted for a talk IEEE eScience 2018. The paper is about "Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations". The IEEE eScience conference 2018 takes place in Amsterdam on 29 October - 1 November 2018.

 

  • Roger Highfield, Director of External Affairs at the Science Museum Group, has just been named as Visiting Professor in the UCL Department of Chemistry. Welcome to UCL, Roger!

 

 

 

  • Peter Coveney and Chris Greenwell have authored an article "The cross-subsidy of research by teaching is a myth" on Times Higher Education (THE), the article addresses the fiction of academic research being loss-making, which is used to draw more money to the centres of universities.

 

 

  • On 27 September 2017 at the London Science Museum IMAX theatre, CompBioMed held a special event "How to build a Virtual Human" during one of the Science Museum Lates events. The hour-long feature described recreating a human being in silico, including IMAX video composited on the Marenostrum supercomputer. Find out more on the CompBioMed Twitter account.

 

 

  • Ruth Eccleston, Peter Coveney, and Neil Dalchau have had their paper accepted into Scientific Reports, the paper is titled "Host genotype and time dependent antigen presentation of viral peptides: predictions from theory".

 

 

  • Peter Coveney has joined the Institute of Advanced Study (IAS) Advisory Council. The IAS Advisory Council meets once a year to support the Directors in delivering an exciting academic programme and to promote the IAS. The role of the Council is to comment on the academic plan and progress, act as ambassadors, and advise on how the national and international standing of the IAS might be improved.

 

 

  • The CCS has been awarded a two year project at Leibniz Supercomputing Centre with an allocation on SuperMUC of 28 million core hours over two years, effective immediately. The project is led by Prof Dr Dieter Kranzmüller, Director of LRZ and Professor of Computer Science at Ludwig Maximillians Universitet, Munich. Partners include Prof Peter Coveney of the Centre for Computational Science at UCL, together with Dr Herman van Vlijmen of Janssen.

 

 

  • Microsoft have awarded the CCS $20,000 for use on Azure to use for binding affinity calculations using BAC. In future simulations of how drugs bind to their targets may have applications ranging from drug design to the tailoring of treatment regimes to specific patients. This project focuses on developing tools that facilitate the use of the Azure cloud to enable simulations of anti-cancer drugs and the proteins they are designed to inhibit. Use of Azure will allow the UCL team to access market leading performance from Nvidia GPUs, in an environment where the resources available can be scaled to match the demands of the study at any given time.

 

 

 

 

  • The Journal of Chemical Theory and Computation have awarded the cover (shown below) for their April issue to the CCS paper from Agastya Bhati, Shunzou Wan, David Wright, and Peter Coveney, "Rapid, accurate, precise and reliable relative free energy prediction using ensemble based thermodynamic integration".

 

 

  • Robbie Sinclair has won first prize in the Computer-Based Modeling and Experiment for the Design of Soft Materials Symposium Student Presentation Contest held at the 2017 MRS Spring Meeting. His paper “New Insights into Graphene Exfoliation with Molecular Dynamics” represents the first public exposure of a scientific development in the understanding of graphene properties which is of central importance to understanding its formation, synthesis and role in nanocomposites.

 

 

 

 

  • Kristof Farkas-Poll has just won an EPSRC Vacation Bursary to work in CCS this summer on a stipend. He will be working on the Binding Affinity Calculator and science applications pertaining to it.

 

 

 

 

 

 

  • Peter Coveney is to give three talks at the 253rd ACS National Meeting in San Francisco, California, April 2-6, 2017. The first talk will be audio-recorded and be made available shortly after the event. The talk titles are as follows:
    1. Computer-based design of advanced materials: Chemically specific multiscale modelling of polymer-clay nanocomposites
    2. High performance and/or cloud computing for free energy prediction using molecular dynamics simulations?
    3. Rapid, accurate, precise and reliable relative free energy prediction using ensemble based thermodynamic integration

 

 

 

 

 

 

  • The 14th International Workshop on Multiscale Modelling and Simulation will be running as part of ICCS 2017, which will take place in Switzerland. Please find the call for papers here, along with further details about the workshop. The deadline for short abstracts is December 15, 2016.

 

 

calculation eq thermo

 

 

 

  • The CompBioMed Centre of Excellence officially launched on October 1st 2016. CompBioMed is a user-driven Centre of Excellence in Computational Biomedicine, to nurture and promote the uptake and exploitation of high performance computing within the biomedical modelling community. The CompBioMed user communities come from academia, industry and clinical practice.

 

 

 

 

 

 

  • Distinguished science writer and journalist Dr Roger Highfield has written a blog post about the experience of running a Giant Workflow on Phases 1 and 2 of SuperMUC. The activity turned out to be a big success for the CCS. About 60 free energy calculations were performed. We not only managed to realise all our objectives but even did more than anticipated, thanks to the exceptional performance of the computer.

 

 

  • A webpage has been created for the Solvay Symposium on "Bridging the Gaps at the PCB Interface" that took place on 19-21 April 2016. It includes a gallery of pictures.

 

 

  • COST Action CA15120 on Open Multiscale Systems Medicine (OpenMultiMed) started on April 5th 2016, with Peter Coveney as a participant. The overarching aim OpenMultiMed is to gather a critical mass of international researchers and coordinate them as a team that develops and evaluates a transdisciplinary framework for multiscale systems medicine, consisting of novel concepts, methodologies and technologies.

 

 

 

 

 

 

 

 

  • Peter Coveney is featuring in a US television show called "Life’s Rocky Start". The 50 minute programme is airing on Wednesday 13th January at 9pm EST across the USA on PBS NOVA. On the NOVA website you can find additional materials, video, and information on getting DVDs. Peter Coveney features in segments filmed in the UCL Chemistry Department.

lifesrockystart

 

  • James Suter, Derek Groen, and Peter Coveney have published a paper titled "Mechanism of exfoliation and prediction of materials properties of clay-polymer nanocomposites from multiscale modeling" in ACS Nano Letters. The paper represents a major breakthrough in the development and application of multiscale modelling and simulation for accelerating materials design and discovery based on the concept of a “virtual laboratory”. They show how commercial companies, manufacturers worldwide, and government laboratories and university researchers can can use advanced modelling methods to enhance their productivity.

 

 

  • The Solvay Symposium on "Bridging the Gaps at the PCB Interface" will take place on 19-21 April 2016 at the International Solvay Institutes Brussels. The Symposium will be centred about the rising multi-modelling paradigm, with special focus on emergent phenomena flourishing at the PCB interface.

Bridging the Gaps at the PCB Interface

 

  • Derek Groen has received an ARCHER Early Career Impact Award. The award recognises an early career researcher who has achieved exceptional economic and/or societal impact. The awards showcase the researchers, their work and the impact of the science that the UK National HPC facility, ARCHER, has enabled.

 

 

  • Peter Coveney will appear in the NOVA TV programme entitled "Life's Rocky Start”, to be broadcast across the USA on Saturday 12th January 2016. NOVA is the award-winning American Public Television science series

liferockystart

 

 

  • The Alan Turing Institute will be launched on the 11th November 2015. The institute will position the UK as a world leader in data science research. The vision is to bring together the best people, organisations and technologies in data science to address business and societal challenges using large-scale and diverse digital data in the 'age of algorithms'. Various meetings, workshops, and summits are being arranged in order to help find the direction of research activity for the institute. Peter Coveney is involved in organising an ATI Summit on Big Data in the Physical Sciences on 13th January 2016. He is also involved in another meeting now being organised on "Data Intensive and Extreme Scale Numerical Simulation in Physics, Materials Science and Chemistry".

 

 

 

  • Introducing the COMPAT project. The 3-year Horizon 2020 funded COMPAT project launched on October 1st 2015, and the CCS leads the Applications Work Package. The main motivation of COMPAT is the urgent need to push the science forward, and stay world leading in simulation driven science and engineering. The ambition is to establish new standards for multiscale computing at exascale, and provision a robust and reliable software technology stack that empowers multiscale modellers to transform computer simulations into predictive science. The kick-off meeting for COMPAT took place in Amsterdam on October 5th and 6th 2015. Find out more at our twitter account (@compatproject).

 

 

  • Peter Coveney has featured in a video, within the Economist's Scientific Mysteries series, entitled "Why does time pass? The moving finger writes". The video is concerned with the nature of time and why travelling through time, unlike travelling through space, is unidirectional.

 

 

  • Peter Coveney has appeared in an article on HPC wire titled "The Era of Personalized Medicine: An Interview with Peter Coveney". The article relates to Peter's keynote lecture on “The Virtual Human: In Silico Methods for Personalized Medicine” at the ISC Cloud & Big Data Conference September 28 – 30 in Frankfurt, Germany.

 

 

  • An article titled "The Virtual Laboratory" featuring Derek Groen, James Suter and Peter Coveney leads the new PRACE newsletter for September 2015. The article follows CCS research into multiscale simulations of clay-polymer nanocomposites.

 

 

  • James Suter, Derek Groen and Peter Coveney have won first prize in the 2015 Journal of Polymer Science award for best presentation in the Theory and Modeling of Nanoparticles: Interactions with Biomolecules and Polymers Session at the American Chemical Society Fall 2015 meeting in Boston, August 2016. The title of their paper was “Towards the Virtual Laboratory: Modelling Clay-Polymer Nanocomposites Using a Multiscale Approach".

 

 

  • Former CCS member Dr Jens Harting (2002-05) has been appointed as head of the department of “Modelling Thin Films” at the Helmholtz Institute Erlangen-Nürnberg (HI ERN) and full professor at the Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU). The HI ERN is a branch office of Forschungszentrum Jülich operated in close cooperation with the Friedrich-Alexander-Universität Erlangen-Nürnberg and Helmholtz-Zentrum Berlin (HZB). The institute’s main facilities will be sited on FAU’s southern campus, while Jens’ working group is located in the “Auf AEG” business park in Nuremberg.

 

 

  • Shunzhou Wan, Peter Coveney et al. have published a paper in the Journal of Chemical Theory and Computation on Rapid, Precise and Reproducible Prediction of Peptide-MHC Binding Affinities from Molecular Dynamics that Correlate Well with Experiment.

    In this study, we rank the binding affinities of 12 diverse peptides bound by a class I MHC molecule HLA-A*02:01 using our “enhanced sampling of molecular dynamics with the approximation of continuum solvent” (ESMACS) protocol. The capability of the binding affinity calculator (BAC) is further tested here with yet more challenging molecular systems than previously studied.

    The ligands--peptides in this case--are larger in size and much more flexible than most small molecular drugs. Our study produces precise and reproducible free energy estimates which correlate well with experimental measurements. If the results are combined with an amino acid hydrophobicity scale, then an extremely good ranking of peptide binding affinities emerges. Our ESMACS approach is rapid, robust, and applicable to a wide range of ligand−receptor interactions without further adjustment.

 

 

  • CCS alumnis Chris Greenwell has been made Professor in the Department of Earth Sciences at Durham University.

 

 

 

 

  • James Suter, Derek Groen and Peter Coveney have published a paper -- the first ever Feature Article -- in Advanced Materials on "Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties". The paper features on the front cover of Volume 27, Issue 6 of Advanced Materials.

adv materials

 

 

 

 

 

 

 

  • The CCS's research on computing patient-specific HIV treatment methods has appeared in a Huffington Post article on "Computing a Cure for HIV: 9 Ways Supercomputers Help Scientists Understand and Treat the Virus" (our research features at #7 in the list). NSF have noted that the article is one of their most popular in recent months.

 

 

  • The Centre for Computational Science has been awarded fellowship and visitor funds from UCLQ for a project titled "New Directions in Quantum Simulation for Quantum Chemistry". The project is a collaboration between Peter Love of Harvard University and Peter Coveney of UCL.

 

 

  • Peter Coveney, Sergey Karabasov, Dmitry Nerukh, Alfons Hoekstra, and Bastien Chopard have edited a special issue of Philosophical Transactions of the Royal Society A, titled "Multiscale systems in fluids and soft matter: approaches, numerics and applications". The issue will be available online from June 30th 2014.

 

 

  • "Computational Biomedicine" has been published by Oxford University Press. The textbook was edited by Peter Coveney, Vanessa Díaz-Zuccarini, Peter Hunter, and Marco Viceconti. See the cover image below:

compbiomed

 

  • Peter Coveney will be presenting the paper “p-medicine: A Medical Informatics Platform for Integrated Large Scale Heterogeneous Patient Data” at the AMIA 2014 conference in DC in November 2014. AMIA is the academic home for informatics and the Symposium is the world's leading scientific conference for medical informatics. The paper will be published in AMIA Annual Symposium Proceedings.

 

 

 

  • Miguel O. Bernabeu, Timm Krüger (University of Edinburgh), and Peter Coveney secured funding from ARCHER, UK’s national supercomputing service, to implement advanced models of rheology and oxygen transport in HemeLB. HemeLB is an open source, parallel, lattice-Boltzmann blood flow simulator currently developed at the CCS. This project wil be undertaken in collaboration with UCL's Research Software Development Team.

 

 

  • Peter Coveney's forthcoming textbook "Computational Biomedicine" is due for release in June 2014. The book was edited by Peter Coveney, Vanessa Díaz-Zuccarini, Peter Hunter, and Marco Viceconti.

 

 

 

  • The UCL Big Data Symposium will take place on 7th April 2014 at UCL’s Bloomsbury Campus, London, UK. Organised by the Computational Life and Medical Sciences Network in partnership with the UCL Big Data Institute and sponsored by OCF, EUDAT, and the Research Data Alliance, the UCL Big Data Symposium is a one-day event showcasing the important role of big data analytics in a broad range of sectors including biomedical research, astronomy, retail sector finance, retail, social media, telecommunications, and security & resilience. The broad and diverse programme aims to highlight to researchers across the piece the breadth of multi-disciplinary research currently being undertaken in this rapidly growing field, and to illustrate the value of collaboration across the different sectors.

 

 

  • Following on from Prof Coveney's talk at the annual conference of the world's largest and most prestigious general scientific society, the American Association for the Advancement of Science (AAAS 2014) in Chicago, Peter was featured on BBC News in an article about computational science for personalised medicine. The article was based in large part on his talk at AAAS, entitled "Computational Biomedicine: Towards the Virtual Human", and on his recent publication in the Journal of Chemical Theory and Computation.

 

 

 

 

  • Peter Coveney will be giving a talk at AAAS 2014 in Chicago - the annual conference of the world's largest and most prestigious general scientific society, the American Association for the Advancement of Science. Peter's talk, "Computational Biomedicine: Towards the Virtual Human", will take place in the session "Virtual Humans: Helping Facilitate Breakthroughs in Medicine" on Friday, 14 February 2014: 1:30 PM-4:30 PM. Peter will also sit on the panel for a news briefing at 11am on Friday 14th.

 

 

  • Dr Joanna Lewis has been awarded £1000 by the British Society for Immunology, towards a visit to the South African Centre for Epidemiological Modelling and Analysis (SACEMA) and the CHER clinical trial. At SACEMA she will work with Dr Martin Nieuwoudt to apply mathematical models of immune recovery to data collected from HIV-infected children and adults starting antiretroviral therapy (ART). By doing so, they hope to better understand some of the effects of age and perinatal versus later infection on the dynamics of the HIV-infected immune system. Work she is carrying out in collaboration with the CHER trial examines the effect on long-term immunological health of different ART regimes during infancy. Infancy is likely to be a critical period in the development of T-cell dynamics because the thymus is highly active. In addition, ART administered to HIV-infected infants very soon after birth may prevent early exposure to HIV-derived antigen, and the effect of this delay on the development of the T-cell pool is as yet unknown.

 

 

  • Dr Derek Groen has been awarded a Software Sustainability Institute Fellowship for a duration of 15 months, starting in January 2014. The Software Sustainability Institute has been funded by EPSRC to cultivate world-class research with software. Derek will use the fellowship to participate in meetings and workshops related to software sustainability (e.g., those organized by the SSI), and to make himself available to teach in software carpentry. In addition, he will use the fellowship funds to finance focus meetings to make software tools more deployable and future-proof. These tools include, but are not necessarily limited to, the open-source HemeLB lattice-Boltzmann simulation environment, and a Fabric-based toolkit for managing scientific (multiscale) simulation workflows.

 

 

 

 

  • Open access funding is now available for all UCL research (not just RCUK and Wellcome outputs).

 

 

  • The CCS has appeared on BBC Arabic TV, it was broadcast at 1730 hrs on November 9th 2013. To view the CCS segment, scroll through to 6m30s.

 

 

 

 

  • Genome England - The health secretary is launching a new government organisation to oversee the creation of a genomic revolution in healthcare, "by 2015 the aim is to put the UK at the forefront of the genome revolution worldwide, with whole-genome sequencing linked to patient diagnosis, treatment and care".

 

 

 

 

  • The Minister for Science and Universities, Rt Hon David Willetts, has announced that the Medical Research Council (MRC) will invest £20m capital funding (£5M going to UCL) in the establishment of a UK health informatics research institute, to be known as the Farr Institute. The Institute will add to an existing investment by charities, Research Councils and Government. Peter Coveney is an investigator on this award.

     

 

 

 

  • The House of Lords Science and Technology Committee launched an inquiry into Scientific Infrastructure on May 29, 2013. This inquiry seeks to identify whether a suitable long-term plan is in place for the initial investment, use, operational costs and upgrades of scientific infrastructure. Prof Peter Coveney was invited to an initial seminar and discussion meeting at the House of Lords on 11 June.

    The e-Infrastructure Academic User Community Forum Steering Committee has submitted a copy of the Strategy for the UK Research Computing Ecosystem as written evidence to the inquiry on behalf of the eIAUCF community.

    As additional evidence for this submission, a recent letter to the Prime Minister from the Council for Science and Technology dated 7 June 2013 was included. This letter represents the consensus of a working group on Data, Algorithms and Modelling, of which Prof Peter Coveney was a member, and further emphasises the vital importance of education and training to equip future generations not just to function but to excel in an information economy.

 

 

  • Peter Coveney and Miguel Bernabeu's work on Blood Flow Modelling has appeared in an article at New Scientist.

     

 

  • Peter Coveney made an appearance on the BBC Radio 4 Today show to talk about prosthetic limbs in relation to the Virtual Physiological Human; skip to 54:00 to hear his segment. The Royal Society have posted a video podcast on the theme issue of Interface Focus "The virtual physiological human: integrative approaches to computational biomedicine", featuring Peter Coveney.

 

 

  • We are pleased to announce the release, under LGPL, of the source code of HemeLB, our high performance fluid dynamics application. HemeLB is optimised for flow at physiologically realistic conditions (such as intracranial arteries) and includes tools for defining simulation domains, visualising the simulation as it runs, and offline post-processing.

     

 

  • Micha Kunze, Dave Wright, Flemming Hansen, and Peter Coveney have received an NIH (National Institutes of Health) award for the third consecutive year, consisting of a large allocation of cycles on Anton from the DE Shaw Group in New York City, for the period 2012-13. The project will substantially develop and extend research we have underway on the human histone deacetylase 8, extending our investigations from regulation to substrate binding, and complemented using NMR spectroscopy . This enzyme and its family members play an important role in histone post-translational modification, and are thus potential targets for cancer chemotherapeutic agents.

 

 

 

 

 

 

  • The Medical Research Council (MRC) has awarded £4.3 million towards the development of the Centre for Health service and Academic Partnership in Translational E-Health Research (CHAPTER) in London. CHAPTER aims to harness the wealth of data found in UK electronic health records to improve patient care and public health. Prof P V Coveney is an Investigator who will be playing a central role in this project.

 

 

 

 

  • Professor Peter Coveney has been nominated as an Academy Expert to the UK Prime Minister's Council for Science and Technology in the domain of Data, Algorithms and Modelling.

 

 

  • UCL is one of eight universities that has been recognised by the EPSRC and the UK Government Communications Headquarters (GCHQ) as an Academic Centre of Excellence in Cyber Security Research. Sources: UCL News and Computer World UK

 

 

 

  • Professor Peter V Coveney has accepted an invitation from the Right Honourable David Willetts MP, Minister of Science & Universities, to become a Founding Member of the UK E-Leadership Council, a body created as a key element of the governance system under which UK e-Infrastructure will be organised in the future. The inaugural meeting of the E-Leadership Council takes place in London on 8 March 2012.

 

 

  • The INBIOMEDvision project has produced reports on two of the project's think tank sessions. The reports have been requested by the European Commission in order to ascertain the status of the bioinformatics/biomedical informatics interface today within Europe and globally; future funding will benefit from the opportunities and gaps identified within these reports. Please contact Nour Shublaq for more information.

 

 

  • Digital Research 2012 is taking place on 10-12 September 2012 at St Catherine’s College, Oxford, UK.

 

 

  • UCL is now hiring for a Reader or Chair in Computational Physiology, and a Reader or Chair in Biomolecular Modelling across Multi-scales, see the vacancies page for details of these posts and instructions on how to apply.

 

 

 

 

 

 

 

  • October 3rd 2011: £145 million boost to improve Britain’s e-infrastructure was announced by the Department for Business, Innovation and Skills. For more information see the following website. The allocation of these sums is in part due to the eSI minitheme and associated activities, outlined below: ...

 

  • Peter Coveney recently discussed the future of computational science at the Durham University workshop Research Achievement through Advanced Computing. You can view the video in S3D or you can deactivate the 3D perspective in the video options.
  • The final version of the "Strategy for the UK Research Computing Ecosystem" is now available. A printed version of the Strategy for the UK Research Computing Ecosystem is now available on request (contact h.s.martin "at" ucl.ac.uk).
  • Prof Peter Coveney has accepted an invitation to join an Editorial Board being assembled by UK Government Department of Business, Innovation & Skills to prepare a Report at the behest of the Right Honourable David Willetts MP, Minister for Science & Universities. This report is intended to lay out a grand strategy for e-infrastructure across the whole of UK academe, industry and commerce and aims to influence UK government policy and thinking from the autumn onward. The Board will be chaired by Dominic Tildesley, VP for the Discover Platform at Unilever. Prof Coveney is the sole academic member of the Board, others being drawn from funding agencies and industry.

  • A podcast from the University of Warwick's A Symposium on Time event featuring Peter Coveney has been published online.

  • The CCS has been awarded 50,000 node hours at the National Resource for Biomedical Supercomputing (NRBSC), located within the Pittsburgh Supercomputing Center (PSC). The project is entitled "Unraveling the Structure – Dynamics – Function Relationship of Human Histone Deacetylase 8". See our projects page for more information.

  • The CCS has been awarded 40.5M CPU hrs on PRACE's JUGENE (> 1 petaflops machine in Jülich) between 1 May 2011 and 30 April 2012 for work in the nanomaterials domain, based on the use of large scale molecular dynamics.

  • The Virtual Physiological Human Network of Excellence (VPH NoE) will hold the second of the series of VPH Conferences on 18th – 20th September 2012.