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Bioscience and medicine

Teaming Up to Drive New Nanoelectronics Discoveries

By | Bioscience and medicine, Uncategorised | No Comments
UCL and Cambridge University are spearheading inter-institutional research aimed at generating new knowledge on the properties of electrons in nanoscale semiconductors – with equipment-sharing making a critical contribution to their pioneering work. Funded by the Engineering and Physical Sciences Research Council (EPSRC), this research – which also involves Royal Holloway, University of London – is led by world-renowned physicist Sir Michael Pepper, Pender Professor of Nanoelectronics at UCL. The aim is not simply to identify unknown physical phenomena at the very smallest scale and enhance understanding of ‘spintronics’ – the intrinsic spin exhibited by electrons. It is to use these discoveries...
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Imaging Software Bring the Brain into Fuller Focus

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Innovative software developed at the Oxford Centre for Functional MRI of the Brain (FMRIB) is on track to improve our understanding of the mind’s innermost wirings – opening up exciting possibilities in neuroscience. Funded by the University of Oxford and the Human Connectome Project (see below), a team including research student Moisés Hernández Fernández,  research fellow Dr Stamatios Sotiropoulos, Prof. Stephen Smith and Prof. Michael Giles has developed parallel computation algorithms that vastly accelerate the processing of Data Mountains generated by a key medical imaging technology. This breakthrough, in which the Emerald supercomputer funded by the Engineering and Physical Sciences Research Council...
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Computing Power Helps Researchers Unlock DNA’s Mysteries

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oxDNA, a novel computer model developed at the University of Oxford, is shedding important new light on how DNA behaves – underpinning valuable breakthroughs in fields such as improved drug delivery within the human body. Working at the interface between chemistry, physics and biology, a multidisciplinary team led by Professor Jonathan Doye and Professor Ard Louis has established oxDNA as the world’s premier modelling & simulation tool of its kind. Key to success has been the High Performance Computing capability of both the university’s own Advanced Research Computing (ARC) resource and the Emerald supercomputer funded by the Engineering and Physical Sciences Research...
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Combined codes for chemistry research

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Andrew Logsdail, Postdoc to Richard Catlow, Head of the MAPs facility with the Department of Chemistry at UCL, has been using the Iridis distributed memory computing cluster to help develop new methodologies for chemistry calculations. Logsdail’s team focus on research into catalysis and chemistry defects, with a view to creating better software to be used in the development of tools such as catalytic converters, and photovoltaic and photocatalytic cells as used in solar power. To do so, they perform vast calculations, and need software that can handle their needs. Their aim has therefore been to integrate their own code –...
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Slowing the aging process

By | Bioscience and medicine, Cities and supporting life | No Comments
By 2024, it’s estimated that over half of the population of the UK will be over 50 years old. That statistic has implications both for healthcare and for the benefits and pension costs that the UK will face: age-related illnesses that prevent people from working are expensive for society as a whole. One of the most challenging aspects of aging, currently, is deterioration in skeletal tissue mechanical function. Tendon disease is painful and debilitating, and its impact on mobility can contribute to a general health decline. With that in mind, researchers at UCL are attempting to identify causes of the...
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Patient-specific Drug Choice

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Choosing the right drug for a patient with cancer is a complicated challenge. There is such a wide range of options, and it can be very difficult for a clinician to identify the best option for each individual case. Shunzhou Wan, senior research associate in the Department of Chemistry at UCL, aims to create a tool to help in that decision making process, using the Iridis supercomputer. “We use Iridis to simulate the interaction of drugs with target proteins. What we’re doing is trying to build a workflow. That involves building the model, then submitting the jobs to run large-scale...
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Modelling mutations for cancer cure

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The p53 tumour suppressor protein, when it works properly, helps to prevent cancer. It does so by inducing the arrest of the cell cycle, by repairing DNA, and by causing apoptosis – a process of programmed cell death. However, p53 also regularly mutates, and either loses the ability to bind DNA, or is destabilised and unfolds, which induces the growth of DNA-damaged cells. Half of all cancers are due to this mutation – so Zohra Ouaray, a PhD Research Student in the School of Chemistry at the University of Southampton, is using Emerald to model what happens and look at...
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Designing better drugs, faster

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Chris Skylaris, Reader in Computational Chemistry at the University of Southampton, develops quantum mechanical calculations for chemistry simulation and drug discovery. He has developed a quantum mechanical method that dramatically cuts the computing time needed for large-scale calculations – expanding research possibilities, and attracting interest from drugs companies who are looking for more accurate molecular simulation tools for their research. The theory of quantum mechanics is necessary if you want to do any simulation of microscopic particles, he says. “You can’t do it with classical mechanics – if you want to describe how atoms and electrons move, they don’t follow...
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Using HPC to improve cancer treatments

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Professor Francesco Gervasio of UCL’s Department of Chemistry used the Emerald supercomputer to simulate the effect of gene mutations linked to the spread of cancer. His research could help develop more robust and effective cancer treatments. Background Epidermal Growth Factor Receptor (EGFR) is a protein that causes cell growth and differentiation. Gene mutations that lead to EGFR over-activity have been associated with a number of cancers, particularly lung cancer. Not surprisingly, EGFR is the target of a rapidly expanding class of anti-cancer drugs. Recent efforts in treating cancer have focused on a part of the EGFR: the tyrosine kinase enzyme, which functions...
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How the “Swine” flu virus develops drug resistance

By | Bioscience and medicine, News | No Comments
A University of Bristol team used the Emerald GPU supercomputer to investigate how mutations of a key enzyme of H1N1 “Swine” flu lead to the development of resistance to current antiviral flu treatments. H1N1-2009 is a highly adaptive virus derived from different gene segments of swine, avian and human influenza. Within months of its appearance in early 2009, the H1N1-2009 strain caused the first flu pandemic of the 21st-century. The antiviral drugs zanamivir (Relenza) and oseltamivir (Tamiflu), which target the neuraminidase enzyme in influenza, successfully treated the infection but widespread use of these drugs led to a series of mutations in...
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