Diamond Light Source is the UK's national synchrotron science facility located in Oxfordshire, United Kingdom. Its purpose is to produce intense beams of light whose special characteristics are useful in many areas of scientific research. In particular it can be used to investigate the structure and properties of a wide range of materials from proteins , and engineering components to conservation of archeological artifacts . The facility's name is abbreviated to Diamond throughout this article. Wikipedia.
Diamond Light Source | Date: 2015-05-19
The invention relates to signals representing energy of photons or particles of ionising radiation incident on pixels of a semiconductor detector. Cross talk between the signals from different pixels is compensated using cross talk compensation signatures in the form of time domain series or functions which are aligned and applied to the cross talk signal in accordance with timing of the event which gave rise to the cross talk.
Agency: GTR | Branch: EPSRC | Program: | Phase: Training Grant | Award Amount: 4.16M | Year: 2014
Recently, an influential American business magazine, Forbes, chose Quantum Engineering as one of its top 10 majors (degree programmes) for 2022. According to Forbes magazine (September 2012): a need is going to arise for specialists capable of taking advantage of quantum mechanical effects in electronics and other products. We propose to renew the CDT in Controlled Quantum Dynamics (CQD) to continue its success in training students to develop quantum technologies in a collaborative manner between experiment and theory and across disciplines. With the ever growing demand for compactness, controllability and accuracy, the size of opto-electronic devices in particular, and electronic devices in general, is approaching the realm where only fully quantum mechanical theory can explain the fluctuations in (and limitations of) these devices. Pushing the frontiers of the very small and very fast looks set to bring about a revolution in our understanding of many fundamental processes in e.g. physics, chemistry and even biology with widespread applications. Although the fundamental basis of quantum theory remains intact, more recent theoretical and experimental developments have led researchers to use the laws of quantum mechanics in new and exciting ways - allowing the manipulation of matter on the atomic scale for hitherto undreamt of applications. This field not only holds the promise of addressing the issue of quantum fluctuations but of turning the quantum behaviour of nano- structures to our advantage. Indeed, the continued development of high-technology is crucial and we are convinced that our proposed CDT can play an important role. When a new field emerges a key challenge in meeting the current and future demands of industry is appropriate training, which is what we propose to achieve in this CDT. The UK plays a leading role in the theory and experimental development of CQD and Imperial College is a centre of excellence within this context. The team involved in the proposed CDT covers a wide range of key activities from theory to experiment. Collectively we have an outstanding track record in research, training of postgraduate students and teaching. The aim of the proposed CDT is to provide a coherent training environment bringing together PhD students from a wide variety of backgrounds and giving them an appreciation of experiment and theory of related fields under the umbrella of CQD. Students graduating from our programme will subsequently find themselves in high-demand both by industry and academia. The proposed CDT addresses the EPSRC strategic area Quantum Information Processing and Quantum Optics and one of the priority areas of the CDT call, Towards Quantum Technologies. The excellence of our doctoral training has been recognised by the award of a highly competitive EU Innovative Doctoral Programme (IDP) in Frontiers of Quantum Technology, which will start in October 2013 running for four years with the budget around 3.8 million euros. The new CDT will closely work with the IDP to maximise synergy. It is clear that other high-profile activities within the general area of CQD are being undertaken in a range of other UK universities and within Imperial College. A key aim of our DTC is inclusivity. We operate a model whereby academics from outside of Imperial College can act as co-supervisors for PhD students on collaborative projects whereby the student spends part of the PhD at the partner institution whilst remaining closely tied to Imperial College and the student cohort. Many of the CDT activities including lectures and summer schools will be open to other PhD students within the UK. Outreach and transferable skills courses will be emphasised to provide a set of outreach classes and to organise various outreach activities including the CDT in CQD Quantum Show to the general public and CDT Festivals and to participate in Imperials Science Festivals.
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: INFRAIA-1-2014-2015 | Award Amount: 10.00M | Year: 2015
Structural biology provides insight into the molecular architecture of cells up to atomic resolution, revealing the biological mechanisms that are fundamental to life. It is thus key to many innovations in chemistry, biotechnology and medicine such as engineered enzymes, new potent drugs, innovative vaccines and novel biomaterials. iNEXT (infrastructure for NMR, EM and X-rays for Translational research) will provide high-end structural biology instrumentation and expertise, facilitating expert and non-expert European users to translate their fundamental research into biomedical and biotechnological applications. iNEXT brings together leading European structural biology facilities under one interdisciplinary organizational umbrella and includes synchrotron sites for X-rays, NMR centers with ultra-high field instruments, and, for the first time, advanced electron microscopy and light imaging facilities. Together with key partners in biological and biomedical institutions, partners focusing on training and dissemination activities, and ESFRI projects (Instruct, Euro-BioImaging, EU-OPENSCREEN and future neutron-provider ESS), iNEXT forms an inclusive European network of world class. iNEXT joint research projects (fragment screening for drug development, membrane protein structure, and multimodal cellular imaging) and networking, training and transnational access activities will be important for SMEs, established industries and academics alike. In particular, iNEXT will provide novel access modes to attract new and non-expert users, which are often hindered from engaging in structural biology projects through lack of instrumentation and expertise: a Structural Audit procedure, whereby a sample is assessed for its suitability for structural studies; Enhanced Project Support, allowing users to get expert help in an iNEXT facility; and High-End Data Collection, enabling experienced users to take full benefit of the iNEXT state-of-the-art equipment.
Agency: GTR | Branch: EPSRC | Program: | Phase: Training Grant | Award Amount: 3.99M | Year: 2014
The Scottish Doctoral Training Centre in Condensed Matter Physics, known as the CM-DTC, is an EPSRC-funded Centre for Doctoral Training (CDT) addressing the broad field of Condensed Matter Physics (CMP). CMP is a core discipline that underpins many other areas of science, and is one of the Priority Areas for this CDT call. Renewal funding for the CM-DTC will allow five more annual cohorts of PhD students to be recruited, trained and released onto the market. They will be highly educated professionals with a knowledge of the field, in depth and in breadth, that will equip them for future leadership in a variety of academic and industrial careers. Condensed Matter Physics research impacts on many other fields of science including engineering, biophysics, photonics, chemistry, and materials science. It is a significant engine for innovation and drives new technologies. Recent examples include the use of liquid crystals for displays including flat-screen and 3D television, and the use of solid-state or polymeric LEDs for power-saving high-illumination lighting systems. Future examples may involve harnessing the potential of graphene (the worlds thinnest and strongest sheet-like material), or the creation of exotic low-temperature materials whose properties may enable the design of radically new types of (quantum) computer with which to solve some of the hardest problems of mathematics. The UKs continued ability to deliver transformative technologies of this character requires highly trained CMP researchers such as those the Centre will produce. The proposed training approach is built on a strong framework of taught lecture courses, with core components and a wide choice of electives. This spans the first two years so that PhD research begins alongside the coursework from the outset. It is complemented by hands-on training in areas such as computer-intensive physics and instrument building (including workshop skills and 3D printing). Some lecture courses are delivered in residential schools but most are videoconferenced live, using the well-established infrastructure of SUPA (the Scottish Universities Physics Alliance). Students meet face to face frequently, often for more than one day, at cohort-building events that emphasise teamwork in science, outreach, transferable skills and careers training. National demand for our graduates is demonstrated by the large number of companies and organisations who have chosen to be formally affiliated with our CDT as Industrial Associates. The range of sectors spanned by these Associates is notable. Some, such as e2v and Oxford Instruments, are scientific consultancies and manufacturers of scientific equipment, whom one would expect to be among our core stakeholders. Less obviously, the list also represents scientific publishers, software houses, companies small and large from the energy sector, large multinationals such as Solvay-Rhodia and Siemens, and finance and patent law firms. This demonstrates a key attraction of our graduates: their high levels of core skills, and a hands-on approach to problem solving. These impart a discipline-hopping ability which more focussed training for specific sectors can complement, but not replace. This breadth is prized by employers in a fast-changing environment where years of vocational training can sometimes be undermined very rapidly by unexpected innovation in an apparently unrelated sector. As the UK builds its technological future by funding new CDTs across a range of priority areas, it is vital to include some that focus on core discipline skills, specifically Condensed Matter Physics, rather than the interdisciplinary or semi-vocational training that features in many other CDTs. As well as complementing those important activities today, our highly trained PhD graduates will be equipped to lay the foundations for the research fields (and perhaps some of the industrial sectors) of tomorrow.
Agency: GTR | Branch: EPSRC | Program: | Phase: Training Grant | Award Amount: 4.28M | Year: 2014
Condensed matter physics is a major underpinning area of science and technology. For example, the physics of electrons in solids underpins much of modern technology and will continue to do so for the foreseeable future. We propose to create a Centre for Doctoral Training (CDT) which will address the national need to develop researchers equipped with the skill sets and perspective to make worldwide impact in this area. The research themes covered address some very fundamental questions in science such as the physics of superconductors, novel magnetic materials, single atomic layer crystals, plasmonic structures, and metamaterials, and also more applied topics in the power electronics, optoelectronics and sensor development fields. There are strong connections between fundamental and applied condensed matter physics. The goal of the Centre is to provide high calibre graduates with a focussed but comprehensive training programme in the most important physical aspects of these important materials, from intelligent design (first principles electronic structure calculations and modelling), via cutting-edge materials synthesis, characterisation and sophisticated instrumentation, through to identification and realisation of exciting new applications. In addition programme development will emphasise transferable skills including business & enterprise, outreach and communication. As stated in the impact section, physics-dependent businesses are of major importance to the UK economy.
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: FETHPC-1-2014 | Award Amount: 7.88M | Year: 2015
Worldwide data volumes are exploding and islands of storage remote from compute will not scale. We will demonstrate the first instance of intelligent data storage, uniting data processing and storage as two sides of the same rich computational model. This will enable sophisticated, intention-aware data processing to be integrated within a storage systems infrastructure, combined with the potential for Exabyte scale deployment in future generations of extreme scale HPC systems. Enabling only the salient data to flow in and out of compute nodes, from a sea of devices spanning next generation solid state to low performance disc we enable a vision of a new model of highly efficient and effective HPC and Big Data demonstrated through the SAGE project. Objectives - Provide a next-generation multi-tiered object-based data storage system (hardware and enabling software) supporting future-generation multi-tier persistent storage media supporting integral computational capability, within a hierarchy. - Significantly improve overall scientific output through advancements in systemic data access performance and drastically reduced data movements. - Provides a roadmap of technologies supporting data access for both Exascale/Exabyte and High Performance Data Analytics. - Provide programming models, access methods and support tools validating their usability, including Big-Data access and analysis methods - Co-Designing and validating on a smaller representative system with earth sciences, meteorology, clean energy, and physics communities - Projecting suitability for extreme scaling through simulation based on evaluation results. Call Alignment: We address storage data access with optimised systems for converged Big Data and HPC use, in a co-design process with scientific partners and applications from many domains. System effectiveness and power efficiency are dramatically improved through minimized data transfer, with extreme scaling and resilience.
Winter G.,Diamond Light Source |
Lobley C.M.C.,Diamond Light Source |
Prince S.M.,University of Manchester
Acta Crystallographica Section D: Biological Crystallography | Year: 2013
xia2 is an expert system for the automated reduction of macromolecular crystallography (MX) data employing well trusted existing software. The system can process a full MX data set consisting of one or more sequences of images at one or more wavelengths from images to structure-factor amplitudes with no user input. To achieve this many decisions are made, the rationale for which is described here. In addition, it is critical to support the testing of hypotheses and to allow feedback of results from later stages in the analysis to earlier points where decisions were made: the flexible framework employed by xia2 to support this feedback is summarized here. While the decision-making protocols described here were developed for xia2, they are equally applicable to interactive data reduction.
Agency: GTR | Branch: EPSRC | Program: | Phase: Research Grant | Award Amount: 970.77K | Year: 2015
This project seeks to develop new algorithms, supporting theory and software for solving least squares problems that arise in science, engineering, planning and economics. Least squares involves finding an approximate solution of overdetermined or inexactly specified systems of equations. Real-life applications abound. Weather forecasters want to produce more accurate forecasts; climatologists want a better understanding of climate change; medics want to produce more accurate images in real time; financiers want to analyse and quantify the systematic risk of an investment by fitting a capital asset pricing model to observed financial data. Finding the best solution commonly involves constructing a mathematical model to describe the problem and then fitting this model to observed data. Such models are usually complicated; models with millions of variables and restrictions are not uncommon, but neither are relatively small but fiendishly difficult ones. It is therefore imperative to implement the model on a computer and to use computer algorithms for solving it. The latter task is at the core of the proposed activities. Nearly all such large-scale problems exhibit an underlying mathematical structure such as sparsity. That is to say, the interactions between the parameters of a large system are often localised and do not involve any direct interaction between all the components. To solve the systems and models represented in this way efficiently involves developing algorithms that are able to exploit these underlying simpler structures, which often reduces the scale of the problems, and thus speeds up their solution. This enterprise commonly leads not only to new software that implements existing methods, but to the creation of new theoretical and practical algorithms. At the other extreme, some problems involve interaction between all components, and while the underlying structure is less transparent, it is nonetheless present. In these cases, the computational burden may be very high and such problems may generally only be solved by sophisticated use of massively parallel computers. The methods we will develop will aim to solve the given problem efficiently and robustly. Since computers cannot solve most mathematical problems exactly, only approximately, a priority will be to ensure the solution obtained by applying our algorithms is highly accurate, that is, close to the true solution of the problem. But it is also vital that we solve problems fast without sacrificing accuracy; this is particularly true if a simulation requires us to investigate a large number of different scenarios, or if the problem we seek to solve is simply a component in an overall vastly more complicated computation, or if new data arrives in real time and we need to adapt the model accordingly. Developing algorithms that are both fast and accurate on multicore machines presents a key challenge. We aim to improve upon existing algorithms from several different angles, exploiting new mathematical techniques from areas such as optimization and the solution of partial differential equations. Parallelism will be designed into our new algorithms, allowing modern computer hardware to be exploited. These generic improvements will be coupled with the development of new techniques to exploit special features of problems from important application areas, including X-ray microscopy, crystallography and radiative transfer modelling. Our new software will be made available through the internationally renowned mathematical software libraries HSL, GALAHAD and SPRAL. These are extensively used by the scientific and engineering research community in the UK and abroad, as well as by some commercial companies. Since 2010, more than 50 UK university departments have used HSL for teaching or research in a wide range of disciplines that includes computational chemistry, engineering design, fluid dynamics, portfolio optimization, and circuit theory.
Agency: GTR | Branch: EPSRC | Program: | Phase: Research Grant | Award Amount: 465.60K | Year: 2016
Establishing the atomic arrangements in a molecule or a solid has been feasible for about 100 years by X-ray diffraction; most pictures (stills) of the structure of, for example, salt, insulin, haemoglobin and foot and mouse disease virus are based on this technique of scattering X-ray from crystals. For less ordered materials, like glasses and liquid solutions, partial, local structures can be derived from X-ray absorption spectroscopy. Both techniques require scattering off electrons and thus tell us about the atomic arrangements and some insight into electronic distributions. Chemical and light-induced changes are movements of electrons and atoms to new sites and so visualizing these evolutions by X-ray methods can provide chemical videos of reactions which have greater richness than before and after stills; this is the molecular parallel of picturing a galloping horse. Generally changes on the timescales of atomic motion occur between a 1/100 and 1 picosecond (1 ps = 1 millionth of a microsecond), and this has been monitored by changes in the uv and visible spectrum (colour). This provides little information about structure. Infra-red spectroscopy can be used for timescales greater than 1 ps, and is characteristic of functional groups within molecules. This proposal provides a means of approaching the detail of a molecular still through chemical changes. The Diamond Light Source is the brightest X-ray source in the UK, and provides the opportunity of studying structures on a timescale of 10s of picoseconds. This is fast enough to catch many excited states of fluorescent materials, and to observe the reactions of the most reactive of transient molecules. UV-visible and infrared spectroscopies will be monitored after changes induced by a laser pulse of about 1/5 of a picosecond. The fast laser spectroscopy will be combined with the rapidly developing technique of photocrystallography, where it is possible to obtain full 3-D solid-state structures of photoactivated species that have lifetimes in the nanosecond to millisecond range, so that it will be possible to make molecular movies showing how key chemical and biological processes occur. Thus, it will be possible to study important catalytic, sensor and non-linear materials across the time scales from picoseconds to milliseconds, to see how properties and functions develop over time. Sampling procedures for crystals, solutions and films will be developed and made available to other research groups. The whole approach should transform the way we think about chemical reactions. From such an approach there will be a fraction of problems for which even faster measurements would be fascinating. In recent years laser light in the X-ray region has become available in the USA and Japan (by X-ray free electron lasers, XFELs), and sources are being built in Europe (Germany and Switzerland). They provide an X-ray pulse of about 1/50 of a picosecond, faster than most molecular vibrations, and thus the X-ray movie of a chemical reaction is feasible. This proposal will provide a test-bed for researchers in the chemical sciences to develop their technique for visualizing their reactions. The facility will be based on the Harwell site adjacent to the equipment and expertise of the Diamond Light Source and Central Laser Facility, both of which are user facilities of the highest rank.
Agency: GTR | Branch: MRC | Program: | Phase: Research Grant | Award Amount: 585.00K | Year: 2015
In the cells of every living organism, a myriad of tasks needs to be carried out to sustain the processes of life. Proteins do most of this work - they contribute to the structure and functioning of the cell and regulate many of its processes. Scientists can use X-rays and electrons to visualize proteins to a level which allows them to distinguish the individual atoms that make up their structures and aids in understanding their mechanisms of action. Using this knowledge we can then design molecules (drugs) that can interfere with the cell machinery to treat disease. This can significantly reduce the time required to develop a drug - examples are medicine for the treatment of flu (e.g. Tamiflu) and HIV. Methods for determining protein structures by X-ray crystallography and electron microscopy and applying them to aid design of new drugs have become faster and more reliable; which is important in the race to develop novel antibiotics to combat the worrying rise in bacterial resistance. Here, we have chosen to determine the structure and mode of action of a protein system called SAP which is vital for the survival of the bacterium Haemophilus influenzae. This bacterium is a major causative agent of respiratory disease, the third leading cause of death worldwide. This bacterium co-exists harmlessly in most individuals in the nose and throat but can become invasive and cause disease. It is particularly prevalent in young children, the elderly, cystic fibrosis sufferers and smokers. In young children middle ear infections (otitis) often precede glue ear and are a major concern, as this can lead to hearing loss, problems with speech development and educational problems. Indeed otitis is the primary cause for the prescription of antibiotics for children in developed countries. SAP in this bacterium, assists in bacterial nutrition and as a defence mechanism to our innate immune response. Virtually all forms of life depend on iron for survival. For H. influenzae to survive and cause disease it is essential that it obtains iron from its environment but bacteria like us (our skin) have a protective coat. This protective coat, made up of lipids, is called a membrane. Membrane proteins are embedded in this coat and some of them act like gateways for the entry or exit of various molecules. These gateways are critical for life because it is through them that the cell can get essential nutrients or throw out harmful substances like antibiotics. SAP is a membrane protein that can transport iron into the bacterial cell so it can grow and multiply. SAP also transports small molecules that are produced by the human immune system. Without the SAP transporter these molecules would tear the protective bacterial membrane, which in turn would kill the invading bacteria. The overall aim of our research is to look at the structure of the SAP transporter to understand how it transports these diverse compounds and with that knowledge contribute to the design, in essence, of plugs to block its ability to function. To do this we need to obtain high resolution pictures to enable us to see the atomic interactions responsible for transport. Membrane proteins cannot easily be removed from the cell membrane without the use of harsh detergents. Additionally they do not like water and this makes it difficult to get the proteins to form crystals which are needed to visualize their structure at high resolution by the diffraction of X-rays. We have obtained crystals of a part of the SAP transporter which shows we can use this technique to obtain high resolution data. In parallel we are using the technique of electron microscopy which can also provide high resolution images of the protein structure but does not require the protein(s) to be crystallized. The structural data obtained will enable us to fully understand how SAP works and help in antibiotic discovery.