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Seddon G.M.,Adelard Institute | Bywater R.P.,Adelard Institute | Bywater R.P.,Magdalen College
Open Biology | Year: 2012

We have developed novel strategies for contracting simulation times in protein dynamics that enable us to study a complex protein with molecular weight in excess of 34 kDa. Starting from a crystal structure, we produce unfolded and then refolded states for the protein. We then compare these quantitatively using both established and new metrics for protein structure and quality checking. These include use of the programs CONCOORD and DARVOLS. Simulation of protein-folded structure well beyond the molten globule state and then recovery back to the folded state is itself new, and our results throw new light on the protein-folding process. We accomplish this using a novel cooling protocol developed for this work. © 2012 The Authors.


Seddon G.M.,Adelard Institute | Bywater R.P.,Adelard Institute | Bywater R.P.,Magdalen College
Open Biology | Year: 2012

The year 2011 marked the half-centenary of the publication of what came to be known as the Anfinsen postulate, that the tertiary structure of a folded protein is prescribed fully by the sequence of its constituent amino acid residues. This postulate has become established as a credo, and, indeed, no contradictions seem to have been found to date. However, the experiments that led to this postulate were conducted on only a single protein, bovine ribonuclease A (RNAse). We conduct molecular dynamics (MD) simulations on this protein with the aim of mimicking this experiment as well as making the methodology available for use with basically any protein. There have been many attempts to model denaturation and refolding processes of globular proteins in silico using MD, but only a few examples where disulphide-bond containing proteins were studied. We took the view that if the reductive deactivation and oxidative reactivation processes of RNAse could be modelled in silico, this would provide valuable insights into the workings of the classical Anfinsen experiment. © 2012 The Authors.


Oxford was chosen to lead one of four EPSRC-funded 'Hubs' looking at different aspects of quantum technology - in Oxford's case, shaping the future of quantum networking and computing, towards the ultimate goal of developing a functioning quantum computer. Since then, the Networked Quantum Information Technologies (NQIT - pronounced 'N-kit') Hub, based at Oxford but involving nearly 30 academic and industrial partners, has been focusing on developing quantum technologies that could dwarf the processing power of today's supercomputers. A new paper by Oxford researchers, published in the journal Nature, demonstrates how the work of the Hub is progressing. Professor David Lucas of Oxford's Department of Physics, co-leader, with Professor Andrew Steane, of the ion trap quantum computing group, explains: 'The development of a "quantum computer" is one of the outstanding technological challenges of the 21st century. A quantum computer is a machine that processes information according to the rules of quantum physics, which govern the behaviour of microscopic particles at the scale of atoms and smaller. 'An important point is that it is not merely a different technology for computing in the same way our everyday computers work; it is at a very fundamental level a different way of processing information. It turns out that this quantum-mechanical way of manipulating information gives quantum computers the ability to solve certain problems far more efficiently than any conceivable conventional computer. One such problem is related to breaking secure codes, while another is searching large data sets. Quantum computers are naturally well-suited to simulating other quantum systems, which may help, for example, our understanding of complex molecules relevant to chemistry and biology.' One of the leading technologies for building a quantum computer is trapped atomic ions, and a principal goal of the NQIT project is to develop the constituent elements of a quantum computer based on these ions. Professor Lucas says: 'Each trapped ion (a single atom, with one electron removed) is used to represent one "quantum bit" of information. The quantum states of the ions are controlled with laser pulses of precise frequency and duration. Two different species of ion are needed in the computer: one to store information (a "memory qubit") and one to link different parts of the computer together via photons (an "interface qubit").' The Nature paper, whose lead author is Magdalen College Junior Research Fellow Chris Ballance, demonstrates the all-important quantum 'logic gate' between two different species of ion - in this case two isotopes of calcium, the abundant isotope calcium-40 and the rare isotope calcium-43. Professor Lucas says: 'The Oxford team has previously shown that calcium-43 makes the best single-qubit memory ever demonstrated, across all physical systems, while the calcium-40 ion has a simpler structure which is well-suited for use as an "interface qubit". The logic gate, which was first demonstrated for same-species ions at NIST Boulder (USA) in 2003, allows quantum information to be transferred from one qubit to another; in the present work, the qubits reside in the two different isotopes, stored in the same ion trap. The Oxford work was the first to demonstrate that this type of logic gate is possible with the demanding precision necessary to build a quantum computer. 'In a nice piece of "spin-off science" from this technological achievement, we were able to perform a "Bell test", by first using the high-precision logic gate to generate an entangled state of the two different-species ions, then manipulating and measuring them independently. This is a test which probes the non-local nature of quantum mechanics; that is, the fact that an entangled state of two separated particles has properties that cannot be mimicked by a classical system. This was the first time such a test had been performed on two different species of atom separated by many times the atomic size.' While Professor Lucas cautions that the so-called 'locality loophole' is still present in this experiment, there is no doubt the work is an important contribution to the growing body of research exploring the physics of entanglement. He says: 'The significance of the work for trapped-ion quantum computing is that we show that quantum logic gates between different isotopic species are possible, can be driven by a relatively simple laser system, and can work with precision beyond the so-called "fault-tolerant threshold" precision of approximately 99% - the precision necessary to implement the techniques of quantum error correction, without which a quantum computer of useful size cannot be built.' In the long term, it is likely that different atomic elements will be required, rather than different isotopes. In closely related work published in the same issue of Nature, by Ting Rei Tan et al, the NIST Ion Storage group has demonstrated a different type of quantum logic gate using ions of two different elements (beryllium and magnesium). More information: Hybrid quantum logic and a test of Bell's inequality using two different atomic isotopes, nature.com/articles/doi:10.1038/nature16184


News Article | December 17, 2015
Site: www.scientificcomputing.com

Just over a year ago, the UK government announced an investment of £270m over five years to help get quantum technology out of laboratories and into the marketplace. Oxford was chosen to lead one of four EPSRC-funded 'Hubs' looking at different aspects of quantum technology — in Oxford's case, shaping the future of quantum networking and computing, towards the ultimate goal of developing a functioning quantum computer. Since then, the Networked Quantum Information Technologies (NQIT — pronounced 'N-kit') Hub, based at Oxford but involving nearly 30 academic and industrial partners, has been focusing on developing quantum technologies that could dwarf the processing power of today's supercomputers. A new paper by Oxford researchers, published in the journal Nature, demonstrates how the work of the Hub is progressing. Professor David Lucas of Oxford's Department of Physics, co-leader, with Professor Andrew Steane, of the ion trap quantum computing group, explains: “The development of a quantum computer is one of the outstanding technological challenges of the 21st century. A quantum computer is a machine that processes information according to the rules of quantum physics, which govern the behavior of microscopic particles at the scale of atoms and smaller. “An important point is that it is not merely a different technology for computing in the same way our everyday computers work; it is at a very fundamental level a different way of processing information. It turns out that this quantum-mechanical way of manipulating information gives quantum computers the ability to solve certain problems far more efficiently than any conceivable conventional computer. One such problem is related to breaking secure codes, while another is searching large data sets. Quantum computers are naturally well-suited to simulating other quantum systems, which may help, for example, our understanding of complex molecules relevant to chemistry and biology.” One of the leading technologies for building a quantum computer is trapped atomic ions, and a principal goal of the NQIT project is to develop the constituent elements of a quantum computer based on these ions. Professor Lucas says: “Each trapped ion (a single atom, with one electron removed) is used to represent one quantum bit of information. The quantum states of the ions are controlled with laser pulses of precise frequency and duration. Two different species of ion are needed in the computer: one to store information (a "memory qubit") and one to link different parts of the computer together via photons (an "interface qubit").' The Nature paper, whose lead author is Magdalen College Junior Research Fellow Chris Ballance, demonstrates the all-important quantum 'logic gate' between two different species of ion — in this case two isotopes of calcium, the abundant isotope calcium-40 and the rare isotope calcium-43. Professor Lucas says: “The Oxford team has previously shown that calcium-43 makes the best single-qubit memory ever demonstrated, across all physical systems, while the calcium-40 ion has a simpler structure which is well-suited for use as an "interface qubit." The logic gate, which was first demonstrated for same-species ions at NIST Boulder (USA) in 2003, allows quantum information to be transferred from one qubit to another; in the present work, the qubits reside in the two different isotopes, stored in the same ion trap. The Oxford work was the first to demonstrate that this type of logic gate is possible with the demanding precision necessary to build a quantum computer. “In a nice piece of "spin-off science" from this technological achievement, we were able to perform a "Bell test," by first using the high-precision logic gate to generate an entangled state of the two different-species ions, then manipulating and measuring them independently. This is a test which probes the non-local nature of quantum mechanics; that is, the fact that an entangled state of two separated particles has properties that cannot be mimicked by a classical system. This was the first time such a test had been performed on two different species of atom separated by many times the atomic size.” While Professor Lucas cautions that the so-called 'locality loophole' is still present in this experiment, there is no doubt the work is an important contribution to the growing body of research exploring the physics of entanglement. He says: “The significance of the work for trapped-ion quantum computing is that we show that quantum logic gates between different isotopic species are possible, can be driven by a relatively simple laser system, and can work with precision beyond the so-called "fault-tolerant threshold" precision of approximately 99 percent — the precision necessary to implement the techniques of quantum error correction, without which a quantum computer of useful size cannot be built.” In the long term, it is likely that different atomic elements will be required, rather than different isotopes. In closely related work published in the same issue of Nature, by Ting Rei Tan et al, the NIST Ion Storage group has demonstrated a different type of quantum logic gate using ions of two different elements (beryllium and magnesium).


News Article | August 22, 2016
Site: www.scientificcomputing.com

Researchers at the University of Oxford have achieved a quantum logic gate with record-breaking 99.9% precision, reaching the benchmark required theoretically to build a quantum computer. Quantum computers, which function according to the laws of quantum physics, have the potential to dwarf the processing power of today's computers, able to process huge amounts of information all at once. The team achieved the logic gate, which places two atoms in a state of quantum entanglement and is the fundamental building block of quantum computing, with a precision (or fidelity) substantially greater than the previous world record. Quantum entanglement – a phenomenon described by Einstein as 'spooky' but which is at the heart of quantum technologies – occurs when two particles stay connected, such that an action on one affects the other, even when they are separated by great distances. The research, carried out by scientists from the Engineering and Physical Sciences Research Council (EPSRC)-funded Networked Quantum Information Technologies Hub (NQIT), which is led by Oxford University, is reported in the journal Physical Review Letters. Dr Chris Ballance, a research fellow at Magdalen College, Oxford and lead author of the paper, said: 'The development of a "quantum computer" is one of the outstanding technological challenges of the 21st century. A quantum computer is a machine that processes information according to the rules of quantum physics, which govern the behaviour of microscopic particles at the scale of atoms and smaller. 'An important point is that it is not merely a different technology for computing in the same way our everyday computers work; it is at a very fundamental level a different way of processing information. It turns out that this quantum-mechanical way of manipulating information gives quantum computers the ability to solve certain problems far more efficiently than any conceivable conventional computer. One such problem is related to breaking secure codes, while another is searching large data sets. Quantum computers are naturally well-suited to simulating other quantum systems, which may help, for example, our understanding of complex molecules relevant to chemistry and biology.' Quantum technology is a complex area, but one analogy that has been used to explain the concept of quantum computing is that it is like being able to read all of the books in a library at the same time, whereas conventional computing is like having to read them one after another. This may be over-simplistic, but it is useful in conveying the way in which quantum computing has the potential to revolutionise the field. Professor David Lucas, of Oxford University's Department of Physics and Balliol College, Oxford, a co-author of the paper, said: 'The concept of "quantum entanglement" is fundamental to quantum computing and describes a situation where two quantum objects – in our case, two individual atoms – share a joint quantum state. That means, for example, that measuring a property of one of the atoms tells you something about the other. 'A quantum logic gate is an operation which can take two independent atoms and put them into this special entangled state. The precision of the gate is a measure of how well this works: in our case, 99.9% precision means that, on average, 999 times out of 1,000 we will have generated the entangled state correctly, and one time out of 1,000 something went wrong. 'To put this in context, quantum theory says that – as far as anyone has found so far – you simply can't build a quantum computer at all if the precision drops below about 99%. At the 99.9% level you can build a quantum computer in theory, but in practice it could be very difficult and thus enormously expensive. If, in the future, a precision of 99.99% can be attained, the prospects look a lot more favourable.' Professor Lucas added: 'Achieving a logic gate with 99.9% precision is another important milestone on the road to developing a quantum computer. A quantum logic gate on its own does not constitute a quantum computer, but you can't build the computer without them. 'An analogy from conventional computing hardware would be that we have finally worked out how to build a transistor with good enough performance to make logic circuits, but the technology for wiring thousands of those transistors together to build an electronic computer is still in its infancy.' The method used by the Oxford team was invented at NIST in Boulder, USA, and, in a paper published alongside Oxford's in Physical Review Letters, the NIST team also reports the achievement of 99.9% precision.


News Article | November 16, 2016
Site: physicsworld.com

Magnonics 2017 is the latest conference in the biennial series focussing on fundamental and applied aspects of magnon and spin-wave dynamics and nanomagnetism. The meeting will take place in the beautiful surroundings of Magdalen College, Oxford. Magdalen is within easy reach of London, and London’s Heathrow and Gatwick airports.


Bywater R.P.,Magdalen College | Veryazov V.,Lund University
Naturwissenschaften | Year: 2013

Globular proteins are folded polypeptide structures comprising stretches of secondary structures (helical (α- or 310 helix type), polyproline helix or β-strands) interspersed by regions of less well-ordered structure ("random coil"). Protein fold prediction is a very active field impacting inte alia on protein engineering and misfolding studies. Apart from the many studies of protein refolding from the denatured state, there has been considerable interest in studying the initial formation of peptides during biosynthesis, when there are at the outset only a few residues in the emerging polypeptide. Although there have been many studies employing quantum chemical methods of the conformation of dipeptides, these have mostly been carried out in the gas phase or simulated water. None of these conditions really apply in the interior confines of the ribosome. In the present work, we are concerned with the conformation of dipeptides in this low dielectric environment. Furthermore, only the residue types glycine and alanine have been studied by previous authors, but we extend this repertoire to include leucine and isoleucine, position isomers which have very different structural propensities. © 2013 Springer-Verlag Berlin Heidelberg.


Bywater R.P.,Magdalen College
Naturwissenschaften | Year: 2012

The notion that RNA must have had a unique and decisive role in the development of life needs hardly be questioned. However, the chemical complexity and other properties of RNA, such as high solubility in water and vulnerability to degradation, make it improbable that RNA could have had an early presence in the development of life on Earth or on any comparable telluric planet. Rather, the task of origin of life research must surely be to identify those chemical processes which could have taken place on Earth that could accumulate the complexity and rich molecular information content needed to sustain primitive life, and ultimately give rise to RNA. A collection of likely chemical precursors to modern biomolecules is listed here together with calculations of their molecular complexity. These complexity scores are then used to propose an ordering, on a timescale, of when they might have appeared on Earth. These pre-RNA living systems would have flourished during the first ~0.3 Gyrs after the start of the Archaean era (~4.2 Gyr ago). If there ever was an "RNA-world" it could have started after that initial period (~3.9 Gyrs ago), later to be complemented with the appearance of duplex DNA at about ~3.6 Gyrs ago, some time before the earliest known stromatolites (~3.4 Gyr). © Springer-Verlag 2012.


While the genome for a given organism stores the information necessary for the organism to function and flourish it is the proteins that are encoded by the genome that perhaps more than anything else characterize the phenotype for that organism. It is therefore not surprising that one of the many approaches to understanding and predicting protein folding and properties has come from genomics and more specifically from multiple sequence alignments. In this work I explore ways in which data derived from sequence alignment data can be used to investigate in a predictive way three different aspects of protein structure: Secondary structures, inter-residue contacts and the dynamics of switching between different states of the protein. In particular the use of Kolmogorov complexity has identified a novel pathway towards achieving these goals. © 2015 Robert Paul Bywater.


Jacobs B.M.,Magdalen College
Schizophrenia Research | Year: 2015

Schizophrenia is a devastating and prevalent psychiatric illness. Progress in understanding the basic pathophysiological processes underlying this disorder has been hindered by the lack of appropriate models. With the advent of induced pluripotent stem cell (iPSC) technology, it is now possible to generate live neurons in vitro from somatic tissue of schizophrenia patients. Despite its several limitations, this revolutionary technology has already helped to advance our understanding of schizophrenia. The phenotypic insights garnered with iPSC models of schizophrenia include transcriptional dysregulation, oxidative stress synaptic dysregulation, and neurodevelopmental abnormalities. Potential pitfalls of this work include the possibility of introducing random genetic mutations during the reprogramming process, the inadequacy of using neurons from other patients as controls, the inability to capture the complex environmental contribution to schizophrenia pathogenesis, the difficulty in modelling neurodevelopment, and the difficulty in modelling the interaction of multiple neuronal and non-neuronal cell types. However, with the increasing sophistication of available reprogramming techniques, co-culture technology, and gene correction strategies, iPSC-derived neurons will continue to elucidate how neuronal function is disrupted in schizophrenia. © 2015 Elsevier B.V.

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