A new theoretical model of DNA as a "recolourable" polymer may explain why specific "epigenetic" patterns on the genome can survive from one cell generation to the next and allow cellular memory.

    Every cell in our body contains the same DNA. Nevertheless, a brain cell is clearly very different from, say, a liver cell, in terms of which genes are active and inactive. The specialisation into different types of cells is made possible by "epigenetics" (literally, "beyond the genetic information"). Epigenetics acts through biochemical markers called "post-translational modifications" which are deposited onto histone proteins -- the proteins needed to package the DNA inside the nucleus. Epigenetic marks vary from cell to cell, allowing each cell to have its own identity. Nonetheless, epigenetic marks are very dynamic: they are gained and lost by histones all the time, and many are removed during replication. This then begs the questions, how does a cell remember its own identity throughout its life and how is its identity passed down to the progeny cells when it divides?

    Davide Michieletto, in collaboration with Davide Marenduzzo and Enzo Orlandini (Padova) have formulated a new model to address these questions. The model treats the complex of DNA and histones (also called "chromatin")  as a polymer made of beads, where each bead corresponding to a few histones (with their corresponding DNA). In the model, the polymer beads are "coloured" based on their epigenetic state, and this can be changed dynamically mimicking the action of "writer" proteins, enzymes found in the cell. The epigenetic colour is then recognised by "readers", which model chromatin-bridging proteins which have an affinity for a given epigenetic mark. The model displays an abrupt first-order-like transition between a swollen and epigenetically "disordered" chromatin and a collapsed and "ordered" one, where the whole polymer has the same colour. The first order nature of the transition is important: it implies that there is hysteresis and memory, and the researchers have shown that, following a (simulated) replication event, the system is able to return to the same ordered state (so the corresponding cell will keep its identity).

    The findings therefore strongly suggest that epigenetic memory may be made possible through a positive feedback loop between "reader" and "writer" proteins which couple the 1D epigenetic patterning to the 3D chromatin folding.

    Dark matter, the elusive material that accounts for much of the Universe, is less dense and more smoothly distributed throughout space than previously thought, according to a new study co-led by astronomers at the University of Edinburgh. The international team of scientists studied wide-area images of the distant universe, taken from the European Southern Observatory in Chile. They applied a technique based on the bending of light by gravity - known as weak gravitational lensing - to map out the distribution of dark matter in the Universe today. Their study represents the largest area of the sky to be mapped using this technique to date.

    The new results contradict previous predictions from a survey of the far-off universe, representing a point in time soon after the Big Bang, imaged by the European Space Agency's Planck satellite. This previous study used a theoretical model to project how the Universe should appear today.   The disagreement between this prediction and the latest direct measurements suggests that scientists' understanding of the evolving modern day Universe is incomplete and needs more research.

    This map of dark matter in the Universe was obtained from data from the KiDS survey, using the VLT Survey Telescope at ESO’s Paranal Observatory in Chile. It reveals an expansive web of dense (light) and empty (dark) regions. This image is one out of five patches of the sky observed by KiDS. Here the invisible dark matter is seen rendered in pink, covering an area of sky around 420 times the size of the full moon. This image reconstruction was made by analysing the light collected from over three million distant galaxies more than 6 billion light-years away. The observed galaxy images were warped by the gravitational pull of dark matter as the light travelled through the Universe.

    The latest study, published in Monthly Notices of the Royal Astronomical Society, was carried out by a team jointly led by the University of Edinburgh, the Argelander Institute for Astronomy in Germany, Leiden University in the Netherlands and Swinburne University of Technology, Australia in an ongoing project called the Kilo Degree Survey, or KiDS. It was supported by the European Research Council.

    "Our findings will help to refine our theoretical model for how the Universe has grown since its inception, improving our understanding of the modern day Universe.”  says Dr Hendrik Hildebrandt of the Argelander Institute for Astronomy in Germany.
    "This latest result indicates that the cosmic web dark matter, which accounts for about one-quarter of the Universe, is less clumpy than we previously believed.” said Dr Massimo Viola of Leiden University in the Netherlands.
    "Unravelling what has happened since the Big Bang is a complex challenge, but by continuing to study the distant skies, we can build a picture of how our modern Universe has evolved.” said Professor Catherine Heymans of the University of Edinburgh's School of Physics and Astronomy.

    Water inside Earth’s interior is crucial to assist mantle convection. Without it, mantle convection would be inefficient, volcanic activity would cease, as would plate tectonics on the surface.

    Hydrous minerals help transport water deep into Earth’s mantle, and form part of a cycle that regulates the sustained presence of water, both in the interior and on the surface, on geological time scales. To understand the deep-water cycle, it is crucial to study the properties of hydrous minerals under the conditions present in Earth’s mantle. Brucite, chemical formula Mg(OH)2, is one of the simplest hydrous minerals and stores significant amounts of water in the form of hydroxyl groups. It is assumed to decompose in the mantle transition zone, but recent work by Dr Andreas Hermann, with collaborators from Florida State University, shows that the mineral can exist in a more compact high-pressure phase instead, which pushes the stability region of brucite several hundreds of kilometers deeper and into the lower mantle. Brucite might be present at much greater depths, and in much larger quantities, than previously thought. This changes the current thinking about the water storage capacity of the deep Earth, and the role hydrous minerals play in transporting and holding water inside our planet.

    The work involved quantum-mechanical calculations that screened thousands of potential crystal structures of brucite under extreme pressure conditions. The new phase, which has a network structure akin to anatase, emerged eventually from those calculations. Besides being more stable than the known brucite structure at high pressures and temperatures, Dr Hermann and his collaborator showed that the new phase has a unique elastic response, which might enable its direct detection in seismic signatures, as well as specific vibrational properties that should make its detection in laboratory experiments straightforward.

    The research is published in the Proceedings of the National Academy of Sciences.

    Presentation slide.

    Flaviu, who is a final year CASE student with NPL has won the thesis presentation award at the first NPL Post Graduate Institute for his presentation titled 'Electronically Coarse Grained Molecular Modelling'.

    Congratulations to Flaviu for winning the best presentation award at the first annual Postgraduate Institute conference at NPL. The conference was attended by 150 delegates over two days, comprising postgraduate researchers based both at NPL and partner universities, their supervisors, invited guests and speakers. 

    A number of the postgraduates also took part in a challenge to describe their doctoral work comprehensively in just three minutes, with just one slide. The winner was Flaviu Cipcigan, for his presentation 'Electronically Coarse Grained Molecular Modelling', 

    Warm inflation is an alternative and simpler dynamical picture for the the early Universe, in which the dominant expansion period occurs in a warm phase, whereas in the standard inflation picture, accepted for over three decades, it occurs in a cold phase. This leads to distinct differences in the history of the early Universe and present-day observational signatures.

    For over the two decades since warm inflation was suggested by Arjun Berera, experts in the fields of cosmology and particle physics have regarded it as almost impossible to realize this idea in a simple first principles model. This paper has confounded these expectations and developed a simple and compelling first principles model of warm inflation.   This now provides a solid theoretical foundation to an alternative paradigm for the early Universe, which shows excellent agreement with large scale observational data (see figure below).

    Results from the model and comparison of cosmic microwave background observational data.

    In standard inflation, any preexisting radiation is stretched and dispersed during a brief cosmic phase and no new radiation is produced. The Universe’s temperature plummets by several orders of magnitude, and an ensuing reheating period fills the Universe with radiation again. Warm inflation is simpler. New radiation is constantly produced by the decay of the scalar field that triggers inflation, the inflaton; the temperature remains large; and there is no reheating phase. Ironically, however, models of warm inflation have so far required thousands of additional fields to be coupled to the inflaton to avoid large corrections to its mass.

    This paper treats the field driving inflation as a pseudo Nambu-Goldstone boson of a broken gauge symmetry and its mass is naturally protected against large quantum and thermal corrections. The model is similar to the Little Higgs mechanism for electroweak symmetry breaking.  Using this idea Berera and colleagues built a model involving only four additional fields and no mass corrections. The researchers then compared the model’s observational predictions with constraints on inflation derived from Planck satellite measurements of the cosmic microwave background radiation and found good agreement between the two.  The presence of radiation during inflation has been known from very earlier work by Berera and colleagues to lower the tensor-scalar ratio.  This model realises this result in a compelling first principles model, thus accommodates the possibility for a tensor mode anywhere from the present upper bound to a value extremely below that.

    The latest research is published in Physical Review Letters and was highlighted by the journal as an Editors' Suggestion, which recognises its important contribution to the field.

    "We are pleased to have formed a theoretical model for this phase of the Universe, which is based on first principles. This could be a valuable theory for improving our understanding of how the early Universe took shape."   Professor Arjun Berera, School of Physics and Astronomy

    On Saturday 26th September the School took part in Door Open Day with two popular exhibits and a successful recruitment day.

    Institute for Condensed Matter and Complex Systems once again threw open the doors to its laboratories for Doors Open Day 2016. Visitors were able to see how complex fluids are studied using rheology, watch food based capsules being made and see the group’s new confocal microscope in action. In the foyer, younger visitors made slime and lava lamps, learning about non newtonian fluids and interfacial phenomena. A popular favourite, a large bucket of corn flour in water dramatically illustrated shear thickening. Well away from the corn starch, highlighted the biophysics research of the group, including an interactive simulation of bacterial population dynamics. A team of 12 PhD students and postdocs from the ICMCS ran the event and talked enthusiastically to visitors about their work. 

    PP4SS (Particle Physics for Scottish Schools) had successful display in the JCMB cafe with good in visitor numbers. 

    A new experiment carried out in the underground Gran Sasso Laboratory of the Italian National Institute for Nuclear Physics (INFN) could help scientists uncover the origin of some rare elements in the universe.

    Nuclear fusion reactions provide the source of energy that makes stars shine. Like gigantic alchemists of the cosmos, they also create new elements from the hydrogen and helium left over by the Big Bang.

    Understanding the complex pattern of reactions that leads to the abundances of elements and isotopes that we observe today requires detailed models of stellar evolution and extensive laboratory experiments on individual nuclear reactions. For some time, astronomers have been puzzled by anomalous abundances of rare isotopes of carbon, nitrogen, and oxygen in the atmospheres of some stars and in tiny grains that reach the Earth inside meteorites. In particular, the amount of oxygen-17 – a rare, heavier form of the oxygen we breathe – observed in some red giants and massive stars can provide important clues on the mixing processes that occur inside these stars and bring to their surfaces the debris of nuclear reactions. By measuring the tiny particles released by the fusion of hydrogen and oxygen-17, the study – published in the journal Physical Review Letters – reveals that oxygen-17 is destroyed twice as fast as previously expected: a result that may help reconcile the puzzling abundances observed in stellar atmospheres and stardust grains.

    The experiment, which took place at the LUNA (Laboratory for Underground Nuclear Astrophysics) accelerator of the Gran Sasso Laboratory, detected the feeble signals of the fusion reaction with unprecedented precision. Such studies can only be performed in the absence of radiation from space, and the shielding provided by the 1.4km of rock under the Gran Sasso mountain is ideal to suppress the background induced by cosmic rays.

    “This work represents another key milestone in the scientific activity of the LUNA collaboration – says Paolo Prati, spokesperson of LUNA – and provides another crucial input to help us understand the origin of the elements in the universe’’.

    LUNA is an international collaboration of about 40 scientists from the INFN (Italy), the Helmholtz-Zentrum Dresden-Rossendorf (Germany), MTA-ATOMKI (Hungary) and the School of Physics and Astronomy of the University of Edinburgh (UK).

    The UK team, led by Professor Marialuisa Aliotta, played a key role in the planning and execution of the experiment and provided the detectors and related instrumentation.

    “This work provides an important piece in the puzzle of the origin of the elements in the universe – says Professor Aliotta, from the School of Physics and Astronomy of the University of Edinburgh – and represents the culmination of four years of careful planning and intense experimental activity. The successful outcome of this project reflects the contributions of a number of individuals and organisations. In particular, Mr Carlo Bruno (SUPA-funded PhD student and first author of the paper) made outstanding contributions to the extensive data taking campaigns and painstaking data analysis. We would also like to say a huge thank-you to the mechanical workshop of the School of Physics and Astronomy for the design and construction of the purpose-built scattering chamber used for the measurements.”

    An international team of astronomers, led by Edinburgh, has gained a new view of the evolution of distant galaxies. Their study focuses on a region of the Universe previously studied using the deepest observations of the Hubble Space Telescope.

    The team has traced the previously unknown abundance of star-forming gas and dust over cosmic time. This provides new insights into what is known as the golden age of galaxy formation - approximately 10 billion years ago. The new observations of a well-studied area of sky, known as the Hubble Ultra Deep Field, were taken with the ALMA (Atacama Large Millimetre/submillimetre Array) telescope, located high in the Atacama Desert in Chile. The resulting images are significantly deeper and sharper than those from previous surveys undertaken at these long wavelengths. Astronomers have used their findings to show for the first time how the rate of star formation in young galaxies is closely related to their total mass in stars, which is assembled from previous star-formation events.

    The findings will be published in in the Monthly Notices of the Royal Astronomical Society.

    The first Hubble Ultra Deep Field images, pioneering deep-field observations at optical wavelengths, were captured with the NASA/ESA Hubble Space Telescope and published in 2004. Hubble was refurbished in 2009 and since then, it has captured near-infrared images. The result is the deepest view of the Universe to achieved date, revealing early galaxies that existed less than a billion years after the Big Bang. However, Hubble cannot reveal the emission from young stars that is absorbed and then re-emitted by clouds of interstellar gas and dust, within which the youngest stars form. To do this, astronomers have had to await the advent of ALMA, which for the first time enables the warm glow of dust-enshrouded star-formation activity to be imaged with a depth and clarity comparable to Hubble imaging. The team, led by the University of Edinburgh, used ALMA to obtain the first deep, homogeneous image of the entire Hubble Ultra Deep Field region. This enabled them to clearly match the galaxies detected by ALMA with objects already known from the Hubble imaging. This showed clearly, for the first time, that the mass of stars already existing within a galaxy is the best indicator of how quickly stars are forming in the very distant Universe. The team was able to detect virtually all of the high-mass galaxies and very little else.

    Professor Jim Dunlop, of the School of Physics and Astronomy, said: “This is a breakthrough result. For the first time we are properly connecting the visible and ultraviolet light view of the distant Universe from Hubble and far-infrared views of the Universe from ALMA.”

    According to researchers, the new ALMA results imply a rapidly rising gas content in galaxies as we look back further in time. This is likely the root of a remarkable increase in star formation rates during the peak of galaxy formation some 10 billion years ago. The results are the first in a series of planned observations of the distant Universe using ALMA. Astronomers hope the forthcoming program of surveys will complete their view of the galaxies in the Hubble Ultra Deep Field.

    Scientists have refined their search for dark matter with the completion of a sophisticated experiment.

    An international team of researchers, including from Edinburgh, has completed a series of tests for dark matter – which is thought to account for more than four-fifths of the Universe – using an underground detector in the US.

    Although the experiment did not yield any direct evidence of dark matter, the results have enabled scientists to refine their models for dark matter particles.

    It will also inform the next generation of experiments that plan to further the search for the material.

    Long-term testing

    The Large Underground Xenon (LUX) dark matter experiment, at the Sanford Underground Research Facility in the Black Hills of South Dakota, has been operating a series of experiments over the past three years.

    The experiment was designed to look for so-called weakly interacting massive particles, or WIMPs, which scientists believe are the most likely fit for a dark matter particle.

    Their interaction with ordinary matter is expected to be very faint and difficult to detect.

    Sensitive detector

    LUX consists of a large tank of cooled liquid xenon surrounded by powerful sensors.

    These are designed to detect the tiny flash of light and electrical charge emitted if a WIMP collides with a xenon atom in the tank.

    Radiation that might interfere with a dark matter signal, such as cosmic rays, are kept out by the detector’s location a mile underground.

    The detector’s extreme sensitivity ensures that if dark matter particles had interacted with the xenon target, the detector would almost certainly have seen it.


    Dark matter is thought to account for more than four-fifths of the mass in the universe.

    Scientists are confident of its existence because its effects can be seen in the behaviour of galaxies and in the way light bends as it travels through the universe. However, experiments have yet to find a dark matter particle.

    The latest results are from the detector’s final 20-month run, which is one of the largest experiments of its type.

    Analysis of nearly a half-million gigabytes of data from the detector made use of advanced computer facilities.

    Next steps

    Future experiments will include the LUX-ZEPLIN (LZ) experiment, which will replace LUX at the Sanford Underground Research Facility.

    LZ will have a larger liquid xenon capacity than LUX, to help fend off external radiation.

    The LUX scientific collaboration, which is supported by the DOE and National Science Foundation (NSF), includes 20 research universities and national laboratories in the US, UK and Portugal.

    "These latest findings about what dark matter is, and what it isn’t, are the best yet, and will help improve the next generation of experiments to detect this elusive substance." Prof. Alex Murphy, Professor of Nuclear & Particle Astrophysics, School of Physics & Astronomy