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News Article | November 17, 2016
Site: www.eurekalert.org

X-ray technique at Berkeley Lab provides high-res views of the structure and movement of genetic material in cell nuclei Scientists have mapped the reorganization of genetic material that takes place when a stem cell matures into a nerve cell. Detailed 3-D visualizations show an unexpected connectivity in the genetic material in a cell's nucleus, and provide a new understanding of a cell's evolving architecture. These unique 3-D reconstructions of mouse olfactory cells, which govern the sense of smell, were obtained using X-ray imaging tools at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab). The results could help us understand how patterning and reorganization of DNA-containing material called chromatin in a cell's nucleus relate to a cell's specialized function as specific genes are activated or silenced. Chromatin is compacted to form chromosomes, which pass along an organism's genetic fingerprint to newly formed cells during cell division. The results were published this week in a special edition of Cell Reports that highlights epigenetics, a field of study focused on a layer of biochemistry that affects gene expression and that is closely coupled to DNA but does not alter the genetic code. Researchers used a powerful X-ray microscope at Berkeley Lab's Advanced Light Source (ALS) to capture images of nerve cell samples at different stages of maturity as they became more specialized in their function -- this process is known as "differentiation." Cells at each stage were imaged from dozens of different angles using X-rays. Each set of 2-D images was used to calculate a 3-D reconstruction of a cell detailing the changing chromatin formations in the nuclei. They also were able to measure the dense packing in a form of chromatin called heterochromatin, and they learned about the importance of a specific protein in controlling the compaction of heterochromatin and its confinement to the nucleus. "It's a new way of looking at the nucleus where we don't have to chemically treat the cell," said Carolyn Larabell, director of the National Center for X-ray Tomography (NCXT), a joint program of Berkeley Lab and UC San Francisco (UCSF). "Being able to directly image and quantify changes in the nucleus is enormously important and has been on cell biologists' wish list for many years." Chromatin is "notoriously sensitive," she said, to chemical stains and other chemical additives that are often used in biological imaging to highlight regions of interest in a given sample. "Until now, it has only been possible to image the nucleus indirectly by staining it, in which case the researcher has to take a leap of faith that the stain was evenly distributed." Larabell, a faculty scientist at Berkeley Lab and a UCSF professor, said it was previously thought that chromatin existed as a series of disconnected islands, though the latest study showed how the chromatin is compartmentalized into two distinct regions of "crowding" that form a continuous network throughout the nucleus. "We were really surprised: There are no islands, it's all connected," she said, adding, "We could see how chromatins pack through the nucleus and how molecules move through the nucleus, and we found that heterochromatin is 30 percent more crowded than the region where active genes are. That cannot be done with any other imaging techniques." Two-dimensional images would have shown the nucleus as a "flat, confusing mess," she said. One aim of the latest study was to gain new insight into gene expression in mice specific to olfactory genes. Mice have about 1,500 genes related to smell. Each olfactory nerve cell expresses just one of these olfactory genes to produce a receptor that recognizes a related set of odors. The many receptors in a mouse's nasal cavity allow it to detect a wide range of smells. "We're trying to understand how the reorganization of chromatin affects gene expression," Larabell said. "No one's been able to study this at the human level yet." This research will hopefully lead to new insights about diseases and disorders that relate to gene expression. Already, the study's results are being incorporated into models of cell development. One of the precursors to Alzheimer's disease, which attacks the brain's nerve cells, is a loss of smell, so understanding this connection to olfactory nerve cells could perhaps serve as a diagnostic tool and perhaps unlock a deeper understanding of the degenerative disorder. The latest study used a microscopy technique known as soft X-ray tomography to record a series of images from small groups of dozens of frozen olfactory nerve cells in three separate stages of development. The technique, which is unique to Berkeley Lab's ALS, captured details as small as tens of nanometers, or tens of billionths of a meter. Researchers visually distinguished regions of highly compacted heterochromatin from other chromatin types. With the proven success of the imaging technique, Larabell said it's possible to perform statistical analyses based on large collections of cell nuclei images sorted by different stages of development. Coupled with other types of imaging techniques, researchers hope to isolate individual gene-selection processes in upcoming work. "This work highlights the power of multidisciplinary research," said Mark Le Gros, associate director of the NCXT and a physicist who was responsible for the design and construction of the X-ray microscope. Le Gros, the lead author in this research, added, "This is an example of work that required a combination of molecular biologists and cell biologists with physicists and computer scientists." The Advanced Light Source is a DOE Office of Science User Facility. The latest work also featured participation from researchers at the Foundation for Research and Technology-Hellas in Greece, Massachusetts Institute of Technology, and University of Jyväskylä in Finland. The work was supported by the National Institutes of Health. Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy's Office of Science. For more, visit http://www. . DOE's Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit http://science. .

News Article | August 29, 2016
Site: www.sciencenews.org

Scientists have created giant molecules — the size of bacteria — that may be useful in future quantum computers. The molecules of unusual size are formed from pairs of Rydberg atoms — atoms with an electron that has been boosted into a high-energy state. Such electrons orbit far from their atom’s nucleus and, as a result, can feel the influence of faraway atoms. To create the molecules, researchers cooled cesium atoms nearly to absolute zero, hitting them with lasers to form Rydberg atoms that bound together in pairs. These molecules are about one thousandth of a millimeter in size — a thousand times the size of a typical molecule — scientists report August 19 in Physical Review Letters. “I think it’s fundamentally interesting and important because it’s such a curious thing,” says physicist David Petrosyan of the Institute of Electronic Structure & Laser at the Foundation for Research and Technology–Hellas in Heraklion, Greece. “The size of these molecules is huge.” This is not the first time such molecules have been created, but the previous evidence was not clear-cut. “Before, maybe it wasn’t clear if this is really a molecule in the sense that it’s vibrating and rotating. It could have been just two atoms sitting therewith very weak interactions or no interactions,” says Johannes Deiglmayr, a physicist at ETH Zürich and a coauthor of the study. Deiglmayr and collaborators measured the molecules’ binding energies — the energy that holds the two atoms together. Additionally, the scientists made detailed calculations to predict the molecules’ properties. These calculations were “extensive and seemed to match really well with their measurements,” says physicist Phillip Gould of the University of Connecticut in Storrs. The result has practical implications, Petrosyan notes. In quantum computers that use atoms as quantum bits, scientists perform computations by allowing atoms to interact. Rydberg atoms can interact with their neighbors over long distances, and when bound together, the atoms stay put at a consistent distance from one another — a feature that may improve the accuracy of calculations. Previously, researchers have used rubidium atoms to make another type of large molecule, formed from Rydberg atoms bonded with normal atoms. But these wouldn’t be useful for quantum computation, Petrosyan says, as they rely on a different type of bonding mechanism.

Ponti G.,University of Southampton | Papadakis I.,University of Crete | Papadakis I.,Foundation for Research and Technology | Bianchi S.,Third University of Rome | And 4 more authors.
Astronomy and Astrophysics | Year: 2012

Context. We report on the results of the first XMM-Newton systematic "excess variance" study of all the radio quiet, X-ray un-obscured AGN. The entire sample consist of 161 sources observed by XMM-Newton for more than 10 ks in pointed observations, which is the largest sample used so far to study AGN X-ray variability on time scales less than a day. Aims. Recently it has been suggested that the same engine might be at work in the core of every black hole (BH) accreting object. In this hypothesis, the same variability should be observed in all AGN, once rescaled by the M BH (M BH) and accretion rate (ṁ). Methods. We systematically compute the excess variance for all AGN, on different time-scales (10, 20, 40 and 80 ks) and in different energy bands (0.3-0.7, 0.7-2 and 2-10 keV). Results. We observe a highly significant and tight (∼0.7 dex) correlation between σ 2 rms and M BH. The subsample of reverberation mapped AGN shows an even smaller scatter (only a factor of 2-3) comparable to the one induced by the M BH uncertainties. This implies that X-ray variability can be used as an accurate tool to measure M BH and this method is more accurate than the ones based on single epoch optical spectra. This allows us to measure M BH for 65 AGN and estimate lower limits for the remaining 96 AGN. On the other hand, the σ 2 rms vs. accretion rate dependence is weaker than expected based on the PSD break frequency scaling. This strongly suggests that both the PSD high frequency break and the normalisation depend on accretion rate in such a way that they almost completely counterbalance each other (PSD amp ∞ ṁ -0.8). A highly significant correlation between σ 2 rms and 2-10 keV spectral index is observed. The highly significant correlations between σ 2 rms and both the L Bol and the FWHM Hβ are consistent with being just by-products of the σ 2 rms vs. M BH relation. The soft and medium σ 2 rms is very well correlated with the hard σ 2 rms, with no deviations from a linear one to one correlation. This suggests that the additional soft components (i.e. soft excess, warm absorber) add a minor contribution to the total variability. Once the variability is rescaled for M BH and ṁ, no significant difference between narrow-line and broad-line Seyfert 1 is observed. Conclusions. The results are in agreement with a picture where, to first approximation, all local AGN have the same variability properties once rescaled for M BH and ṁ. © 2012 ESO.

Emmanoulopoulos D.,University of Southampton | Papadakis I.E.,University of Crete | Papadakis I.E.,Foundation for Research and Technology | McHardy I.M.,University of Southampton | And 3 more authors.
Monthly Notices of the Royal Astronomical Society | Year: 2012

We present the first robust evidence of an anticorrelation between the X-ray photon index, Γ, and the X-ray luminosity in a single low-luminosity active galactic nucleus (LLAGN), NGC7213. Until today, such anticorrelation trends have been seen only in large samples of LLAGN that span a wide range of X-ray fluxes, although the opposite behaviour (i.e. a positive correlation between Γ and X-ray luminosity) has been extensively studied for individual X-ray bright active galactic nuclei. For NGC7213, we use the long-term X-ray monitoring data of the Rossi X-ray Timing Explorer (RXTE), regularly obtained on average every two days from 2006 March to 2009 December. Based on our X-ray data, we derive the Γ versus flux and the hardness ratio versus flux relations, indicating clearly that NGC7213 follows a 'harder when brighter' spectral behaviour. Additionally, by analysing radio and optical data, and combining data from the literature, we form the most complete spectral energy distribution (SED) of the source across the electromagnetic spectrum yielding a bolometric luminosity of 1.7 × 10 43erg s -1. Phenomenologically, the SED of NGC7213 is similar to that of a low-ionization nuclear emission-line region. The robust anticorrelation trend that we find between Γ and X-ray luminosity together with the low accretion rate of the source, 0.14percent that of the Eddington limit, makes NGC7213 the first LLAGN exhibiting a similar spectral behaviour with that of black hole X-ray binaries in the 'hard state'. © 2012 The Authors Monthly Notices of the Royal Astronomical Society © 2012 RAS.

Emmanoulopoulos D.,University of Southampton | Papadakis I.E.,University of Crete | Papadakis I.E.,Foundation for Research and Technology | Dovciak M.,Czech Republic Astronomical Institute | McHardy I.M.,University of Southampton
Monthly Notices of the Royal Astronomical Society | Year: 2014

We present the first systematic physical modelling of the time-lag spectra between the soft (0.3-1 keV) and the hard (1.5-4 keV) X-ray energy bands, as a function of Fourier frequency, in a sample of 12 active galactic nuclei which have been observed by XMM-Newton. We concentrate particularly on the negative X-ray time-lags (typically seen above 10-4 Hz), i.e. soft-band variations lag the hard-band variations, and we assume that they are produced by reprocessing and reflection by the accretion disc within a lamp-post X-ray source geometry. We also assume that the response of the accretion disc, in the soft X-ray bands, is adequately described by the response in the neutral Fe Kα line at 6.4 keV for which we use fully general relativistic ray-tracing simulations to determine its time evolution. These response functions, and thus the corresponding time-lag spectra, yield much more realistic results than the commonly used, but erroneous, top-hat models. Additionally, we parametrize the positive part of the time-lag spectra (typically seen below 10-4 Hz) by a power law. We find that the bestfitting black hole (BH) masses, M, agree quite well with those derived by other methods, thus providing us with a new tool for BH mass determination. We find no evidence for any correlation between M and the BH spin parameter, α, the viewing angle, θ, or the height of the X-ray source above the disc, h. Also on average, the X-ray source lies only around 3.7 gravitational radii above the accretion disc and θ is distributed uniformly between 20° and 60°. Finally, there is a tentative indication that the distribution of α may be bimodal above and below 0.62. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Fragos T.,Harvard - Smithsonian Center for Astrophysics | Lehmer B.D.,Johns Hopkins University | Lehmer B.D.,NASA | Naoz S.,Harvard - Smithsonian Center for Astrophysics | And 4 more authors.
Astrophysical Journal Letters | Year: 2013

X-ray photons, because of their long mean-free paths, can easily escape the galactic environments where they are produced, and interact at long distances with the intergalactic medium, potentially having a significant contribution to the heating and reionization of the early universe. The two most important sources of X-ray photons in the universe are active galactic nuclei (AGNs) and X-ray binaries (XRBs). In this Letter we use results from detailed, large scale population synthesis simulations to study the energy feedback of XRBs, from the first galaxies (z ∼ 20) until today. We estimate that X-ray emission from XRBs dominates over AGN at z ≳ 6-8. The shape of the spectral energy distribution of the emission from XRBs shows little change with redshift, in contrast to its normalization which evolves by ∼4 orders of magnitude, primarily due to the evolution of the cosmic star-formation rate. However, the metallicity and the mean stellar age of a given XRB population affect significantly its X-ray output. Specifically, the X-ray luminosity from high-mass XRBs per unit of star-formation rate varies an order of magnitude going from solar metallicity to less than 10% solar, and the X-ray luminosity from low-mass XRBs per unit of stellar mass peaks at an age of ∼300 Myr and then decreases gradually at later times, showing little variation for mean stellar ages ≳ 3 Gyr. Finally, we provide analytical and tabulated prescriptions for the energy output of XRBs, that can be directly incorporated in cosmological simulations. © 2013. The American Astronomical Society. All rights reserved.

Emmanoulopoulos D.,University of Southampton | Mchardy I.M.,University of Southampton | Papadakis I.E.,University of Crete | Papadakis I.E.,Foundation for Research and Technology
Monthly Notices of the Royal Astronomical Society: Letters | Year: 2011

We present an X-ray time lag analysis, as a function of Fourier frequency, for MCG-6-30-15 and Mrk766 using long-termXMM-Newtonlight curves in the 0.5-1.5 and the 2-4keV energy bands, together with some physical modelling of the corresponding time lag spectra. Both the time lag spectra of MCG-6-30-15 and Mrk766 show negative values (i.e. soft band variations lag behind the corresponding hard band variations) at high frequencies, around 10-3Hz, similar to those previously observed from 1H0707-495. The remarkable morphological resemblance between the time lag spectra of MCG-6-30-15 and Mrk766 indicate that the physical processes responsible for the observed soft time delays are very similar in the two sources, favouring a reflection scenario from material situated very nearby to the central black hole. © 2011 The Authors Monthly Notices of the Royal Astronomical Society © 2011 RAS.

Arndt M.,University of Vienna | Ekers A.,European Science Foundation | Ekers A.,University of Latvia | Klitzing W.V.,Foundation for Research and Technology | Ulbricht H.,University of Southampton
New Journal of Physics | Year: 2012

The level of experimental control and the detailed theoretical understanding of matter wave physics have led to a renaissance of experiments testing the very foundations of quantum mechanics and general relativity, as well as to applications in metrology. A variety of interferometric quantum sensors surpasses, or will surpass, the limits of their classical counterparts, for instance in the measurement of frequency and time or forces such as accelerations due to rotation and gravity with applications in basic science, navigation and the search for natural resources. The collection of original articles published in this focus issue of New Journal of Physics is intended as a snapshot of the current research pursued by a number of leading teams working on the development of new matter wave physics, devices and techniques. A number of contributions also stress the close relation between the historic roots of quantum mechanics and aspects of modern quantum information science which are relevant for matter wave physics.

Emmanoulopoulos D.,University of Southampton | McHardy I.M.,University of Southampton | Papadakis I.E.,University of Crete | Papadakis I.E.,Foundation for Research and Technology
Monthly Notices of the Royal Astronomical Society | Year: 2013

The production of artificial light curves with known statistical and variability properties is of great importance in astrophysics. Consolidating the confidence levels during cross-correlation studies, understanding the artefacts induced by sampling irregularities, establishing detection limits for future observatories are just some of the applications of simulated data sets. Currently, the widely used methodology of amplitude and phase randomization is able to produce artificial light curves which have a given underlying power spectral density (PSD) but which are strictly Gaussian distributed. This restriction is a significant limitation, since the majority of the light curves, e.g. active galactic nuclei, X-ray binaries, gamma-ray bursts, show strong deviations from Gaussianity exhibiting 'burst-like' events in their light curves yielding longtailed probability density functions (PDFs). In this study, we propose a simple method which is able to precisely reproduce light curves which match both the PSD and the PDF of either an observed light curve or a theoretical model. The PDF can be representative of either the parent distribution or the actual distribution of the observed data, depending on the study to be conducted for a given source. The final artificial light curves contain all of the statistical and variability properties of the observed source or theoretical model, i.e. the same PDF and PSD, respectively. Within the framework of Reproducible Research, the code and the illustrative example used in this paper are both made publicly available in the form of an interactive MATHEMATICA notebook. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Rath C.,Max Planck Institute for Extraterrestrial Physics | Gliozzi M.,George Mason University | Papadakis I.E.,University of Crete | Papadakis I.E.,Foundation for Research and Technology | Brinkmann W.,Max Planck Institute for Extraterrestrial Physics
Physical Review Letters | Year: 2012

The method of surrogates is one of the key concepts of nonlinear data analysis. Here, we demonstrate that commonly used algorithms for generating surrogates often fail to generate truly linear time series. Rather, they create surrogate realizations with Fourier phase correlations leading to nondetections of nonlinearities. We argue that reliable surrogates can only be generated, if one tests separately for static and dynamic nonlinearities. © 2012 American Physical Society.

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