TY - JOUR A1 - Trinh, Christopher Q. A1 - Ellis, Simon C. A1 - Bland-Hawthorn, Joss A1 - Lawrence, Jon S. A1 - Horton, Anthony J. A1 - Leon-Saval, Sergio G. A1 - Shortridge, Keith A1 - Bryant, Julia A1 - Case, Scott A1 - Colless, Matthew A1 - Couch, Warrick A1 - Freeman, Kenneth A1 - Löhmannsröben, Hans-Gerd A1 - Gers, Luke A1 - Glazebrook, Karl A1 - Haynes, Roger A1 - Lee, Steve A1 - O'Byrne, John A1 - Miziarski, Stan A1 - Roth, Martin M. A1 - Schmidt, Brian A1 - Tinney, Christopher G. A1 - Zheng, Jessica T1 - Gnosis - the first instrument to use fiber bragg gratings for OH suppression JF - The astronomical journal N2 - The near-infrared is an important part of the spectrum in astronomy, especially in cosmology because the light from objects in the early universe is redshifted to these wavelengths. However, deep near-infrared observations are extremely difficult to make from ground-based telescopes due to the bright background from the atmosphere. Nearly all of this background comes from the bright and narrow emission lines of atmospheric hydroxyl (OH) molecules. The atmospheric background cannot be easily removed from data because the brightness fluctuates unpredictably on short timescales. The sensitivity of ground-based optical astronomy far exceeds that of near-infrared astronomy because of this long-standing problem. GNOSIS is a prototype astrophotonic instrument that utilizes "OH suppression fibers" consisting of fiber Bragg gratings and photonic lanterns to suppress the 103 brightest atmospheric emission doublets between 1.47 and 1.7 mu m. GNOSIS was commissioned at the 3.9 m Anglo-Australian Telescope with the IRIS2 spectrograph to demonstrate the potential of OH suppression fibers, but may be potentially used with any telescope and spectrograph combination. Unlike previous atmospheric suppression techniques GNOSIS suppresses the lines before dispersion and in a manner that depends purely on wavelength. We present the instrument design and report the results of laboratory and on-sky tests from commissioning. While these tests demonstrated high throughput (approximate to 60%) and excellent suppression of the skylines by the OH suppression fibers, surprisingly GNOSIS produced no significant reduction in the interline background and the sensitivity of GNOSIS+IRIS2 is about the same as IRIS2. It is unclear whether the lack of reduction in the interline background is due to physical sources or systematic errors as the observations are detector noise dominated. OH suppression fibers could potentially impact ground-based astronomy at the level of adaptive optics or greater. However, until a clear reduction in the interline background and the corresponding increasing in sensitivity is demonstrated optimized OH suppression fibers paired with a fiber-fed spectrograph will at least provide a real benefit at low resolving powers. KW - atmospheric effects KW - infrared: diffuse background KW - instrumentation: miscellaneous Y1 - 2013 U6 - https://doi.org/10.1088/0004-6256/145/2/51 SN - 0004-6256 VL - 145 IS - 2 PB - IOP Publ. Ltd. CY - Bristol ER - TY - BOOK A1 - Rüdiger, Günther A1 - Kitchatinov, Leonid L. A1 - Hollerbach, Rainer T1 - Magnetic processes in astrophysics : theory, simulations, experiments Y1 - 2013 SN - 978-3-527-41034-7 PB - Wiley-VCH CY - Weinheim, Bergstr. ER - TY - THES A1 - Menon, Arathy T1 - Indian summer monsoon : future variability, extreme events and effects of lagged adaptation Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Ohliger, Matthias A1 - Nesme, V. A1 - Eisert, J. T1 - Efficient and feasible state tomography of quantum many-body systems JF - New journal of physics : the open-access journal for physics N2 - We present a novel method for performing quantum state tomography for many-particle systems, which are particularly suitable for estimating the states in lattice systems such as of ultra-cold atoms in optical lattices. We show that the need to measure a tomographically complete set of observables can be overcome by letting the state evolve under some suitably chosen random circuits followed by the measurement of a single observable. We generalize known results about the approximation of unitary two-designs, i.e. certain classes of random unitary matrices, by random quantum circuits and connect our findings to the theory of quantum compressed sensing. We show that for ultra-cold atoms in optical lattices established experimental techniques such as optical super-lattices, laser speckles and time-of-flight measurements are sufficient to perform fully certified, assumption-free tomography. This is possible without the need to address single sites in any step of the procedure. Combining our approach with tensor network methods-in particular, the theory of matrix product states-we identify situations where the effort of reconstruction is even constant in the number of lattice sites, allowing, in principle, to perform tomography on large-scale systems readily available in present experiments. Y1 - 2013 U6 - https://doi.org/10.1088/1367-2630/15/1/015024 SN - 1367-2630 VL - 15 IS - 5 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Herenz, Peter A1 - Richter, Philipp A1 - Charlton, Jane C. A1 - Masiero, Joseph R. T1 - The milky way halo as a QSO absorption-line system new results from an HST/STIS absorption-line catalogue of galactic high-velocity clouds JF - Astronomy and astrophysics : an international weekly journal N2 - We use archival UV absorption-line data from HST/STIS to statistically analyse the absorption characteristics of the high-velocity clouds (HVCs) in the Galactic halo towards more than 40 extragalactic background sources. We determine absorption covering fractions of low-and intermediate ions (Oi, Cii, Si ii, Mgii, Feii, Si iii, Civ, and Si iv) in the range f(c) = 0.20-0.70. For detailed analysis we concentrate on Si ii absorption components in HVCs, for which we investigate the distribution of column densities, b-values, and radial velocities. Combining information for Si ii and Mg II, and using a geometrical HVC model we investigate the contribution of HVCs to the absorption cross section of strong Mg ii absorbers in the local Universe. We estimate that the Galactic HVCs would contribute on average similar to 52 percent to the total strong Mg ii cross section of the Milky Way, if our Galaxy were to be observed from an exterior vantage point. We further estimate that the mean projected covering fraction of strong Mg ii absorption in the Milky Way halo and disc from an exterior vantage point is < f(c,sMgII)> = 0.31 for a halo radius of R = 61 kpc. These numbers, together with the observed number density of strong Mg ii absorbers at low redshift, indicate that the contribution of infalling gas clouds (i.e., HVC analogues) in the halos of Milky Way-type galaxies to the cross section of strong Mgii absorbers is < 34 percent. These findings are in line with the idea that outflowing gas (e. g., produced by galactic winds) in the halos of more actively star-forming galaxies dominate the absorption-cross section of strong Mgii absorbers in the local Universe. KW - ISM: structure KW - Galaxy: halo KW - galaxies: halos Y1 - 2013 U6 - https://doi.org/10.1051/0004-6361/201220531 SN - 0004-6361 VL - 550 PB - EDP Sciences CY - Les Ulis ER - TY - JOUR A1 - van Loon, J. Th. A1 - Bailey, M. A1 - Tatton, B. L. A1 - Apellaniz, Jesus Maiz A1 - Crowther, P. A. A1 - de Koter, A. A1 - Evans, C. J. A1 - Henault-Brunet, V. A1 - Howarth, I. D. A1 - Richter, Philipp A1 - Sana, Hugues A1 - Simon Díaz, Sergio A1 - Taylor, W. A1 - Walborn, N. R. T1 - The VLT-FLAMES tarantula survey IX. - the interstellar medium seen through diffuse interstellar bands and neutral sodium JF - Astronomy and astrophysics : an international weekly journal N2 - Context. The Tarantula Nebula (a.k.a. 30 Dor) is a spectacular star-forming region in the Large Magellanic Cloud (LMC), seen through gas in the Galactic disc and halo. Diffuse interstellar bands (DIBs) offer a unique probe of the diffuse, cool-warm gas in these regions. Aims. The aim is to use DIBs as diagnostics of the local interstellar conditions, whilst at the same time deriving properties of the yet-unknown carriers of these enigmatic spectral features. Methods. Spectra of over 800 early-type stars from the Very Large Telescope Flames Tarantula Survey (VFTS) were analysed. Maps were created, separately, for the Galactic and LMC absorption in the DIBs at 4428 and 6614 angstrom and - in a smaller region near the central cluster R 136 - neutral sodium (the Na ID doublet); we also measured the DIBs at 5780 and 5797 angstrom. Results. The maps show strong 4428 and 6614 angstrom DIBs in the quiescent cloud complex to the south of 30 Dor but weak absorption in the harsher environments to the north (bubbles) and near the OB associations. The Na maps show at least five kinematic components in the LMC and a shell-like structure surrounding R 136, and small-scale structure in the Milky Way. The strengths of the 4428, 5780, 5797 and 6614 angstrom DIBs are correlated, also with Na absorption and visual extinction. The strong 4428 angstrom DIB is present already at low Na column density but the 6614, 5780 and 5797 angstrom DIBs start to be detectable at subsequently larger Na column densities. Conclusions. The carriers of the 4428, 6614, 5780 and 5797 angstrom DIBs are increasingly prone to removal from irradiated gas. The relative strength of the 5780 and 5797 angstrom DIBs clearly confirm the Tarantula Nebula as well as Galactic high-latitude gas to represent a harsh radiation environment. The resilience of the 4428 angstrom DIB suggests its carrier is large, compact and neutral. Structure is detected in the distribution of cool-warm gas on scales between one and > 100 pc in the LMC and as little as 0.01 pc in the Sun's vicinity. Stellar winds from the central cluster R 136 have created an expanding shell; some infalling gas is also detected, reminiscent of a galactic "fountain". KW - ISM: individual objects: Tarantula Nebula (30 Doradus Nebula) KW - ISM: molecules KW - ISM: kinematics and dynamics KW - ISM: lines and bands KW - ISM: structure KW - local insterstellar matter Y1 - 2013 U6 - https://doi.org/10.1051/0004-6361/201220210 SN - 0004-6361 VL - 550 IS - 9 PB - EDP Sciences CY - Les Ulis ER - TY - JOUR A1 - Eliazar, Iddo A1 - Metzler, Ralf T1 - Anomalous statistics of random relaxations in random environments JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - We comprehensively analyze the emergence of anomalous statistics in the context of the random relaxation ( RARE) model [Eliazar and Metzler, J. Chem. Phys. 137, 234106 ( 2012)], a recently introduced versatile model of random relaxations in random environments. The RARE model considers excitations scattered randomly across a metric space around a reaction center. The excitations react randomly with the center, the reaction rates depending on the excitations' distances from this center. Relaxation occurs upon the first reaction between an excitation and the center. Addressing both the relaxation time and the relaxation range, we explore when these random variables display anomalous statistics, namely, heavy tails at zero and at infinity that manifest, respectively, exceptionally high occurrence probabilities of very small and very large outliers. A cohesive set of closed-form analytic results is established, determining precisely when such anomalous statistics emerge. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.87.022141 SN - 1539-3755 SN - 1550-2376 VL - 87 IS - 2 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Schick, Daniel A1 - Bojahr, Andre A1 - Herzog, Marc A1 - Gaal, P. A1 - Vrejoiu, I. A1 - Bargheer, Matias T1 - Following Strain-Induced Mosaicity Changes of Ferroelectric Thin Films by Ultrafast Reciprocal Space Mapping JF - Physical review letters N2 - We investigate coherent phonon propagation in a thin film of ferroelectric PbZr0.2Ti0.8O3 (PZT) by ultrafast x-ray diffraction experiments, which are analyzed as time-resolved reciprocal space mapping in order to observe the in-and out-of-plane structural dynamics, simultaneously. The mosaic structure of the PZT leads to a coupling of the excited out-of-plane expansion to in-plane lattice dynamics on a picosecond time scale, which is not observed for out-of-plane compression. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.110.095502 SN - 0031-9007 SN - 1079-7114 VL - 110 IS - 9 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Hoffmann, H. A1 - Seiß, Martin A1 - Spahn, Frank T1 - Vertical relaxation of a moonlet propeller in Saturn's a ring JF - The astrophysical journal : an international review of spectroscopy and astronomical physics ; Part 2, Letters N2 - Two images, taken by the Cassini spacecraft near Saturn's equinox in 2009 August, show the Earhart propeller casting a 350 km long shadow, offering the opportunity to watch how the ring height, excited by the propeller moonlet, relaxes to an equilibrium state. From the shape of the shadow cast and a model of the azimuthal propeller height relaxation, we determine the exponential cooling constant of this process to be lambda = 0.07 +/- 0.02 km(-1), and thereby determine the collision frequency of the ring particles in the vertically excited region of the propeller to be omega(c)/Omega = 0.9 +/- 0.2. KW - planets and satellites: individual (Saturn) KW - planets and satellites: rings Y1 - 2013 U6 - https://doi.org/10.1088/2041-8205/765/1/L4 SN - 2041-8205 VL - 765 IS - 1 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Kursawe, Jochen A1 - Schulz, Johannes H. P. A1 - Metzler, Ralf T1 - Transient aging in fractional brownian and langevin-equation motion JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - Stochastic processes driven by stationary fractional Gaussian noise, that is, fractional Brownian motion and fractional Langevin-equation motion, are usually considered to be ergodic in the sense that, after an algebraic relaxation, time and ensemble averages of physical observables coincide. Recently it was demonstrated that fractional Brownian motion and fractional Langevin-equation motion under external confinement are transiently nonergodic-time and ensemble averages behave differently-from the moment when the particle starts to sense the confinement. Here we show that these processes also exhibit transient aging, that is, physical observables such as the time-averaged mean-squared displacement depend on the time lag between the initiation of the system at time t = 0 and the start of the measurement at the aging time t(a). In particular, it turns out that for fractional Langevin-equation motion the aging dependence on ta is different between the cases of free and confined motion. We obtain explicit analytical expressions for the aged moments of the particle position as well as the time-averaged mean-squared displacement and present a numerical analysis of this transient aging phenomenon. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.88.062124 SN - 1539-3755 SN - 1550-2376 VL - 88 IS - 6 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Ovsyannikov, Ruslan A1 - Karlsson, P. A1 - Lundqvist, M. A1 - Lupulescu, C. A1 - Eberhardt, W. A1 - Föhlisch, Alexander A1 - Svensson, S. A1 - Martensson, N. T1 - Principles and operation of a new type of electron spectrometer - ArTOF JF - Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy N2 - A new energy and angular electron analyzer ArTOF (Angular Resolved Time of Flight) is described. The analyzer is based on simultaneous measurement of flight times and angles in an advanced electron lens system. In angular modes the new analyzer combines an increase in transmission by almost three orders of magnitude with improved resolution, in comparison to standard state-of-the-art electron spectrometers. In this report we describe some design principles and we give a review of calibration and alignment procedures necessary for the use of the ArTOF on a synchrotron radiation facility. Our program scripts to handle the large datasets are also discussed. Furthermore we give a broad description of the new research fields that benefit from the use of the ArTOF and give a short summary of the first results of angle resolved photoemission measurement with ArTOF using the single-bunch X-ray pulses from the BESSY II storage ring facility. (C) 2013 Published by Elsevier B.V. KW - ARPES KW - Time of flight KW - Synchrotron KW - Electron spectroscopy Y1 - 2013 U6 - https://doi.org/10.1016/j.elspec.2013.08.005 SN - 0368-2048 SN - 1873-2526 VL - 191 IS - 12 SP - 92 EP - 103 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Kunnus, Kristjan A1 - Josefsson, Ida A1 - Schreck, Simon A1 - Quevedo, Wilson A1 - Miedema, Piter S. A1 - Techert, Simone A1 - de Groot, Frank M. F. A1 - Odelius, Michael A1 - Wernet, Philippe A1 - Föhlisch, Alexander T1 - From Ligand Fields to Molecular Orbitals: Probing the Local Valence Electronic Structure of Ni2+ in Aqueous Solution with Resonant Inelastic X-ray Scattering JF - The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces & biophysical chemistry N2 - Bonding of the Ni2+(aq) complex is investigated with an unprecedented combination of resonant inelastic X-ray scattering (RIXS) measurements and ab initio calculations at the Ni L absorption edge. The spectra directly reflect the relative energies of the ligand-field and charge-transfer valence-excited states. They give element-specific access with atomic resolution to the ground-state electronic structure of the complex and allow quantification of ligand-field strength and 3d-3d electron correlation interactions in the Ni2+(aq) complex. The experimentally determined ligand-field strength is 10Dq = 1.1 eV. This and the Racah parameters characterizing 3d-3d Coulomb interactions B = 0.13 eV and C = 0.42 eV as readily derived from the measured energies match very well with the results from UV-vis spectroscopy. Our results demonstrate how L-edge RIXS can be used to complement existing spectroscopic tools for the investigation of bonding in 3d transition-metal coordination compounds in solution. The ab initio RASPT2 calculation is successfully used to simulate the L-edge RIXS spectra. Y1 - 2013 U6 - https://doi.org/10.1021/jp4100813 SN - 1520-6106 VL - 117 IS - 51 SP - 16512 EP - 16521 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Kliem, Bernhard A1 - Su, Y. N. A1 - van Ballegooijen, A. A. A1 - DeLuca, E. E. T1 - Magnetohydrodynamic modeling of the solar eruption on 2010 APRIL 8 JF - The astrophysical journal : an international review of spectroscopy and astronomical physics N2 - The structure of the coronal magnetic field prior to eruptive processes and the conditions for the onset of eruption are important issues that can be addressed through studying the magnetohydrodynamic (MHD) stability and evolution of nonlinear force-free field (NLFFF) models. This paper uses data-constrained NLFFF models of a solar active region (AR) that erupted on 2010 April 8 as initial conditions in MHD simulations. These models, constructed with the techniques of flux rope insertion and magnetofrictional relaxation (MFR), include a stable, an approximately marginally stable, and an unstable configuration. The simulations confirm previous related results of MFR runs, particularly that stable flux rope equilibria represent key features of the observed pre-eruption coronal structure very well, and that there is a limiting value of the axial flux in the rope for the existence of stable NLFFF equilibria. The specific limiting value is located within a tighter range, due to the sharper discrimination between stability and instability by the MHD description. The MHD treatment of the eruptive configuration yields a very good agreement with a number of observed features, like the strongly inclined initial rise path and the close temporal association between the coronal mass ejection and the onset of flare reconnection. Minor differences occur in the velocity of flare ribbon expansion and in the further evolution of the inclination; these can be eliminated through refined simulations. We suggest that the slingshot effect of horizontally bent flux in the source region of eruptions can contribute significantly to the inclination of the rise direction. Finally, we demonstrate that the onset criterion, formulated in terms of a threshold value for the axial flux in the rope, corresponds very well to the threshold of the torus instability in the considered AR. KW - magnetohydrodynamics (MHD) KW - Sun: corona KW - Sun: coronal mass ejections (CMEs) KW - Sun: filaments, prominences KW - Sun: flares KW - Sun: magnetic fields Y1 - 2013 U6 - https://doi.org/10.1088/0004-637X/779/2/129 SN - 0004-637X SN - 1538-4357 VL - 779 IS - 2 PB - IOP Publ. Ltd. CY - Bristol ER - TY - THES A1 - Galeazzi, Filippo T1 - Towards realistic modeling of relativistic stars Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Stoyanov, Hristiyan A1 - Kollosche, Matthias A1 - Risse, Sebastian A1 - Wache, Remi A1 - Kofod, Guggi T1 - Soft conductive elastomer materials for stretchable electronics and voltage controlled artificial muscles JF - Advanced materials N2 - Block copolymer elastomer conductors (BEC) are mixtures of block copolymers grafted with conducting polymers, which are found to support very large strains, while retaining a high level of conductivity. These novel materials may find use in stretchable electronics. The use of BEC is demonstrated in a capacitive strain sensor and in an artificial muscle of the dielectric elastomer actuator type, supporting more than 100% actuation strain and capacity strain sensitivity up to 300%. KW - soft electrical connections KW - stretchable electronics KW - elastic conductor KW - compliant electrodes Y1 - 2013 U6 - https://doi.org/10.1002/adma.201202728 SN - 0935-9648 VL - 25 IS - 4 SP - 578 EP - 583 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Huebener, R. A1 - Mari, Andrea A1 - Eisert, Jens T1 - Wick's theorem for matrix product states JF - Physical review letters N2 - Matrix product states and their continuous analogues are variational classes of states that capture quantum many-body systems or quantum fields with low entanglement; they are at the basis of the density-matrix renormalization group method and continuous variants thereof. In this work we show that, generically, N-point functions of arbitrary operators in discrete and continuous translation invariant matrix product states are completely characterized by the corresponding two- and three-point functions. Aside from having important consequences for the structure of correlations in quantum states with low entanglement, this result provides a new way of reconstructing unknown states from correlation measurements, e. g., for one-dimensional continuous systems of cold atoms. We argue that such a relation of correlation functions may help in devising perturbative approaches to interacting theories. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.110.040401 SN - 0031-9007 VL - 110 IS - 4 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Bauer, Maximilian A1 - Metzler, Ralf T1 - In vivo facilitated diffusion model JF - PLoS one N2 - Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and one-dimensional sliding along the DNA contour is still beneficial in the crowded interior of cells is highly disputed. Here we use a simple model for the bacterial genome inside the cell and present a semi-analytical model for the in vivo target search of transcription factors within the facilitated diffusion framework. Without having to resort to extensive simulations we determine the mean search time of a lac repressor in a living E. coli cell by including parameters deduced from experimental measurements. The results agree very well with experimental findings, and thus the facilitated diffusion picture emerges as a quantitative approach to gene regulation in living bacteria cells. Furthermore we see that the search time is not very sensitive to the parameters characterizing the DNA configuration and that the cell seems to operate very close to optimal conditions for target localization. Local searches as implied by the colocalization mechanism are only found to mildly accelerate the mean search time within our model. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0053956 SN - 1932-6203 VL - 8 IS - 1 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Godec, Aljaz A1 - Metzler, Ralf T1 - Finite-Time effects and ultraweak ergodicity breaking in superdiffusive dynamics JF - Physical review letters N2 - We study the ergodic properties of superdiffusive, spatiotemporally coupled Levy walk processes. For trajectories of finite duration, we reveal a distinct scatter of the scaling exponents of the time averaged mean squared displacement (delta x(2)) over bar around the ensemble value 3 - alpha (1 < alpha < 2) ranging from ballistic motion to subdiffusion, in strong contrast to the behavior of subdiffusive processes. In addition we find a significant dependence of the average of (delta x(2)) over bar over an ensemble of trajectories as a function of the finite measurement time. This so-called finite-time amplitude depression and the scatter of the scaling exponent is vital in the quantitative evaluation of superdiffusive processes. Comparing the long time average of the second moment with the ensemble mean squared displacement, these only differ by a constant factor, an ultraweak ergodicity breaking. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.110.020603 SN - 0031-9007 VL - 110 IS - 2 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Schulz, Johannes H. P. A1 - Barkai, Eli A1 - Metzler, Ralf T1 - Aging effects and population splitting in single-particle trajectoryaverages JF - Physical review letters N2 - We study time averages of single particle trajectories in scale-free anomalous diffusion processes, in which the measurement starts at some time t(a) > 0 after initiation of the process at t = 0. Using aging renewal theory, we show that for such nonstationary processes a large class of observables are affected by a unique aging function, which is independent of boundary conditions or the external forces. Moreover, we discuss the implications of aging induced population splitting: with growing age ta of the process, an increasing fraction of particles remains motionless in a measurement of fixed duration. Consequences for single biomolecule tracking in live cells are discussed. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.110.020602 SN - 0031-9007 SN - 1079-7114 VL - 110 IS - 2 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Barbosa Pfannes, Eva Katharina A1 - Anielski, Alexander A1 - Gerhardt, Matthias A1 - Beta, Carsten T1 - Intracellular photoactivation of caged cGMP induces myosin II and actin responses in motile cells JF - Integrative biology N2 - Cyclic GMP (cGMP) is a ubiquitous second messenger in eukaryotic cells. It is assumed to regulate the association of myosin II with the cytoskeleton of motile cells. When cells of the social amoeba Dictyostelium discoideum are exposed to chemoattractants or to increased osmotic stress, intracellular cGMP levels rise, preceding the accumulation of myosin II in the cell cortex. To directly investigate the impact of intracellular cGMP on cytoskeletal dynamics in a living cell, we released cGMP inside the cell by laser-induced photo-cleavage of a caged precursor. With this approach, we could directly show in a live cell experiment that an increase in intracellular cGMP indeed induces myosin II to accumulate in the cortex. Unexpectedly, we observed for the first time that also the amount of filamentous actin in the cell cortex increases upon a rise in the cGMP concentration, independently of cAMP receptor activation and signaling. We discuss our results in the light of recent work on the cGMP signaling pathway and suggest possible links between cGMP signaling and the actin system. Y1 - 2013 U6 - https://doi.org/10.1039/c3ib40109j SN - 1757-9694 SN - 1757-9708 VL - 5 IS - 12 SP - 1456 EP - 1463 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf T1 - Population splitting, trapping, and non-ergodicity in heterogeneous diffusion processes JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - We consider diffusion processes with a spatially varying diffusivity giving rise to anomalous diffusion. Such heterogeneous diffusion processes are analysed for the cases of exponential, power-law, and logarithmic dependencies of the diffusion coefficient on the particle position. Combining analytical approaches with stochastic simulations, we show that the functional form of the space-dependent diffusion coefficient and the initial conditions of the diffusing particles are vital for their statistical and ergodic properties. In all three cases a weak ergodicity breaking between the time and ensemble averaged mean squared displacements is observed. We also demonstrate a population splitting of the time averaged traces into fast and slow diffusers for the case of exponential variation of the diffusivity as well as a particle trapping in the case of the logarithmic diffusivity. Our analysis is complemented by the quantitative study of the space coverage, the diffusive spreading of the probability density, as well as the survival probability. Y1 - 2013 U6 - https://doi.org/10.1039/c3cp53056f SN - 1463-9076 SN - 1463-9084 VL - 15 IS - 46 SP - 20220 EP - 20235 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Schleussner, Carl-Friedrich A1 - Feulner, G. T1 - A volcanically triggered regime shift in the subpolar North Atlantic Ocean as a possible origin of the Little Ice Age JF - Climate of the past : an interactive open access journal of the European Geosciences Union N2 - Among the climatological events of the last millennium, the Northern Hemisphere Medieval Climate Anomaly succeeded by the Little Ice Age are of exceptional importance. The origin of these regional climate anomalies remains a subject of debate and besides external influences like solar and volcanic activity, internal dynamics of the climate system might have also played a dominant role. Here, we present transient last millennium simulations of the fully coupled model of intermediate complexity Climber 3a forced with stochastically reconstructed wind-stress fields. Our results indicate that short-lived volcanic eruptions might have triggered a cascade of sea ice ocean feedbacks in the North Atlantic, ultimately leading to a persistent regime shift in the ocean circulation. We find that an increase in the Nordic Sea sea-ice extent on decadal timescales as a consequence of major volcanic eruptions in our model leads to a spin-up of the subpolar gyre and a weakened Atlantic meridional overturning circulation, eventually causing a persistent, basin-wide cooling. These results highlight the importance of regional climate feedbacks such as a regime shift in the subpolar gyre circulation for understanding the dynamics of past and future climate. Y1 - 2013 U6 - https://doi.org/10.5194/cp-9-1321-2013 SN - 1814-9324 SN - 1814-9332 VL - 9 IS - 3 SP - 1321 EP - 1330 PB - Copernicus CY - Göttingen ER - TY - THES A1 - Brödel, Andreas K. T1 - Novel cell-free systems for increasing efficiency and versatility of protein synthesis Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Dell'Angela, M. A1 - Anniyev, Toyli A1 - Beye, Martin A1 - Coffee, Ryan A1 - Föhlisch, Alexander A1 - Gladh, J. A1 - Katayama, T. A1 - Kaya, S. A1 - Krupin, O. A1 - LaRue, J. A1 - Mogelhoj, A. A1 - Nordlund, D. A1 - Norskov, J. K. A1 - Oberg, H. A1 - Ogasawara, H. A1 - Ostrom, H. A1 - Pettersson, Lars G. M. A1 - Schlotter, W. F. A1 - Sellberg, J. A. A1 - Sorgenfrei, Florian A1 - Turner, J. J. A1 - Wolf, M. A1 - Wurth, W. A1 - Nilsson, A. T1 - Real-time observation of surface bond breaking with an X-ray Laser JF - Science N2 - We used the Linac Coherent Light Source free-electron x-ray laser to probe the electronic structure of CO molecules as their chemisorption state on Ru(0001) changes upon exciting the substrate by using a femtosecond optical laser pulse. We observed electronic structure changes that are consistent with a weakening of the CO interaction with the substrate but without notable desorption. A large fraction of the molecules (30%) was trapped in a transient precursor state that would precede desorption. We calculated the free energy of the molecule as a function of the desorption reaction coordinate using density functional theory, including van der Waals interactions. Two distinct adsorption wells-chemisorbed and precursor state separated by an entropy barrier-explain the anomalously high prefactors often observed in desorption of molecules from metals. Y1 - 2013 U6 - https://doi.org/10.1126/science.1231711 SN - 0036-8075 VL - 339 IS - 6125 SP - 1302 EP - 1305 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Jechow, Andreas A1 - Norton, B. G. A1 - Händel, S. A1 - Blums, V. A1 - Streed, E. W. A1 - Kielpinski, D. T1 - Controllable optical phase shift over one radian from a single isolated atom JF - Physical review letters N2 - Fundamental optics such as lenses and prisms work by applying phase shifts of several radians to incoming light, and rapid control of such phase shifts is crucial to telecommunications. However, large, controllable optical phase shifts have remained elusive for isolated quantum systems. We have used a single trapped atomic ion to induce and measure a large optical phase shift of 1.3 +/- 0.1 radians in light scattered by the atom. Spatial interferometry between the scattered light and unscattered illumination light enables us to isolate the phase shift in the scattered component. The phase shift achieves the maximum value allowed by atomic theory over the accessible range of laser frequencies, pointing out new opportunities in microscopy and nanophotonics. Single-atom phase shifts of this magnitude open up new quantum information protocols, in particular long-range quantum phase-shift-keying cryptography. DOI: 10.1103/PhysRevLett.110.113605 Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.110.113605 SN - 0031-9007 VL - 110 IS - 11 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Beye, Martin A1 - Föhlisch, Alexander T1 - Soft X-ray probes of ultrafast dynamics for heterogeneous catalysis JF - Chemical physics : a journal devoted to experimental and theoretical research involving problems of both a chemical and physical nature N2 - Soft X-ray spectroscopy is one of the best tools to directly address the electronic structure, the driving force of chemical reactions. It enables selective studies on sample surfaces to single out reaction centers in heterogeneous catalytic reactions. With core-hole clock methods, specific dynamics are related to the femtosecond life time of a core-hole. Typically, this method is used with photoemission spectroscopy, but advancements in soft X-ray emission techniques render more specific studies possible. With the advent of bright femtosecond pulsed soft X-ray sources, highly selective pump-probe X-ray emission studies are enabled with temporal resolutions down to tens of femtoseconds. This finally allows to study dynamics in the electronic structure of adsorbed reaction centers on the whole range of relevant time scales - closing the gap between kinetic soft X-ray studies and the atto- to femtosecond core-hole clock techniques. KW - Core-hole clock KW - Resonant inelastic X-ray scattering KW - Ultrafast surface science KW - Photoelectron spectroscopy Y1 - 2013 U6 - https://doi.org/10.1016/j.chemphys.2012.03.023 SN - 0301-0104 SN - 1873-4421 VL - 414 IS - 5 SP - 130 EP - 138 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Westendorf, Christian A1 - Negrete, Jose A1 - Bae, Albert J. A1 - Sandmann, Rabea A1 - Bodenschatz, Eberhard A1 - Beta, Carsten T1 - Actin cytoskeleton of chemotactic amoebae operates close to the onset of oscillations JF - Proceedings of the National Academy of Sciences of the United States of America N2 - The rapid reorganization of the actin cytoskeleton in response to external stimuli is an essential property of many motile eukaryotic cells. Here, we report evidence that the actin machinery of chemotactic Dictyostelium cells operates close to an oscillatory instability. When averaging the actin response of many cells to a short pulse of the chemoattractant cAMP, we observed a transient accumulation of cortical actin reminiscent of a damped oscillation. At the single-cell level, however, the response dynamics ranged from short, strongly damped responses to slowly decaying, weakly damped oscillations. Furthermore, in a small subpopulation, we observed self-sustained oscillations in the cortical F-actin concentration. To substantiate that an oscillatory mechanism governs the actin dynamics in these cells, we systematically exposed a large number of cells to periodic pulse trains of different frequencies. Our results indicate a resonance peak at a stimulation period of around 20 s. We propose a delayed feedback model that explains our experimental findings based on a time-delay in the regulatory network of the actin system. To test the model, we performed stimulation experiments with cells that express GFP-tagged fusion proteins of Coronin and actin-interacting protein 1, as well as knockout mutants that lack Coronin and actin-interacting protein 1. These actin-binding proteins enhance the disassembly of actin filaments and thus allow us to estimate the delay time in the regulatory feedback loop. Based on this independent estimate, our model predicts an intrinsic period of 20 s, which agrees with the resonance observed in our periodic stimulation experiments. KW - Dictyostelium discoideum KW - microfluidics KW - caged cAMP KW - delay-differential equation Y1 - 2013 U6 - https://doi.org/10.1073/pnas.1216629110 SN - 0027-8424 VL - 110 IS - 10 SP - 3853 EP - 3858 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Vahabi, Mahsa A1 - Schulz, Johannes H. P. A1 - Shokri, Babak A1 - Metzler, Ralf T1 - Area coverage of radial Levy flights with periodic boundary conditions JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - We consider the area coverage of radial Levy flights in a finite square area with periodic boundary conditions. From simulations we show how the fractal path dimension d(f) and thus the degree of area coverage depends on the number of steps of the trajectory, the size of the area, and the resolution of the applied box counting algorithm. For sufficiently long trajectories and not too high resolution, the fractal dimension returned by the box counting method equals two, and in that sense the Levy flight fully covers the area. Otherwise, the determined fractal dimension equals the stable index of the distribution of jump lengths of the Levy flight. We provide mathematical expressions for the turnover between these two scaling regimes. As complementary methods to analyze confined Levy flights we investigate fractional order moments of the position for which we also provide scaling arguments. Finally, we study the time evolution of the probability density function and the first passage time density of Levy flights in a square area. Our findings are of interest for a general understanding of Levy flights as well as for the analysis of recorded trajectories of animals searching for food or for human motion patterns. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.87.042136 SN - 1539-3755 VL - 87 IS - 4 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Tiscareno, Matthew S. A1 - Mitchell, Colin J. A1 - Murray, Carl D. A1 - Di Nino, Daiana A1 - Hedman, Matthew M. A1 - Schmidt, Jürgen A1 - Burns, Joseph A. A1 - Cuzzi, Jeffrey N. A1 - Porco, Carolyn C. A1 - Beurle, Kevin A1 - Evans, Michael W. T1 - Observations of Ejecta clouds produced by impacts onto Saturn's rings JF - Science N2 - We report observations of dusty clouds in Saturn's rings, which we interpret as resulting from impacts onto the rings that occurred between 1 and 50 hours before the clouds were observed. The largest of these clouds was observed twice; its brightness and cant angle evolved in a manner consistent with this hypothesis. Several arguments suggest that these clouds cannot be due to the primary impact of one solid meteoroid onto the rings, but rather are due to the impact of a compact stream of Saturn-orbiting material derived from previous breakup of a meteoroid. The responsible interplanetary meteoroids were initially between 1 centimeter and several meters in size, and their influx rate is consistent with the sparse prior knowledge of smaller meteoroids in the outer solar system. Y1 - 2013 U6 - https://doi.org/10.1126/science.1233524 SN - 0036-8075 VL - 340 IS - 6131 SP - 460 EP - 464 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Isaeva, Olga B. A1 - Kuznetsov, Alexey S. A1 - Kuznetsov, Sergey P. T1 - Hyperbolic chaos of standing wave patterns generated parametrically by a modulated pump source JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - We outline a possibility of hyperbolic chaotic dynamics associated with the expanding circle map for spatial phases of parametrically excited standing wave patterns. The model system is governed by a one-dimensional wave equation with nonlinear dissipation. The phenomenon arises due to the pump modulation providing the alternating excitation of modes with the ratio of characteristic scales 1 : 3. DOI: 10.1103/PhysRevE.87.040901 Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.87.040901 SN - 1539-3755 VL - 87 IS - 4 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Jeon, Jae-Hyung A1 - Leijnse, Natascha A1 - Oddershede, Lene B. A1 - Metzler, Ralf T1 - Anomalous diffusion and power-law relaxation of the time averaged mean squared displacement in worm-like micellar solutions JF - New journal of physics : the open-access journal for physics N2 - We report the results of single tracer particle tracking by optical tweezers and video microscopy in micellar solutions. From careful analysis in terms of different stochastic models, we show that the polystyrene tracer beads of size 0.52-2.5 mu m after short-time normal diffusion turn over to perform anomalous diffusion of the form < r(2)(t)> similar or equal to t(alpha) with alpha approximate to 0.3. This free anomalous diffusion is ergodic and consistent with a description in terms of the generalized Langevin equation with a power-law memory kernel. With optical tweezers tracking, we unveil a power-law relaxation over several decades in time to the thermal plateau value under the confinement of the harmonic tweezer potential, as predicted previously (Phys. Rev. E 85 021147 (2012)). After the subdiffusive motion in the millisecond range, the motion becomes faster and turns either back to normal Brownian diffusion or to even faster superdiffusion, depending on the size of the tracer beads. Y1 - 2013 U6 - https://doi.org/10.1088/1367-2630/15/4/045011 SN - 1367-2630 VL - 15 IS - 4 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Heydari, Esmaeil A1 - Flehr, Roman A1 - Stumpe, Joachim T1 - Influence of spacer layer on enhancement of nanoplasmon-assisted random lasing JF - Applied physics letters N2 - Threshold reduction and emission enhancement are reported for a gold nanoparticle-based waveguided random laser, exploiting the localized surface plasmon resonance excitation. It was experimentally found that a proper thickness of the spacer layer between the gold nanoparticles and the gain layer enhances the random laser performance. It tunes the coupling between the gain polymer and the gold nanoparticles and avoids the quenching of emission in close contact to the gold nanoparticles which is considered as one of the main sources of loss in the current laser system. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4800776] Y1 - 2013 U6 - https://doi.org/10.1063/1.4800776 SN - 0003-6951 VL - 102 IS - 13 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Katayama, T. A1 - Anniyev, Toyli A1 - Beye, Martin A1 - Coffee, Ryan A1 - Dell'Angela, M. A1 - Föhlisch, Alexander A1 - Gladh, J. A1 - Kaya, S. A1 - Krupin, O. A1 - Nilsson, A. A1 - Nordlund, D. A1 - Schlotter, W. F. A1 - Sellberg, J. A. A1 - Sorgenfrei, Florian A1 - Turner, J. J. A1 - Wurth, W. A1 - Öström, H. A1 - Ogasawara, H. T1 - Ultrafast soft X-ray emission spectroscopy of surface adsorbates using an X-ray free electron laser JF - Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy N2 - We report on an experimental system designed to probe chemical reactions on solid surfaces on a sub-picosecond timescale using soft X-ray emission spectroscopy at the Linac Coherent Light Source (LCLS) free electron laser (FEL) at the SLAC National Accelerator Laboratory. We analyzed the O 1s X-ray emission spectra recorded from atomic oxygen adsorbed on a Ru(0001) surface at a synchrotron beamline (SSRL, BL13-2) and an FEL beamline (LCLS, SXR). We have demonstrated conditions that provide negligible amount of FEL induced damage of the sample. In addition we show that the setup is capable of tracking the temporal evolution of electronic structure during a surface reaction of submonolayer quantities of CO molecules desorbing from the surface. KW - X-ray emission spectroscopy KW - Surface science KW - Free electron laser KW - Ultrafast Y1 - 2013 U6 - https://doi.org/10.1016/j.elspec.2013.03.006 SN - 0368-2048 VL - 187 IS - 1 SP - 9 EP - 14 PB - Elsevier CY - Amsterdam ER - TY - THES A1 - Schleussner, Carl-Friedrich T1 - Variability and trend of the North Atlantic ocean circulation in past and future climate Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Anggraini, Ade T1 - The 26 May 2006 yogyakarta earthquake, aftershocks and interactions Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Temirbayev, Amirkhan A. A1 - Nalibayev, Yerkebulan D. A1 - Zhanabaev, Zeinulla Zh. A1 - Ponomarenko, Vladimir I. A1 - Rosenblum, Michael T1 - Autonomous and forced dynamics of oscillator ensembles with global nonlinear coupling an experimental study JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - We perform experiments with 72 electronic limit-cycle oscillators, globally coupled via a linear or nonlinear feedback loop. While in the linear case we observe a standard Kuramoto-like synchronization transition, in the nonlinear case, with increase of the coupling strength, we first observe a transition to full synchrony and then a desynchronization transition to a quasiperiodic state. However, in this state the ensemble remains coherent so that the amplitude of the mean field is nonzero, but the frequency of the mean field is larger than frequencies of all oscillators. Next, we analyze effects of common periodic forcing of the linearly or nonlinearly coupled ensemble and demonstrate regimes when the mean field is entrained by the force whereas the oscillators are not. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.87.062917 SN - 1539-3755 SN - 1550-2376 VL - 87 IS - 6 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Könnecke, Rene A1 - Follath, R. A1 - Pontius, N. A1 - Schlappa, J. A1 - Eggenstein, F. A1 - Zeschke, T. A1 - Bischoff, P. A1 - Schmidt, J. -S. A1 - Noll, T. A1 - Trabant, C. A1 - Schreck, S. A1 - Wernet, Ph. A1 - Eisebitt, S. A1 - Senf, F. A1 - Schuessler-Langeheine, Christian A1 - Erko, A. A1 - Föhlisch, Alexander T1 - The confocal plane grating spectrometer at BESSY II JF - Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy N2 - At BESSY II a confocal plane grating spectrometer for resonant inelastic X-ray scattering (RIXS) is currently under commissioning. The new endstation operates with a source size of 4 x 1 mu m(2) provided by its dedicated beamline. The RIXS-spectrometer covers an energy range from 50 eV to 1000 eV, providing a resolving power E/Delta E of 5000-15,000. The beamline allows full polarization control and gives a photon flux of up to 7 x 10(14) photons/s/0.1 A/0.1%bandwidth by offering a resolving power E/Delta E of 4000-12,000. KW - Resonant inelastic X-ray scattering KW - Soft X-ray monochromator KW - High transmission micro focus beamline KW - Plane grating emission spectrometer Y1 - 2013 U6 - https://doi.org/10.1016/j.elspec.2012.11.003 SN - 0368-2048 VL - 188 SP - 133 EP - 139 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Beye, Martin A1 - Wernet, Ph. A1 - Schüßler-Langeheine, Christian A1 - Föhlisch, Alexander T1 - Time resolved resonant inelastic X-ray scattering: a supreme tool to understand dynamics in solids and molecules JF - Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy N2 - Dynamics in materials typically involve different degrees of freedom, like charge, lattice, orbital and spin in a complex interplay. Time-resolved resonant inelastic X-ray scattering (RIXS) as a highly selective tool can provide unique insight and follow the details of dynamical processes while resolving symmetries, chemical and charge states, momenta, spin configurations, etc. In this paper, we review examples where the intrinsic scattering duration time is used to study femtosecond phenomena. Free-electron lasers access timescales starting in the sub-ps range through pump-probe methods and synchrotrons study the time scales longer than tens of ps. In these examples, time-resolved resonant inelastic X-ray scattering is applied to solids as well as molecular systems. KW - Resonant inelastic X-ray scattering KW - Ultrafast spectroscopy KW - Phase transitions KW - Molecular dynamics Y1 - 2013 U6 - https://doi.org/10.1016/j.elspec.2013.04.013 SN - 0368-2048 VL - 188 IS - 3 SP - 172 EP - 182 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Cherstvy, Andrey G. A1 - Teif, V. B. T1 - Structure-driven homology pairing of chromatin fibers the role of electrostatics and protein-induced bridging JF - Journal of biological physics : emphasizing physical principles in biological research ; an international journal for the formulation and application of mathematical models in the biological sciences N2 - Chromatin domains formed in vivo are characterized by different types of 3D organization of interconnected nucleosomes and architectural proteins. Here, we quantitatively test a hypothesis that the similarities in the structure of chromatin fibers (which we call "structural homology") can affect their mutual electrostatic and protein-mediated bridging interactions. For example, highly repetitive DNA sequences in heterochromatic regions can position nucleosomes so that preferred inter-nucleosomal distances are preserved on the surfaces of neighboring fibers. On the contrary, the segments of chromatin fiber formed on unrelated DNA sequences have different geometrical parameters and lack structural complementarity pivotal for stable association and cohesion. Furthermore, specific functional elements such as insulator regions, transcription start and termination sites, and replication origins are characterized by strong nucleosome ordering that might induce structure-driven iterations of chromatin fibers. We propose that shape-specific protein-bridging interactions facilitate long-range pairing of chromatin fragments, while for closely-juxtaposed fibers electrostatic forces can in addition yield fine-tuned structure-specific recognition and pairing. These pairing effects can account for some features observed for mitotic and inter-phase chromatins. KW - Chromatin pairing KW - Homology KW - Electrostatics KW - Shape recognition KW - Long-range bridging Y1 - 2013 U6 - https://doi.org/10.1007/s10867-012-9294-4 SN - 0092-0606 SN - 1573-0689 VL - 39 IS - 3 SP - 363 EP - 385 PB - Springer CY - Dordrecht ER - TY - THES A1 - Körnig, André T1 - Assembled biogenic magnetic nanoparticles : proberties of magnetosome chains and their stability against external magnetic fields Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Verma, Meetu T1 - The evolution and decay of sunspots : a hight-resolution study of flows and magnetic fields in and around sunspots Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Bromke, Marta T1 - On the localization and physiological function of bitter taste receptors Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Jocher, Georg T1 - Charakterisierung der arktischen bodennahen Turbulenz unter Verwendung verschiedener Methoden der Flussberechnung und daraus resultierende Möglichkeiten für die Berechnung der bodennahen turbulenten Flüsse im regionalen Klimamodell HIRHAM5 Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Heydari, Esmaiel T1 - Optical resonance for label-free biosensing and nanoplasmonic emission enhancement Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Maity, Alok Kumar A1 - Bandyopadhyay, Arnab A1 - Chattopadhyay, Sudip A1 - Chaudhuri, Jyotipratim Ray A1 - Metzler, Ralf A1 - Chaudhury, Pinaki A1 - Banik, Suman K. T1 - Quantification of noise in bifunctionality-induced post-translational modification JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of a bacterial two-component system. The proposed model takes into account post-translational modifications in terms of elementary phosphotransfer kinetics. Sources of fluctuations due to autophosphorylation, kinase, and phosphatase activity of the sensor kinase have been considered in the model via Langevin equations, which are then solved within the framework of linear noise approximation. The resultant analytical expression of phosphorylated response regulators are then used to quantify the noise profile of biologically motivated single and branched pathways. Enhancement and reduction of noise in terms of extra phosphate outflux and influx, respectively, have been analyzed for the branched system. Furthermore, the role of fluctuations of the network output in the regulation of a promoter with random activation-deactivation dynamics has been analyzed. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.88.032716 SN - 1539-3755 VL - 88 IS - 3 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Jeon, Jae-Hyung A1 - Barkai, Eli A1 - Metzler, Ralf T1 - Noisy continuous time random walks JF - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr N2 - Experimental studies of the diffusion of biomolecules within biological cells are routinely confronted with multiple sources of stochasticity, whose identification renders the detailed data analysis of single molecule trajectories quite intricate. Here, we consider subdiffusive continuous time random walks that represent a seminal model for the anomalous diffusion of tracer particles in complex environments. This motion is characterized by multiple trapping events with infinite mean sojourn time. In real physical situations, however, instead of the full immobilization predicted by the continuous time random walk model, the motion of the tracer particle shows additional jiggling, for instance, due to thermal agitation of the environment. We here present and analyze in detail an extension of the continuous time random walk model. Superimposing the multiple trapping behavior with additive Gaussian noise of variable strength, we demonstrate that the resulting process exhibits a rich variety of apparent dynamic regimes. In particular, such noisy continuous time random walks may appear ergodic, while the bare continuous time random walk exhibits weak ergodicity breaking. Detailed knowledge of this behavior will be useful for the truthful physical analysis of experimentally observed subdiffusion. Y1 - 2013 U6 - https://doi.org/10.1063/1.4816635 SN - 0021-9606 SN - 1089-7690 VL - 139 IS - 12 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Rössle, Matthias A1 - Wang, C. N. A1 - Marsik, P. A1 - Yazdi-Rizi, Meghdad A1 - Kim, K. W. A1 - Dubroka, Adam A1 - Marozau, Ivan A1 - Schneider, C. W. A1 - Humlicek, J. A1 - Baeriswyl, D. A1 - Bernhard, C. T1 - Optical probe of ferroelectric order in bulk and thin-film perovskite titanates JF - Physical review : B, Condensed matter and materials physics N2 - We have measured the temperature dependence of the direct band gap Eg in SrTiO3 and BaTiO3 and related materials with quantum-paraelectric and ferroelectric properties using optical spectroscopy. We show that Eg exhibits an anomalous temperature dependence with pronounced changes in the vicinity of the ferroelectric transition that can be accounted for in terms of the Frohlich electron-phonon interaction with an optical phonon mode, the so-called soft mode. In addition, we demonstrate that these characteristic changes of Eg can be readily detected even in very thin films of SrTiO3 with a strain-induced ferroelectric order. Optical spectroscopy thus can be used as a rather sensitive probe of ferroelectric order in very thin films of these titanates and probably also in subsequent multilayers and devices. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevB.88.104110 SN - 1098-0121 VL - 88 IS - 10 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Liu, Rui A1 - Liu, Chang A1 - Xu, Yan A1 - Liu, Wei A1 - Kliem, Bernhard A1 - Wang, Haimin T1 - Observation of a moretown wave and wave-filament interactions associated with the renowned X9 flare on 1990 May 24 JF - The astrophysical journal : an international review of spectroscopy and astronomical physics N2 - Using Big Bear Solar Observatory film data recently digitized at NJIT, we investigate a Moreton wave associated with an X9 flare on 1990 May 24, as well as its interactions with four filaments F1-F4 located close to the flaring region. The interaction yields interesting insight into physical properties of both the wave and the filaments. The first clear Moreton wavefront appears at the flaring-region periphery at approximately the same time as the peak of a microwave burst and the first of two gamma-ray peaks. The wavefront propagates at different speeds ranging from 1500-2600 km s(-1) in different directions, reaching as far as 600 Mm away from the flaring site. Sequential chromospheric brightenings are observed ahead of the Moreton wavefront. A slower diffuse front at 300-600 km s(-1) is observed to trail the fast Moreton wavefront about one minute after the onset. The Moreton wave decelerates to similar to 550 km s(-1) as it sweeps through F1. The wave passage results in F1's oscillation which is featured by similar to 1 mHz signals with coherent Fourier phases over the filament, the activation of F3 and F4 followed by gradual recovery, but no disturbance in F2. Different height and magnetic environment together may account for the distinct responses of the filaments to the wave passage. The wavefront bulges at F4, whose spine is oriented perpendicular to the upcoming wavefront. The deformation of the wavefront is suggested to be due to both the forward inclination of the wavefront and the enhancement of the local Alfven speed within the filament channel. KW - Sun: filaments, prominences KW - Sun: flares KW - Sun: oscillations KW - waves Y1 - 2013 U6 - https://doi.org/10.1088/0004-637X/773/2/166 SN - 0004-637X VL - 773 IS - 2 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Tu, Rui A1 - Zhang, Hongping A1 - Ge, Maorong A1 - Huang, Guanwen T1 - A real-time ionospheric model based on GNSS Precise Point Positioning JF - Advances in space research N2 - This paper proposes a method of real-time monitoring and modeling the ionospheric Total Electron Content (TEC) by Precise Point Positioning (PPP). Firstly, the ionospheric TEC and receiver's Differential Code Biases (DCB) are estimated with the undifferenced raw observation in real-time, then the ionospheric TEC model is established based on the Single Layer Model (SLM) assumption and the recovered ionospheric TEC. In this study, phase observations with high precision are directly used instead of phase smoothed code observations. In addition, the DCB estimation is separated from the establishment of the ionospheric model which will limit the impacts of the SLM assumption impacts. The ionospheric model is established at every epoch for real time application. The method is validated with three different GNSS networks on a local, regional, and global basis. The results show that the method is feasible and effective, the real-time ionosphere and DCB results are very consistent with the IGS final products, with a bias of 1-2 TECU and 0.4 ns respectively. KW - Ionospheric monitoring and modeling KW - Precise Point Positioning (PPP) KW - Real time KW - Total Electron Content (TEC) KW - Global Navigation Satellite System (GNSS) KW - Differential Code Biases (DCB) Y1 - 2013 U6 - https://doi.org/10.1016/j.asr.2013.06.015 SN - 0273-1177 SN - 1879-1948 VL - 52 IS - 6 SP - 1125 EP - 1134 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Beye, Martin A1 - Schreck, S. A1 - Sorgenfrei, Florian A1 - Trabant, C. A1 - Pontius, N. A1 - Schüßler-Langeheine, C. A1 - Wurth, W. A1 - Föhlisch, Alexander T1 - Stimulated X-ray emission for materials science JF - Nature : the international weekly journal of science N2 - Resonant inelastic X-ray scattering and X-ray emission spectroscopy can be used to probe the energy and dispersion of the elementary low-energy excitations that govern functionality in matter: vibronic, charge, spin and orbital excitations(1-7). A key drawback of resonant inelastic X-ray scattering has been the need for high photon densities to compensate for fluorescence yields of less than a per cent for soft X-rays(8). Sample damage from the dominant non-radiative decays thus limits the materials to which such techniques can be applied and the spectral resolution that can be obtained. A means of improving the yield is therefore highly desirable. Here we demonstrate stimulated X-ray emission for crystalline silicon at photon densities that are easily achievable with free-electron lasers(9). The stimulated radiative decay of core excited species at the expense of non-radiative processes reduces sample damage and permits narrow-bandwidth detection in the directed beam of stimulated radiation. We deduce how stimulated X-ray emission can be enhanced by several orders of magnitude to provide, with high yield and reduced sample damage, a superior probe for low-energy excitations and their dispersion in matter. This is the first step to bringing nonlinear X-ray physics in the condensed phase from theory(10-16) to application. Y1 - 2013 U6 - https://doi.org/10.1038/nature12449 SN - 0028-0836 VL - 501 IS - 7466 SP - 191 EP - + PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Bojahr, Andre A1 - Herzog, Marc A1 - Mitzscherling, Steffen A1 - Maerten, Lena A1 - Schick, Daniel A1 - Goldshteyn, J. A1 - Leitenberger, Wolfram A1 - Shayduk, R. A1 - Gaal, P. A1 - Bargheer, Matias T1 - Brillouin scattering of visible and hard X-ray photons from optically synthesized phonon wavepackets JF - Optics express : the international electronic journal of optics N2 - We monitor how destructive interference of undesired phonon frequency components shapes a quasi-monochromatic hypersound wavepacket spectrum during its local real-time preparation by a nanometric transducer and follow the subsequent decay by nonlinear coupling. We prove each frequency component of an optical supercontinuum probe to be sensitive to one particular phonon wavevector in bulk material and cross-check this by ultrafast x-ray diffraction experiments with direct access to the lattice dynamics. Establishing reliable experimental techniques with direct access to the transient spectrum of the excitation is crucial for the interpretation in strongly nonlinear regimes, such as soliton formation. Y1 - 2013 U6 - https://doi.org/10.1364/OE.21.021188 SN - 1094-4087 VL - 21 IS - 18 SP - 21188 EP - 21197 PB - Optical Society of America CY - Washington ER - TY - JOUR A1 - Berenstein, Igal A1 - Beta, Carsten T1 - Cross-diffusion in the two-variable Oregonator model JF - Chaos : an interdisciplinary journal of nonlinear science N2 - We explore the effect of cross-diffusion on pattern formation in the two-variable Oregonator model of the Belousov-Zhabotinsky reaction. For high negative cross-diffusion of the activator (the activator being attracted towards regions of increased inhibitor concentration) we find, depending on the values of the parameters, Turing patterns, standing waves, oscillatory Turing patterns, and quasi-standing waves. For the inhibitor, we find that positive cross-diffusion (the inhibitor being repelled by increasing concentrations of the activator) can induce Turing patterns, jumping waves and spatially modulated bulk oscillations. We qualitatively explain the formation of these patterns. With one model we can explain Turing patterns, standing waves and jumping waves, which previously was done with three different models. Y1 - 2013 U6 - https://doi.org/10.1063/1.4816937 SN - 1054-1500 VL - 23 IS - 3 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Stich, Michael A1 - Casal, Alfonso A1 - Beta, Carsten T1 - Stabilization of standing waves through time-delay feedback JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - Standing waves are studied as solutions of a complex Ginzburg-Landau equation subjected to local and global time-delay feedback terms. The onset is described as an instability of the uniform oscillations with respect to spatially periodic perturbations. The solution of the standing wave pattern is given analytically and studied through simulations. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.88.042910 SN - 1539-3755 SN - 1550-2376 VL - 88 IS - 4 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Theves, Matthias A1 - Taktikos, Johannes A1 - Zaburdaev, Vasily A1 - Stark, Holger A1 - Beta, Carsten T1 - A bacterial swimmer with two alternating speeds of propagation JF - Biophysical journal N2 - We recorded large data sets of swimming trajectories of the soil bacterium Pseudomonas putida. Like other prokaryotic swimmers, P. putida exhibits a motion pattern dominated by persistent runs that are interrupted by turning events. An in-depth analysis of their swimming trajectories revealed that the majority of the turning events is characterized by an angle of phi(1) = 180 degrees (reversals). To a lesser extent, turning angles of phi(2 Sigma Sigma Sigma Sigma) = 00 are also found. Remarkably, we observed that, upon a reversal, the swimming speed changes by a factor of two on average a prominent feature of the motion pattern that, to our knowledge, has not been reported before. A theoretical model, based on the experimental values for the average run time and the rotational diffusion, recovers the mean-square displacement of P. putida if the two distinct swimming speeds are taken into account. Compared to a swimmer that moves with a constant intermediate speed, the mean-square displacement is strongly enhanced. We furthermore observed a negative dip in the directional autocorrelation at intermediate times, a feature that is only recovered in an extended model, where the nonexponential shape of the run-time distribution is taken into account. Y1 - 2013 U6 - https://doi.org/10.1016/j.bpj.2013.08.047 SN - 0006-3495 SN - 1542-0086 VL - 105 IS - 8 SP - 1915 EP - 1924 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - de Jong, S. A1 - Kukreja, R. A1 - Trabant, C. A1 - Pontius, N. A1 - Chang, C. F. A1 - Kachel, T. A1 - Beye, Martin A1 - Sorgenfrei, Florian A1 - Back, C. H. A1 - Braeuer, B. A1 - Schlotter, W. F. A1 - Turner, J. J. A1 - Krupin, O. A1 - Doehler, M. A1 - Zhu, D. A1 - Hossain, M. A. A1 - Scherz, A. O. A1 - Fausti, D. A1 - Novelli, F. A1 - Esposito, M. A1 - Lee, W. S. A1 - Chuang, Y. D. A1 - Lu, D. H. A1 - Moore, R. G. A1 - Yi, M. A1 - Trigo, M. A1 - Kirchmann, P. A1 - Pathey, L. A1 - Golden, M. S. A1 - Buchholz, Marcel A1 - Metcalf, P. A1 - Parmigiani, F. A1 - Wurth, W. A1 - Föhlisch, Alexander A1 - Schuessler-Langeheine, Christian A1 - Duerr, H. A. T1 - Speed limit of the insulator-metal transition in magnetite JF - Nature materials N2 - As the oldest known magnetic material, magnetite (Fe3O4) has fascinated mankind for millennia. As the first oxide in which a relationship between electrical conductivity and fluctuating/localized electronic order was shown(1), magnetite represents a model system for understanding correlated oxides in general. Nevertheless, the exact mechanism of the insulator-metal, or Verwey, transition has long remained inaccessible(2-8). Recently, three- Fe- site lattice distortions called trimeronswere identified as the characteristic building blocks of the low-temperature insulating electronically ordered phase(9). Here we investigate the Verwey transition with pump- probe X- ray diffraction and optical reflectivity techniques, and show how trimerons become mobile across the insulator-metal transition. We find this to be a two- step process. After an initial 300 fs destruction of individual trimerons, phase separation occurs on a 1.5 +/- 0.2 ps timescale to yield residual insulating and metallic regions. This work establishes the speed limit for switching in future oxide electronics(10). Y1 - 2013 U6 - https://doi.org/10.1038/NMAT3718 SN - 1476-1122 SN - 1476-4660 VL - 12 IS - 10 SP - 882 EP - 886 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Thomas, Philipp A1 - Matuschek, Hannes A1 - Grima, Ramon T1 - How reliable is the linear noise approximation of gene regulatory networks? JF - BMC genomics N2 - Background: The linear noise approximation (LNA) is commonly used to predict how noise is regulated and exploited at the cellular level. These predictions are exact for reaction networks composed exclusively of first order reactions or for networks involving bimolecular reactions and large numbers of molecules. It is however well known that gene regulation involves bimolecular interactions with molecule numbers as small as a single copy of a particular gene. It is therefore questionable how reliable are the LNA predictions for these systems. Results: We implement in the software package intrinsic Noise Analyzer (iNA), a system size expansion based method which calculates the mean concentrations and the variances of the fluctuations to an order of accuracy higher than the LNA. We then use iNA to explore the parametric dependence of the Fano factors and of the coefficients of variation of the mRNA and protein fluctuations in models of genetic networks involving nonlinear protein degradation, post-transcriptional, post-translational and negative feedback regulation. We find that the LNA can significantly underestimate the amplitude and period of noise-induced oscillations in genetic oscillators. We also identify cases where the LNA predicts that noise levels can be optimized by tuning a bimolecular rate constant whereas our method shows that no such regulation is possible. All our results are confirmed by stochastic simulations. Conclusion: The software iNA allows the investigation of parameter regimes where the LNA fares well and where it does not. We have shown that the parametric dependence of the coefficients of variation and Fano factors for common gene regulatory networks is better described by including terms of higher order than LNA in the system size expansion. This analysis is considerably faster than stochastic simulations due to the extensive ensemble averaging needed to obtain statistically meaningful results. Hence iNA is well suited for performing computationally efficient and quantitative studies of intrinsic noise in gene regulatory networks. Y1 - 2013 U6 - https://doi.org/10.1186/1471-2164-14-S4-S5 SN - 1471-2164 VL - 14 IS - 4 PB - BioMed Central CY - London ER - TY - JOUR A1 - Rahmani, H. A1 - Wendt, Martin A1 - Srianand, R. A1 - Noterdaeme, P. A1 - Petitjean, P. A1 - Molaro, P. A1 - Whitmore, J. B. A1 - Murphy, M. T. A1 - Centurion, Martin A1 - Fathivavsari, H. A1 - D'Odorico, S. A1 - Evans, T. M. A1 - Levshakov, S. A. A1 - Lopez, S. A1 - Martins, C. J. A. P. A1 - Reimers, D. A1 - Vladilo, G. T1 - The UVES large program for testing fundamental physics - II. Constraints on a change in mu towards quasar HE 0027-1836 JF - Monthly notices of the Royal Astronomical Society N2 - We present an accurate analysis of the H-2 absorption lines from the z(abs) similar to 2.4018 damped Ly alpha system towards HE 0027-1836 observed with the Very Large Telescope Ultraviolet and Visual Echelle Spectrograph (VLT/UVES) as a part of the European Southern Observatory Large Programme 'The UVES large programme for testing fundamental physics' to constrain the variation of proton-to-electron mass ratio, mu m(p)/m(e). We perform cross-correlation analysis between 19 individual exposures taken over three years and the combined spectrum to check the wavelength calibration stability. We notice the presence of a possible wavelength-dependent velocity drift especially in the data taken in 2012. We use available asteroids spectra taken with UVES close to our observations to confirm and quantify this effect. We consider single-and two-component Voigt profiles to model the observed H-2 absorption profiles. We use both linear regression analysis and Voigt profile fitting where Delta mu/mu is explicitly considered as an additional fitting parameter. The two-component model is marginally favoured by the statistical indicators and we get Delta mu/mu = -2.5 +/- 8.1(stat) +/- 6.2(sys) ppm. When we apply the correction to the wavelength-dependent velocity drift, we find Delta mu/mu = -7.6 +/- 8.1(stat) +/- 6.3(sys) ppm. It will be important to check the extent to which the velocity drift we notice in this study is present in UVES data used for previous Delta mu/mu measurements. KW - intergalactic medium KW - quasars: absorption lines KW - quasars: individual: HE 0027-1836 Y1 - 2013 U6 - https://doi.org/10.1093/mnras/stt1356 SN - 0035-8711 SN - 1365-2966 VL - 435 IS - 1 SP - 861 EP - 878 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Kienert, Lars Hendrik T1 - Climate-modelling studies of the faint young Sun problem and of the relation between the AMOC and a regional sea-level gradient Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Schulz, Johannes H. P. A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Correlated continuous time random walks - combining scale-invariance with long-range memory for spatial and temporal dynamics JF - Journal of physics : A, Mathematical and theoretical N2 - Standard continuous time random walk (CTRW) models are renewal processes in the sense that at each jump a new, independent pair of jump length and waiting time are chosen. Globally, anomalous diffusion emerges through scale-free forms of the jump length and/or waiting time distributions by virtue of the generalized central limit theorem. Here we present a modified version of recently proposed correlated CTRW processes, where we incorporate a power-law correlated noise on the level of both jump length and waiting time dynamics. We obtain a very general stochastic model, that encompasses key features of several paradigmatic models of anomalous diffusion: discontinuous, scale-free displacements as in Levy flights, scale-free waiting times as in subdiffusive CTRWs, and the long-range temporal correlations of fractional Brownian motion (FBM). We derive the exact solutions for the single-time probability density functions and extract the scaling behaviours. Interestingly, we find that different combinations of the model parameters lead to indistinguishable shapes of the emerging probability density functions and identical scaling laws. Our model will be useful for describing recent experimental single particle tracking data that feature a combination of CTRW and FBM properties. Y1 - 2013 U6 - https://doi.org/10.1088/1751-8113/46/47/475001 SN - 1751-8113 SN - 1751-8121 VL - 46 IS - 47 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Jechow, Andreas A1 - Seefeldt, Michael A1 - Kurzke, Henning A1 - Heuer, Axel A1 - Menzel, Ralf T1 - Enhanced two-photon excited fluorescence from imaging agents using true thermal light JF - Nature photonics N2 - Two-photon excited fluorescence (TPEF) is a standard technique in modern microscopy(1), but is still affected by photodamage to the probe. It has been proposed that TPEF can be enhanced using entangled photons(2,3), but this has proven challenging. Recently, it was shown that some features of entangled photons can be mimicked with thermal light, which finds application in ghost imaging(4), subwavelength lithography(5) and metrology(6). Here, we use true thermal light from a superluminescent diode to demonstrate TPEF that is enhanced compared to coherent light, using two common fluorophores and luminescent quantum dots, which suit applications in imaging and microscopy. We find that the TPEF rate is directly proportional to the measured(7) degree of second-order coherence, as predicted by theory. Our results show that photon bunching in thermal light can be exploited in two-photon microscopy, with the photon statistic providing a new degree of freedom. Y1 - 2013 U6 - https://doi.org/10.1038/NPHOTON.2013.271 SN - 1749-4885 SN - 1749-4893 VL - 7 IS - 12 SP - 973 EP - 976 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Tepper-Garcia, Thor A1 - Richter, Philipp A1 - Schaye, Joop T1 - Absorption signatures of warm-hot gas at low redshift - ne viii JF - Monthly notices of the Royal Astronomical Society N2 - At z < 1 a large fraction of the baryons is thought to reside in diffuse gas that has been shock-heated to high temperatures (10 (5)-10 (6) K). Absorption by the 770.41, 780.32 A doublet of Ne viii in quasar spectra represents a unique tool to study this elusive warm-hot phase. We have developed an analytic model for the properties of Ne viii absorbers that allows for an inhomogeneous metal distribution. Our model agrees with the predictions of a simulation from the OverWhelmingly Large Simulations project indicating that the average line-of-sight metal-filling fraction within the absorbing gas is low (c(L) similar to 0.1). Most of the Ne viii in our model is produced in low-density, collisionally ionized gas (n(H) = 10(-6)-10(-4) cm(-3), T = 10 (5)-10 (6) K). Strong Ne viii absorbers (log(10)(N-NeVIII/cm(-2))14), like those recently detected by Hubble Space Telescope/Cosmic Origins Spectrograph, are found to arise in higher density gas (n(H) greater than or similar to 10(-4) cm(-3), T approximate to 5 x 10 (5) K). Ne viii cloudlets harbour only 1 per cent of the cosmic baryon budget. The baryon content of the surrounding gas (which has similar densities and temperatures as the Ne viii cloudlets) is a factor c(-1)L higher. We conclude that Ne viii absorbers are robust probes of shock-heated diffuse gas, but that spectra with signal-to-noise ratios S/N > 100 would be required to detect the bulk of the baryons in warm-hot gas. KW - methods: analytical KW - methods: numerical KW - galaxies: formation KW - intergalactic medium KW - quasars: absorption lines KW - cosmology: theory Y1 - 2013 U6 - https://doi.org/10.1093/mnras/stt1712 SN - 0035-8711 SN - 1365-2966 VL - 436 IS - 3 SP - 2063 EP - 2081 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Haakh, Harald R. A1 - Intravaia, Francesco T1 - Mode structure and polaritonic contributions to the Casimir effect in a magnetodielectric cavity JF - Physical review : A, Atomic, molecular, and optical physics N2 - We present a full analysis of the mode spectrum in a cavity formed by two parallel plates, one of which is magnetodielectric (metamaterial) while the other one is metallic, and obtain dispersion relations in closed form. The optical properties of the cavity walls are described in terms of realistic models for effective permittivity and permeability. Surface polaritons, i.e., electromagnetic modes that have at least partly an evanescent character, are shown to dominate the Casimir interaction at small separations. We analyze in detail the s-polarized polaritons, which are a characteristic feature of a magnetodielectric configuration, and discuss their role in the repulsive Casimir force. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevA.88.052503 SN - 1050-2947 SN - 1094-1622 VL - 88 IS - 5 PB - American Physical Society CY - College Park ER - TY - THES A1 - Draganova, Nadya T1 - On the diversity of O VI absorbers at high redshift Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Suárez Velásquez, Isabel Fernanda T1 - The contribution of the warm-hot intergalactic medium to the CMB anisotropies and distortions Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Hoffmann, Holger T1 - Vertical structures induced by embedded propeller moonlets in Saturn's rings Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Baushev, Anton N. T1 - Extragalactic dark matter and direct detection experiments JF - The astrophysical journal : an international review of spectroscopy and astronomical physics N2 - Recent astronomical data strongly suggest that a significant part of the dark matter content of the Local Group and Virgo Supercluster is not incorporated into the galaxy halos and forms diffuse components of these galaxy clusters. A portion of the particles from these components may penetrate the Milky Way and make an extragalactic contribution to the total dark matter containment of our Galaxy. We find that the particles of the diffuse component of the Local Group are apt to contribute similar to 12% to the total dark matter density near Earth. The particles of the extragalactic dark matter stand out because of their high speed (similar to 600 km s(-1)), i.e., they are much faster than the galactic dark matter. In addition, their speed distribution is very narrow (similar to 20 km s(-1)). The particles have an isotropic velocity distribution (perhaps, in contrast to the galactic dark matter). The extragalactic dark matter should provide a significant contribution to the direct detection signal. If the detector is sensitive only to the fast particles (v > 450 km s(-1)), then the signal may even dominate. The density of other possible types of the extragalactic dark matter (for instance, of the diffuse component of the Virgo Supercluster) should be relatively small and comparable with the average dark matter density of the universe. However, these particles can generate anomaly high-energy collisions in direct dark matter detectors. KW - astroparticle physics KW - dark matter KW - elementary particles KW - Local Group Y1 - 2013 U6 - https://doi.org/10.1088/0004-637X/771/2/117 SN - 0004-637X VL - 771 IS - 2 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Poghossian, A. A1 - Weil, M. A1 - Cherstvy, Andrey G. A1 - Schöning, M. J. T1 - Electrical monitoring of polyelectrolyte multilayer formation by means of capacitive field-effect devices JF - Analytical & bioanalytical chemistry N2 - The semiconductor field-effect platform represents a powerful tool for detecting the adsorption and binding of charged macromolecules with direct electrical readout. In this work, a capacitive electrolyte-insulator-semiconductor (EIS) field-effect sensor consisting of an Al-p-Si-SiO2 structure has been applied for real-time in situ electrical monitoring of the layer-by-layer formation of polyelectrolyte (PE) multilayers (PEM). The PEMs were deposited directly onto the SiO2 surface without any precursor layer or drying procedures. Anionic poly(sodium 4-styrene sulfonate) and cationic weak polyelectrolyte poly(allylamine hydrochloride) have been chosen as a model system. The effect of the ionic strength of the solution, polyelectrolyte concentration, number and polarity of the PE layers on the characteristics of the PEM-modified EIS sensors have been studied by means of capacitance-voltage and constant-capacitance methods. In addition, the thickness, surface morphology, roughness and wettabilityof the PE mono- and multilayers have been characterised by ellipsometry, atomic force microscopy and water contact-angle methods, respectively. To explain potential oscillations on the gate surface and signal behaviour of the capacitive field-effect EIS sensor modified with a PEM, a simplified electrostatic model that takes into account the reduced electrostatic screening of PE charges by mobile ions within the PEM has been proposed and discussed. KW - Field-effect KW - Capacitive sensor KW - Polyelectrolyte multilayer KW - Electrical monitoring KW - ConCap Y1 - 2013 U6 - https://doi.org/10.1007/s00216-013-6951-9 SN - 1618-2642 VL - 405 IS - 20 SP - 6425 EP - 6436 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Cherstvy, Andrey G. A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Anomalous diffusion and ergodicity breaking in heterogeneous diffusion processes JF - New journal of physics : the open-access journal for physics N2 - We demonstrate the non-ergodicity of a simple Markovian stochastic process with space-dependent diffusion coefficient D(x). For power-law forms D(x) similar or equal to vertical bar x vertical bar(alpha), this process yields anomalous diffusion of the form < x(2)(t)> similar or equal to t(2/(2-alpha)). Interestingly, in both the sub- and superdiffusive regimes we observe weak ergodicity breaking: the scaling of the time-averaged mean-squared displacement <(delta(2)(Delta))over bar> remains linear in the lag time Delta and thus differs from the corresponding ensemble average < x(2)(t)>. We analyse the non-ergodic behaviour of this process in terms of the time-averaged mean- squared displacement (delta(2)) over bar and its random features, i.e. the statistical distribution of (delta(2)) over bar and the ergodicity breaking parameters. The heterogeneous diffusion model represents an alternative approach to non- ergodic, anomalous diffusion that might be particularly relevant for diffusion in heterogeneous media. Y1 - 2013 U6 - https://doi.org/10.1088/1367-2630/15/8/083039 SN - 1367-2630 VL - 15 IS - 15 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Cherstvy, Andrey G. T1 - Detection of DNA hybridization by field-effect DNA-based biosensors - mechanisms of signal generation and open questions JF - Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics N2 - We model theoretically the electrostatic effects taking place upon DNA hybridization in dense DNA arrays immobilized on a layer of Au nano-particles deposited on the surface of a field-effect-based DNA capacitive biosensor. We consider the influence of separation of a charged analyte from the sensor surface and the salinity of electrolyte solution, in the framework of both linear and nonlinear Poisson-Boltzmann theories. The latter predicts a substantially weaker sensor signals due to electrostatic saturation effects that is the main conclusion of this paper. We analyze how different physical parameters of dense DNA brushes affect the magnitude of hybridization signals. The list includes the fraction of DNA charge neutralization, the length and spatial conformations of adsorbed DNA molecules, as well as the discreteness of DNA charges. We also examine the effect of Donnan ionic equilibrium in DNA lattices on the sensor response. The validity of theoretical models is contrasted against recent experimental observations on detection of DNA hybridization via its intrinsic electric charge. The sensitivity of such biochemical sensing devices, their detection limit, and DNA hybridization efficiency are briefly discussed in the end. KW - DNA hybridization KW - Au nano-particle KW - Bio-electrochemical sensing KW - Electrostatic screening Y1 - 2013 U6 - https://doi.org/10.1016/j.bios.2013.02.026 SN - 0956-5663 VL - 46 IS - 2 SP - 162 EP - 170 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Molaro, P. A1 - Centurion, Martin A1 - Whitmore, J. B. A1 - Evans, T. M. A1 - Murphy, M. T. A1 - Agafonova, I. I. A1 - Bonifacio, P. A1 - D'Odorico, S. A1 - Levshakov, S. A. A1 - Lopez, S. A1 - Martins, C. J. A. P. A1 - Petitjean, P. A1 - Rahmani, H. A1 - Reimers, D. A1 - Srianand, R. A1 - Vladilo, G. A1 - Wendt, Martin T1 - The UVES Large Program for testing fundamental physics I. Bounds on a change in alpha towards quasar HE 221-2818 JF - Astronomy and astrophysics : an international weekly journal N2 - Context. Absorption-line systems detected in quasar spectra can be used to compare the value of the fine-structure constant, alpha, measured today on Earth with its value in distant galaxies. In recent years, some evidence has emerged of small temporal and also spatial variations in alpha on cosmological scales. These variations may reach a fractional level of approximate to 10 ppm (parts per million). Aims. To test these claims we are conducting a Large Program of observations with the Very Large Telescope's Ultraviolet and Visual Echelle Spectrograph (UVES), and are obtaining high-resolution (R approximate to 60 000) and high signal-to-noise ratio (S/N approximate to 100) UVES spectra calibrated specifically for this purpose. Here we analyse the first complete quasar spectrum from this programme, that of HE 2217-2818. Methods. We applied the many multiplet method to measure alpha in five absorption systems towards this quasar: z(abs) = 0.7866, 0.9424, 1.5558, 1.6279, and 1.6919. Results. The most precise result is obtained for the absorber at z(abs) = 1.6919 where 3 Fe II transitions and Al II lambda 1670 have high S/N and provide a wide range of sensitivities to alpha. The absorption profile is complex with several very narrow features, and it requires 32 velocity components to be fitted to the data. We also conducted a range of tests to estimate the systematic error budget. Our final result for the relative variation in alpha in this system is Delta alpha/alpha = +1.3 +/- 2.4(stat) +/- 1.0(sys) ppm. This is one of the tightest current bounds on alpha-variation from an individual absorber. A second, separate approach to the data reduction, calibration, and analysis of this system yielded a slightly different result of -3.8 +/- 2.1(stat) ppm, possibly suggesting a larger systematic error component than our tests indicated. This approach used an additional 3 Fe II transitions, parts of which were masked due to contamination by telluric features. Restricting this analysis to the Fe II transitions alone and using a modified absorption profile model gave a result that is consistent with the first approach, Delta alpha/alpha = +1.1 +/- 2.6(stat) ppm. The four other absorbers have simpler absorption profiles, with fewer and broader features, and offer transitions with a narrower range of sensitivities to alpha. They therefore provide looser bounds on Delta alpha/alpha at the greater than or similar to 10 ppm precision level. Conclusions. The absorbers towards quasar HE 2217-2818 reveal no evidence of any variation in alpha at the 3-ppm precision level (1 sigma confidence). If the recently reported 10-ppm dipolar variation in alpha across the sky is correct, the expectation at this sky position is (3.2-5.4) +/- 1.7 ppm depending on dipole model used. Our constraint of Delta alpha/alpha = +1.3 +/- 2.4(stat) +/- 1.0(sys) ppm is not inconsistent with this expectation. KW - quasars: absorption lines KW - quasars: individual: HE 2217-2818 KW - intergalactic medium KW - cosmology: miscellaneous cosmology KW - observations Y1 - 2013 U6 - https://doi.org/10.1051/0004-6361/201321351 SN - 0004-6361 VL - 555 IS - 4 PB - EDP Sciences CY - Les Ulis ER - TY - JOUR A1 - Nezhadhaghighi, M. Ghasemi A1 - Rajabpour, M. A. T1 - Quantum entanglement entropy and classical mutual information in long-range harmonic oscillators JF - Physical review : B, Condensed matter and materials physics N2 - We study different aspects of quantum von Neumann and Renyi entanglement entropy of one-dimensional long-range harmonic oscillators that can be described by well-defined nonlocal field theories. We show that the entanglement entropy of one interval with respect to the rest changes logarithmically with the number of oscillators inside the subsystem. This is true also in the presence of different boundary conditions. We show that the coefficients of the logarithms coming from different boundary conditions can be reduced to just two different universal coefficients. We also study the effect of the mass and temperature on the entanglement entropy of the system in different situations. The universality of our results is also confirmed by changing different parameters in the coupled harmonic oscillators. We also show that more general interactions coming from general singular Toeplitz matrices can be decomposed to our long-range harmonic oscillators. Despite the long-range nature of the couplings, we show that the area law is valid in two dimensions and the universal logarithmic terms appear if we consider subregions with sharp corners. Finally, we study analytically different aspects of the mutual information such as its logarithmic dependence to the subsystem, effect of mass, and influence of the boundary. We also generalize our results in this case to general singular Toeplitz matrices and higher dimensions. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevB.88.045426 SN - 1098-0121 SN - 1550-235X VL - 88 IS - 4 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Laflamme, Simon A1 - Kollosche, Matthias A1 - Connor, Jerome J. A1 - Kofod, Guggi T1 - Robust flexible capacitive surface sensor for structural health monitoring applications JF - Journal of engineering mechanics N2 - Early detection of possible defects in civil infrastructure is vital to ensuring timely maintenance and extending structure life expectancy. The authors recently proposed a novel method for structural health monitoring based on soft capacitors. The sensor consisted of an off-the-shelf flexible capacitor that could be easily deployed over large surfaces, the main advantages being cost-effectiveness, easy installation, and allowing simple signal processing. In this paper, a capacitive sensor with tailored mechanical and electrical properties is presented, resulting in greatly improved robustness while retaining measurement sensitivity. The sensor is fabricated from a thermoplastic elastomer mixed with titanium dioxide and sandwiched between conductive composite electrodes. Experimental verifications conducted on wood and concrete specimens demonstrate the improved robustness, as well as the ability of the sensing method to diagnose and locate strain. KW - Strain gages KW - Structural health monitoring KW - Monitoring KW - Probe instruments KW - Strain gauge KW - Structural health monitoring KW - Strain monitoring KW - Capacitive sensor KW - Dielectric polymer KW - Stretchable sensor KW - Flexible membrane KW - Sensing skin Y1 - 2013 U6 - https://doi.org/10.1061/(ASCE)EM.1943-7889.0000530 SN - 0733-9399 SN - 1943-7889 VL - 139 IS - 7 SP - 879 EP - 885 PB - American Society of Civil Engineers CY - Reston ER - TY - JOUR A1 - Pfannes, Eva K. A1 - Anielski, Alexander A1 - Gerhardt, Matthias A1 - Beta, Carsten T1 - Intracellular photoactivation of caged-cGMP induces myosin II and actin responses in motile cells N2 - Cyclic GMP (cGMP) is a ubiquitous second messenger in eukaryotic cells. It is assumed to regulate the association of myosin II with the cytoskeleton of motile cells. When cells of the social amoeba Dictyostelium discoideum are exposed to chemoattractants or to increased osmotic stress, intracellular cGMP levels rise, preceding the accumulation of myosin II in the cell cortex. To directly investigate the impact of intracellular cGMP on cytoskeletal dynamics in a living cell, we released cGMP inside the cell by laser-induced photo-cleavage of a caged precursor. With this approach, we could directly show in a live cell experiment that an increase in intracellular cGMP indeed induces myosin II to accumulate in the cortex. Unexpectedly, we observed for the first time that also the amount of filamentous actin in the cell cortex increases upon a rise in the cGMP concentration, independently of cAMP receptor activation and signaling. We discuss our results in the light of recent work on the cGMP signaling pathway and suggest possible links between cGMP signaling and the actin system. Y1 - 2013 UR - http://pubs.rsc.org/en/content/articlehtml/2013/ib/c3ib40109j U6 - https://doi.org/10.1039/C3IB40109J ER - TY - THES A1 - Itoh, Naoki T1 - Applications of developed and extended singular spectrum analysis to monthly precipitation Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Beye, Martin A1 - Anniyev, Toyli A1 - Coffee, Ryan A1 - Dell'Angela, Martina A1 - Föhlisch, Alexander A1 - Gladh, J. A1 - Katayama, T. A1 - Kaya, S. A1 - Krupin, O. A1 - Mogelhoj, A. A1 - Nilsson, A. A1 - Nordlund, D. A1 - Norskov, J. K. A1 - Oberg, H. A1 - Ogasawara, H. A1 - Pettersson, Lars G. M. A1 - Schlotter, W. F. A1 - Sellberg, J. A. A1 - Sorgenfrei, Florian A1 - Turner, J. J. A1 - Wolf, M. A1 - Wurth, Wilfried A1 - Ostrom, H. T1 - Selective ultrafast probing of transient hot chemisorbed and precursor States of CO on Ru(0001) JF - Physical review letters N2 - We have studied the femtosecond dynamics following optical laser excitation of CO adsorbed on a Ru surface by monitoring changes in the occupied and unoccupied electronic structure using ultrafast soft x-ray absorption and emission. We recently reported [M. Dell'Angela et al. Science 339, 1302 (2013)] a phonon-mediated transition into a weakly adsorbed precursor state occurring on a time scale of >2 ps prior to desorption. Here we focus on processes within the first picosecond after laser excitation and show that the metal-adsorbate coordination is initially increased due to hot-electron-driven vibrational excitations. This process is faster than, but occurs in parallel with, the transition into the precursor state. With resonant x-ray emission spectroscopy, we probe each of these states selectively and determine the respective transient populations depending on optical laser fluence. Ab initio molecular dynamics simulations of CO adsorbed on Ru(0001) were performed at 1500 and 3000 K providing insight into the desorption process. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.110.186101 SN - 0031-9007 VL - 110 IS - 18 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Send, Sebastian A1 - Abboud, Ali A1 - Hartmann, Robert A1 - Huth, M. A1 - Leitenberger, Wolfram A1 - Pashniak, N. A1 - Schmidt, J. A1 - Strüder, Lothar A1 - Pietsch, Ullrich T1 - Characterization of a pnCCD for applications with synchrotron radiation JF - Nuclear instruments & methods in physics research : a journal on accelerators, instrumentation and techniques applied to research in nuclear and atomic physics, materials science and related fields in physics ; A, Accelerators, spectrometers, detectors and associated equipment N2 - In this work we study the response of a pnCCD by means of X-ray spectroscopy in the energy range between 6 key and 20 key and by Laue diffraction techniques. The analyses include measurements of characteristic detector parameters like energy resolution, count rate capability and effects of different gain settings. The limit of a single photon counting operation in white beam X-ray diffraction experiments is discussed with regard to the occurrence of pile-up events, for which the energy information about individual photons is lost. In case of monochromatic illumination the pnCCD can be used as a fast conventional CCD with a charge handling capacity (CHC) of about 300,000 electrons per pixel. If the CHC is exceeded, any surplus charge will spill to neighboring pixels perpendicular to the transfer direction due to electrostatic repulsion. The possibilities of increasing the number of storable electrons are investigated for different voltage settings by exposing a single pixel with X-rays generated by a microfocus X-ray source. The pixel binning mode is tested as an alternative approach that enables a pnCCD operation with significantly shorter readout times. KW - pnCCD KW - X-ray spectroscopy KW - X-ray imaging KW - Energy-dispersive Laue diffraction Y1 - 2013 U6 - https://doi.org/10.1016/j.nima.2013.01.044 SN - 0168-9002 VL - 711 IS - 5 SP - 132 EP - 142 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Kharchenko, Vasyl O. A1 - Goychuk, Igor T1 - Subdiffusive rocking ratchets in viscoelastic media transport optimization and thermodynamic efficiency in overdamped regime JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - We study subdiffusive overdamped Brownian ratchets periodically rocked by an external zero-mean force in viscoelastic media within the framework of a non-Markovian generalized Langevin equation approach and associated multidimensional Markovian embedding dynamics. Viscoelastic deformations of the medium caused by the transport particle are modeled by a set of auxiliary Brownian quasiparticles elastically coupled to the transport particle and characterized by a hierarchy of relaxation times which obey a fractal scaling. The most slowly relaxing deformations which cannot immediately follow to the moving particle imprint long-range memory about its previous positions and cause subdiffusion and anomalous transport on a sufficiently long time scale. This anomalous behavior is combined with normal diffusion and transport on an initial time scale of overdamped motion. Anomalously slow directed transport in a periodic ratchet potential with broken space inversion symmetry emerges due to a violation of the thermal detailed balance by a zero-mean periodic driving and is optimized with frequency of driving, its amplitude, and temperature. Such optimized anomalous transport can be low dispersive and characterized by a large generalized Peclet number. Moreover, we show that overdamped subdiffusive ratchets can sustain a substantial load and do useful work. The corresponding thermodynamic efficiency decays algebraically in time since the useful work done against a load scales sublinearly with time following to the transport particle position, but the energy pumped by an external force scales with time linearly. Nevertheless, it can be transiently appreciably high and compare well with the thermodynamical efficiency of the normal diffusion overdamped ratchets on sufficiently long temporal and spatial scales. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.87.052119 SN - 1539-3755 VL - 87 IS - 5 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Lomholt, Michael A. A1 - Lizana, Ludvig A1 - Metzler, Ralf A1 - Ambjoernsson, Tobias T1 - Microscopic origin of the logarithmic time evolution of aging processes in complex systems JF - Physical review letters N2 - There exists compelling experimental evidence in numerous systems for logarithmically slow time evolution, yet its full theoretical understanding remains elusive. We here introduce and study a generic transition process in complex systems, based on nonrenewal, aging waiting times. Each state n of the system follows a local clock initiated at t = 0. The random time tau between clock ticks follows the waiting time density psi (tau). Transitions between states occur only at local clock ticks and are hence triggered by the local forward waiting time, rather than by psi (tau). For power-law forms psi (tau) similar or equal to tau(-1-alpha) (0 < alpha < 1) we obtain a logarithmic time evolution of the state number < n(t)> similar or equal to log(t/t(0)), while for alpha > 2 the process becomes normal in the sense that < n(t)> similar or equal to t. In the intermediate range 1 < alpha < 2 we find the power-law growth < n(t)> similar or equal to t(alpha-1). Our model provides a universal description for transition dynamics between aging and nonaging states. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.110.208301 SN - 0031-9007 VL - 110 IS - 20 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Pulkkinen, Otto A1 - Metzler, Ralf T1 - Distance matters the impact of gene proximity in bacterial gene regulation JF - Physical review letters N2 - Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from analytical and numerical analysis that the distance between a transcription factor (TF) gene and its target gene drastically affects the speed and reliability of transcriptional regulation in bacterial cells. For an explicit model system, we develop a general theory for the interactions between a TF and a transcription unit. The observed variations in regulation efficiency are linked to the magnitude of the variation of the TF concentration peaks as a function of the binding site distance from the signal source. Our results support the role of rapid binding site search for gene colocalization and emphasize the role of local concentration differences. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.110.198101 SN - 0031-9007 VL - 110 IS - 19 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Valori, Gherarod A1 - Demoulin, Pascal A1 - Pariat, E. A1 - Masson, S. T1 - Accuracy of magnetic energy computations JF - Astronomy and astrophysics : an international weekly journal N2 - Context. For magnetically driven events, the magnetic energy of the system is the prime energy reservoir that fuels the dynamical evolution. In the solar context, the free energy (i.e., the energy in excess of the potential field energy) is one of the main indicators used in space weather forecasts to predict the eruptivity of active regions. A trustworthy estimation of the magnetic energy is therefore needed in three-dimensional (3D) models of the solar atmosphere, e. g., in coronal fields reconstructions or numerical simulations. Aims. The expression of the energy of a system as the sum of its potential energy and its free energy (Thomson's theorem) is strictly valid when the magnetic field is exactly solenoidal. For numerical realizations on a discrete grid, this property may be only approximately fulfilled. We show that the imperfect solenoidality induces terms in the energy that can lead to misinterpreting the amount of free energy present in a magnetic configuration. Methods. We consider a decomposition of the energy in solenoidal and nonsolenoidal parts which allows the unambiguous estimation of the nonsolenoidal contribution to the energy. We apply this decomposition to six typical cases broadly used in solar physics. We quantify to what extent the Thomson theorem is not satisfied when approximately solenoidal fields are used. Results. The quantified errors on energy vary from negligible to significant errors, depending on the extent of the nonsolenoidal component of the field. We identify the main source of errors and analyze the implications of adding a variable amount of divergence to various solenoidal fields. Finally, we present pathological unphysical situations where the estimated free energy would appear to be negative, as found in some previous works, and we identify the source of this error to be the presence of a finite divergence. Conclusions. We provide a method of quantifying the effect of a finite divergence in numerical fields, together with detailed diagnostics of its sources. We also compare the efficiency of two divergence-cleaning techniques. These results are applicable to a broad range of numerical realizations of magnetic fields. KW - magnetic fields KW - methods: numerical KW - Sun: surface magnetism KW - Sun: corona Y1 - 2013 U6 - https://doi.org/10.1051/0004-6361/201220982 SN - 0004-6361 VL - 553 IS - 2 PB - EDP Sciences CY - Les Ulis ER - TY - JOUR A1 - Shayduk, Roman A1 - Herzog, Marc A1 - Bojahr, Andre A1 - Schick, Daniel A1 - Gaal, Peter A1 - Leitenberger, Wolfram A1 - Navirian, Hengameh A1 - Sander, Mathias A1 - Goldshteyn, Jevgenij A1 - Vrejoiu, Ionela A1 - Bargheer, Matias T1 - Direct time-domain sampling of subterahertz coherent acoustic phonon spectra in SrTiO3 using ultrafast x-ray diffraction JF - Physical review : B, Condensed matter and materials physics N2 - We synthesize sub-THz longitudinal quasimonochromatic acoustic phonons in a SrTiO3 single crystal using a SrRuO3/SrTiO3 superlattice as an optical-acoustic transducer. The generated acoustic phonon spectrum is determined using ultrafast x-ray diffraction. The analysis of the generated phonon spectrum in the time domain reveals a k-vector dependent phonon lifetime. It is observed that even at sub-THz frequencies the phonon lifetime agrees with the 1/omega(2) power law known from Akhiezer's model for hyper sound attenuation. The observed shift of the synthesized spectrum to the higher q is discussed in the framework of nonlinear effects appearing due to the high amplitude of the synthesized phonons. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevB.87.184301 SN - 1098-0121 VL - 87 IS - 18 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Javanainen, Matti A1 - Hammaren, Henrik A1 - Monticelli, Luca A1 - Jeon, Jae-Hyung A1 - Miettinen, Markus S. A1 - Martinez-Seara, Hector A1 - Metzler, Ralf A1 - Vattulainen, Ilpo T1 - Anomalous and normal diffusion of proteins and lipids in crowded lipid membranes JF - Faraday discussions N2 - Lateral diffusion plays a crucial role in numerous processes that take place in cell membranes, yet it is quite poorly understood in native membranes characterized by, e.g., domain formation and large concentration of proteins. In this article, we use atomistic and coarse-grained simulations to consider how packing of membranes and crowding with proteins affect the lateral dynamics of lipids and membrane proteins. We find that both packing and protein crowding have a profound effect on lateral diffusion, slowing it down. Anomalous diffusion is observed to be an inherent property in both protein-free and protein-rich membranes, and the time scales of anomalous diffusion and the exponent associated with anomalous diffusion are found to strongly depend on packing and crowding. Crowding with proteins also has a striking effect on the decay rate of dynamical correlations associated with lateral single-particle motion, as the transition from anomalous to normal diffusion is found to take place at macroscopic time scales: while in protein-poor conditions normal diffusion is typically observed in hundreds of nanoseconds, in protein-rich conditions the onset of normal diffusion is tens of microseconds, and in the most crowded systems as large as milliseconds. The computational challenge which results from these time scales is not easy to deal with, not even in coarse-grained simulations. We also briefly discuss the physical limits of protein motion. Our results suggest that protein concentration is anything but constant in the plane of cell membranes. Instead, it is strongly dependent on proteins' preference for aggregation. Y1 - 2013 U6 - https://doi.org/10.1039/c2fd20085f SN - 1359-6640 VL - 161 IS - 1 SP - 397 EP - 417 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Menzel, Ralf A1 - Heuer, Axel A1 - Puhlmann, Dirk A1 - Dechoum, K. A1 - Hillery, M. A1 - Spaehn, M. J. A. A1 - Schleich, W. P. T1 - A two-photon double-slit experiment JF - Journal of modern optics N2 - We employ a photon pair created by spontaneous parametric down conversion (SPDC) where the pump laser is in the TEM01 mode to perform a Young's double-slit experiment. The signal photon illuminates the two slits and displays interference fringes in the far-field while the idler photon measured in the near-field in coincidence with the signal photon provides us with which-slit' information. We explain the results of these experiments with the help of an analytical expression for the second-order correlation function derived from an elementary model of SPDC. Our experiment emphasizes the crucial role of the mode function in the quantum theory of radiation. KW - complementarity KW - wave-particle dualism KW - Young's double-slit experiment KW - spontaneous parametric down conversion KW - TEM01 mode Y1 - 2013 U6 - https://doi.org/10.1080/09500340.2012.746400 SN - 0950-0340 VL - 60 IS - 1 SP - 86 EP - 94 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Sliusarenko, O. Yu. A1 - Surkov, D. A. A1 - Gonchar, V. Yu. A1 - Chechkin, Aleksei V. T1 - Stationary states in bistable system driven by Levy noise JF - European physical journal special topics N2 - We study the properties of the probability density function (PDF) of a bistable system driven by heavy tailed white symmetric L,vy noise. The shape of the stationary PDF is found analytically for the particular case of the L,vy index alpha = 1 (Cauchy noise). For an arbitrary L,vy index we employ numerical methods based on the solution of the stochastic Langevin equation and space fractional kinetic equation. In contrast to the bistable system driven by Gaussian noise, in the L,vy case, the positions of maxima of the stationary PDF do not coincide with the positions of minima of the bistable potential. We provide a detailed study of the distance between the maxima and the minima as a function of the depth of the potential and the L,vy noise parameters. Y1 - 2013 U6 - https://doi.org/10.1140/epjst/e2013-01736-0 SN - 1951-6355 VL - 216 IS - 1 SP - 133 EP - 138 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Abboud, Ali A1 - Send, Sebastian A1 - Pashniak, N. A1 - Leitenberger, Wolfram A1 - Ihle, Sebastian A1 - Huth, M. A1 - Hartmann, Robert A1 - Strüder, Lothar A1 - Pietsch, Ullrich T1 - Sub-pixel resolution of a pnCCD for X-ray white beam applications JF - Journal of instrumentation N2 - A new approach to achieve sub-pixel spatial resolution in a pnCCD detector with 75 x 75 mu m(2) pixel size is proposed for X-ray applications in single photon counting mode. The approach considers the energy dependence of the charge cloud created by a single photon and its split probabilities between neighboring pixels of the detector based on a rectangular model for the charge cloud density. For cases where the charge of this cloud becomes distributed over three or four pixels the center position of photon impact can be reconstructed with a precision better than 2 mu m. The predicted charge cloud sizes are tested at selected X-ray fluorescence lines emitting energies between 6.4 keV and 17.4 keV and forming charge clouds with size (rms) varying between 8 mu m and 10 mu m respectively. The 2 mu m enhanced spatial resolution of the pnCCD is verified by means of an x-ray transmission experiment throughout an optical grating. KW - Solid state detectors KW - Interaction of radiation with matter KW - Detector modelling and simulations II (electric fields, charge transport, multiplication and induction, pulse formation, electron emission, etc) Y1 - 2013 U6 - https://doi.org/10.1088/1748-0221/8/05/P05005 SN - 1748-0221 VL - 8 IS - 3 PB - IOP Publ. Ltd. CY - Bristol ER - TY - THES A1 - Marchenko, Dmitry T1 - Rashba effect on Dirac fermions in grahene Y1 - 2013 CY - Potsdam ER - TY - THES A1 - Albrecht, Torsten T1 - A dynamic memory of fracture processes in ice shelves Y1 - 2013 CY - Potsdam ER - TY - JOUR A1 - Pattyn, Frank A1 - Perichon, Laura A1 - Durand, Gael A1 - Favier, Lionel A1 - Gagliardini, Olivier A1 - Hindmarsh, Richard C. A. A1 - Zwinger, Thomas A1 - Albrecht, Torsten A1 - Cornford, Stephen A1 - Docquier, David A1 - Furst, Johannes J. A1 - Goldberg, Daniel A1 - Gudmundsson, Gudmundur Hilmar A1 - Humbert, Angelika A1 - Huetten, Moritz A1 - Huybrechts, Philippe A1 - Jouvet, Guillaume A1 - Kleiner, Thomas A1 - Larour, Eric A1 - Martin, Daniel A1 - Morlighem, Mathieu A1 - Payne, Anthony J. A1 - Pollard, David A1 - Rueckamp, Martin A1 - Rybak, Oleg A1 - Seroussi, Helene A1 - Thoma, Malte A1 - Wilkens, Nina T1 - Grounding-line migration in plan-view marine ice-sheet models: results of the ice2sea MISMIP3d intercomparison JF - Journal of glaciology N2 - Predictions of marine ice-sheet behaviour require models able to simulate grounding-line migration. We present results of an intercomparison experiment for plan-view marine ice-sheet models. Verification is effected by comparison with approximate analytical solutions for flux across the grounding line using simplified geometrical configurations (no lateral variations, no buttressing effects from lateral drag). Perturbation experiments specifying spatial variation in basal sliding parameters permitted the evolution of curved grounding lines, generating buttressing effects. The experiments showed regions of compression and extensional flow across the grounding line, thereby invalidating the boundary layer theory. Steady-state grounding-line positions were found to be dependent on the level of physical model approximation. Resolving grounding lines requires inclusion of membrane stresses, a sufficiently small grid size (<500 m), or subgrid interpolation of the grounding line. The latter still requires nominal grid sizes of <5 km. For larger grid spacings, appropriate parameterizations for ice flux may be imposed at the grounding line, but the short-time transient behaviour is then incorrect and different from models that do not incorporate grounding-line parameterizations. The numerical error associated with predicting grounding-line motion can be reduced significantly below the errors associated with parameter ignorance and uncertainties in future scenarios. Y1 - 2013 U6 - https://doi.org/10.3189/2013JoG12J129 SN - 0022-1430 VL - 59 IS - 215 SP - 410 EP - 422 PB - International Glaciological Society CY - Cambridge ER - TY - JOUR A1 - Feudel, Fred A1 - Seehafer, Norbert A1 - Tuckerman, Laurette S. T1 - Multistability in rotating spherical shell convection Y1 - 2013 UR - http://link.aps.org/doi/10.1103/PhysRevE.87.023021 (9.9.2013) SN - 1539-3755 ER - TY - JOUR A1 - Miranda, Rodrigo A. A1 - Rempel, Erico L. A1 - Chian, Abraham C.-L. A1 - Seehafer, Norbert A1 - Toledo, Benjamin A. T1 - Lagrangian coherent structures at the onset of hyperchaos in the two-dimensional Navier-Stokes equations Y1 - 2013 UR - http://dx.doi.org/10.1063/1.4811297 ER - TY - JOUR A1 - Miranda, Rodrigo A. A1 - Rempel, Erico L. A1 - Chian, Abraham C.-L. A1 - Seehafer, Norbert A1 - Toledo, Benjamin A. A1 - Munoz, Pablo R. T1 - Lagrangian coherent structures at the onset of hyperchaos in the two-dimensional Navier-Stokes equations JF - Chaos : an interdisciplinary journal of nonlinear science N2 - We study a transition to hyperchaos in the two-dimensional incompressible Navier-Stokes equations with periodic boundary conditions and an external forcing term. Bifurcation diagrams are constructed by varying the Reynolds number, and a transition to hyperchaos (HC) is identified. Before the onset of HC, there is coexistence of two chaotic attractors and a hyperchaotic saddle. After the transition to HC, the two chaotic attractors merge with the hyperchaotic saddle, generating random switching between chaos and hyperchaos, which is responsible for intermittent bursts in the time series of energy and enstrophy. The chaotic mixing properties of the flow are characterized by detecting Lagrangian coherent structures. After the transition to HC, the flow displays complex Lagrangian patterns and an increase in the level of Lagrangian chaoticity during the bursty periods that can be predicted statistically by the hyperchaotic saddle prior to HC transition. Y1 - 2013 U6 - https://doi.org/10.1063/1.4811297 SN - 1054-1500 VL - 23 IS - 3 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Feudel, Fred A1 - Seehafer, Norbert A1 - Tuckerman, Laurette S. A1 - Gellert, Marcus T1 - Multistability in rotating spherical shell convection JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - The multiplicity of stable convection patterns in a rotating spherical fluid shell heated from the inner boundary and driven by a central gravity field is presented. These solution branches that arise as rotating waves (RWs) are traced for varying Rayleigh number while their symmetry, stability, and bifurcations are studied. At increased Rayleigh numbers all the RWs undergo transitions to modulated rotating waves (MRWs) which are classified by their spatiotemporal symmetry. The generation of a third frequency for some of the MRWs is accompanied by a further loss of symmetry. Eventually a variety of MRWs, three-frequency solutions, and chaotic saddles and attractors control the dynamics for higher Rayleigh numbers. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.87.023021 SN - 1539-3755 VL - 87 IS - 2 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Meibom, S. A1 - Barnes, Sydney A. A1 - Covey, K. A1 - Jeffries, R. D. A1 - Matt, S. A1 - Morin, J. A1 - Palacios, A. A1 - Reiners, A. A1 - Sicilia-Aguilar, A. A1 - Irwin, J. T1 - Angular momentum evolution of cool stars: Toward a synthesis of observations and theory before and after the ZAMS JF - Astronomische Nachrichten = Astronomical notes N2 - The coexistence of fast and slowly rotating cool stars in ZAMS clusters - forming distinct sequences in the color vs. rotation period plane - is providing clues to differences in their pre main-sequence angular momentum evolution. This Cool Stars 17 splinter was dedicated to a discussion of new observational and theoretical results that may help discriminate between proposed mechanisms for early angular momentum regulation and help us explain the observed ZAMS dichotomy. KW - circumstellar matter KW - stars: late-type KW - stars: magnetic fields KW - stars: pre-main sequence KW - stars: rotation Y1 - 2013 U6 - https://doi.org/10.1002/asna.201211777 SN - 0004-6337 SN - 1521-3994 VL - 334 IS - 1-2 SP - 168 EP - 171 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Ben-Abdallah, Philippe A1 - Messina, Riccardo A1 - Biehs, Svend-Age A1 - Tschikin, Maria A1 - Joulain, Karl A1 - Henkel, Carsten T1 - Heat superdiffusion in plasmonic nanostructure networks JF - Physical review letters N2 - The heat transport mediated by near-field interactions in networks of plasmonic nanostructures is shown to be analogous to a generalized random walk process. The existence of superdiffusive regimes is demonstrated both in linear ordered chains and in three-dimensional random networks by analyzing the asymptotic behavior of the corresponding probability distribution function. We show that the spread of heat in these networks is described by a type of Levy flight. The presence of such anomalous heat-transport regimes in plasmonic networks opens the way to the design of a new generation of composite materials able to transport heat faster than the normal diffusion process in solids. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.111.174301 SN - 0031-9007 SN - 1079-7114 VL - 111 IS - 17 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Pieplow, Gregor A1 - Henkel, Carsten T1 - Fully covariant radiation force on a polarizable particle JF - New journal of physics : the open-access journal for physics N2 - The electromagnetic force on a polarizable particle is calculated in a covariant framework. Local equilibrium temperatures for the electromagnetic field and the particle's dipole moment are assumed, using a relativistic formulation of the fluctuation-dissipation theorem. Two examples illustrate radiative friction forces: a particle moving through a homogeneous radiation background and above a planar interface. Previous results for arbitrary relative velocities are recovered in a compact way. Y1 - 2013 U6 - https://doi.org/10.1088/1367-2630/15/2/023027 SN - 1367-2630 VL - 15 IS - 4 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Kralemann, Bjoern A1 - Fruehwirth, Matthias A1 - Pikovskij, Arkadij A1 - Rosenblum, Michael A1 - Kenner, Thomas A1 - Schaefer, Jochen A1 - Moser, Maximilian T1 - In vivo cardiac phase response curve elucidates human respiratory heart rate variability JF - Nature Communications N2 - Recovering interaction of endogenous rhythms from observations is challenging, especially if a mathematical model explaining the behaviour of the system is unknown. The decisive information for successful reconstruction of the dynamics is the sensitivity of an oscillator to external influences, which is quantified by its phase response curve. Here we present a technique that allows the extraction of the phase response curve from a non-invasive observation of a system consisting of two interacting oscillators-in this case heartbeat and respiration-in its natural environment and under free-running conditions. We use this method to obtain the phase-coupling functions describing cardiorespiratory interactions and the phase response curve of 17 healthy humans. We show for the first time the phase at which the cardiac beat is susceptible to respiratory drive and extract the respiratory-related component of heart rate variability. This non-invasive method for the determination of phase response curves of coupled oscillators may find application in many scientific disciplines. Y1 - 2013 U6 - https://doi.org/10.1038/ncomms3418 SN - 2041-1723 VL - 4 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Montaseri, Ghazal A1 - Yazdanpanah, Mohammad Javad A1 - Pikovskij, Arkadij A1 - Rosenblum, Michael T1 - Synchrony suppression in ensembles of coupled oscillators via adaptive vanishing feedback JF - Chaos : an interdisciplinary journal of nonlinear science N2 - Synchronization and emergence of a collective mode is a general phenomenon, frequently observed in ensembles of coupled self-sustained oscillators of various natures. In several circumstances, in particular in cases of neurological pathologies, this state of the active medium is undesirable. Destruction of this state by a specially designed stimulation is a challenge of high clinical relevance. Typically, the precise effect of an external action on the ensemble is unknown, since the microscopic description of the oscillators and their interactions are not available. We show that, desynchronization in case of a large degree of uncertainty about important features of the system is nevertheless possible; it can be achieved by virtue of a feedback loop with an additional adaptation of parameters. The adaptation also ensures desynchronization of ensembles with non-stationary, time-varying parameters. We perform the stability analysis of the feedback-controlled system and demonstrate efficient destruction of synchrony for several models, including those of spiking and bursting neurons. Y1 - 2013 U6 - https://doi.org/10.1063/1.4817393 SN - 1054-1500 VL - 23 IS - 3 PB - American Institute of Physics CY - Melville ER - TY - JOUR A1 - Krishnan, Giri Panamoottil A1 - Bazhenov, Maxim A1 - Pikovskij, Arkadij T1 - Multipulse phase resetting curves JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - In this paper, we introduce and study systematically, in terms of phase response curves, the effect of dual-pulse excitation on the dynamics of an autonomous oscillator. Specifically, we test the deviations from linear summation of phase advances resulting from two small perturbations. We analytically derive a correction term, which generally appears for oscillators whose intrinsic dimensionality is >1. The nonlinear correction term is found to be proportional to the square of the perturbation. We demonstrate this effect in the Stuart-Landau model and in various higher dimensional neuronal models. This deviation from the superposition principle needs to be taken into account in studies of networks of pulse-coupled oscillators. Further, this deviation could be used in the verification of oscillator models via a dual-pulse excitation. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.88.042902 SN - 1539-3755 SN - 1550-2376 VL - 88 IS - 4 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Komarov, Maxim A1 - Pikovskij, Arkadij T1 - Multiplicity of singular synchronous States in the kuramoto model of coupled oscillators JF - Physical review letters N2 - We study the Kuramoto model of globally coupled oscillators with a biharmonic coupling function. We develop an analytic self-consistency approach to find stationary synchronous states in the thermodynamic limit and demonstrate that there is a huge multiplicity of such states, which differ microscopically in the distributions of locked phases. These synchronous regimes already exist prior to the linear instability transition of the fully asynchronous state. In the presence of white Gaussian noise, the multiplicity is lifted, but the dependence of the order parameters on coupling constants remains nontrivial. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevLett.111.204101 SN - 0031-9007 SN - 1079-7114 VL - 111 IS - 20 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Pikovskij, Arkadij T1 - Robust synchronization of spin-torque oscillators with an LC R load JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - We study dynamics of a serial array of spin-torque oscillators with a parallel inductor-capacitor-resistor (LC R) load. In a large range of parameters the fully synchronous regime, where all the oscillators have the same state and the output field is maximal, is shown to be stable. However, not always such a robust complete synchronization develops from a random initial state; in many cases nontrivial clustering is observed, with a partial synchronization resulting in a quasiperiodic or chaotic mean-field dynamics. Y1 - 2013 U6 - https://doi.org/10.1103/PhysRevE.88.032812 SN - 1539-3755 SN - 1550-2376 VL - 88 IS - 3 PB - American Physical Society CY - College Park ER -