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Sample records for bacteriorhodopsin reveals correlated

  1. All-optical nonlinear holographic correlation using bacteriorhodopsin films

    Science.gov (United States)

    Thoma, Ralph; Dratz, Michael; Hampp, Norbert

    1995-05-01

    Films made of the halobacterial photochrome bacteriorhodopsin (BR) can be used in a number of holographic real-time applications. Their application as active material in a dual-axis joint- Fourier-transform (DAJFT) real-time correlator was shown recently. The BR films have a strong nonlinear intensity dependence on the light-induced absorption and refractive-index changes. Therefore the holographic diffraction efficiency also shows a nonlinear dependence on the writing intensity. We investigate the effect of this nonlinearity on the result of the correlation process in a bacteriorhodopsin-based DAJFT correlator. Numerical models supporting the experimental observations are presented. It was found that the BR film combines the holographic function for most objects with that of a spatial bandpass filter, whose center frequency is tuned by the writing intensity. This results in smaller peak widths and a suppression of the sidelobes. BR films allow the application of this nonlinear behavior in real time to the all-optical correlation process.

  2. Absorption characteristics of bacteriorhodopsin molecules

    Indian Academy of Sciences (India)

    H K T Kumar; K Appaji Gowda

    2000-03-01

    The bacteriorhodopsin molecule absorbs light and undergoes a series of structural transformation following a well-defined photocycle. The complex photocycle is transformed to an equivalent level diagram by considering the lifetime of the intermediate states. Assuming that only and states are appreciably populated at any instant of time, the level diagram is further simplified to two-level system. Based on the rate equations for two-level system, an analytic expression for the absorption coefficient of bacteriorhodopsin molecule is derived. It is applied to study the behaviour of absorption coefficient of bacteriorhodopsin film in the visible wavelength region of 514 nm. The dependence of absorption coefficient of bacteriorhodopsin film on the thickness of the film, total number density of active molecules and initial number density of molecules in -state is presented in the graphical form.

  3. Nonlinear optical properties of bacteriorhodopsin

    Science.gov (United States)

    Hendrickx, Eric; Verbiest, Thierry; Clays, Koen J.; Persoons, Andre P.

    1993-04-01

    In this paper we show the applicability of Hyper-Rayleigh scattering to obtain hyperpolarizabilities of ionic and biochemical compounds. It was found that dark-adapted bacteriorhodopsin and its isolated chromophore have considerable second order nonlinear optical properties. Information obtained from depolarization studies of the scattered light is discussed.

  4. Optical Processing of Speckle Images with Bacteriorhodopsin for Pattern Recognition

    Science.gov (United States)

    Downie, John D.; Tucker, Deanne (Technical Monitor)

    1994-01-01

    Logarithmic processing of images with multiplicative noise characteristics can be utilized to transform the image into one with an additive noise distribution. This simplifies subsequent image processing steps for applications such as image restoration or correlation for pattern recognition. One particularly common form of multiplicative noise is speckle, for which the logarithmic operation not only produces additive noise, but also makes it of constant variance (signal-independent). We examine the optical transmission properties of some bacteriorhodopsin films here and find them well suited to implement such a pointwise logarithmic transformation optically in a parallel fashion. We present experimental results of the optical conversion of speckle images into transformed images with additive, signal-independent noise statistics using the real-time photochromic properties of bacteriorhodopsin. We provide an example of improved correlation performance in terms of correlation peak signal-to-noise for such a transformed speckle image.

  5. Resonant optical rectification in bacteriorhodopsin.

    Science.gov (United States)

    Groma, Géza I; Colonna, Anne; Lambry, Jean-Christophe; Petrich, Jacob W; Váró, György; Joffre, Manuel; Vos, Marten H; Martin, Jean-Louis

    2004-05-25

    The relative role of retinal isomerization and microscopic polarization in the phototransduction process of bacteriorhodopsin is still an open question. It is known that both processes occur on an ultrafast time scale. The retinal trans-->cis photoisomerization takes place on the time scale of a few hundred femtoseconds. On the other hand, it has been proposed that the primary light-induced event is a sudden polarization of the retinal environment, although there is no direct experimental evidence for femtosecond charge displacements, because photovoltaic techniques cannot be used to detect charge movements faster than picoseconds. Making use of the known high second-order susceptibility chi(2) of retinal in proteins, we have used a nonlinear technique, interferometric detection of coherent infrared emission, to study macroscopically oriented bacteriorhodopsin-containing purple membranes. We report and characterize impulsive macroscopic polarization of these films by optical rectification of an 11-fs visible light pulse in resonance with the optical transition. This finding provides direct evidence for charge separation as a precursor event for subsequent functional processes. A simple two-level model incorporating the resonant second-order optical properties of retinal, which are known to be a requirement for functioning of bacteriorhodopsin, is used to describe the observations. In addition to the electronic response, long-lived infrared emission at specific frequencies was observed, reflecting charge movements associated with vibrational motions. The simultaneous and phase-sensitive observation of both the electronic and vibrational signals opens the way to study the transduction of the initial polarization into structural dynamics. PMID:15148391

  6. Nonlinear Optical Studies of Bacteriorhodopsin

    Science.gov (United States)

    Rao, D. V. G. L. N.; Aranda, F. J.; Chen, Z.; Akkara, J. A.; Kaplan, D. L.; Nakashima, M.

    We report interesting results on nonlinear optics at low powers in bacteriorhodopsin films with applications in all-optical switching and modulation. Chemically stabilized films of bacteriorhodopsin in a polymer matrix for which the lifetime of the excited M state is 3 to 4 orders of magnitude longer than that of water solutions of wild-type bR were used in these experiments. Due to the sensitivity of the films, very small powers of order microwatts are required for optical phase conjugation. The influence of the fast photochemical M to B transition induced by blue light on the saturation intensity, phase conjugate intensity and switching time was established. We also report our measurements of the intensity dependence of the self-focusing and self-defocusing properties of wild-type bR in water solution using the Z-scan technique with low power cw lasers at two wavelengths on either side of the absorption band. Our measurements indicate that the sign of the nonlinearity depends on the wavelength and the magnitude depends on the fluence of the incident laser beam. The observed self-focusing and defocusing is not due to the intrinsic electronic nonlinearity. The observations can be explained in terms of the Kramers-Kronig dispersion relation that relates the real and imaginary parts of the complex index of refraction.

  7. Optical limiting by chemically enhanced bacteriorhodopsin films

    Science.gov (United States)

    Song, Q. Wang; Zhang, Chungping; Gross, Richard; Birge, Robert

    1993-05-01

    Measurements of effective nonlinearity of a chemically enhanced bacteriorhodopsin film are presented, using 2-scan method. Optical limiting properties and the film's nonlinear transmission properties of the film are also studied.

  8. Nonlinear Optical Image Processing with Bacteriorhodopsin Films

    Science.gov (United States)

    Downie, John D.; Deiss, Ron (Technical Monitor)

    1994-01-01

    The transmission properties of some bacteriorhodopsin film spatial light modulators are uniquely suited to allow nonlinear optical image processing operations to be applied to images with multiplicative noise characteristics. A logarithmic amplitude transmission feature of the film permits the conversion of multiplicative noise to additive noise, which may then be linearly filtered out in the Fourier plane of the transformed image. The bacteriorhodopsin film displays the logarithmic amplitude response for write beam intensities spanning a dynamic range greater than 2.0 orders of magnitude. We present experimental results demonstrating the principle and capability for several different image and noise situations, including deterministic noise and speckle. Using the bacteriorhodopsin film, we successfully filter out image noise from the transformed image that cannot be removed from the original image.

  9. Novelty filter that uses a bacteriorhodopsin film

    Science.gov (United States)

    Okamoto, Takayuki; Yamaguchi, Ichirou; Boothroyd, Simon A.; Chrostowski, Jacek

    1997-01-01

    We propose a new novelty optical filter that uses a bacteriorhodopsin film. This filter is based on the time-dependent nonlinear diffraction efficiency of real-time holograms recorded in the film. As soon as the signal beam carrying a pattern is diffracted by the polarization hologram recorded in the bacteriorhodopsin film, it begins to erase the hologram and suppresses the diffraction of the beam at the position of the stationary part of the pattern. This filter enhances only leading edges of moving patterns. In this system undesired scattered light, which is orthogonally polarized to the diffracted beam, is discriminated by a polarizer.

  10. Nonlinear transmittance of the 4-keto bacteriorhodopsin

    Science.gov (United States)

    Vanhanen, J.; Leppanen, V. P.; Jaaskelainen, T.; Parkkinen, J. P. S.; Parkkinen, S.

    1999-09-01

    The photocycle of the 4-keto bacteriorhodopsin is investigated. We constructed a multilevel theoretical model for the nonlinear transmittance properties of the material. Adjusting the relaxation parameters we are able to fit the theoretical intensity dependent transmittance curves into the experiments and to determine the photocycle from simple optical measurements.

  11. Tryptophan fluorescence quenching by alkaline earth metal cations in deionized bacteriorhodopsin.

    Science.gov (United States)

    Wang, G; Wang, A J; Hu, K S

    2000-12-01

    Tryptophan quenching by the addition of alkaline earth metal cations to deionized bacteriorhodopsin suspensions was determined. The results show that the addition of cation primarily quenches fluorescence from surface tryptophan residues. The quenched intensity exhibits a 1/R dependence, where R is the ionic radius of the corresponding metal ion. This observation results from a stronger energy transfer coupling between the tryptophan and the retinal. The membrane curvature may be involved as a result of cations motion and correlated conformational changes. PMID:11332888

  12. Detecting conformational change by current transport in Bacteriorhodopsin

    CERN Document Server

    Alfinito, Eleonora

    2008-01-01

    Charge transport modification exhibiting an increase of conductance activated by an external green light in Bacteriorhodopsin is correlated to its conformational change. A theoretical model based on a map of the protein structure into a resistor network is implemented to account for a sequential tunneling mechanism of charge transfer through neighbouring amino-acids. The model is validated by comparison with current-voltage experiments and provides for the potential barriers involved in the charge transfer an average height of 69 meV over an interacting radius of 6 \\aa. The predictability of the model is also tested on bovine rhodopsin, the prototype of the G protein coupled receptor (GPCR) family also sensitive to the light, with results exhibiting the opposite behaviour of a decrease of conductance in the presence of light.

  13. Dynamics of Primary Events in the Photocycle of Excited Bacteriorhodopsin

    Institute of Scientific and Technical Information of China (English)

    Jun-Jun LU; Ming MING; Yi YANG; Jia WU; Bo LI; Jian-Dong DING; Qing-Guo LI; Shi-Xiong QIAN

    2004-01-01

    Transient dynamic behavior of the excited bacteriorhodopsin (BR), which was isolated from the strain H. salinarum, was studied at excitation wavelength from 585 to 639 nm. With the one-color femtosecond (fs) pump-probe technique, we revealed the primary events in BR's photocycle that took place in an ultrafast time scale. From the analysis of the decay components of the dynamical traces, it was evident that the isomerization of the retinal chromophore in BR and the intermediate J's formation occurred within 500 fs. BR exhibited pH-dependent dynamical behaviors. When the medium pH was between 5 and 9, the BR ultrafast dynamics has no obvious change. In contrast, the dynamical curves were obviously affected when the pH was out of that region.

  14. Nonlinear transmission properties in bacteriorhodopsin-embedded photonic crystal

    Science.gov (United States)

    Okada-Shudo, Yoshiko; Ishihara, Teruya

    2003-11-01

    Transmission spectra and photoinduced transmission change are observed in periodic waveguide which consist of a quartz grating substrate and a thin protein film of bacteriorhodopsin. We propose a scheme to achieve all optical switching using the photoinduced refractive index change of bacteriorhodopsin.

  15. Revealing quantum correlation by negativity of the Wigner function

    Science.gov (United States)

    Taghiabadi, Razieh; Akhtarshenas, Seyed Javad; Sarbishaei, Mohsen

    2016-05-01

    We analyze two two-mode continuous variable separable states with the same marginal states. We adopt the definition of classicality in the form of well-defined positive Wigner function describing the state and find that although the states possess positive local Wigner functions, they exhibit negative Wigner functions for the global states. Using the negativity of Wigner function as an indicator of nonclassicality, we show that despite these states possess different negativities of the Wigner function, they do not reveal this difference as phase space nonclassicalities such as negativity of the Mandel Q parameter or quadrature squeezing. We then concentrate on quantum correlation of these states and show that quantum discord and local quantum uncertainty, as two well-defined measures of quantum correlation, manifest the difference between negativity of the Wigner functions. The non-Gaussianity of these states is also examined and show that the difference in behavior of their non-Gaussianity is the same as the difference between negativity of their Wigner functions. We also investigate the influence of correlation rank criterion and find that when the states can be produced locally from classical states, the Wigner functions cannot reveal their quantum correlations.

  16. Kinetic vs. Thermodynamic Control of Bacteriorhodopsin Pumping

    Science.gov (United States)

    Gunner, Marilyn

    2011-03-01

    Bacteriorhodopsin is a transmembrane proton pump that converts light energy to a transmembrane electrochemical gradient. Retinal, bound in the center of the protein, absorbs light and isomerizes from the all-trans to 13-cis configuration. A series of conformational changes and proton transfers then restores the structure to the all-trans ground state while pumping one proton from the high pH cell interior to the low pH exterior, saving energy in an electrochemical gradient. Poorly understood gating elements control key steps where incorrect proton transfer would return the protein to the ground state without pumping. The gate's barrier height determines how much the pump leaks. Analysis of high-resolution structures trapped in different intermediates has produced ideas for how bacteriorhodopsin ensures pumping. There are two contrasting strategies, one primarily thermodynamic and the other relying on kinetic control to ensure that protons are moved uphill. With thermodynamic control, residue protonation states always remain in quasi-equilibrium. Relatively slow conformational changes shift the energy landscape modifying site pKas. Residues then change ionization remaining in equilibrium in each metastable intermediate. The sequence of intermediates imparts the directionality to the transfers. Alternatively, the direction of transfer is determined by the accessibility of low energy pathways so is thus is under kinetic control. We will discuss which steps in the bacteriorhodopsin photocycle are under thermodynamic or under kinetic control. The role of three specific conformational changes (retinal isomerization, Arg82 reorientation and Glu194 and 204 separations) on the degree of proton transfer will be described. Supported by NFS MCB 1022208. Carried out with Yifan Song now at the University of Washington Department of Biochemistry.

  17. Retinal isomerization dynamics in dry bacteriorhodopsin films

    Science.gov (United States)

    Colonna, Anne; Groma, Géza I.; Vos, Marten H.

    2005-10-01

    The primary photoprocesses in neutral and acid forms of oriented dried bacteriorhodopsin films were investigated by femtosecond absorption spectroscopy. The excitation energy dependence of the signals was used to distinguish photochemistry from processes involving photophysics of photocycle intermediates. Both the kinetics and the quantum yield of all- trans excited state decay by retinal photoisomerization and subsequent J → K transition were found to be very similar as in hydrated environments. Therefore, unlike slower photocycle phases, communication of the retinal with the environment does not play a role in retinal isomerization. Our results are important for understanding recent nonlinear optical applications of such films.

  18. Ultrafast all-optical switching in bacteriorhodopsin

    Science.gov (United States)

    Roy, Sukhdev; Singh, C. P.; Reddy, K. P. J.

    2001-04-01

    All-optical switching has been demonstrated in bacteriorhodopsin based on excited-state nonlinear absorption. A probe laser beam at 640 nm corresponding to the O-state absorption maximum is switched due to a strong pulsed pump laser beam at 570 nm, that corresponds to the maximum ground state absorption. We have studied the effect of variation in pulse width and in small signal absorption coefficient on the switching characteristics. The switching time decreases as the pulse width of the pump beam decreases and the small signal absorption coefficient increases. The switching contrast depends mainly on the peak pumping intensity.

  19. Neural correlates of the LSD experience revealed by multimodal neuroimaging.

    Science.gov (United States)

    Carhart-Harris, Robin L; Muthukumaraswamy, Suresh; Roseman, Leor; Kaelen, Mendel; Droog, Wouter; Murphy, Kevin; Tagliazucchi, Enzo; Schenberg, Eduardo E; Nest, Timothy; Orban, Csaba; Leech, Robert; Williams, Luke T; Williams, Tim M; Bolstridge, Mark; Sessa, Ben; McGonigle, John; Sereno, Martin I; Nichols, David; Hellyer, Peter J; Hobden, Peter; Evans, John; Singh, Krish D; Wise, Richard G; Curran, H Valerie; Feilding, Amanda; Nutt, David J

    2016-04-26

    Lysergic acid diethylamide (LSD) is the prototypical psychedelic drug, but its effects on the human brain have never been studied before with modern neuroimaging. Here, three complementary neuroimaging techniques: arterial spin labeling (ASL), blood oxygen level-dependent (BOLD) measures, and magnetoencephalography (MEG), implemented during resting state conditions, revealed marked changes in brain activity after LSD that correlated strongly with its characteristic psychological effects. Increased visual cortex cerebral blood flow (CBF), decreased visual cortex alpha power, and a greatly expanded primary visual cortex (V1) functional connectivity profile correlated strongly with ratings of visual hallucinations, implying that intrinsic brain activity exerts greater influence on visual processing in the psychedelic state, thereby defining its hallucinatory quality. LSD's marked effects on the visual cortex did not significantly correlate with the drug's other characteristic effects on consciousness, however. Rather, decreased connectivity between the parahippocampus and retrosplenial cortex (RSC) correlated strongly with ratings of "ego-dissolution" and "altered meaning," implying the importance of this particular circuit for the maintenance of "self" or "ego" and its processing of "meaning." Strong relationships were also found between the different imaging metrics, enabling firmer inferences to be made about their functional significance. This uniquely comprehensive examination of the LSD state represents an important advance in scientific research with psychedelic drugs at a time of growing interest in their scientific and therapeutic value. The present results contribute important new insights into the characteristic hallucinatory and consciousness-altering properties of psychedelics that inform on how they can model certain pathological states and potentially treat others. PMID:27071089

  20. Neural correlates of the LSD experience revealed by multimodal neuroimaging

    Science.gov (United States)

    Carhart-Harris, Robin L.; Muthukumaraswamy, Suresh; Roseman, Leor; Kaelen, Mendel; Droog, Wouter; Murphy, Kevin; Tagliazucchi, Enzo; Schenberg, Eduardo E.; Nest, Timothy; Orban, Csaba; Leech, Robert; Williams, Luke T.; Williams, Tim M.; Bolstridge, Mark; Sessa, Ben; McGonigle, John; Sereno, Martin I.; Nichols, David; Hobden, Peter; Evans, John; Singh, Krish D.; Wise, Richard G.; Curran, H. Valerie; Feilding, Amanda; Nutt, David J.

    2016-01-01

    Lysergic acid diethylamide (LSD) is the prototypical psychedelic drug, but its effects on the human brain have never been studied before with modern neuroimaging. Here, three complementary neuroimaging techniques: arterial spin labeling (ASL), blood oxygen level-dependent (BOLD) measures, and magnetoencephalography (MEG), implemented during resting state conditions, revealed marked changes in brain activity after LSD that correlated strongly with its characteristic psychological effects. Increased visual cortex cerebral blood flow (CBF), decreased visual cortex alpha power, and a greatly expanded primary visual cortex (V1) functional connectivity profile correlated strongly with ratings of visual hallucinations, implying that intrinsic brain activity exerts greater influence on visual processing in the psychedelic state, thereby defining its hallucinatory quality. LSD’s marked effects on the visual cortex did not significantly correlate with the drug’s other characteristic effects on consciousness, however. Rather, decreased connectivity between the parahippocampus and retrosplenial cortex (RSC) correlated strongly with ratings of “ego-dissolution” and “altered meaning,” implying the importance of this particular circuit for the maintenance of “self” or “ego” and its processing of “meaning.” Strong relationships were also found between the different imaging metrics, enabling firmer inferences to be made about their functional significance. This uniquely comprehensive examination of the LSD state represents an important advance in scientific research with psychedelic drugs at a time of growing interest in their scientific and therapeutic value. The present results contribute important new insights into the characteristic hallucinatory and consciousness-altering properties of psychedelics that inform on how they can model certain pathological states and potentially treat others. PMID:27071089

  1. Electron microscopic observation and rotational diffusion measurement of bacteriorhodopsin in lipid vesicles

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The morphology of bacteriorhodopsin reconstituted into dimyristoylphosphatidylcholine and egg-phosphatidylcholine vesicles was observed by freeze-fracture electron microscopy. The rotational diffusion of bacteriorhodopsin at different concentrations of melittin was measured by observing flash-induced transient dichroism in dimyristoylphosphatidylcholine vesicles. In the presence of melittin, bacteriorhodopsin molecules in dimyristoylphosphatidylcholine vesicles were aggregated into large particles or patches, and the ability of rotational diffusion of bacteriorhodop sin in vesicles was decreased. This suggests that melittin produces its effect via direct electrostatic interaction with bacteriorhodopsin. Low temperature-induced aggregation of bacteriorhodopsin was also observed in dimyristoylphosphatidylcholine vesicles. Low temperature may cause phase separation. Bacteriorhodopsin was also successfully reconstituted into egg-phosphatidylcholine vesicles, but Iow temperature-induced aggregation of bacteriorhodopsin in dimyristoylphosphati dylcholine cannot appear in egg-phosphatidylcholine vesicles. This suggests that different lipids have different effects on bacteriorhodopsin in vesicles.

  2. Multi-exponentially Photoelectric Response of Bacteriorhodopsin

    Institute of Scientific and Technical Information of China (English)

    姚保利; 徐大纶; 侯洵; 胡坤生; 王敖金

    2001-01-01

    A thin oriented bacteriorhodopsin (bR) film is deposited on a stainless steel slide by use of the electrophoretic sedimentation method. A junction is made with electrolyte gels having a counterelectrode to construct a bRbased photoelectric detector. The photoelectric response signal to a 10ns laser pulse is measured. A theory on the photoelectric kinetics of bR is developed based on the concept of the charge displacement current and the bR photocycle rate equations. Comparison between the theoretical and experimental results proves that the bR photoelectric response to a short laser pulse is a multi-exponential process. The decay time constants and amplitudes of each exponential component are obtained by data fitting.

  3. Bacteriorhodopsin: Tunable Optical Nonlinear Magnetic Response

    CERN Document Server

    Bovino, F A; Sibilia, C; Giardina, M; Váró, G; Gergely, C

    2011-01-01

    We report on a strong and tunable magnetic optical nonlinear response of Bacteriorhodopsin (BR) under "off resonance" femtosecond (fs) pulse excitation, by detecting the polarization map of the noncollinear second harmonic signal of an oriented BR film, as a function of the input beam power. BR is a light-driven proton pump with a unique photochemistry initiated by the all trans retinal chromophore embedded in the protein. An elegant application of this photonic molecular machine has been recently found in the new area of optogenetics, where genetic expression of BR in brain cells conferred a light responsivity to the cells enabling thus specific stimulation of neurons. The observed strong tunable magnetic nonlinear response of BR might trigger promising applications in the emerging area of pairing optogenetics and functional magnetic resonance imaging susceptible to provide an unprecedented complete functional mapping of neural circuits.

  4. Numerical simulation of the nonlinear optical response of bacteriorhodopsin

    Science.gov (United States)

    Kowalski, Gregory J.

    1996-10-01

    The numerical simulation of the nonlinear optical behavior of bacteriorhodopsin in a solution of water is described. Relationships for the intensity dependent absorption coefficient and index of refraction are developed and used in the numerical simulation of bacteriorhodopsin as an optical limiter and as defocussing element for laser pulses in the picosecond regime. The algorithm is a transient finite volume method that is coupled with a 'ray model' of the radiation which simultaneously solves the heat transfer and Maxwell's equations. The nonlinear behavior of the material is included in this analysis using a modified Euler predictor-corrector integration technique. Calculated power limiting and z-scan curves are in qualitative agreement with experiments. These results indicate that the code can be used to investigate and optimize optical systems which use the nonlinear behavior of bacteriorhodopsin.

  5. Bacteriorhodopsin overview of fundamentals and applications

    Science.gov (United States)

    Thai, Serey

    1999-07-01

    Bacteriorhodopsin (BR) is a light transducing photochromic protein in the purple membrane of a salt-loving microorganism that inhabits salt marshes. It has strong absorption in a broad region of the visible spectrum. The B- state in the photocycle can be considered to be the ground state, which has absorption maxima at 570 nm. Perhaps, the most intriguing features of this organic photopolymer are its extraordinary stability in the chemical, thermal and photochemical sense, its large optical nonlinearity, dynamic nature, durability, real-time holographic recording capabilities, and information storage potential. Furthermore, BR-doped polymer film can be fabricated for a large-scale application, whereas photorefractive crystals like BSO or KNSBM cannot be grown easily to the same dimension as BR. Hence, BR's potential in optical system includes transient dynamic applications of an M-type hologram and 3D optical memories of a branched photocycle that shows a great promise for data storage and retrieval due to its high capacity. The major advantages of this organic photopolymer include high density, low cost, low weight and portability which are a projected requirement for the Air Force and commercial applications.

  6. Enhancement of photoanisotropy in Bacteriorhodopsin films

    Science.gov (United States)

    Rao, D. V. G. L. N.; Wu, Pengfei

    2003-03-01

    The biological material of Bacteriorhodopsin (bR) and its derivatives are among the most promising candidates for potential applications in photonics in view of their large optical nonlinearity, ease of optimization and tailoring optical properties. We report a novel scheme for significant enhancement of photo-anisotropic effects in bR films using two exciting beams at different wavelengths with orthogonal polarization. We monitor the photoinduced anisotropy with a probe beam passing through the bR film placed between two crossed polarizers. Near twenty times enhancement of probe beam intensity has been observed as compared with the case of only one exciting beam. The mechanism of the enhancement originates from optimization of direction-selected photo-isomerization of the biomaterial controlled by the polarized exciting beams. We also demonstrate an all-optical switch with the additional novel feature of output sign-control by applying this technique. It is possible to achieve fast optical switching since the photo-isomerization of M to B state of the bR molecule may be as fast as nanoseconds.

  7. Measurements of photoinduced refractive index changes in bacteriorhodopsin films

    Science.gov (United States)

    Banyal, Ravinder Kumar; Raghavendra Prasad, B.

    2007-03-01

    We report the pump--probe measurements of nonlinear refractive index changes in photochromic bacteriorhodopsin films. The photoinduced absorption is caused by pump beam at 532 nm and the accompanying refractive index changes are studied using a probe beam at 633 nm. The proposed technique is based on a convenient and accurate determination of optical path difference using digital interferometry-based local fringe shift. The results are presented for the wild-type as well as genetically modified D96N variant of the bacteriorhodopsin.

  8. Fast integrated optical switching by the protein bacteriorhodopsin

    Science.gov (United States)

    Fábián, László; Wolff, Elmar K.; Oroszi, László; Ormos, Pál; Dér, András

    2010-07-01

    State-of-the-art photonic integration technology is ready to provide the passive elements of optical integrated circuits, based either on silicon, glass or plastic materials. The bottleneck is to find the proper nonlinear optical (NLO) materials in waveguide-based integrated optical circuits for light-controlled active functions. Recently, we proposed an approach where the active role is performed by the chromoprotein bacteriorhodopsin as an NLO material, that can be combined with appropriate integrated optical devices. Here we present data supporting the possibility of switching based on a fast photoreaction of bacteriorhodopsin. The results are expected to have important implications for photonic switching technology.

  9. Measurements of photoinduced refractive index changes in bacteriorhodopsin films

    Indian Academy of Sciences (India)

    Ravinder Kumar Banyal; B Raghavendra Prasad

    2007-03-01

    We report the pump-probe measurements of nonlinear refractive index changes in photochromic bacteriorhodopsin films. The photoinduced absorption is caused by pump beam at 532 nm and the accompanying refractive index changes are studied using a probe beam at 633 nm. The proposed technique is based on a convenient and accurate determination of optical path difference using digital interferometry-based local fringe shift. The results are presented for the wild-type as well as genetically modified D96N variant of the bacteriorhodopsin.

  10. Wavelet correlations to reveal multiscale coupling in geophysical systems

    CERN Document Server

    Casagrande, Erik; Miralles, Diego; Entekhabi, Dara; Molini, Annalisa

    2015-01-01

    The interactions between climate and the environment are highly complex. Due to this complexity, process-based models are often preferred to estimate the net magnitude and directionality of interactions in the Earth System. However, these models are based on simplifications of our understanding of nature, thus are unavoidably imperfect. Conversely, observation-based data of climatic and environmental variables are becoming increasingly accessible over large scales due to the progress of space-borne sensing technologies and data-assimilation techniques. Albeit uncertain, these data enable the possibility to start unraveling complex multivariable, multiscale relationships if the appropriate statistical methods are applied. Here, we investigate the potential of the wavelet cross-correlation method as a tool for identifying multiscale interactions, feedback and regime shifts in geophysical systems. The ability of wavelet cross-correlation to resolve the fast and slow components of coupled systems is tested on syn...

  11. Clique topology reveals intrinsic geometric structure in neural correlations.

    Science.gov (United States)

    Giusti, Chad; Pastalkova, Eva; Curto, Carina; Itskov, Vladimir

    2015-11-01

    Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonlinear monotone transformations. These features can be used to detect both random and geometric structure, and depend only on the relative ordering of matrix entries. We then analyzed the activity of pyramidal neurons in rat hippocampus, recorded while the animal was exploring a 2D environment, and confirmed that our method is able to detect geometric organization using only the intrinsic pattern of neural correlations. Remarkably, we found similar results during nonspatial behaviors such as wheel running and rapid eye movement (REM) sleep. This suggests that the geometric structure of correlations is shaped by the underlying hippocampal circuits and is not merely a consequence of position coding. We propose that clique topology is a powerful new tool for matrix analysis in biological settings, where the relationship of observed quantities to more meaningful variables is often nonlinear and unknown.

  12. Dynamic and unique nucleolar microenvironment revealed by fluorescence correlation spectroscopy.

    Science.gov (United States)

    Park, Hweon; Han, Sung-Sik; Sako, Yasushi; Pack, Chan-Gi

    2015-03-01

    Organization and functions of the nucleolus is maintained by mobilities and interactions of nucleolar factors. Because the nucleolus is a densely packed structure, molecular crowding effects determined by the molecular concentrations and mobilities in the nucleolus should also be important for regulating nucleolar organization and functions. However, such molecular property of nucleolar organization is not fully understood. To understand the biophysical property of nucleolar organization, the diffusional behaviors of inert green fluorescent protein (GFP) oligomers with or without nuclear localization signals (NLSs) were analyzed under various conditions by fluorescence correlation spectroscopy. Our result demonstrates that the mobility of GFPs inside the nucleolus and the nucleoplasm can be represented by single free diffusion under normal conditions, even though the mobility in the nucleolus is considerably slower than that in the chromatin region. Moreover, the free diffusion of GFPs is found to be significantly size- and NLS-dependent only in the nucleolus. Interestingly, the mobility in the nucleolus is highly sensitive to ATP depletion, as well as actinomycin D (ActD) treatment. In contrast, the ultra-structure of the nucleolus was not significantly changed by ATP depletion but was changed by ActD treatment. These results suggest that the nucleolus behaves similarly to an open aqueous-phase medium with an increased molecular crowding effect that depends on both energy and transcription.

  13. Can strong correlations be experimentally revealed for Ҡ -mesons?

    Directory of Open Access Journals (Sweden)

    Hiesmayr Beatrix C.

    2014-01-01

    Full Text Available In 1964 the physicists John St. Bell working at CERN took the 1935-idea of Einstein-Podolsky-Rosen seriously and found that all theories based on local realism have to satisfy a certain inequality, nowadays dubbed Bell’s inequality. Experiments with ordinary matter systems or light show violations of Bell’s inequality favouring the quantum theory though a loophole free experiment has not yet been performed. This contribution presents an experimentally feasible Bell inequality for systems at higher energy scales, i.e. entangled neutral Ҡ -meson pairs that are typically produced in Φ -mesons decays or proton-antiproton annihilation processes. Strong requirements have to be overcome in order to achieve a conclusive tests, such a proposal was recently published. Surprisingly, this new Bell inequality reveals new features for weakly decaying particles, in particular, a strong sensitivity to the combined charge-conjugation-parity (CP symmetry. Here-with, a puzzling relation between a symmetry breaking for mesons and Bell’s inequality—which is a necessary and sufficient condition for the security of quantum cryptography protocols— is established. This becomes the more important since CP symmetry is related to the cosmological question why the antimatter disappeared after the Big Bang.

  14. Nonlinear optical properties of bacteriorhodopsin, retinal, and related molecules

    Science.gov (United States)

    Hendrickx, Eric; Clays, Koen J.; Vinckier, A.; Persoons, Andre P.; Dehu, Christophe; Bredas, Jean-Luc

    1995-10-01

    The first hyperpolarizabilities, (beta) , of bacteriorhodopsin, retinal, and related molecules were determined experimentally by using the hyper-Rayleigh scattering technique and compared to the calculated values obtained with the semiempirical intermediate neglect of differential overlap/configuration interaction/sum-over-states method. The experimental and theoretical results are in excellent mutual agreeement. The hyper-Rayleigh scattering technique is shown to be very sensitive to the degree of solubilization of bacteriorhodopsin. Theoretical and experimental data confirm the expected dependence of (beta) on the first transition energy as well as an exponential increase of (beta) with the number of double bonds. It was found that, upon trans to 13-cis or 9-cis isomerization of a retinal double bond, a constant fraction of the (beta) value is lost, regardless of the nature of the electron withdrawing group or the solvent of choice.

  15. Do Cation-π Interactions Exist in Bacteriorhodopsin

    Institute of Scientific and Technical Information of China (English)

    HU Kun-Sheng; WANG Guang-Yu; HE Jin-An

    2001-01-01

    Metal ions are essential to the structure and physiological functions of bacteriorhodopsin. Experimental evidence suggests the existence of specific cation binding to the negatively charged groups of Asp85 and Asp212 via an electrostatic interaction. However, only using electrostatic force is not enough to explain the role of the metal cations because the carboxylate of Asp85 is well known to be protonated in the M intermediate. Considering the presence of some aromatic amino acid residues in the vicinity of the retinal pocket, the existence of cation-π interactions between the metal cation and aromatic amino acid residues is suggested. Obviously, introduction of this kind of interaction is conducive to understanding the effects of the metal cations and aromatic amino acid residues inside the protein on the structural stability and proton pumping of bacteriorhodopsin.

  16. Nonlinear polarization interaction in bacteriorhodopsin films with anisotropically saturating absorption

    Science.gov (United States)

    Korchemskaya, Elena Y.; Soskin, Marat S.; Stepanchikov, Dmitriy A.; Druzhko, Anna B.; Dyukova, Tatyana V.

    1996-06-01

    The effect of protein and matrix modifications on the photoanisotropic properties is studied for developing the concept of impact upon the main optical properties of the dynamic optical material based on bacteriorhodopsin (BR) both interaction of transmembrane protein--chromophore complex BR with matrix and interaction of protein opsin with chromophore retinal. Also possibility of the application of BR-films for the light polarization modulator is proposed.

  17. Nonlinear polarization-modulated spectroscopy of bacteriorhodopsin and its analogues

    Science.gov (United States)

    Taranenko, V. B.; Bazhenov, V. Yu; Kulikovskaya, O. A.

    1996-09-01

    We report on a novel nonlinear polarization-modulated spectroscopic method for an accurate measurement of the nonlinear change of both real and imaginary parts of the complex refractive index in isotropic materials having either scalar or tensor photoresponse. It is based on a vector two-wave-mixing interaction and heterodyne detection of dynamic change of optical polarization. New data on steady-state and transient nonlinear characteristics of bacteriorhodopsin-based materials (suspensions and polymer films) are obtained using this method.

  18. All-optical logic-gates based on bacteriorhodopsin film

    Institute of Scientific and Technical Information of China (English)

    Chen Gui-Ying; Zhang Chun-Ping; Guo Zong-Xia; Tian Jian-Guo; Zhang Guang-Yin; Song Qi-Wang

    2005-01-01

    Based on self-diffraction in bacteriorhodopsin (bR) film, we propose all-optical NOT, XOR, half adder and XNOR logic operations. Using the relation between diffraction light and the polarization states of recording beams, we demonstrate NOT and XNOR logic operations. Studying the relation of polarization states among the diffracting, recording and reading beams, we implement XOR logic and half adder operations with three inputs. The methods are simple and practicable.

  19. Cooperative phenomena in the photocycle of D96N mutant bacteriorhodopsin.

    Science.gov (United States)

    Radionov, A N; Kaulen, A D

    1995-12-27

    The M intermediate decay in the photocycle of D96N mutant bacteriorhodopsin does not depend on the light intensity of the exciting flash. Cooperative phenomena in the photocycle are revealed after addition of azide causing acceleration of the M decay and making it kinetically well separated from the N decay. Increase in the light intensity induces slight deceleration of the M decay and significant acceleration of the N decay. The data obtained directly confirm our recent model [Komrakov and Kaulen (1995) Biophys. Chem. 56, 113-119], according to which appearance of the Mslow intermediate in the photocycle of the wild type bR at high light intensity is due to destabilization of the N intermediate leading to the acceleration of the N-->M and N-->bR reactions. PMID:8549749

  20. Rate Constant Change of Photo Reaction of Bacteriorhodopsin Observed in Trimeric Molecular System.

    Science.gov (United States)

    Tsujiuchi, Yutaka; Masumoto, Hiroshi; Goto, Takashi

    2016-04-01

    To elucidate the time evolution of photo reaction of bacteriorhodopsin in glycerol mixed purple membrane at around 196 K under irradiation by red light, a kinetic model was constructed. The change of absorption with irradiation at times of 560 nm and 412 nm was analyzed for the purpose of determining reaction rates of photo reaction of bacteriorhodopsin and its product M intermediate. In this study it is shown that reaction rates of conversion from bacteriorhodopsin to the M intermediate can be explained by a set of linear differential equations. This model analysis concludes that bacteriorhodopsin in which constitutes a trimer unit with other two bacteriorhodopsin molecules changes into M intermediates in the 1.73 of reaction rate, in the initial step, and according to the number of M intermediate in a trimer unit, from three to one, the reaction rate of bacteriorhodopsin into M intermediates smaller as 1.73, 0.80, 0.19 which caused by influence of inter-molecular interaction between bacteriorhodopsin. PMID:27451646

  1. Light-Induced Charge Separation and Transfer in Bacteriorhodopsin

    Institute of Scientific and Technical Information of China (English)

    HUANG Yu-Hua; LI Qing-Guo; ZHAO You-Yuan; ZHANG Zhong-Bin; OU-YANG Xiao-Ping; GONG Qin-Gan; CHEN Ling-Bing; LI Fu-Ming; LIU Jian; DING Jian-Dong

    2000-01-01

    The photo-voltage signals in bacteriorhodopsin(bR) excited by 1064nm pulse laser are different from those by 532 or 355 nm. It shows that the positive and negative photoelectric signals are produced by the motion of the positive and negative charges, respectively, and more energy is needed for producing the positive charges than the negative. The mechanism of light-induced charge generation and charge transfer in bR was studied and analyzed by measuring the photoelectric signals with different impedance of measuring circuit and different pulse-width of 532 nm laser as pump light.

  2. The behaviours of optical novelty filter based on bacteriorhodopsin film

    Institute of Scientific and Technical Information of China (English)

    Chen Gui-Ying; Yuan Yi-Zhe; Liang Xin; Xu Tang; Zhang Chun-Ping; Song Qi-Wang

    2006-01-01

    The quality of the novelty filter image is investigated at different intensities of the incident blue and yellow beams irradiating a bacteriorhodopsin (bR) film. The relationship between the transmitted blue beams and the incident yellow beams is established. The results show that the contrast of the novelty filter image depends on the lifetime of longest lived photochemical state (M state). These results enable one to identify the direction of a moving object and to improve the quality of the novel filter image by prolonging the lifetime of M state.

  3. Engineering a Robust Photovoltaic Device with Quantum Dots and Bacteriorhodopsin

    OpenAIRE

    Renugopalakrishnan, Venkatesan; Barbiellini, Bernardo; King, Chris; Molinari, Michael; Mochalov, Konstantin; Sukhanova, Alyona; Nabiev, Igor; Fojan, Peter; Tuller, Harry L.; Chin, Michael; Somasundaran, Ponisseril; Padrós, Esteve; Ramakrishna, Seeram

    2014-01-01

    We present a route toward a radical improvement in solar cell efficiency using resonant energy transfer and sensitization of semiconductor metal oxides with a light-harvesting quantum dot (QD)/bacteriorhodopsin (bR) layer designed by protein engineering. The specific aims of our approach are (1) controlled engineering of highly ordered bR/QD complexes; (2) replacement of the liquid electrolyte by a thin layer of gold; (3) highly oriented deposition of bR/QD complexes on a gold layer; and (4) ...

  4. Effective photochromic nonlinearity of dried blue-membrane bacteriorhodopsin films

    Science.gov (United States)

    Tallent, Jack; Song, Q. Wang; Li, Zengfa; Stuart, Jeff; Birge, R. R.

    1996-09-01

    We report the effective nonlinearity for photochromic conversion in a blue-membrane bacteriorhodopsin film hosted in a dry polyvinyl alcohol matrix. The shift in absorption maximum on photoconversion in this film is larger than that of the same material in hydrated form, thus offering a larger modulation of the refractive index. The photoexcited index modulation is stable for several months, which provides for holographic data recording and long-term photochromic data storage. The effective index modulation is experimentally measured and is in good agreement with the theoretical predictions based on the Kramers-Kronig transformation.

  5. Spontaneous pattern formation in a thin film of bacteriorhodopsin with mixed absorptive-dispersive nonlinearity

    Science.gov (United States)

    Glückstad, J.; Saffman, M.

    1995-03-01

    We have observed the spontaneous formation of transverse spatial patterns in a thin film of bacteriorhodopsin with a feedback mirror. Bacteriorhodopsin has a mixed absorptive-dispersive nonlinearity at the wavelength used in the experiments (633 nm). Threshold values of the incident intensity for observation of pattern formation are found from a linear stability analysis of a model that describes bacteriorhodopsin as a sluggish saturable nonlinear medium with a complex Kerr coefficient. The calculated threshold intensity is in good agreement with the experimental observations, and the patterns are predicted to be frequency offset from the pump radiation.

  6. Mixed Potential Energy Surfaces of the Ultrafast Isomerization of Retinal in Bacteriorhodopsin

    Directory of Open Access Journals (Sweden)

    Prokhorenko Valentyn I.

    2013-03-01

    Full Text Available We observe, using electronic two-dimensional photon echo spectroscopy, that the cis and trans potential energy surfaces of the ultrafast isomerization of retinal in bacteriorhodopsin are mixed via the hydrogen out of plane (HOOP mode.

  7. Metabolomics reveals significant variations in metabolites and correlations regarding the maturation of walnuts (Juglans regia L.).

    Science.gov (United States)

    Rao, Guodong; Sui, Jinkai; Zhang, Jianguo

    2016-01-01

    The content of walnut metabolites is related to its nutritive value and physiological characteristics, however, comprehensive information concerning the metabolome of walnut kernels is limited. In this study we analyzed the metabolites of walnut kernels at five developmental stages from filling to ripening using GC-MS-based untargeted metabolomics; of a total 252 peaks identified, 85 metabolites were positively identified. Further statistical analysis revealed that these 85 metabolites covered different types of metabolism pathways. PCA scores revealed that the metabolic compositions of the embryo are different at each stage, while the metabolic composition of the endotesta could not be significantly separated into distinct groups. Additionally, 7225 metabolite-metabolite correlations were detected in walnut kernel by a Pearson correlation coefficient approach; during screening of the calculated correlations, 463 and 1047 were determined to be significant with r(2)≥0.49 and had a false discovery rate (FDR) ≤0.05 in endotesta and embryo, respectively. This work provides the first comprehensive metabolomic study of walnut kernels and reveals that most of the carbohydrate and protein-derived carbon was transferred into other compounds, such as fatty acids, during the maturation of walnuts, which may potentially provide the basis for further studies on walnut kernel metabolism.

  8. Metabolomics reveals significant variations in metabolites and correlations regarding the maturation of walnuts (Juglans regia L.

    Directory of Open Access Journals (Sweden)

    Guodong Rao

    2016-06-01

    Full Text Available The content of walnut metabolites is related to its nutritive value and physiological characteristics, however, comprehensive information concerning the metabolome of walnut kernels is limited. In this study we analyzed the metabolites of walnut kernels at five developmental stages from filling to ripening using GC-MS-based untargeted metabolomics; of a total 252 peaks identified, 85 metabolites were positively identified. Further statistical analysis revealed that these 85 metabolites covered different types of metabolism pathways. PCA scores revealed that the metabolic compositions of the embryo are different at each stage, while the metabolic composition of the endotesta could not be significantly separated into distinct groups. Additionally, 7225 metabolite-metabolite correlations were detected in walnut kernel by a Pearson correlation coefficient approach; during screening of the calculated correlations, 463 and 1047 were determined to be significant with r2≥0.49 and had a false discovery rate (FDR ≤0.05 in endotesta and embryo, respectively. This work provides the first comprehensive metabolomic study of walnut kernels and reveals that most of the carbohydrate and protein-derived carbon was transferred into other compounds, such as fatty acids, during the maturation of walnuts, which may potentially provide the basis for further studies on walnut kernel metabolism.

  9. Bacteriorhodopsin films for optical signal processing and data storage

    Science.gov (United States)

    Walkup, John F. (Principal Investigator); Mehrl, David J. (Principal Investigator)

    1996-01-01

    This report summarizes the research results obtained on NASA Ames Grant NAG 2-878 entitled 'Investigations of Bacteriorhodopsin Films for Optical Signal Processing and Data Storage.' Specifically we performed research, at Texas Tech University, on applications of Bacteriorhodopisin film to both (1) dynamic spatial filtering and (2) holographic data storage. In addition, measurements of the noise properties of an acousto-optical matrix-vestor multiplier built for NASA Ames by Photonic Systems Inc. were performed at NASA Ames' Photonics Laboratory. This research resulted in two papers presented at major optical data processing conferences and a journal paper which is to appear in APPLIED OPTICS. A new proposal for additional BR research has recently been submitted to NASA Ames Research Center.

  10. Bacteriorhodopsin-based bipolar photosensor for biomimetic sensing

    Science.gov (United States)

    Kasai, Katsuyuki; Haruyama, Yoshihiro; Yamada, Toshiki; Akiba, Makoto; Tominari, Yukihiro; Kaji, Takahiro; Terui, Toshifumi; Peper, Ferdinand; Tanaka, Shukichi; Katagiri, Yoshitada; Kikuchi, Hiroshi; Okada-Shudo, Yoshiko; Otomo, Akira

    2013-10-01

    Bacteriorhodopsin (bR) is a promising biomaterial for several applications. Optical excitation of bR at an electrode-electrolyte interface generates differential photocurrents while an incident light is turned on and off. This unique functional response is similar to that seen in retinal neurons. The bR-based bipolar photosensor consists of the bR dip-coated thin films patterned on two ITO plates and the electrolyte solution. This bipolar photocell will function as a biomimetic photoreceptor cell. The bipolar structure, due to the photocurrent being generated in alignment with the cathodic direction, makes the excitatory and inhibitory regions possible. This scheme shows our bipolar cell can act as a basic unit of edge detection and forms the artificial visual receptive field.

  11. Thermochromism of bacteriorhodopsin and its pH dependence.

    Science.gov (United States)

    Neebe, Martin; Rhinow, Daniel; Schromczyk, Nina; Hampp, Norbert A

    2008-06-12

    Purple membranes (PMs), which consist of the photochromic membrane protein bacteriorhodopsin (BR) and lipids only, show complex thermochromic properties. Three different types of reversible temperature-dependent spectral transitions were found, involving spectral states absorbing at 460, 519, and 630 nm. These thermochromic absorption changes were analyzed in the range from 10 to 80 degrees C. In dependence on the bulk pH value, hypsochromic or bathochromic shifts in the BR absorption spectra are observed in BR gels as well as in BR films. The thermochromic changes between both purple and blue or purple and red were quantified in the CIE color system. The molecular changes causing these effects are discussed, and a model is presented in terms of intramolecular protonation equilibriums. The thermochromic properties of BR may be of interest in applications like security tags, as this feature may complement the well-known photochromic properties of BR. PMID:18491932

  12. Integrated optical switching based on the protein bacteriorhodopsin.

    Science.gov (United States)

    Dér, András; Valkai, Sándor; Fábián, László; Ormos, Pál; Ramsden, Jeremy J; Wolff, Elmar K

    2007-01-01

    According to our earlier pioneering study, a dry film containing native bacteriorhodopsin (bR) shows unique nonlinear optical properties (refractive index change, controllable by light of different colors, greater than 2 x 10(-3)) that are in many respects superior to those of the materials presently applied in integrated optics. Here, we report on the first integrated optical application based on a miniature Mach-Zehnder interferometer (see Figs. 1 and 2) demonstrating a real switching effect by bR (efficiency higher than 90%) due to the M-state. Our results also imply that the refractive index change of the K-state (9 x 10(-4)) is high enough for fast switching. PMID:17132043

  13. Generalized model for all-optical light modulation in bacteriorhodopsin

    Science.gov (United States)

    Roy, Sukhdev; Singh, C. P.; Reddy, K. P. J.

    2001-10-01

    We present a generalized model for the photochemical cycle of bacteriorhodopsin (bR) protein molecule. Rate equations have been solved for the detailed light-induced processes in bR for its nine states: B→K↔L↔MI→MII↔N↔O↔P→Q→B. The complete steady-state intensity-induced population densities in various states of the molecule have been computed to obtain a general, exact, and analytical expression for the nonlinear absorption coefficient for multiple modulation pump laser beams. All-optical light modulation of different probe laser beam transmissions by intensity induced population changes due to one and two modulation laser beams has been analyzed. The proposed model has been shown to accurately model experimental results.

  14. Bacteriorhodopsin-the basis of molecular superfast nanoelectronics

    Science.gov (United States)

    Samoilovich, M. I.; Belyanin, A. F.; Grebennikov, E. P.; Guriyanov, A. V.

    2002-12-01

    We give some perspectives on the possibilities for application of the bacteriorhodopsin (BR) molecule in the development of nanoelectronic devices in conjunction with photonic crystals-materials with inhibited photonic band. This involves the use of a single BR molecule by `changing' the photon gradient formation with externally initiated electric fields, preserving the mechanisms of negative reverse communication, or the use of an intermolecular mechanism of photo transitions and dependence on the electric field. Greatly enhanced optical responses, linear and nonlinear, in metal nanocomposites and nanodiamond containing nanoscale surface features have been intensively studied in recent years. These results foreshadow fascinating possibilities for linear and nonlinear local spectroscopy of single molecules. Use of photonic crystals (at present the only technologically realized three-dimensional photonic crystals are the opal matrices) suggests the possible application of a number of physical phenomena.

  15. High-contrast, all-optical switching in bacteriorhodopsin films

    Science.gov (United States)

    Banyal, Ravinder Kumar; Raghavendra Prasad, B.

    2005-09-01

    We report experiments with nonlinear-absorption-based, high-contrast, all-optical switching in photochromic bacteriorhodopsin (BR) films. The switching action is accomplished by control of the transmission of a weak probe beam through a BR sample with the help of strong pump beam illumination at 532 nm wavelength. We found that the switching properties of BR films depend on several experimentally controllable parameters such as probe wavelength, pump beam intensity, and excitation rate. A comparative study of the switching behavior and other parameters of practical use was carried out at three probe wavelengths (543, 594, and 633 nm) and various beam powers and pump excitation rates. The results are presented for commercially available wild-type and D96N variant BR films.

  16. Nonlinear Optical Interactions in Bacteriorhodopsin Using Z-Scan

    Science.gov (United States)

    Aranda, Francisco J.; Rao, Devulapalli V. G. L. N.; Wong, Chi L.; Zhou, Ping; Chen, Zhong; Akkara, Joseph A.; Kaplan, David L.; Roach, Joseph F.

    1995-06-01

    Nonlinear refractive index coefficient n2 of bacteriorhodopsin suspensions in water is measured by the Z-scan technique with a low power continuous wave laser at 647.1 manometer wavelength. Our results indicate that both the magnitude and the sign of n2 depend strongly on the light intensity. Negative values for n2 are obtained for on axis laser irradiance at the focus above 3 W/cm2. The observed self-defocusing phenomena can be attributed to the index change due to the light induced transition between the photochromic states. The results elucidate the origin of n2 and offer a plausible explanation for the differences in the reported n2 measurements.

  17. Effect of different agents onto multidrug resistant cells revealed by fluorescence correlation spectroscopy

    Science.gov (United States)

    Boutin, C.; Roche, Y.; Jaffiol, R.; Millot, J.-M.; Millot, C.; Plain, J.; Deturche, R.; Jeannesson, P.; Manfait, M.; Royer, P.

    Fluorescence correlation spectroscopy (FCS), which is a sensitive and non invasive technique, has been used to characterize the plasma membrane fluidity and heterogeneity of multidrug resistant living cells. At the single cell level, the effects of different membrane agents present in the extra-cellular medium have been analyzed. Firstly, we reveal a modification of plasma membrane microviscosity according to the addition of a fluidity modulator, benzyl alcohol. In the other hand, revertant such as verapamil and cyclosporin-A appears to act more specifically on the slow diffusion sites as microdomains.

  18. Bacteriorhodopsin-based Langmuir-Schaefer films for solar energy capture.

    Science.gov (United States)

    Bertoncello, Paolo; Nicolini, Davide; Paternolli, Cristina; Bavastrello, Valter; Nicolini, Claudio

    2003-06-01

    The photovoltaic (PV) solar cell, converting incident solar radiation directly into electrical energy, today represents the most common power source for the earth-orbiting spacecraft, and the utilization of organic materials in this context is here explored in comparison with the present state of the art placing emphasis in organic nanotechnology. Poly[3-3'(vinylcarbazole)] (PVK) was synthesized by oxidative polymerization with ferric chloride of N-vinylcarbazole. The resulting polymer was then deposited on solid support by using the Langmuir-Schaefer (LS) technique. The pressure-area isotherm of PVK revealed the possibility of compact monolayer formation at the air-water interface. Different layers of PVK were doped with iodine vapors. The cyclic voltammetry investigation of PVK-doped I2 showed a distinctive electrochemical behavior. The photoinduced charge transfer across a donor/acceptor (D/A) hybrid interface provided an effective method to study the PV properties of the composite LS films. The results are compared with other approaches within the biological framework, such as bacteriorhodopsin (BR), and organic nanostructured materials. PMID:15382669

  19. Revealing a universal planet-metallicity correlation for planets of different solar-type stars

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ji; Fischer, Debra A., E-mail: ji.wang@yale.edu [Department of Astronomy, Yale University, New Haven, CT 06511 (United States)

    2015-01-01

    The metallicity of exoplanet systems serves as a critical diagnostic of planet formation mechanisms. Previous studies have demonstrated the planet–metallicity correlation for large planets (R{sub P} ⩾ 4 R{sub E}); however, a correlation has not been found for smaller planets. With a sample of 406 Kepler objects of interest whose stellar properties are determined spectroscopically, we reveal a universal planet–metallicity correlation: not only gas-giant planets (3.9 R{sub E}

  20. Correlative nonlinear optical microscopy and infrared nanoscopy reveals collagen degradation in altered parchments

    Science.gov (United States)

    Latour, Gaël; Robinet, Laurianne; Dazzi, Alexandre; Portier, François; Deniset-Besseau, Ariane; Schanne-Klein, Marie-Claire

    2016-05-01

    This paper presents the correlative imaging of collagen denaturation by nonlinear optical microscopy (NLO) and nanoscale infrared (IR) spectroscopy to obtain morphological and chemical information at different length scales. Such multiscale correlated measurements are applied to the investigation of ancient parchments, which are mainly composed of dermal fibrillar collagen. The main issue is to characterize gelatinization, the ultimate and irreversible alteration corresponding to collagen denaturation to gelatin, which may also occur in biological tissues. Key information about collagen and gelatin signatures is obtained in parchments and assessed by characterizing the denaturation of pure collagen reference samples. A new absorbing band is observed near the amide I band in the IR spectra, correlated to the onset of fluorescence signals in NLO images. Meanwhile, a strong decrease is observed in Second Harmonic signals, which are a structural probe of the fibrillar organization of the collagen at the micrometer scale. NLO microscopy therefore appears as a powerful tool to reveal collagen degradation in a non-invasive way. It should provide a relevant method to assess or monitor the condition of collagen-based materials in museum and archival collections and opens avenues for a broad range of applications regarding this widespread biological material.

  1. Substrate-tuning of correlated spin-orbit oxides revealed by optical conductivity calculations

    Science.gov (United States)

    Kim, Bongjae; Kim, Beom Hyun; Kim, Kyoo; Min, B. I.

    2016-06-01

    We have systematically investigated substrate-strain effects on the electronic structures of two representative Sr-iridates, a correlated-insulator Sr2IrO4 and a metal SrIrO3. Optical conductivities obtained by the ab initio electronic structure calculations reveal that the tensile strain shifts the optical peak positions to higher energy side with altered intensities, suggesting the enhancement of the electronic correlation and spin-orbit coupling (SOC) strength in Sr-iridates. The response of the electronic structure upon tensile strain is found to be highly correlated with the direction of magnetic moment, the octahedral connectivity, and the SOC strength, which cooperatively determine the robustness of Jeff = 1/2 ground states. Optical responses are analyzed also with microscopic model calculation and compared with corresponding experiments. In the case of SrIrO3, the evolution of the electronic structure near the Fermi level shows high tunability of hole bands, as suggested by previous experiments.

  2. Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins.

    Science.gov (United States)

    Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud

    2015-02-01

    Protein conformation has been recognized as the key feature determining biological function, as it determines the position of the essential groups specifically interacting with substrates. Hence, the shape of the cavities or grooves at the protein surface appears to drive those functions. However, only a few studies describe the geometrical evolution of protein cavities during molecular dynamics simulations (MD), usually with a crude representation. To unveil the dynamics of cavity geometry evolution, we developed an approach combining cavity detection and Principal Component Analysis (PCA). This approach was applied to four systems subjected to MD (lysozyme, sperm whale myoglobin, Dengue envelope protein and EF-CaM complex). PCA on cavities allows us to perform efficient analysis and classification of the geometry diversity explored by a cavity. Additionally, it reveals correlations between the evolutions of the cavities and structures, and can even suggest how to modify the protein conformation to induce a given cavity geometry. It also helps to perform fast and consensual clustering of conformations according to cavity geometry. Finally, using this approach, we show that both carbon monoxide (CO) location and transfer among the different xenon sites of myoglobin are correlated with few cavity evolution modes of high amplitude. This correlation illustrates the link between ligand diffusion and the dynamic network of internal cavities.

  3. Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

    Directory of Open Access Journals (Sweden)

    Heidi Koldsø

    2014-10-01

    Full Text Available Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2, in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

  4. Transient Fourier holography with bacteriorhodopsin films for breast cancer diagnostics

    Science.gov (United States)

    Rao, Devulapalli; Kothapalli, Sri-Rajasekar; Wu, Pengfei; Yelleswarapu, Chandra

    X-ray mammography is the current gold standard for breast cancer screening. Microcalcifications and other features which are helpful to the radiologist for early diagnostics are often buried in the noise generated by the surrounding dense tissue. So image processing techniques are required to enhance these important features to improve the sensitivity of detection. An innovative technique is demonstrated for recording a hologram of the mammogram. It is recorded on a thin polymer film of Bacteriorhodopsin (bR) as photo induced isomerization grating containing the interference pattern between the object beam containing the Fourier spatial frequency components of the mammogram and a reference beam. The hologram contains all the enhanced features of the mammogram. A significant innovation of the technique is that the enhanced components in the processed image can be viewed by the radiologist in time scale. A technician can record the movie and when the radiologist looks at the movie at his convenience, freezing the frame as and when desired, he would see the microcalcifications as the brightest and last long in time. He would also observe lesions with intensity decreasing as their size increases. The same bR film can be used repeatedly for recording holograms with different mammograms. The technique is versatile and a different frequency band can be chosen to be optimized by changing the reference beam intensity. The experimental arrangement can be used for mammograms in screen film or digital format.

  5. Engineering a Robust Photovoltaic Device with Quantum Dots and Bacteriorhodopsin.

    Science.gov (United States)

    Renugopalakrishnan, Venkatesan; Barbiellini, Bernardo; King, Chris; Molinari, Michael; Mochalov, Konstantin; Sukhanova, Alyona; Nabiev, Igor; Fojan, Peter; Tuller, Harry L; Chin, Michael; Somasundaran, Ponisseril; Padrós, Esteve; Ramakrishna, Seeram

    2014-07-31

    We present a route toward a radical improvement in solar cell efficiency using resonant energy transfer and sensitization of semiconductor metal oxides with a light-harvesting quantum dot (QD)/bacteriorhodopsin (bR) layer designed by protein engineering. The specific aims of our approach are (1) controlled engineering of highly ordered bR/QD complexes; (2) replacement of the liquid electrolyte by a thin layer of gold; (3) highly oriented deposition of bR/QD complexes on a gold layer; and (4) use of the Forster resonance energy transfer coupling between bR and QDs to achieve an efficient absorbing layer for dye-sensitized solar cells. This proposed approach is based on the unique optical characteristics of QDs, on the photovoltaic properties of bR, and on state-of-the-art nanobioengineering technologies. It permits spatial and optical coupling together with control of hybrid material components on the bionanoscale. This method paves the way to the development of the solid-state photovoltaic device with the efficiency increased to practical levels. PMID:25383133

  6. Integrated optical devices using bacteriorhodopsin as active nonlinear optical material

    Science.gov (United States)

    Dér, András; Fábián, László; Valkai, Sándor; Wolff, Elmar; Ramsden, Jeremy; Ormos, Pál

    2006-08-01

    Coupling of optical data-processing devices with microelectronics, telecocommunication and sensory functions, is among the biggest challenges in molecular electronics. Intensive research is going on to find suitable nonlinear optical materials that could meet the demanding requirements of optoelectronic applications, especially regarding high sensitivity and stability. In addition to inorganic and organic crystals, biological molecules have also been considered for use in integrated optics, among which the bacterial chromoprotein, bacteriorhodopsin (bR) generated the most interest. bR undergoes enormous absorption and concomitant refractive index changes upon initiation of a cyclic series of photoreactions by a burst of actinic light. This effect can be exploited to create highly versatile all-optical logical elements. We demonstrate the potential of this approach by investigating the static and dynamic response of several basic elements of integrated optical devices. Our results show that, due to its relatively high refractive index changes, bR can be used as an active nonlinear optical material to produce a variety of integrated optical switching and modulation effects.

  7. All-optical biomolecular parallel logic gates with bacteriorhodopsin.

    Science.gov (United States)

    Sharma, Parag; Roy, Sukhdev

    2004-06-01

    All-optical two input parallel logic gates with bacteriorhodopsin (BR) protein have been designed based on nonlinear intensity-induced excited-state absorption. Amplitude modulation of a continuous wave (CW) probe laser beam transmission at 640 nm corresponding to the peak absorption of O intermediate state through BR, by a modulating CW pump laser beam at 570 nm corresponding to the peak absorption of initial BR state has been analyzed considering all six intermediate states in its photocycle using the rate equation approach. The transmission characteristics have been shown to exhibit a dip, which is sensitive to normalized small-signal absorption coefficient (beta), rate constants of O and N intermediate states and absorption of the O state at 570 nm. There is an optimum value of beta for a given pump intensity range for which maximum modulation can be achieved. It is shown that 100% modulation can be achieved if the initial state of BR does not absorb the probe beam. The results have been used to design low-power all-optical parallel NOT, AND, OR, XNOR, and the universal NAND and NOR logic gates for two cases: 1) only changing the output threshold and 2) considering a common threshold with different beta values. PMID:15382746

  8. Dynamic Behaviour of Self-Diffraction in Bacteriorhodopsin Film

    Institute of Scientific and Technical Information of China (English)

    GUO Zong-Xia; CHEN Gui-Ying; ZHANG Chun-Ping; TIAN Jian-Guo; Q. Wang Song; SHEN Bin; FU Guang-Hua

    2004-01-01

    @@ We investigate the dependences of the diffraction efficiency of the first order self-diffracted beam in bacteriorhodopsin (bR) films on the illumination time, the intensity and wavelength of the incident light. When the blue light (λ = 488 nm) and low intensity red light (λ = 632.8 nm) are incident on the bR film respectively,the diffraction efficiencies increase from zero to a stable value with the illumination time. When the green light (λ = 533 nm) and high-intensity red light illuminate the bR film respectively, the diffraction efficiencies increase from zero to the maximum and then decrease to a stable value with the illumination time. Rise and decay times are dependent on the intensity and wavelength of the incident light. The maximaldiffraction efficiency of the red light is twice as high as that of the green light. The highest diffraction efficiency of 5.4% is obtained at 633nm.The diffraction efficiency change with the time for the green light is larger than that for the blue and red light.

  9. Electron microscopic observation and rotational diffusion measurement of bacteriorhodopsin in lipid vesicles

    Institute of Scientific and Technical Information of China (English)

    HU; Kunsheng

    2001-01-01

    [1]Stoeckenius, W.. Bacterial rhodopsins: Evolution of a mechanistic model for the ion pumps, Protein Science, 1999, 8: 447.[2]Ebrey. T. G, Light energy transduction in bacteriorhodopsin, in Thermodynamics of Membranes, Receptors and Channels (ed. Jackson. M.), New York: CRC Press, 1993. 353-387.[3]Lanyi. J. K.. Understanding structure and function in the light-driven proton pump bacteriorhodopsin, J. Struct. Biol., 1998,l24: 164.[4]Quay. S. C., Condie. C. C., Conformational studies of aqueous melittin: Thermodynamic parameters of the monomer-tetramer self-association reaction. Biochemistry, 1983, 22: 695.[5]Habermann. E.. Bee and wasp venoms. Science, 1972, 177: 314.[6]Tosteson. M. T., Holmes. S. J., Razin. M. et al., Melitton lysis of red cells, J. Membr. Biol., 1985, 87: 35.[7]Hu, K. S., Dufton, M. J., Morrison, I. E. G. et al., Cherry interaction of bee venom melittin with bacteriorhodopsin in lipid vesicles: Protein rotational diffusion measurement. Biochem. Biophys. Acta, 1985, 816(2): 358.[8]Shi, H., Hu, K. S., Huang, Y. et al., Effect of melittin on photocycle and photoresponse of purple membrane: sites of interaction between bacteriorhodopsin and melittin, Photochemistry and Photobiology, 1993, 58(3): 413.[9]Jiang. Q. X., Hu, K. S.. Shi. H., Interaction of both melittin and its site-specific mutants with bacteriorhodopsin of Halobacterium halobium: sites of electrostatic interaction on melittin Photochemistry and Photobiology, 1994, 60(2): 175.[10]Doebler, R., Basaran. N.. Goldston H. et al., Effect of protein aggregation into aqueous phase on the binding of membrane proteins to membranes, Biophys. J., 1999, 76: 928.[11]Rehorek, M., Heyn, M. P, Binding of all-trans-retinal to the purple membrane, Evidence for cooperativity and determination of the extinction coefficient, Biochemistry, 1979, 18: 4977.[12]Chen. P. S. Jr.. Toribara, T. Y., Warner, H., Microdetermination of phosphorous, Anal. Chem., t956, 28

  10. Nonlinear coherent optical image processing using logarithmic transmittance of bacteriorhodopsin films

    Science.gov (United States)

    Downie, John D.

    1995-08-01

    The transmission properties of some bacteriorhodopsin-film spatial light modulators are uniquely suited to allow nonlinear optical image-processing operations to be applied to images with multiplicative noise characteristics. A logarithmic amplitude-transmission characteristic of the film permits the conversion of multiplicative noise to additive noise, which may then be linearly filtered out in the Fourier plane of the transformed image. I present experimental results demonstrating the principle and the capability for several different image and noise situations, including deterministic noise and speckle. The bacteriorhodopsin film studied here displays the logarithmic transmission response for write intensities spanning a dynamic range greater than 2 orders of magnitude.

  11. Spatial light modulation based on photoinduced change in the complex refractive index of bacteriorhodopsin

    Science.gov (United States)

    Takei, Hiroyuki; Shimizu, Norio

    1996-04-01

    Bacteriorhodopsin exhibits photoinduced changes in both absorption and refractive index at 633 nm. To explore the possibility of exploiting this property in constructing a photoaddressed spatial light modulator, we investigated the transmission property of a Fabry-Perot interferometer containing a bacteriorhodopsin thin film. Film was formed that had a phase shift of pi /4 and sufficient interference fringe contrast for spatial light modulation. This establishes the possibility of constructing a spatial light modulator that features nonlinear input-output characteristics and can operate at moderate light intensities of the order of tens of milliwatts per centimeter square. spatial light modulation, complex refractive index.

  12. Neural correlates of intelligence as revealed by fMRI of fluid analogies.

    Science.gov (United States)

    Geake, John G; Hansen, Peter C

    2005-06-01

    It has been conjectured that the cognitive basis of intelligence is the ability to make fluid or creative analogical relationships between distantly related concepts or pieces of information (Hofstadter, D.R. 1995. Fluid Concepts and Creative Analogies. Basic Books, New York., Hofstadter, D.R. 2001. Analogy as the Core of Cognition. In The Analogical Mind: Perspectives from Cognitive Science (D. Gentner, K. J. Holyoak and B. N. Kokinov, Ed.). pp. 504-537. MIT Press, Cambridge, Mass.). We hypothesised that fluid analogy-making tasks would activate specific regions of frontal cortex that were common to those of previous inferential reasoning tasks. We report here a novel self-paced event-related fMRI study employed to investigate the neural correlates of intelligence associated with undertaking fluid letter string analogy tasks. Stimuli were adapted from items of the AI program Copycat (Mitchell, M. 1993. Analogy-making as Perception: A computer model. The MIT Press, Cambridge MA.). Twelve right-handed adults chose their own "best" completions from four plausible response choices to 55 fluid letter string analogies across a range of analogical depths. An analysis using covariates determined per subject by analogical depth revealed significant bilateral neural activations in the superior, inferior, and middle frontal gyri and in the anterior cingulate/paracingulate cortex. These frontal areas have been previously associated with reasoning tasks involving inductive syllogisms, syntactic hierarchies, and linguistic creativity. A higher-order analysis covarying participants' verbal intelligence measures found correlations with individual BOLD activation strengths in two ROIs within BA 9 and BA 45/46. This is a provocative result given that verbal intelligence is conceptualised as being a measure of crystallised intelligence, while analogy making is conceptualised as requiring fluid intelligence. The results therefore support the conjecture that fluid analogising could

  13. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen

    Directory of Open Access Journals (Sweden)

    Hibret A. Adissu

    2014-05-01

    Full Text Available The Mouse Genetics Project (MGP at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30 or without (n=20 clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3% in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14% presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.

  14. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen.

    Science.gov (United States)

    Adissu, Hibret A; Estabel, Jeanne; Sunter, David; Tuck, Elizabeth; Hooks, Yvette; Carragher, Damian M; Clarke, Kay; Karp, Natasha A; Newbigging, Susan; Jones, Nora; Morikawa, Lily; White, Jacqueline K; McKerlie, Colin

    2014-05-01

    The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.

  15. Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars

    Institute of Scientific and Technical Information of China (English)

    Hong Lin; Jun Rao; Jianxin Shi; Chaoyang Hu; Fang Cheng; Zoe AWilson; Dabing Zhang; Sheng Quan

    2014-01-01

    Soybean [Glycine max (L.) Merr.] is one of the world’s major crops, and soybean seeds are a rich and important resource for proteins and oils. While “omics”studies, such as genomics, transcriptomics, and proteomics, have been widely applied in soybean molecular research, fewer metabolomic studies have been conducted for large-scale detection of low molecular weight metabolites, especial y in soybean seeds. In this study, we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry. One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed. Among the 169 detected metabolites, 104 were found to be significantly variable in their levels across tested cultivars. Metabolite markers that could be used to distinguish genetical y related soybean cultivars were also identified, and metabolite-metabolite correlation analysis revealed some significant associations within the same or among different metabolite groups. Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.

  16. Part I. Bacteriorhodopsin-related materials work for molecular electronics. Part II. Volumetric optical memory based on the branched photocycle of bacteriorhodopsin. Part III. The role of calcium in the bacteriorhodopsin binding site

    Science.gov (United States)

    Stuart, Jeffrey Alan

    Part I. A protocol for the routine isolation and purification of purple membrane sheets containing the integral membrane protein, bacteriorhodopsin, was developed based upon modifications of protocols already in the literature. This simplified protocol is geared toward the facile isolation of protein for use in molecular electronic devices. Methods for the incorporation of bacteriorhodopsin into various polymeric supports were also developed, primarily in the form of dried films and hydrated cubes. This work also represents the first reported production of dried films of the deionized protein, or blue membrane. Part II. An architecture for a volumetric optical memory based on the branched-photocycle of bacteriorhodopsin is presented. The branching reaction circumvents problems associated with destructive reading and writing processes and allows access to a stable, long-lived state, separated both temporally and energetically from the main photocycle, thereby making long-term data storage possible. The state, denoted as Q, can only be accessed by exposing the protein to two different wavelengths of light in the proper sequence, with the appropriate temporal separation (roughly 2 ms between the light pulses). The Q-state (assigned as a binary one) is transparent to both writing and reading processes, making them rigorously non-destructive. Bacteriorhodopsin in its resting state is assigned as a binary zero. A differential absorption reading process is used to determine the state of each volumetric binary element. Preliminary results are reported. Part III. The nature of the chromophore binding site of light-adapted bacteriorhodopsin is analyzed by using all-valence electron MNDO and MNDO-PSDCI molecular orbital theory to interpret previously reported linear and nonlinear optical spectroscopic measurements. It is concluded that the unique two-photon properties of the chromophore are due in part to the electrostatic field associated with a Casp{2+} ion near the

  17. Theoretical and experimental analysis of the propagation of sinusoidal signals in Bacteriorhodopsin films

    Science.gov (United States)

    Blaya, S.; Candela, M.; Acebal, P.; Carretero, L.; Gomariz, M.; Madrigal, R. F.; Fimia, A.

    2014-05-01

    Time-delay of transmitted pulses with respect to the incident pulse in bacteriorhodopsin films has been studied without the use of a pump beam. Based on a modified saturable absorber model, analytical expressions of the transmitted pulse have been obtained. As a result, time delay, distortion and fractional delay have been theoretically analyzed for sinusoidal pulses with a low background.

  18. Fundamentals of photoelectric effects in molecular electronic thin film devices: applications to bacteriorhodopsin-based devices.

    Science.gov (United States)

    Hong, F T

    1995-01-01

    This tutorial lecture focuses on the fundamental mechanistic aspects of light-induced charge movements in pigment-containing membranes. The topic is relevant to molecular electronics because many prototypes optoelectronic devices are configured as pigment-containing thin films. We use reconstituted bacteriorhodopsin membranes as an example to illustrate the underlying principle of measurements and data interpretation. Bacteriorhodopsin, a light-driven proton pump, is the only protein component in the purple membrane of Halobacterium halobium. It resembles the visual pigment rhodopsin chemically but performs the function of photosynthesis. Bacteriorhodopsin thus offers an unprecedented opportunity for us to compare the visual photoreceptor and the photosynthetic apparatus from a mechanistic point of view. Bacteriorhodopsin, well known for its exceptional chemical and mechanical stability, is also a popular advanced biomaterial for molecular device construction. The tutorial approaches the subject from two angles. First, the fundamental photoelectric properties are exploited for device construction. Second, basic design principles for photosensors and photon energy converters can be elucidated via 'reverse engineering'. The concept of molecular intelligence and the principle of biomimetic science are discussed.

  19. Study of nonlinear optical properties of multilayer Langmuir-Blodgett films containing bacteriorhodopsin.

    Science.gov (United States)

    Barmenkov Yu, O; Kir'yanov, A V; Starodumov, A N; Maslyanitsyn, I A; Shigorin, V D; Lemmetyinen, H

    2000-08-01

    Multilayer oriented Langmuir-Blodgett films of bacteriorhodopsin were prepared and their nonlinear optical properties, including second harmonic generation and photoresponse at a two phase-modulated beams mixing, were investigated. The nonlinear component of refractive index of the films was measured. PMID:10946566

  20. Real-time self-induced nonlinear optical Zernike-type filter in a bacteriorhodopsin film

    Science.gov (United States)

    Iturbe Castillo, David; Sanchez-de-la-Llave, David; Garcia, Ruben R.; Olivos-Perez, L. I.; Gonzalez, Luis A.; Rodriguez-Ortiz, M.

    2001-11-01

    We propose the use of a nonlinear bacteriorhodopsin film to self-induce a Zernike-type filter in robust optical phase-contrast systems. The device requires relatively low light intensity levels (as low as 200 nW/cm2) at wavelengths around 633 nm and can contrast dynamical phase distributions.

  1. Determination of the thermal expansion and thermo-optic coefficients of a bacteriorhodopsin film

    Science.gov (United States)

    Wang Song, Q.; Zhang, Chunping; Ku, Chin-Yu; Huang, Ming-Chieh; Gross, Richard B.; Birge, Robert R.

    1995-02-01

    The linear expansion and thermo-optic coefficients of a bacteriorhodopsin film were measured by using an interferometric method. The experimental results confirm the previous suspicions that the large refractive nonlinearity which occurs at high illumination intensities arises form a thermal effect. The results also suggest a possible way to increase the usable thermal nonlinearity by four times.

  2. Optical switching in bistable active cavity containing nonlinear absorber on bacteriorhodopsin

    Science.gov (United States)

    Bazhenov, Vladimir Y.; Taranenko, Victor B.; Vasnetsov, Mikhail V.

    1993-04-01

    The transverse nonlinear dynamics of switchings in an active system (laser with nonlinear saturable absorber on bacteriorhodopsin in a self-imaging cavity) is studied both experimentally and theoretically. The soliton-like light field structure formation and continuously cycled self-switching process are investigated.

  3. Evidence of multipolar response of Bacteriorhodopsin by noncollinear second harmonic generation.

    Science.gov (United States)

    Bovino, F A; Larciprete, M C; Sibilia, C; Váró, G; Gergely, C

    2012-06-18

    Noncollinear second harmonic generation from a Bacteriorhodopsin (BR) oriented multilayer film was systematically investigated by varying the polarization state of both fundamental beams. Both experimental results and theoretical simulations, show that the resulting polarization mapping is an useful tool to put in evidence the optical chirality of the investigated film as well as the corresponding multipolar contributions to the nonlinear. PMID:22714524

  4. pH-Sensitive photoinduced energy transfer from bacteriorhodopsin to single-walled carbon nanotubes in SWNT-bR hybrids.

    Science.gov (United States)

    El Hadj, Karim; Bertoncini, Patricia; Chauvet, Olivier

    2013-10-22

    Energy transfer mechanisms in noncovalently bound bacteriorhodopsin/single-walled carbon nanotube (SWNT) hybrids are investigated using optical absorption and photoluminescence excitation measurements. The morphology of the hybrids was investigated by atomic force microscopy. In this study, proteins are immobilized onto the sidewall of the carbon nanotubes using a sodium cholate suspension-dialysis method that maintains the intrinsic optical and fluorescence properties of both molecules. The hybrids are stable in aqueous solutions for pH ranging from 4.2 to 9 and exhibit photoluminescence properties that are pH-dependent. The study reveals that energy transfer from bacteriorhodopsin to carbon nanotubes takes place. So, at pH higher than 5 and up to 9, the SWNTs absorb the photons emitted by the aromatic residues of the protein, inducing a strong increase in intensity of the E11 emissions of SWNTs through their E33 and E44 excitations. From pH = 4.2 to pH = 5, the protein fluorescence is strongly quenched whatever the emission wavelengths, while additional fluorescence features appear at excitation wavelengths ranging from 660 to 680 nm and at 330 nm. The presence of these features is attributed to a resonance energy transfer mechanism that has an efficiency of 0.94 ± 0.02. More, by increasing the pH of the dispersion, the fluorescence characteristics become those observed at higher pH values and vice versa.

  5. Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea.

    Directory of Open Access Journals (Sweden)

    Kirill Borziak

    Full Text Available Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs, is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA, which in archaea is typically encoded by two genes (LplA-N and LplA-C, or by a lipoyl(octanoyl transferase (LipB or LipM plus a lipoic acid synthetase (LipA. Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across

  6. Correlating chemical sensitivity and basal gene expression reveals mechanism of action | Office of Cancer Genomics

    Science.gov (United States)

    Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal gene expression could be correlated with patterns of small-molecule sensitivity across many cell lines to illuminate the actions of compounds whose MoA are unknown.

  7. NMR cross-correlated relaxation rates reveal ion coordination sites in DNA

    NARCIS (Netherlands)

    Fiala, R.; Spackova, N.; Foldynová-Trantírková, S.; Sponer, J.; Sklenár, V.; Trantirek, L.

    2011-01-01

    In this work, a novel NMR method for the identification of preferential coordination sites between physiologically relevant counterions and nucleic acid bases is demonstrated. In this approach, the NMR cross-correlated relaxation rates between the aromatic carbon chemical shift anisotropy and the pr

  8. Proteomic analysis of saliva in HIV-positive heroin addicts reveals proteins correlated with cognition.

    Directory of Open Access Journals (Sweden)

    Stephen S Dominy

    Full Text Available The prevalence of HIV-associated neurocognitive disorders (HAND remains high despite effective antiretroviral therapies. Multiple etiologies have been proposed over the last several years to account for this phenomenon, including the neurotoxic effects of antiretrovirals and co-morbid substance abuse; however, no underlying molecular mechanism has been identified. Emerging evidence in several fields has linked the gut to brain diseases, but the effect of the gut on the brain during HIV infection has not been explored. Saliva is the most accessible gut biofluid, and is therefore of great scientific interest for diagnostic and prognostic purposes. This study presents a longitudinal, liquid chromatography-mass spectrometry-based quantitative proteomics study investigating saliva samples taken from 8 HIV-positive (HIV+, 11 -negative (HIV- heroin addicts. In addition, saliva samples were investigated from 11 HIV-, non-heroin addicted healthy controls. In the HIV+ group, 58 proteins were identified that show significant correlations with cognitive scores, implicating disruption of protein quality control pathways by HIV. Notably, only one protein from the HIV- heroin addict cohort showed a significant correlation with cognitive scores, and no proteins correlated with cognitive scores in the healthy control group. In addition, the majority of correlated proteins have been shown to be associated with exosomes, allowing us to propose that the salivary glands and/or oral epithelium may modulate brain function during HIV infection through the release of discrete packets of proteins in the form of exosomes.

  9. Body Waves Revealed by Spatial Stacking on Long-Term Cross-Correlation of Ambient Noise

    Institute of Scientific and Technical Information of China (English)

    Kai Wang; Yinhe Luo; Kaifeng Zhao; Limeng Zhang

    2014-01-01

    ABSTRCT: Theoretical and experimental studies indicate that complete Green’s Function can be retrieved from cross-correlation in a diffuse field. High SNR (signal-to-noise ratio) surface waves have been extracted from cross-correlations of long-duration ambient noise across the globe. Body waves, not extracted in most of ambient noise studies, are thought to be more difficult to retrieve from regular ambient noise data processing. By stacking cross-correlations of ambient noise in 50 km inter-station distance bins in China, western United States and Europe, we observed coherent 20–100 s core phases (ScS, PKIKPPKIKP, PcPPKPPKP) and crustal-mantle phases (Pn, P, PL, Sn, S, SPL, SnSn, SS, SSPL) at distances ranging from 0 to 4 000 km. Our results show that these crustal-mantle phases show diverse characteristics due to different substructure and sources of body waves beneath different regions while the core phases are relatively robust and can be retrieved as long as stations are available. Further analysis indicates that the SNR of these body-wave phases depends on a compromise between stacking fold in spatial domain and the coherence of pre-stacked cross-correlations.Spatially stacked cross-correlations of seismic noise can provide new virtual seismograms for paths that complement earthquake data and that contain valuable information on the structure of the Earth. The extracted crustal-mantle phases can be used to study lithospheric heterogeneities and the robust core phases are significantly useful to study the deep structure of the Earth, such as detecting fine heterogeneities of the core-mantle boundary and constraining differential rotation of the inner core.

  10. Quantum yields for the light adaptations in Anabaena sensory rhodopsin and bacteriorhodopsin

    Science.gov (United States)

    Wada, Yoichiro; Kawanabe, Akira; Furutani, Yuji; Kandori, Hideki; Ohtani, Hiroyuki

    2008-02-01

    Archael-type rhodopsin has an all- trans or a 13- cis retinal. The light-induced interconversion between these two forms has been found in Anabaena sensory rhodopsin, even though only the photoreaction from the 13- cis form to the all- trans form exists in bacteriorhodopsin. In this study, we obtained the quantum yields for the 13- cis → all- trans and all- trans → 13- cis reactions of Anabaena sensory rhodopsin (0.24 ± 0.03 and 0.38 ± 0.07, respectively) and concluded that these values were independent of the wavelength of the excitation light as well as bacteriorhodopsin. In other words, no excess energy effects can be found in these reactions.

  11. Metal ion binding sites of bacteriorhodopsin. Laser-induced lanthanide luminescence study

    International Nuclear Information System (INIS)

    Laser-excited luminescence lifetimes of lanthanide ions bound to bacteriorhodopsin have been measured in deionized membranes. The luminescence titration curve, as well as the binding curve of apomembrane (retinal-free) with Eu3+, has shown that the removal of the retinal does not significantly affect the affinity of Eu3+ for the two high affinity sites of bacteriorhodopsin. The D2O effects on decay rate constants indicate that Eu3+ bound to the high affinity sites of native membrane or apomembrane is coordinated by about six ligands in the first coordination sphere. Tb3+ is shown to be coordinated by four ligands. The data indicate that metal ions bind to the protein with a specific geometry. From intermetal energy transfer experiments using Eu3+-Pr3+, Tb3+-Ho3+, and Tb3+-Er3+, the distance between the two high affinity sites is estimated to be 7-8 A

  12. Whole-brain analytic measures of network communication reveal increased structure-function correlation in right temporal lobe epilepsy

    Directory of Open Access Journals (Sweden)

    Jonathan Wirsich

    2016-01-01

    In rTLE patients, we found a widespread hypercorrelated functional network. Network communication analysis revealed greater unspecific branching of the shortest path (search information in the structural connectome and a higher global correlation between the structural and functional connectivity for the patient group. We also found evidence for a preserved structural rich-club in the patient group. In sum, global augmentation of structure-function correlation might be linked to a smaller functional repertoire in rTLE patients, while sparing the central core of the brain which may represent a pathway that facilitates the spread of seizures.

  13. The 3rd-order nonlinearity of bacteriorhodopsin by four-wave mixing

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The 3rd-order nonlinear optical susceptibility X(3) and the response time of the light-transducing biomolecule bacteriorhodopsin were measured with the four-wave mixing technique and a picosecond frequency-doubled Nd:YAG laser(532nm).The X(3) and the response time measured are 10-9 esu and 20 ps,respectively.The possible mechanism for generating the 3rd-order nonlinear optical susceptibility X(3) and response time were discussed.

  14. Can the Low-Resolution Structures of Photointermediates of Bacteriorhodopsin Explain Their Crystal Structures?

    OpenAIRE

    Kamikubo, Hironari; Kataoka, Mikio

    2004-01-01

    To understand the molecular mechanism of light-driven proton pumps, the structures of the photointermediates of bacteriorhodopsin have been intensively investigated. Low-resolution diffraction techniques have demonstrated substantial conformational changes at the helix level in the M and N intermediates, between which there are noticeable differences. The intermediate structures at atomic resolution have also been solved by x-ray crystallography. Although the crystal structures have demonstra...

  15. Optical signal processing on photorefractive crystal substrate and bacteriorhodopsin thin film

    Science.gov (United States)

    Azimipour, Mehdi; Pashaie, Ramin

    2013-03-01

    In this article we present a new approach for implementation of computation algorithms to perform nonlinear signal processing with light on the surface of a photorefractive crystal and Bacteriorhodopsin thin film. Using the developed mathematical models for the photodynamics of these materials, we demonstrate a specific operation mode and a design procedure to obtain nonlinear response which can be used for implementation of high-performance photonic computers.

  16. Polarization properties of four-wave interaction in dynamic recording material based on bacteriorhodopsin

    Science.gov (United States)

    Korchemskaya, Ellen Y.; Soskin, Marat S.

    1994-10-01

    The polarization properties of four-wave interaction on polymer films with bacteriorhodopsin that possess anisotropically saturating nonlinearity are studied both theoretically and experimentally. The amplitude and the polarization of the diffracted wave for recording material with anisotropically saturating nonlinearity are calculated. Low saturation intensity allows the operation of the polarization of low-intensity signals to be realized. It is shown that control of the diffractive wave polarization is possible only with the variation of the light recording intensity.

  17. Optical chirality of bacteriorhodopsin films via second harmonic Maker's fringes measurements

    Science.gov (United States)

    Larciprete, M. C.; Belardini, A.; Sibilia, C.; Saab, M.-b.; Váró, G.; Gergely, C.

    2010-05-01

    We experimentally investigated second harmonic generation from an oriented multilayer film of bacteriorhodopsin protein, deposited onto a charged surface. The generated signal is obtained as a function of incidence angle, at different polarization state of both fundamental and generated beams. We show that the measurements, together with the analytical curves, allow to retrieve the nonvanishing elements of the nonlinear optical tensor, including the ones introduced by optical chirality.

  18. Light-induced changes in the absorption spectrum of bacteriorhodopsin under two-wavelength excitation

    Science.gov (United States)

    Koklyushkin, A. V.; Korolev, A. E.

    2004-09-01

    The results of spectrophotometric measurements of nonlinear light-induced changes in the absorption spectrum of bacteriorhodopsin D96N occurring upon simultaneous excitation at the wavelengths 633 and 441 nm in the excitation intensity range typical for recording of dynamic holograms are presented. The quantitative conditions under which the action of the radiation at one wavelength reduces the change in the optical density caused by the radiation at the other wavelength are determined.

  19. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    OpenAIRE

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U. (Udo); Elsen, A.; Baumann, Ph.; Nuzzo, R.G.; Stach, E A; Frenkel, A. I.

    2015-01-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—e...

  20. Proteomic Analysis of Saliva in HIV-positive Heroin Addicts Reveals Proteins Correlated with Cognition

    Energy Technology Data Exchange (ETDEWEB)

    Dominy, Stephen; Brown, Joseph N.; Ryder, Mark I.; Gritsenko, Marina A.; Jacobs, Jon M.; Smith, Richard D.

    2014-04-01

    The prevalence of HIV-associated neurocognitive disorders (HAND) remains high despite effective antiretroviral therapies. Multiple etiologies have been proposed over the last few years to account for this phenomenon, including the neurotoxic effects of antiretrovirals and co-morbid substance abuse. However, no underlying molecular mechanism has been identified. Emerging evidence in several fields has linked the gut to brain diseases, but the effect of the gut on the brain during HIV infection has not been explored. Saliva is the most accessible gut biofluid, and is therefore of great scientific interest for diagnostic and prognostic purposes. This study presents a longitudinal, liquid chromatography-mass spectrometry-based quantitative proteomics study investigating saliva samples taken from 8 HIV-positive (HIV+) and 11 -negative (HIV-) heroin addicts. In the HIV+ group, 58 proteins were identified that show significant correlations with cognitive scores and that implicate disruption of protein quality control pathways by HIV. Notably, no proteins from the HIV- heroin addict cohort showed significant correlations with cognitive scores. In addition, the majority of correlated proteins have been shown to be associated with exosomes, allowing us to propose that the salivary glands and/or oral epithelium may modulate brain function during HIV infection through the release of discrete packets of proteins in the form of exosomes.

  1. Correlation of transcriptomic responses and metal bioaccumulation in Mytilus edulis L. reveals early indicators of stress

    Energy Technology Data Exchange (ETDEWEB)

    Poynton, Helen C., E-mail: helen.poynton@umb.edu; Robinson, William E.; Blalock, Bonnie J.; Hannigan, Robyn E.

    2014-10-15

    Highlights: • Gene expression and metal tissue concentrations were compared in Mytilus edulis. • Expression levels of several transcripts correlated with metal concentrations. • Transcripts involved in the unfolded protein response (UPR) were induced. • Integration of transcriptomics and tissue levels provides insight to toxicity. - Abstract: Marine biomonitoring programs in the U.S. and Europe have historically relied on monitoring tissue concentrations of bivalves to monitor contaminant levels and ecosystem health. By integrating ‘omic methods with these tissue residue approaches we can uncover mechanistic insight to link tissue concentrations to potential toxic effects. In an effort to identify novel biomarkers and better understand the molecular toxicology of metal bioaccumulation in bivalves, we exposed the blue mussel, Mytilus edulis L., to sub-lethal concentrations (0.54 μM) of cadmium, lead, and a Cd + Pb mixture. Metal concentrations were measured in gill tissues at 1, 2, and 4 weeks, and increased linearly over the 4 week duration. In addition, there was evidence that Pb interfered with Cd uptake in the mixture treatment. Using a 3025 sequence microarray for M. edulis, we performed transcriptomic analysis, identifying 57 differentially expressed sequences. Hierarchical clustering of these sequences successfully distinguished the different treatment groups demonstrating that the expression profiles were reproducible among the treatments. Enrichment analysis of gene ontology terms identified several biological processes that were perturbed by the treatments, including nucleoside phosphate biosynthetic processes, mRNA metabolic processes, and response to stress. To identify transcripts whose expression level correlated with metal bioaccumulation, we performed Pearson correlation analysis. Several transcripts correlated with gill metal concentrations including mt10, mt20, and contig 48, an unknown transcript containing a wsc domain. In addition

  2. Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form.

    Directory of Open Access Journals (Sweden)

    Vitaly Shevchenko

    Full Text Available Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.

  3. Neural correlates reveal sub-lexical orthography and phonology during reading aloud: A review

    Directory of Open Access Journals (Sweden)

    Kalinka eTimmer

    2014-08-01

    Full Text Available The sub-lexical conversion of graphemes-to-phonemes (GPC during reading has been investigated extensively with behavioral measures, as well as event-related potentials (ERPs. Most research utilizes silent reading (e.g., lexical decision task for which phonological activation is not a necessity. However, recent research employed reading aloud to capture sub-lexical GPC. The masked priming paradigm avoids strategic processing and is therefore well suitable for capturing sub-lexical processing instead of lexical effects. By employing ERPs, the on-line time course of sub-lexical GPC can be observed before the overt response. ERPs have revealed that besides phonological activation, as revealed by behavioral studies, there is also early orthographic activation. This review describes studies in one’s native language, in one’s second language, and in a cross-language situation. We discuss the implications the ERP results have on different (computational models. First, the ERP results show that computational models should assume an early locus of the grapheme-to-phoneme-conversion (GPC. Second, cross-language studies reveal that the phonological representations from both languages of a bilingual become activated automatically and the phonology belonging to the context is selected rapidly. Therefore, it is important to extend the scope of computational models of reading (aloud to multiple lexicons.

  4. Voltage dependence of proton pumping by bacteriorhodopsin mutants with altered lifetime of the M intermediate.

    Directory of Open Access Journals (Sweden)

    Sven Geibel

    Full Text Available The light-driven proton pump bacteriorhodopsin (BR from Halobacterium salinarum is tightly regulated by the [H(+] gradient and transmembrane potential. BR exhibits optoelectric properties, since spectral changes during the photocycle are kinetically controlled by voltage, which predestines BR for optical storage or processing devices. BR mutants with prolonged lifetime of the blue-shifted M intermediate would be advantageous, but the optoelectric properties of such mutants are still elusive. Using expression in Xenopus oocytes and two-electrode voltage-clamping, we analyzed photocurrents of BR mutants with kinetically destabilized (F171C, F219L or stabilized (D96N, D96G M intermediate in response to green light (to probe H(+ pumping and blue laser flashes (to probe accumulation/decay of M. These mutants have divergent M lifetimes. As for BR-WT, this strictly correlates with the voltage dependence of H(+ pumping. BR-F171C and BR-F219L showed photocurrents similar to BR-WT. Yet, BR-F171C showed a weaker voltage dependence of proton pumping. For both mutants, blue laser flashes applied during and after green-light illumination showed reduced M accumulation and shorter M lifetime. In contrast, BR-D96G and BR-D96N exhibited small photocurrents, with nonlinear current-voltage curves, which increased strongly in the presence of azide. Blue laser flashes showed heavy M accumulation and prolonged M lifetime, which accounts for the strongly reduced H(+ pumping rate. Hyperpolarizing potentials augmented these effects. The combination of M-stabilizing and -destabilizing mutations in BR-D96G/F171C/F219L (BR-tri shows that disruption of the primary proton donor Asp-96 is fatal for BR as a proton pump. Mechanistically, M destabilizing mutations cannot compensate for the disruption of Asp-96. Accordingly, BR-tri and BR-D96G photocurrents were similar. However, BR-tri showed negative blue laser flash-induced currents even without actinic green light, indicating

  5. Probing bacteriorhodopsin photochemistry with nonlinear optics. Comparing the second harmonic generation of bR and the photochemically induced intermediate K

    Energy Technology Data Exchange (ETDEWEB)

    Bouevitch, O.; Lewis, A. [Hebrew Univ., Jerusalem (Israel); Sheves, M. [Weizmann Inst. of Science, Rehevot (Israel)

    1995-06-29

    The nonlinear optical properties of the bacteriorhodopsin chromophore in the bR568 and K states are investigated by second harmonic generation. The comparison of amplitudes and phases of the second-order nonlinear optical polarizabilities of the retinal chromophore in the two states has revealed a noticeable increase of the induced dipole of the retinal as a result of the bR568 $YLD K transition. The results have been explained in terms of recent theoretical understandings of the nonlinear optical properties of polyenes. Within the context of these understandings we have discussed the molecular origins of the light-induced color changes and the possible mechanism of photon energy storage observed in this protein. 54 refs., 8 figs., 3 tabs.

  6. Correlating chemical sensitivity and basal gene expression reveals mechanism of action

    Science.gov (United States)

    Rees, Matthew G.; Seashore-Ludlow, Brinton; Cheah, Jaime H.; Adams, Drew J.; Price, Edmund V.; Gill, Shubhroz; Javaid, Sarah; Coletti, Matthew E.; Jones, Victor L.; Bodycombe, Nicole E.; Soule, Christian K.; Alexander, Benjamin; Li, Ava; Montgomery, Philip; Kotz, Joanne D.; Hon, C. Suk-Yee; Munoz, Benito; Liefeld, Ted; Dančík, Vlado; Haber, Daniel A.; Clish, Clary B.; Bittker, Joshua A.; Palmer, Michelle; Wagner, Bridget K.; Clemons, Paul A.; Shamji, Alykhan F.; Schreiber, Stuart L.

    2015-01-01

    Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal gene expression could be correlated with patterns of small-molecule sensitivity across many cell lines to illuminate the actions of compounds whose MoA are unknown. To test this idea, we correlated the sensitivity patterns of 481 compounds with ~19,000 basal transcript levels across 823 different human cancer cell lines and identified selective outlier transcripts. This process yielded many novel mechanistic insights, including the identification of activation mechanisms, cellular transporters, and direct protein targets. We found that ML239, originally identified in a phenotypic screen for selective cytotoxicity in breast cancer stem-like cells, most likely acts through activation of fatty acid desaturase 2 (FADS2). These data and analytical tools are available to the research community through the Cancer Therapeutics Response Portal. PMID:26656090

  7. Correlation in the sequential evolutionary pattern of influenza hemagglutinin reveals its immunogenic and structural characters

    Science.gov (United States)

    Pan, Keyao; Deem, Michael

    2010-03-01

    The immune system recognizes the hemagglutinin (HA) protein on the surface of the influenza virus. It is this protein that evolves to escape immune recognition. Correlation analysis is performed for all pairs of positions in the alignment of HA sequences collected in history. Spectral decomposition of the resulting matrix yields several independent eigenvectors that clusters those positions into several sectors, each of which corresponds to a subset of the positions and follows a relatively independent evolutionary pattern. Some of the obtained sectors match well with the five experimentally and statistically (using Shannon entropy) determined epitopes that are the sites of antibody binding. This result implies that different immunogenic epitopes of HA have characteristic patterns of escape mutation, arguably due to the distinct structures of the epitopes and properties of corresponding antibodies. In the three dimensional structure of HA, each sector is located in a compact surface region, thus the correlations in the evolution pattern occur locally in the tertiary structure. Novel sectors found, beyond the five known HA epitopes, may also possess certain biophysical functions.

  8. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes.

    Science.gov (United States)

    Li, Y; Zakharov, D; Zhao, S; Tappero, R; Jung, U; Elsen, A; Baumann, Ph; Nuzzo, R G; Stach, E A; Frenkel, A I

    2015-01-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction-ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes. PMID:26119246

  9. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    Science.gov (United States)

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction--ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  10. A New Planet around an M Dwarf: Revealing a Correlation between Exoplanets and Stellar Mass

    OpenAIRE

    Johnson, John A.; Butler, R. Paul; Marcy, Geoffrey W.; Fischer, Debra A.; Vogt, Steven S.; Wright, Jason T.; Peek, Kathryn M. G.

    2007-01-01

    We report precise Doppler measurements of GJ 317 (M3.5 V) that reveal the presence of a planet with a minimum mass M_P sin i = 1.2 M_(Jup) in an eccentric, 692.9 day orbit. GJ 317 is only the third M dwarf with a Doppler-detected Jovian planet. The residuals to a single-Keplerian fit show evidence of a possible second orbital companion. The inclusion of a second Jupiter-mass planet (P ≈ 2700 days, M_P sin i = 0.83 M_(Jup)) decreases √X_v^2 from 2.02 to 1.23, and reduces the rms from 12.5 to 6...

  11. Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish.

    Science.gov (United States)

    Kok, Fatma O; Shin, Masahiro; Ni, Chih-Wen; Gupta, Ankit; Grosse, Ann S; van Impel, Andreas; Kirchmaier, Bettina C; Peterson-Maduro, Josi; Kourkoulis, George; Male, Ira; DeSantis, Dana F; Sheppard-Tindell, Sarah; Ebarasi, Lwaki; Betsholtz, Christer; Schulte-Merker, Stefan; Wolfe, Scot A; Lawson, Nathan D

    2015-01-12

    The widespread availability of programmable site-specific nucleases now enables targeted gene disruption in the zebrafish. In this study, we applied site-specific nucleases to generate zebrafish lines bearing individual mutations in more than 20 genes. We found that mutations in only a small proportion of genes caused defects in embryogenesis. Moreover, mutants for ten different genes failed to recapitulate published Morpholino-induced phenotypes (morphants). The absence of phenotypes in mutant embryos was not likely due to maternal effects or failure to eliminate gene function. Consistently, a comparison of published morphant defects with the Sanger Zebrafish Mutation Project revealed that approximately 80% of morphant phenotypes were not observed in mutant embryos, similar to our mutant collection. Based on these results, we suggest that mutant phenotypes become the standard metric to define gene function in zebrafish, after which Morpholinos that recapitulate respective phenotypes could be reliably applied for ancillary analyses.

  12. Revealing the Eruptive History of Volcanoes from Massive Cross-Correlation of Seismic Signal at Global Scale

    Science.gov (United States)

    Dupont, A.; Gaillard, P.; Grenouille, A.; Bui-Quang, P.; Guilhem, A.; Bobrov, D.; Kitov, I. O.; Rozhkov, M.

    2015-12-01

    We propose here a massive cross-correlation technique applied to seismic events located around volcanoes and recorded at teleseismic distance. Multichannel cross-correlations are performed between 2002 to 2012 using seismic templates occurring at the time of moderate to large volcanic eruptions. The volcanic periods are reported from the Global Volcanism Program database while the waveform data are obtained from the Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO). The temporal distribution of new seismic events, built from the association of teleseismic detections reveals acceleration patterns, which are highly correlated to the past eruptive activities. These newly detected events are relocated using Bayesian approach and leads to preliminary interpretation of the volcanic plumbing system. Two examples are presented. First, the large 2008 eruption (Volcanic Explosivity Index, VEI4) of Kasatochi (Aleutian Islands, 52.10°N/175.31°W) is used to demonstrate that only few seismic templates (~3) help to reveal the time scale of the eruption. Results are compared to hydroacoustic signal, which is highly correlated to the distribution of new seismic events prior and during eruption. We also show that after the peaked seismic activity (i.e., ~ 100 seismic events in 1 hour) the infrasound signal starts and signs the volcanic plume activity. The second case example reveals with success seven past volcanic eruptions of lower magnitude (VEI1 to VEI2) of the Karangetang volcano (Siau Island in Indonesia, 2.46°N/125.24°E). We show the potential of this method to detect volcanic eruptions in isolated areas. This is of special interest especially when there is no volcano observatory to monitor the volcanic activity, or when the last eruptive period is unknown.

  13. Exploratory Metabolomic Analyses Reveal Compounds Correlated with Lutein Concentration in Frontal Cortex, Hippocampus, and Occipital Cortex of Human Infant Brain.

    Directory of Open Access Journals (Sweden)

    Jacqueline C Lieblein-Boff

    Full Text Available Lutein is a dietary carotenoid well known for its role as an antioxidant in the macula, and recent reports implicate a role for lutein in cognitive function. Lutein is the dominant carotenoid in both pediatric and geriatric brain tissue. In addition, cognitive function in older adults correlated with macular and postmortem brain lutein concentrations. Furthermore, lutein was found to preferentially accumulate in the infant brain in comparison to other carotenoids that are predominant in diet. While lutein is consistently related to cognitive function, the mechanisms by which lutein may influence cognition are not clear. In an effort to identify potential mechanisms through which lutein might influence neurodevelopment, an exploratory study relating metabolite signatures and lutein was completed. Post-mortem metabolomic analyses were performed on human infant brain tissues in three regions important for learning and memory: the frontal cortex, hippocampus, and occipital cortex. Metabolomic profiles were compared to lutein concentration, and correlations were identified and reported here. A total of 1276 correlations were carried out across all brain regions. Of 427 metabolites analyzed, 257 were metabolites of known identity. Unidentified metabolite correlations (510 were excluded. In addition, moderate correlations with xenobiotic relationships (2 or those driven by single outliers (3 were excluded from further study. Lutein concentrations correlated with lipid pathway metabolites, energy pathway metabolites, brain osmolytes, amino acid neurotransmitters, and the antioxidant homocarnosine. These correlations were often brain region-specific. Revealing relationships between lutein and metabolic pathways may help identify potential candidates on which to complete further analyses and may shed light on important roles of lutein in the human brain during development.

  14. Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions.

    Science.gov (United States)

    Lin, Aijing; Liu, Kang K L; Bartsch, Ronny P; Ivanov, Plamen Ch

    2016-05-13

    Within the framework of 'Network Physiology', we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain-heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain-heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems. PMID:27044991

  15. Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions.

    Science.gov (United States)

    Lin, Aijing; Liu, Kang K L; Bartsch, Ronny P; Ivanov, Plamen Ch

    2016-05-13

    Within the framework of 'Network Physiology', we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain-heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain-heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems.

  16. Quantitative Neuropeptidome Analysis Reveals Neuropeptides Are Correlated with Social Behavior Regulation of the Honeybee Workers.

    Science.gov (United States)

    Han, Bin; Fang, Yu; Feng, Mao; Hu, Han; Qi, Yuping; Huo, Xinmei; Meng, Lifeng; Wu, Bin; Li, Jianke

    2015-10-01

    Neuropeptides play vital roles in orchestrating neural communication and physiological modulation in organisms, acting as neurotransmitters, neuromodulators, and neurohormones. The highly evolved social structure of honeybees is a good system for understanding how neuropeptides regulate social behaviors; however, much knowledge on neuropeptidomic variation in the age-related division of labor remains unknown. An in-depth comparison of the brain neuropeptidomic dynamics over four time points of age-related polyethism was performed on two strains of honeybees, the Italian bee (Apis mellifera ligustica, ITb) and the high royal jelly producing bee (RJb, selected for increasing royal jelly production for almost four decades from the ITb in China). Among the 158 identified nonredundant neuropeptides, 77 were previously unreported, significantly expanding the coverage of the honeybee neuropeptidome. The fact that 14 identical neuropeptide precursors changed their expression levels during the division of labor in both the ITb and RJb indicates they are highly related to task transition of honeybee workers. These observations further suggest the two lines of bees employ a similar neuropeptidome modification to tune their respective physiology of age polyethism via regulating excretory system, circadian clock system, and so forth. Noticeably, the enhanced level of neuropeptides implicated in regulating water homeostasis, brood pheromone recognition, foraging capacity, and pollen collection in RJb signify the fact that neuropeptides are also involved in the regulation of RJ secretion. These findings gain novel understanding of honeybee neuropeptidome correlated with social behavior regulation, which is potentially important in neurobiology for honeybees and other insects.

  17. Neuronal Correlates of Cognitive Control during Gaming Revealed by Near-Infrared Spectroscopy.

    Directory of Open Access Journals (Sweden)

    Matthias Witte

    Full Text Available In everyday life we quickly build and maintain associations between stimuli and behavioral responses. This is governed by rules of varying complexity and past studies have identified an underlying fronto-parietal network involved in cognitive control processes. However, there is only limited knowledge about the neuronal activations during more natural settings like game playing. We thus assessed whether near-infrared spectroscopy recordings can reflect different demands on cognitive control during a simple game playing task. Sixteen healthy participants had to catch falling objects by pressing computer keys. These objects either fell randomly (RANDOM task, according to a known stimulus-response mapping applied by players (APPLY task or according to a stimulus-response mapping that had to be learned (LEARN task. We found an increased change of oxygenated and deoxygenated hemoglobin during LEARN covering broad areas over right frontal, central and parietal cortex. Opposed to this, hemoglobin changes were less pronounced for RANDOM and APPLY. Along with the findings that fewer objects were caught during LEARN but stimulus-response mappings were successfully identified, we attribute the higher activations to an increased cognitive load when extracting an unknown mapping. This study therefore demonstrates a neuronal marker of cognitive control during gaming revealed by near-infrared spectroscopy recordings.

  18. Neural correlates of apathy revealed by lesion mapping in participants with traumatic brain injuries.

    Science.gov (United States)

    Knutson, Kristine M; Monte, Olga Dal; Raymont, Vanessa; Wassermann, Eric M; Krueger, Frank; Grafman, Jordan

    2014-03-01

    Apathy, common in neurological disorders, is defined as disinterest and loss of motivation, with a reduction in self-initiated activity. Research in diseased populations has shown that apathy is associated with variations in the volume of brain regions such as the anterior cingulate and the frontal lobes. The goal of this study was to determine the neural signatures of apathy in people with penetrating traumatic brain injuries (pTBIs), as to our knowledge, these have not been studied in this sample. We studied 176 male Vietnam War veterans with pTBIs using voxel-based lesion-symptom mapping (VLSM) and apathy scores from the UCLA Neuropsychiatric Inventory (NPI), a structured inventory of symptoms completed by a caregiver. Our results revealed that increased apathy symptoms were associated with brain damage in limbic and cortical areas of the left hemisphere including the anterior cingulate, inferior, middle, and superior frontal regions, insula, and supplementary motor area. Our results are consistent with the literature, and extend them to people with focal pTBI. Apathy is a significant symptom since it can reduce participation of the patient in family and other social interactions, and diminish affective decision-making.

  19. An innovative experimental design reveals the spatial correlation between landuse, irrigation properties, and bromide leaching

    Science.gov (United States)

    Schwen, A.; Yang, Y.; Walton, J.; Wendroth, O.

    2012-04-01

    Understanding the relationship between leaching of pesticides and soil hydraulic properties under different land use conditions is critical to our understanding of the flow of water and solutes in soils and efforts to model these flow characteristics. One problem inherent in the measurement of solute leaching in field experiments is the considerable high natural spatial variability of flow-controlling soil properties. Thus, analyzing treatment effects based on the mean and the variance of observations can become obsolete if there is a huge inherent variance in the set of measurements. Moreover, no spatial range of influence can be derived from the observations. To overcome this limitation, the spatial covariance and cross-variance between measurements was used as decision and quality criteria in the present study. This study aims to demonstrate that focussing on the spatial covariance of observations and considering their spatial process can provide a measure of spatial representativity or scale-specific variance. We introduce a novel experimental scheme, where the treatments are arranged in a scale-dependent manner. In a field trial in Lexington, Kentucky, bromide leaching under two contrasting land use systems (no-till agricultural crops vs. pasture) was compared. After surface application of tracer solution (KBr), the experimental field was irrigated using different time-delays (1, 4 and 24 hours) as well as two different irrigation amounts and two different intensities. At the end, the KBr-concentration in the soil profile was determined using auger samplings. The data was correlated with the applied boundary conditions by spatial statistical methods such as semivariograms, cross-semivariograms and spectral analysis. Our results show distinct differences in the leaching behaviour between the two analyzed land uses with an deeper infiltration in the no-till agricultural field. This can be partly related to a higher initial soil water content in this treatment

  20. Two-photon polarization data storage in bacteriorhodopsin films and its potential use in security applications

    International Nuclear Information System (INIS)

    Bacteriorhodopsin (BR) films allow write-once-read-many recording of polarization data by a two-photon-absorption (TPA) process. The optical changes in BR films induced by the TPA recording were measured and the Müller matrix of a BR film was determined. A potential application of BR films in security technology is shown. Polarization data can be angle-selective retrieved with high signal-to-noise ratio. The BR film does not only carry optical information but serves also as a linear polarizer. This enables that polarization features recorded in BR films may be retrieved by merely using polarized light from a mobile phone display

  1. Two-photon polarization data storage in bacteriorhodopsin films and its potential use in security applications

    Energy Technology Data Exchange (ETDEWEB)

    Imhof, Martin; Hampp, Norbert, E-mail: hampp@staff.uni-marburg.de [Department of Chemistry, Material Sciences Center, University of Marburg, Hans-Meerwein-Str., D-35032 Marburg (Germany); Rhinow, Daniel [Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt (Germany)

    2014-02-24

    Bacteriorhodopsin (BR) films allow write-once-read-many recording of polarization data by a two-photon-absorption (TPA) process. The optical changes in BR films induced by the TPA recording were measured and the Müller matrix of a BR film was determined. A potential application of BR films in security technology is shown. Polarization data can be angle-selective retrieved with high signal-to-noise ratio. The BR film does not only carry optical information but serves also as a linear polarizer. This enables that polarization features recorded in BR films may be retrieved by merely using polarized light from a mobile phone display.

  2. Förster Resonance Energy Transfer between Core/Shell Quantum Dots and Bacteriorhodopsin

    OpenAIRE

    Karna, Shashi P.; Craig R. Friedrich; Garrett, Gregory A.; Lueking, Donald R.; Winder, Eric M.; Griep, Mark H.

    2012-01-01

    An energy transfer relationship between core-shell CdSe/ZnS quantum dots (QDs) and the optical protein bacteriorhodopsin (bR) is shown, demonstrating a distance-dependent energy transfer with 88.2% and 51.1% of the QD energy being transferred to the bR monomer at separation distances of 3.5 nm and 8.5 nm, respectively. Fluorescence lifetime measurements isolate nonradiative energy transfer, other than optical absorptive mechanisms, with the effective QD excited state lifetime reducing from 18...

  3. Photoinduced Birefringence and Broadband All-Optical Photonic Switch in a Bacteriorhodopsin/Polymer Composite Film

    Institute of Scientific and Technical Information of China (English)

    WEI Lai; TENG Xue-Lei; Lu Ming; ZHAO You-Yuan; MA De-Wang; DING Jian-Dong

    2007-01-01

    Photoinduced birefringence with large optical nonlinearity in a bacteriorhodopsin/polymer composite film is observed.A high refractive index change of 8.5×10-5 photoinduced by 476nm pumping beam is reached at the low intensity of 6.5mW/cm2.Based on it,a broadband all-optical photonic switch is realized with an optical controlling switch system.Because of controlling beam's selectivity in switching,the transporting beams of different wavelengths with different intensities and shapes can be modulated by adjusting the wavelength and intensity of the controlling beam.

  4. Nonlinear photoinduced anisotropy and modifiable optical image display in a bacteriorhodopsin/polymer composite film

    Science.gov (United States)

    Wei, Lai; Luo, Jia; Zhu, Jiang; Lu, Ming; Zhao, You-yuan; Ma, De-wang; Ding, Jian-dong

    2007-04-01

    The nonlinear photoinduced anisotropy with large birefringence in a bacteriorhodopsin/polymer composite (bR/PC) film was observed. The contrast ratio, a ratio of the maximum to the minimum intensity of transmitted probe light through the bR/PC film within the linear gray scale range could reach ˜350:1. An all-optical image display in different colors was performed. The intensity of the transmitted signal could be modulated by adjusting the multibeam polarization states and intensities. Therefore, the positive image, negative image, and image erasure in display were demonstrated.

  5. A Novel Optical Filter for Removing Bright-Background Using an Enhanced Bacteriorhodopsin Thin Film

    Institute of Scientific and Technical Information of China (English)

    ZHANG Chun-Ping(张春平); GU Li-Qun(顾立群); CHEN Gm-Ying(陈桂英); GUO Zong-Xia(郭宗霞); FU Guang-Hua(富光华); ZHANG Guang-Yin(张光寅); ZHANG Tian-Hao(张天浩); LI Yu-Dong(李玉栋); Q. Wang SONG

    2003-01-01

    We found that the bacteriorhodopsin (bR) film has a special property of complementary suppression modulated transmission (CSMT). The yellow and the blue beams can be suppressed mutually when both the beams illuminate the bR film simultaneously. When the blue beam carrying an image with a bright-background noise illuminates on the bR film and then a yellow beam with uniform intensity distribution illuminates the same area, the brightbackground can be removed due to the CSMT. In our demonstration, the pattern model is letters "VLSI" with ground noise of small words and the ground noise is removed from the pattern by the new optical filter.

  6. Enhancement of photoelectric response of bacteriorhodopsin by multilayered WO3 x H2O nanocrystals/PVA membrane.

    Science.gov (United States)

    Li, Rui; Hu, Fengping; Bao, Qiaoliang; Bao, Shujuan; Qiao, Yan; Yu, Shucong; Guo, Jun; Li, Chang Ming

    2010-02-01

    For the first time, a multilayered WO(3) x H(2)O/PVA membrane on bacteriorhodopsin (bR) is constructed to significantly enhance the photoelectric response of bR by the spillover effect of WO(3) x H(2)O nanocrystals, providing great potential in its important applications in bioelectronics and proton exchange membrane fuel cells.

  7. Contrast enhancement and phase conjugation low-power optical signal in dynamic recording material based on bacteriorhodopsin

    Science.gov (United States)

    Korchemskaya, Elena Y.; Soskin, Marat S.; Dukova, Tatjana V.; Vsevolodov, Nicolai N.

    1994-02-01

    Polymer films with fragments of the purple membranes containing protein bacteriorhodopsin (BR) have been used for the real-time optical information processing of low-power (several milliwatt) cw gas laser signals. The nonlinear recording media with BR have a potential in microscopic techniques for in-vivo diagnosis of the crystalline lens.

  8. Studying of Phototransformation of Light Signal by Photoreceptor Pigments - Rhodopsin, Iodopsin and Bacteriorhodopsin

    Directory of Open Access Journals (Sweden)

    Ignat Ignatov

    2014-09-01

    Full Text Available This review article views predominately the structure and function of animal and bacterial photoreceptor pigments (rhodopsin, iodopsin, bacteriorhodopsin and their aspects of nano- and biotechnological usage. On an example of bacteriorhodopsin is described the method of its isolation from purple membranes of photo-organotrophic halobacterium Halobacterium halobium by cellular autolysis by distilled water, processing of bacterial biomass by ultrasound at 22 KHz, alcohol extraction of low and high-weight molecular impurities, cellular RNA, carotenoids and lipids, the solubilization with 0,5 % (w/v SDS-Na and subsequent fractionation by methanol and gel filtration chromatography on Sephadex G-200 Column balanced with 0.09 M Tris-borate buffer (pH = 8,35 with 0,1 % (w/v SDS-Na and 2,5 mM EDTA. Within the framework of the research the mechanism of color perception by the visual analyzer having the ability to analyze certain ranges of the optical spectrum, as colors was studied along with an analysis of the additive mixing of two colors. It was shown that at the mixing of electromagnetic waves with different wavelengths, the visual analyzer perceive them as separate or average wave length corresponding to mix color.

  9. New Nano- and Biotechnological Applications of Bacterial and Animal Photoreceptor Pigments  Bacteriorhodopsin, Rhodopsin and Iodopsin

    Directory of Open Access Journals (Sweden)

    Ignat Ignatov

    2016-03-01

    Full Text Available This paper views predominately the structure and function of animal and bacterial photoreceptor pigments (rhodopsin, iodopsin, bacteriorhodopsin and new aspects of their nano- and biotechnological usage. On an example of bacteriorhodopsin was described the method of its isolation from purple membranes of photo-organotrophic halobacterium Halobacterium halobium by cellular autolysis by distilled water, processing of bacterial biomass by ultrasound at 22 KHz, alcohol extraction of low and high-weight molecular impurities, cellular RNA, carotenoids and lipids, the solubilization with 0,5 % (w/v SDS-Na and subsequent fractionation by methanol and gel filtration chromatography on Sephadex G-200 Column balanced with 0.09 M Tris-HCl buffer (pH = 6,76 with 0,1 % (w/v SDS-Na and 2,5 mM EDTA. Within the framework of the research the mechanism of color perception by the visual analyzer having the ability to analyze certain ranges of the optical spectrum, as colors was studied along with an analysis of the additive mixing of two colors. It was shown that at the mixing of electromagnetic waves with different wavelengths, the visual analyzer perceive them as separate or average wave length corresponding to mix color.

  10. Systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution.

    Directory of Open Access Journals (Sweden)

    Erez Persi

    Full Text Available We present a novel analysis of compositional order (CO based on the occurrence of Frequent amino-acid Triplets (FTs that appear much more than random in protein sequences. The method captures all types of proteomic compositional order including single amino-acid runs, tandem repeats, periodic structure of motifs and otherwise low complexity amino-acid regions. We introduce new order measures, distinguishing between 'regularity', 'periodicity' and 'vocabulary', to quantify these phenomena and to facilitate the identification of evolutionary effects. Detailed analysis of representative species across the tree-of-life demonstrates that CO proteins exhibit numerous functional enrichments, including a wide repertoire of particular patterns of dependencies on regularity and periodicity. Comparison between human and mouse proteomes further reveals the interplay of CO with evolutionary trends, such as faster substitution rate in mouse leading to decrease of periodicity, while innovation along the human lineage leads to larger regularity. Large-scale analysis of 94 proteomes leads to systematic ordering of all major taxonomic groups according to FT-vocabulary size. This is measured by the count of Different Frequent Triplets (DFT in proteomes. The latter provides a clear hierarchical delineation of vertebrates, invertebrates, plants, fungi and prokaryotes, with thermophiles showing the lowest level of FT-vocabulary. Among eukaryotes, this ordering correlates with phylogenetic proximity. Interestingly, in all kingdoms CO accumulation in the proteome has universal characteristics. We suggest that CO is a genomic-information correlate of both macroevolution and various protein functions. The results indicate a mechanism of genomic 'innovation' at the peptide level, involved in protein elongation, shaped in a universal manner by mutational and selective forces.

  11. Correlations between Photovoltaic Characteristics, Adsorption Number, and Regeneration Kinetics in Dye-Sensitized Solar Cells Revealed by Scanning Photocurrent Microscopy.

    Science.gov (United States)

    Mitsui, Masaaki; Kawano, Yuya; Mori, Kyosuke; Wakabayashi, Naoto

    2015-06-30

    Newly developed simultaneous scanning photocurrent and luminescence microscopy was applied to ruthenium-based dye-sensitized solar cells (DSCs) comprising a cover glass photoanode with a 100 nm thick TiO2 layer. Using this, we have investigated the lateral variations of several parameters of these DSCs under short-circuit conditions. Simultaneous measurement of photocurrent and luminescence images for the same area of the DSC demonstrated submicrometric lateral resolution of our photocurrent microscopy, which is approximately 10 times better than the resolution of photocurrent microscopy used in past studies. The photovoltaic parameters, such as short-circuit current density, open-circuit voltage, and charge-collection efficiency, were thus evaluated for local (or submicrometric) regions of the DSCs. Furthermore, the photocurrent saturation behavior of the DSCs was examined as a function of the excitation rate and analyzed on the basis of a three-state kinetic model. This protocol allowed for quantification of the dye-adsorption number and dye-regeneration rate constant for any local area of the DSCs. Consequently, the correlations between the dye adsorption number, photovoltaic parameters, and regeneration rate constant, which are difficult to address through examination of the entire cell, were revealed by the "zoom-in" approach utilizing this high-resolution photocurrent microscopy.

  12. Spectral Signatures of the Pentagonal Water Cluster in Bacteriorhodopsin

    Energy Technology Data Exchange (ETDEWEB)

    Baer, M; Mathias, G; Kuo, I W; Tobias, D J; Mundy, C J; Marx, D

    2008-07-25

    The exchange of protons between basic and acidic groups within proteins often involves transient protonation of amino acids and water molecules embedded in the protein matrix. One of the best studied proteins in this respect is Bacteriorohodopsin (BR), which works in the membrane of Halobacterium salinarium as a light-driven proton pump. The pumping process is triggered in the initial bR state by a photon absorption of an all-trans retinylidene chromophore, which is linked via a protonated Schiff base (pRSB) to the sidechain of Lys216. The subsequent photocycle comprises a series of intermediate states J, K, L, M, N and O, which are characterized by conformational and absorbance changes of the chromophore accompanying several elementary proton transfer processes. Upon completion of the photocycle one net proton has been transferred from the cyctoplasmic to the extracellular side against the proton gradient across the membrane. These proton exchange reactions can be monitored by time resolved infrared (IR) spectroscopy of the BR wild type and site specific mutants, which allow the localization of absorbance changes within the protein. Furthermore, these measurements have revealed the fundamental importance of internal water molecules in these processes as supported by recent large-scale QM/MM molecular dynamics studies of anharmonic IR spectra.

  13. Solid-state NMR studies of bacteriorhodopsin and the purple membrane

    CERN Document Server

    Mason, A J

    2001-01-01

    proteins. This technique may prove particularly useful when studying large proteins that are difficult to orient where the MAS lineshapes will remain relatively unaffected in comparison with current static NMR methods. Finally the MAOSS method was extended to the study of the lipid components of the purple membrane and the feasibility of determining structural constraints from phospholipid headgroups was assessed. The potential of using sup 3 sup 1 P NMR to observe qualitative protein-lipid interactions in both the purple membrane and reconstituted membranes containing bovine rhodopsin was also demonstrated. Following the demonstration of a new MAS NMR method for resolving orientational constraints in uni-axially oriented biological membranes (Glaubitz and Watts, 1998), experiments were performed to realise the potential of the new method on large, oriented membrane proteins. Using bacteriorhodopsin in the purple membrane as a paradigm for large membrane proteins, the protein was specifically labelled with de...

  14. Generation and analysis of bacteriorhodopsin mutants with the potential for biotechnological applications.

    Science.gov (United States)

    Saeedi, P; Moosaabadi, J Mohammadian; Sebtahmadi, S Sina; Mehrabadi, J Fallah; Behmanesh, M; Nejad, H Rouhani; Nazaktabar, A

    2012-01-01

    The properties of bacteriorhodopsin (BR) can be manipulated by genetic engineering. Therefore, by the methods of gene engineering, Asp85 was replaced individually by two other amino acids (D85V, D85S). The resulting recombinant proteins were assembled into soybean vesicles retinylated to form functional BR-like nano-particles. Proton translocation was almost completely abrogated by the mutant D85S, while the D85V mutant was partially active in pumping protons. Compared with wild type, maximum absorption of the mutants, D85V and D85S, were 563 and 609 nm, which illustrated 5 nm reductions (blue shift) and 41 nm increases (red shift), respectively. Since proton transport activity and spectroscopic activities of the mutants are different, a wide variety of membrane bioreactors (MBr) have been developed. Modified proteins can be utilized to produce unique photo/Electro-chromic materials and tools. PMID:22976247

  15. High-effective cultivation of Halobacterium salinarum providing with bacteriorhodopsin production under controlled stress.

    Science.gov (United States)

    Kalenov, Sergei V; Baurina, Marina M; Skladnev, Dmitry A; Kuznetsov, Alexander Ye

    2016-09-10

    Submerged growth of Halobacterium salinarum and therefore synthesis of bacteriorhodopsin (BR) and carotenoids depend greatly on products of both chemical and/or photochemical oxidation of medium components and cellular metabolism which act as inhibitors. Some cultivation variants which allowed eliminating an adverse effect of inhibitors on biomass accumulation and BR synthesis are reviewed. The application of activated charcoal or ion exchange resin as adsorbents at preparing inoculums and the main cultivation stages was shown to allow controlling, namely lowering overstress of the halobacterial cells by metabolites. The halobacterial biomass containing BR up to 1,750mgL(-1) and the minimum amount of carotinoids that would BR greatly facilitate isolation was accumulated up to 45gL(-1) during eight-day cultivation with cell recycling through adsorbent suspension in a fed-batch mode. To control BR biosynthesis the express method of BR quantification based on colour shades of cell suspension was developed. PMID:27449487

  16. Calibration of Membrane Viscosity of the Reconstituted Vesicles by Measurement of the Rotational Diffusion of Bacteriorhodopsin

    Institute of Scientific and Technical Information of China (English)

    王敖金; 胡坤生

    2002-01-01

    Membrane viscosity of the reconstituted vesicles was calibrated by rotational diffusion of bacteriorhodopsin (BR) in dimyristoylphosphatidylcholine (DMPC) and egg phosphatidylcholine (PC) vesicles. Rotational diffusion of BR in the vesicles was measured by flash-induced absorption anisotropy decay. BR was, for the first time, reconstituted successfully into DMPC and egg PC vesicles. From the measurement of flash-induced absorption anisotropy decay of BR, the value of rotational diffusion coefficient D was obtained from each curve fitting by a global fitting procedure and, in turn, membrane viscosity η was estimated from D. The results have shown that membrane viscosity is temperature-dependent. It was decreased as temperature increased, but a transition occurred in the region of the respective phase transition of DMPC and egg PC, respectively. The decrease of η was fast near the phase transition for DMPC and egg PC. Few effects of lipid/BR ratio and glycerol or sucrose in suspension medium on membrane viscosity were found.

  17. High-speed integrated optical logic based on the protein bacteriorhodopsin.

    Science.gov (United States)

    Mathesz, Anna; Fábián, László; Valkai, Sándor; Alexandre, Daniel; Marques, Paulo V S; Ormos, Pál; Wolff, Elmar K; Dér, András

    2013-08-15

    The principle of all-optical logical operations utilizing the unique nonlinear optical properties of a protein was demonstrated by a logic gate constructed from an integrated optical Mach-Zehnder interferometer as a passive structure, covered by a bacteriorhodopsin (bR) adlayer as the active element. Logical operations were based on a reversible change of the refractive index of the bR adlayer over one or both arms of the interferometer. Depending on the operating point of the interferometer, we demonstrated binary and ternary logical modes of operation. Using an ultrafast transition of the bR photocycle (BR-K), we achieved high-speed (nanosecond) logical switching. This is the fastest operation of a protein-based integrated optical logic gate that has been demonstrated so far. The results are expected to have important implications for finding novel, alternative solutions in all-optical data processing research. PMID:23500476

  18. Broadband optical limiter based on nonlinear photoinduced anisotropy in bacteriorhodopsin film

    Science.gov (United States)

    Huang, Yuhua; Siganakis, Georgios; Moharam, M. G.; Wu, Shin-Tson

    2004-11-01

    Nonlinear photoinduced anisotropy in a bacteriorhodopsin film was theoretically and experimentally investigated and a broadband active optical limiter was demonstrated in the visible spectral range. A diode-pumped second harmonic yttrium aluminum garnet laser was used as a pumping beam and three different wavelengths at λ =442, 532, and 655nm from different lasers were used as probing beams. The pump and probe beams overlap at the sample. When the pumping beam is absent, the probing beam cannot transmit the crossed polarizers. With the presence of the pumping beam, a portion of the probing light is detected owing to the photoinduced anisotropy. Due to the optical nonlinearity, the transmitted probing beam intensity is clamped at a certain value, which depends on the wavelength, when the pumping beam intensity exceeds 5mW/mm2. Good agreement between theory and experiment is found.

  19. An all-optical time-delay relay based n a bacteriorhodopsin film

    Institute of Scientific and Technical Information of China (English)

    Chen Gui-Ying; Xu Xu-Xu; Zhang Chun-Ping; Qi Shen-Wen; Song Qi-Wang

    2008-01-01

    Using a special property of dynamic complementary-suppression-modulated transmission (DCSMT) in the bacteriorhodopsin (bR) film,we have demonstrated an all-optical time-delay relay.To extend our work,the relationship between the delay time of the all-optical time-delay relay and parameters of a bR film is numerically studied.We show how the delay time changes with the product of concentration and thickness (PCT) of a bR film.Furthermore,the shortest and longest delay times are given for the relay of 'switch off'.The saturable delay time and maximum delaytime of 'switch on' are also given.How the wavelengths (632.8,568,533 and 412 nm) and intensities of the illuminating light influence the delay time is also discussed.The simulation results are useful for optimizing the design of all-optical time-delay relays.

  20. All-optical switching characteristics in bacteriorhodopsin and its applications in integrated optics

    Science.gov (United States)

    Huang, Yuhua; Wu, Shin-Tson; Zhao, Youyuan

    2004-03-01

    We experimentally and theoretically investigated the optical switching characteristics of bacteriorhodopsin (bR) at l=633 nm using the pump-probe method. A diode-pumped second harmonic YAG laser (l=532 nm which is located around the maximum initial Br state absorption) was used as a pumping beam and a cw He-Ne laser (l=633 nm which is around the peaks of K and O states) was used as a probe. Due to the nonlinear intensity induced excited state absorption of the K, L, M, N, and O states in the bR photocycle, the switching characteristics are sensitive to the intensity of the probe and pump beams. Based on this property, we have demonstrated an all-optical device functioning as 11 kinds of variable binary all-optical logic gates.

  1. Photoinduced nonlinear refraction in a polymeric film encapsulating a bacteriorhodopsin mutant

    Science.gov (United States)

    Teng, Xue-lei; Lu, Ming; Zhao, You-yuan; Ma, De-wang; Zhao, Ying-chun; Ding, Jian-dong; Huang, Wei-da

    2010-08-01

    The absorption change versus time after switching off the illumination on a polymeric film that contained a bacteriorhodopsin (BR) mutant has been measured. The M-lifetime of this BR mutant is ˜320 s. A pertinent Z-scan was performed to study the BR optical nonlinearity. A physical model with multi-level transitions in the Z-scan was suggested. The minimum saturated light intensity measured at 633 nm is ˜0.9 mW/cm2. A low intensity of 70 μW/cm2 has been used for recording in this film. The change in refraction index Δn633 is -3.0×10-3 and Δn476 is 8.5×10-3 with the intensity all at ˜100 mW/cm2.

  2. What Do Statistics Reveal About the Black Hole versus the Bulge Mass Correlation and Co-evolution?

    CERN Document Server

    Peng, Chien Y

    2010-01-01

    Observational data show that the correlation between supermassive black holes (MBH) and galaxy bulge (Mbulge) masses follows a nearly linear trend, and that the correlation is strongest with the bulge rather than the total stellar mass (Mgal). With increasing redshift, the ratio Gamma=MBH/Mbulge relative to z=0 also seems to be larger for MBH >~ 10^{8.5} Msol. This study looks more closely at statistics to better understand the creation and observations of the MBH-Mbulge correlation. It is possible to show that if galaxy merging statistics can drive the correlation, minor mergers are responsible for causing a *convergence to linearity* most evident at high masses, whereas major mergers have a central limit convergence that more strongly *reduces the scatter*. This statistical reasoning is agnostic about galaxy morphology. Therefore, combining statistical prediction (more major mergers ==> tighter correlation) with observations (bulges = tightest correlation), would lead one to conclude that more major mergers...

  3. Metabolic Profiling in Chinese Cabbage (Brassica rapa L. subsp. pekinensis) Cultivars Reveals that Glucosinolate Content Is Correlated with Carotenoid Content.

    Science.gov (United States)

    Baek, Seung-A; Jung, Young-Ho; Lim, Sun-Hyung; Park, Sang Un; Kim, Jae Kwang

    2016-06-01

    A total of 38 bioactive compounds, including glucosinolates, carotenoids, tocopherols, sterols, and policosanols, were characterized from nine varieties of Chinese cabbage (Brassica rapa L. subsp. pekinensis) to determine their phytochemical diversity and analyze their abundance relationships. The metabolite profiles were evaluated with principal component analysis (PCA), Pearson correlation analysis, and hierarchical clustering analysis (HCA). PCA and HCA identified two distinct varieties of Chinese cabbage (Cheonsangcheonha and Waldongcheonha) with higher levels of glucosinolates and carotenoids. Pairwise comparisons of the 38 metabolites were calculated using Pearson correlation coefficients. The HCA, which used the correlation coefficients, clustered metabolites that are derived from closely related biochemical pathways. Significant correlations were discovered between chlorophyll and carotenoids. Additionally, aliphatic glucosinolate and carotenoid levels were positively correlated. The Cheonsangcheonha and Waldongcheonha varieties appear to be good candidates for breeding because they have high glucosinolate and carotenoid levels. PMID:27172980

  4. Identification of Specific Effect of Chloride on the Spectral Properties and Structural Stability of Multiple Extracellular Glutamic Acid Mutants of Bacteriorhodopsin

    Science.gov (United States)

    Lazarova, Tzvetana; Mlynarczyk, Krzysztof; Querol, Enric; Tenchov, Boris; Filipek, Slawomir; Padrós, Esteve

    2016-01-01

    In the present work we combine spectroscopic, DSC and computational approaches to examine the multiple extracellular Glu mutants E204Q/E194Q, E204Q/E194Q/E9Q and E204Q/E194Q/E9Q/E74Q of bacteriorhodopsin by varying solvent ionic strength and composition. Absorption spectroscopy data reveal that the absorption maxima of multiple EC Glu mutants can be tuned by the chloride concentration in the solution. Visible Circular dichroism spectra imply that the specific binding of Cl- can modulate weakened exciton chromophore coupling and reestablish wild type-like bilobe spectral features of the mutants. The DSC data display reappearance of the reversible thermal transition, higher Tm of denaturation and an increase in the enthalpy of unfolding of the mutants in 1 M KCl solutions. Molecular dynamics simulations indicate high affinity binding of Cl- to Arg82 and to Gln204 and Gln194 residues in the mutants. Analysis of the experimental data suggests that simultaneous elimination of the negatively charged side chain of Glu194 and Glu204 is the major cause for mutants’ alterations. Specific Cl- binding efficiently coordinates distorted hydrogen bonding interactions of the EC region and reconstitutes the conformation and structure stability of mutated bR in WT-like fashion. PMID:27657718

  5. The neuronal correlates of digits backward are revealed by voxel-based morphometry and resting-state functional connectivity analyses.

    Directory of Open Access Journals (Sweden)

    Rui Li

    Full Text Available Digits backward (DB is a widely used neuropsychological measure that is believed to be a simple and effective index of the capacity of the verbal working memory. However, its neural correlates remain elusive. The aim of this study is to investigate the neural correlates of DB in 299 healthy young adults by combining voxel-based morphometry (VBM and resting-state functional connectivity (rsFC analyses. The VBM analysis showed positive correlations between the DB scores and the gray matter volumes in the right anterior superior temporal gyrus (STG, the right posterior STG, the left inferior frontal gyrus and the left Rolandic operculum, which are four critical areas in the auditory phonological loop of the verbal working memory. Voxel-based correlation analysis was then performed between the positive rsFCs of these four clusters and the DB scores. We found that the DB scores were positively correlated with the rsFCs within the salience network (SN, that is, between the right anterior STG, the dorsal anterior cingulate cortex and the right fronto-insular cortex. We also found that the DB scores were negatively correlated with the rsFC within an anti-correlation network of the SN, between the right posterior STG and the left posterior insula. Our findings suggest that DB performance is related to the structural and functional organizations of the brain areas that are involved in the auditory phonological loop and the SN.

  6. Studying proton pumping mechanism of bacteriorhodopsin and cytochrome c oxidase with multi-conformation continuum electrostatics

    Science.gov (United States)

    Song, Yifan

    The proton gradient across the biological membrane is important for the biological systems. Bacteriorhodopsin and cytochrome c oxidase convert different energy sources into this gradient. The focus of this thesis is to understand the mechanism of these proteins using computational methods. In bacteriorhodopsin, residue ionization states were calculated in 9 crystal structures trapped in bR, early M and late M states by Multi-Conformation Continuum Electrostatics (MCC). The three groups in the central cluster are ionized in bR structures while a proton has transferred from the SB+ to Asp 85 - in the late M structures matching prior experimental results. The proton release cluster binds one proton in bR structure which is lost to water by pH 8 in late M. Modest changes in intra-protein interactions cause the charge shifts within the clusters. Motions of Arg 82 couple the proton shift in the central cluster to proton release. Changes in the total charge of the two clusters are coupled by direct long-range interactions. Cytochrome c oxidase is a transmembrane proton pump that builds an electrochemical gradient using chemical energy from the reduction of O2. Ionization states of all residues were calculated with MCCE in seven anaerobic oxidase redox states ranging from fully oxidized to fully reduced in Rb. sphaeroides cytochrome c oxidase. At pH 7, only a hydroxide coordinated to CuB shifts its pKa from below 7 to above 7, and so picks up a proton when Heme a3 and CuB are reduced. Glu I-286, Tyr I-288, His I-334 and a second hydroxide on Heme a3 all have pKas above 7. The propionic acids near the BNC are deprotonated with pKas well below 7. This suggests electroneutrality in the BNC is not maintained during the anaerobic reduction. The electrochemical midpoint potential (E m) of Heme a is calculated to shift down when the BNC is reduced, which agrees with prior experiments. If the BNC reduction is electroneutral, then the Heme a Em is independent of the BNC redox state.

  7. Effective atomic numbers and electron densities of bacteriorhodopsin and its comprising amino acids in the energy range 1 keV–100 GeV

    Energy Technology Data Exchange (ETDEWEB)

    Ahmadi, Morteza; Lunscher, Nolan [Waterloo Institute for Nanotechnology and Department of Systems Design Engineering, University of Waterloo, 200 University Ave., W., Waterloo, Ontario, Canada N2L 3G1 (Canada); Yeow, John T.W., E-mail: jyeow@uwaterloo.ca [Waterloo Institute for Nanotechnology and Department of Systems Design Engineering, University of Waterloo, 200 University Ave., W., Waterloo, Ontario, Canada N2L 3G1 (Canada)

    2013-04-01

    Recently, there has been an interest in fabrication of X-ray sensors based on bacteriorhodopsin, a proton pump protein in cell membrane of Halobacterium salinarium. Therefore, a better understanding of interaction of X-ray photons with bacteriorhodopsin is required. We use WinXCom program to calculate the mass attenuation coefficient of bacteriorhodopsin and its comprising amino acids for photon energies from 1 keV to 100 GeV. These amino acids include alanine, arginine, asparagine, aspartic acid, glutamine, glutamic acid, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine, Asx1, Asx2, Glx1 and Glx2. We then use that data to calculate effective atomic number and electron densities for the same range of energy. We also emphasize on two ranges of energies (10–200 keV and 1–20 MeV) in which X-ray imaging and radiotherapy machines work.

  8. Effective atomic numbers and electron densities of bacteriorhodopsin and its comprising amino acids in the energy range 1 keV-100 GeV

    Science.gov (United States)

    Ahmadi, Morteza; Lunscher, Nolan; Yeow, John T. W.

    2013-04-01

    Recently, there has been an interest in fabrication of X-ray sensors based on bacteriorhodopsin, a proton pump protein in cell membrane of Halobacterium salinarium. Therefore, a better understanding of interaction of X-ray photons with bacteriorhodopsin is required. We use WinXCom program to calculate the mass attenuation coefficient of bacteriorhodopsin and its comprising amino acids for photon energies from 1 keV to 100 GeV. These amino acids include alanine, arginine, asparagine, aspartic acid, glutamine, glutamic acid, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine, Asx1, Asx2, Glx1 and Glx2. We then use that data to calculate effective atomic number and electron densities for the same range of energy. We also emphasize on two ranges of energies (10-200 keV and 1-20 MeV) in which X-ray imaging and radiotherapy machines work.

  9. Exploratory metabolomic analyses reveal compounds correlated with lutein concentration in frontal cortex, hippocampus, and occipital cortex of human infant brain

    Science.gov (United States)

    Lutein is a dietary carotenoid well known for its role as an antioxidant in the macula and recent reports implicate a role for lutein in cognitive function. Lutein is the dominant carotenoid in both pediatric and geriatric brain tissue. In addition, cognitive function in older adults correlated with...

  10. Correlative atomic force microscopy and localization-based super-resolution microscopy: revealing labelling and image reconstruction artefacts.

    Science.gov (United States)

    Monserrate, Aitor; Casado, Santiago; Flors, Cristina

    2014-03-17

    Hybrid microscopy: A correlative microscopy tool that combines in situ super-resolution fluorescence microscopy based on single-molecule localization and atomic force microscopy is presented. Direct comparison with high- resolution topography allows the authors to improve fluorescence labeling and image analysis in super-resolution imaging.

  11. Enhanced photocurrent generation in bacteriorhodopsin based bio-sensitized solar cells using gel electrolyte.

    Science.gov (United States)

    Chellamuthu, Jeganathan; Nagaraj, Pavithra; Chidambaram, Sabari Girisun; Sambandam, Anandan; Muthupandian, Ashokkumar

    2016-09-01

    High purity light sensitive photoactive protein Bacteriorhodopsin (BR) was isolated successfully via a simple two phase extraction technique (ATPS) as an alternate method for the tedious sucrose gradient ultracentrifugation procedure (SGU). Bio sensitized solar cells (BSSCs) were fabricated by the integration of BR into TiO2 (photo anode) with acetamide based gel electrolytes and platinum (photo cathode) as a counter electrode. The structural and photoelectrical behaviours of BR and BSSCs were analyzed by Atomic Force Microscopy, Raman spectroscopy, photocurrent and photovoltage (IV) measurement and electrochemical impedance spectroscopy. The short circuit photocurrent (Jsc) and photoelectric conversion efficiency (η) of acetamide based gel electrolyte (AG) (1.08mAcm(-2), 0.49%) are twice higher than that of traditional triiodide based liquid electrolyte (LE) (0.62mAcm(-2), 0.19%). Also, quasi-Fermi level and lifetime of photogenerated electrons in acetamide based gel electrolyte is about four times higher than that observed in traditional triiodide redox electrolyte. A comparison of the observed results with similar BSSCs made of other natural photoactive protein systems shows that BR as sensitizer has better photovoltaic performance. The enhanced photocurrent generation of the BSSC constructed in our study could be due to the interaction of BR with acetamide based modified poly(ethylene)oxide (PEO) gel electrolyte. PMID:27380296

  12. The effect of silver nanoparticles on the photocycle of bacteriorhodopsin of purple membranes of Halobacterium salinarum

    Science.gov (United States)

    Oleinikov, V. A.; Mochalov, K. E.; Solovyeva, D. O.; Chistyakov, A. A.; Lukashev, E. P.; Nabiev, I. R.

    2016-08-01

    The effect of silver nanoparticles (AgNPs) that are adsorbed on the surface of the purple membranes of Halobacterium salinarium bacteria on the optical properties and functional peculiarities of the lightsensitive protein bacteriorhodopsin (BR) has been demonstrated for the first time. Two mechanisms of the effect of AgNPs on the protein photocycle have been demonstrated using Raman scattering, giant Raman scattering, flash photolysis, and atomic force microscopy. It has been shown that the nanoparticles in the immediate spatial vicinity of BR fix its photocycle at the stage where it was at the moment of interaction with the nanoparticles. At greater distances, which reach three radii of an AgNPs, they have a weaker effect on BR, under which it retains the ability to be involved in the photocycle, however, has its parameters significantly changed. Thus, in the case of wild-type BR the photocycle accelerates and for the BR-D96N mutant it becomes slower. The data that are obtained could be of significance for creation of such optoelectronic hybrid systems with BR, where the parameters of its photocycle can be controlled using NPs. The results of the study may also be used in the field of nanobioengineering research, which is directed to creation of unique materials with controlled properties for recording and storage of information, energy transformation, and identification and characterization of trace amounts of analytes.

  13. Photosensory behaviour of a bacteriorhodopsin-deficient mutant, ET-15, of Halobacterium halobium

    Energy Technology Data Exchange (ETDEWEB)

    Hildebrand, E.; Schimz, A. (Kernforschungsanlage Juelich G.m.b.H. (Germany, F.R.). Inst. fuer Neurobiologie)

    1983-05-01

    Halobacterium halobium, strain ET-15, which does not contain detectable amounts of bacteriorhodopsin (BR) shows behavioral responses to UV and yellow-green light. Attractant stimuli, i.e. light-increases in the yellow-green range or light-decreases in the UV, suppress the spontaneous reversals of the swimming direction for a certain time. Repellent stimuli, i.e. light-decreases in the yellow-green range or light-increases in the UV, elicit an additional reversal response after a few seconds. Action spectra of both sensory photosystems, PS 370 and PS 565, were measured with attractant as well as with repellent stimuli. As in BR-containing cells, maximal sensitivity was always found at 370 nm for the UV-system and at 565 nm for the long-wavelength system. Fluence-response curves at 370 and 565 nm obtained with strain ET-15 and with a BR-containing strain show that the sensitivity of both photosystems is not reduced in the absence of BR. It is concluded that BR is required neither for PS 565 nor for PS 370. Instead retinal-containing pigments different from BR have to be assumed to mediate photosensory behavior.

  14. Schiff base switch II precedes the retinal thermal isomerization in the photocycle of bacteriorhodopsin.

    Directory of Open Access Journals (Sweden)

    Ting Wang

    Full Text Available In bacteriorhodopsin, the order of molecular events that control the cytoplasmic or extracellular accessibility of the Schiff bases (SB are not well understood. We use molecular dynamics simulations to study a process involved in the second accessibility switch of SB that occurs after its reprotonation in the N intermediate of the photocycle. We find that once protonated, the SB C15 = NZ bond switches from a cytoplasmic facing (13-cis, 15-anti configuration to an extracellular facing (13-cis, 15-syn configuration on the pico to nanosecond timescale. Significantly, rotation about the retinal's C13 = C14 double bond is not observed. The dynamics of the isomeric state transitions of the protonated SB are strongly influenced by the surrounding charges and dielectric effects of other buried ions, particularly D96 and D212. Our simulations indicate that the thermal isomerization of retinal from 13-cis back to all-trans likely occurs independently from and after the SB C15 = NZ rotation in the N-to-O transition.

  15. Deposition of bacteriorhodopsin protein in a purple membrane form on nitrocellulose membranes for enhanced photoelectric response.

    Science.gov (United States)

    Kim, Young Jun; Neuzil, Pavel; Nam, Chang-Hoon; Engelhard, Martin

    2012-12-27

    Bacteriorhodopsin protein (bR)-based systems are one of the simplest known biological energy converters. The robust chemical, thermal and electrochemical properties of bR have made it an attractive material for photoelectric devices. This study demonstrates the photoelectric response of a dry bR layer deposited on a nitrocellulose membrane with indium tin oxide (ITO) electrodes. Light-induced electrical current as well as potential and impedance changes of dried bR film were recorded as the function of illumination. We have also tested bR in solution and found that the electrical properties are strongly dependent on light intensity changing locally proton concentration and thus pH of the solution. Experimental data support the assumption that bR protein on a positively charged nitrocellulose membrane (PNM) can be used as highly sensitive photo- and pH detector. Here the bR layer facilitates proton translocation and acts as an ultrafast optoelectric signal transducer. It is therefore useful in applications related to bioelectronics, biosensors, bio-optics devices and current carrying junction devices.

  16. Deposition of Bacteriorhodopsin Protein in a Purple Membrane Form on Nitrocellulose Membranes for Enhanced Photoelectric Response

    Directory of Open Access Journals (Sweden)

    Chang-Hoon Nam

    2012-12-01

    Full Text Available Bacteriorhodopsin protein (bR-based systems are one of the simplest known biological energy converters. The robust chemical, thermal and electrochemical properties of bR have made it an attractive material for photoelectric devices. This study demonstrates the photoelectric response of a dry bR layer deposited on a nitrocellulose membrane with indium tin oxide (ITO electrodes. Light-induced electrical current as well as potential and impedance changes of dried bR film were recorded as the function of illumination. We have also tested bR in solution and found that the electrical properties are strongly dependent on light intensity changing locally proton concentration and thus pH of the solution. Experimental data support the assumption that bR protein on a positively charged nitrocellulose membrane (PNM can be used as highly sensitive photo- and pH detector. Here the bR layer facilitates proton translocation and acts as an ultrafast optoelectric signal transducer. It is therefore useful in applications related to bioelectronics, biosensors, bio-optics devices and current carrying junction devices.

  17. Kinetics of picosecond laser pulse induced charge separation and proton transfer in bacteriorhodopsin.

    Science.gov (United States)

    Yao, Baoli; Xu, Dalun; Hou, Xun; Hu, Kunsheng; Wang, Aojin

    2003-01-01

    Bacteriorhodopsin (BR) films oriented by an electrophoretic method are deposited on a transparent conductive ITO glass. A counterelectrode of copper and gelose gel is used to compose a sandwich-type photodetector with the structure of ITO/BR film/gelose gel/Cu. A single 30-ps laser pulse and a mode-locked pulse train are respectively used to excite the BR photodetector. The ultrafast falling edge and the bipolar response signal are measured by the digital oscilloscope under seven different time ranges. Marquardt nonlinear least squares fitting is used to fit all the experimental data and a good fitting equation is found to describe the kinetic process of the photoelectric signal. Data fitting resolves six exponential components that can be assigned to a seven-step BR photocycle model: BR-->K-->KL-->L-->M-->N-->O-->BR. Comparing tests of the BR photodetector with a 100-ps Si PIN photodiode demonstrates that this type of BR photodetector has at least 100-ps response time and can also serve as a fast photoelectric switch. PMID:12542379

  18. B-M-type anisotropy in bacteriorhodopsin films for nonlinear spatial light modulation

    Science.gov (United States)

    Korchemskaya, Elena Y.; Stepanchikov, Dmitriy A.; Dyukova, Tatyana V.; Shakhbazian, Valery Y.

    2003-02-01

    Bacteriorhodopsin (BR), a photoreceptor protein possesses a photochemical cycle of several distinct intermediates; all of them are photoactive. The BR molecules both in the initial form of the photocycle, BR570 (absorption maximum around 570 nm) and longest-lived (in films) intermediate M412 (absorption maximum at 412 nm) possess anisotropic absorption. Under the action of linearly polarized light, the reversible anisotropic photoselection of BR molecules takes place. So far only the method of photoinduced anisotropy based on anisotropic properties of BR570 was applied to realtime optical processing. In the present work, the potentialities for the use of photoinduced anisotropy in the BR-films based on both BR570 and M412 for the spatial light modulation are demonstrated. The overall blocking of highintensity features from an image is shown. Mixed B-M-type anisotropy in the chemically modified BR films, as applied to the edge enhancement, can provide a contrast ratio as high as 250:1. Low saturation intensity of the BR-films allows for the blocking of any intensity feature from an image that is carried out by choosing an appropriate intensity level of a controlling He-Ne laser beam without analyzer rotation. The photoanisotropic incoherent-to-coherent optical conversion with concurrent spatial-intensity modulation is also performed on the BR-films.

  19. Polarization multiplexed write-once-read-many optical data storage in bacteriorhodopsin films

    Science.gov (United States)

    Yao, Baoli; Lei, Ming; Ren, Liyong; Menke, Neimule; Wang, Yingli; Fischer, Thorsten; Hampp, Norbert

    2005-11-01

    In polymeric films of bacteriorhodopsin (BR) a photoconversion product, which was named the F620 state, was observed on excitation of the film with 532 nm nanosecond laser pulses. This photoproduct shows a strong nonlinear absorption. Such BR films can be used for write-once-read-many (WORM) optical data storage. We demonstrate that a photoproduct similar or even identical to that obtained with nanosecond pulses is generated on excitation with 532 nm femtosecond pulses. This photoproduct also shows strong anisotropic absorption, which facilitates polarization storage of data. The product is thermally stable and is irretrievable to the initial B state either by photochemical reaction or through a thermal pathway. The experimental results indicate that the product is formed by a two-photon absorption process. Optical WORM storage is demonstrated by use of two polarization states, but more polarization states may be used. The combination of polarization data multiplexing and extremely short recording time in the femtosecond range enables very high data volumes to be stored within a very short time.

  20. All-optical switching and all-optical logic gates based on bacteriorhodopsin

    Science.gov (United States)

    Huang, Yuhua; Wu, Shin-Tson; Zhao, Youyuan

    2004-06-01

    We demonstrate an all-optical switching using a bacteriorhodopsin (bR) film. The transmission of the bR film is investigated using the pump-probe method. A diode-pumped second harmonic YAG laser (λ = 532nm which is around the maximum initial B state absorption) was used as a pumping beam and a cw He-Ne laser (λ = 632 nm which is around the peaks of K and O states) was used as a probe. Due to the nonlinear intensity induced excited state absorption of the K, L, M, N, and O states in the bR photocycle, the switching characteristics are sensitive to the intensity of the probe and pump beams. Based on this property, we design an all-optical operating device functioning as 11 kinds of variable binary all-optical logic gates. The incident 532nm beam acts as an input to the logic gate and the transmission of the 632nm bears the output of the gate.

  1. Förster Resonance Energy Transfer between Core/Shell Quantum Dots and Bacteriorhodopsin

    Directory of Open Access Journals (Sweden)

    Mark H. Griep

    2012-01-01

    Full Text Available An energy transfer relationship between core-shell CdSe/ZnS quantum dots (QDs and the optical protein bacteriorhodopsin (bR is shown, demonstrating a distance-dependent energy transfer with 88.2% and 51.1% of the QD energy being transferred to the bR monomer at separation distances of 3.5 nm and 8.5 nm, respectively. Fluorescence lifetime measurements isolate nonradiative energy transfer, other than optical absorptive mechanisms, with the effective QD excited state lifetime reducing from 18.0 ns to 13.3 ns with bR integration, demonstrating the Förster resonance energy transfer contributes to 26.1% of the transferred QD energy at the 3.5 nm separation distance. The established direct energy transfer mechanism holds the potential to enhance the bR spectral range and sensitivity of energies that the protein can utilize, increasing its subsequent photocurrent generation, a significant potential expansion of the applicability of bR in solar cell, biosensing, biocomputing, optoelectronic, and imaging technologies.

  2. Enhanced Photocurrent Generation from Bacteriorhodopsin Photocells Using Grating-Structured Transparent Conductive Oxide Electrodes.

    Science.gov (United States)

    Kaji, Takahiro; Kasai, Katsuyuki; Haruyama, Yoshihiro; Yamada, Toshiki; Inoue, Shin-Ichiro; Tominari, Yukihiro; Ueda, Rieko; Terui, Toshifumi; Tanaka, Shukichi; Otomo, Akira

    2016-04-01

    We fabricated a grating-structured electrode made of indium-doped zinc oxide (IZO) with a high refractive index (approximately 2) for a bacteriorhodopsin (bR) photocell. We investigated the photocurrent characteristics of the bR photocell and demonstrated that the photocurrent values from the bR/IZO electrode with the grating structure with a grating period of 340 nm were more than 3.5-4 times larger than those without the grating structure. The photocurrent enhancement was attributed to the resonance effect due to light coupling to the grating structure as well as the scattering effect based on the experimental results and analysis using the photonic band structure determined using finite-difference time-domain (FDTD) simulations. The refractive index of the bR film in electrolyte solution (1.40) used in the FDTD simulations was estimated by analyzing the extinction peak wavelength of 20-nm gold colloids in the bR film. Our results indicate that the grating- or photonic-crystal-structured transparent conductive oxide (TCO) electrodes can increase the light use efficiency of various bR devices such as artificial photosynthetic devices, solar cells, and light-sensing devices. PMID:27451605

  3. Correlative Light-Electron Microscopy Reveals the Tubular-Saccular Ultrastructure of Carriers Operating between Golgi Apparatus and Plasma Membrane

    OpenAIRE

    Polishchuk, Roman S.; Polishchuk, Elena V.; Marra, Pierfrancesco; Alberti, Saverio; Buccione, Roberto; Luini, Alberto; Mironov, Alexander A.

    2000-01-01

    Transport intermediates (TIs) have a central role in intracellular traffic, and much effort has been directed towards defining their molecular organization. Unfortunately, major uncertainties remain regarding their true structure in living cells. To address this question, we have developed an approach based on the combination of the green fluorescent protein technology and correlative light-electron microscopy, by which it is possible to monitor an individual carrier in vivo and then take a p...

  4. Correlative and quantitative 1H NMR-based metabolomics reveals specific metabolic pathway disturbances in diabetic rats

    OpenAIRE

    Zhang, Shucha; Gowda, G. A. Nagana; Asiago, Vincent; Shanaiah, Narasimhamurthy; Barbas, Coral; Raftery, Daniel

    2008-01-01

    Type 1 diabetes was induced in Sprague–Dawley rats using streptozotocin. Rat urine samples (8 diabetic and 10 control) were analyzed by 1H nuclear magnetic resonance (NMR) spectroscopy. The derived metabolites using univariate and multivariate statistical analysis were subjected to correlative analysis. Plasma metabolites were measured by a series of bioassays. A total of 17 urinary metabolites were identified in the 1H NMR spectra and the loadings plots after principal components analysis. D...

  5. "Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution.

    Directory of Open Access Journals (Sweden)

    Jordi Silvestre-Ryan

    2011-03-01

    Full Text Available The mechanism of intra-protein communication and allosteric coupling is key to understanding the structure-property relationship of protein function. For subtilisin Carlsberg, the Ca²+-binding loop is distal to substrate-binding and active sites, yet the serine protease function depends on Ca²+ binding. The atomic molecular dynamics (MD simulations of apo and Ca²+-bound subtilisin show similar structures and there is no direct evidence that subtilisin has alternative conformations. To model the intra-protein communication due to Ca²+ binding, we transform the sequential segments of an atomic MD trajectory into separate elastic network models to represent anharmonicity and nonlinearity effectively as the temporal and spatial variation of the mechanical coupling network. In analogy to the spectrogram of sound waves, this transformation is termed the "fluctuogram" of protein dynamics. We illustrate that the Ca²+-bound and apo states of subtilisin have different fluctuograms and that intra-protein communication proceeds intermittently both in space and in time. We found that residues with large mechanical coupling variation due to Ca²+ binding correlate with the reported mutation sites selected by directed evolution for improving the stability of subtilisin and its activity in a non-aqueous environment. Furthermore, we utilize the fluctuograms calculated from MD to capture the highly correlated residues in a multiple sequence alignment. We show that in addition to the magnitude, the variance of coupling strength is also an indicative property for the sequence correlation observed in a statistical coupling analysis. The results of this work illustrate that the mechanical coupling networks calculated from atomic details can be used to correlate with functionally important mutation sites and co-evolution.

  6. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates.

    Science.gov (United States)

    Weng, Mao-Lun; Blazier, John C; Govindu, Madhumita; Jansen, Robert K

    2014-03-01

    Geraniaceae plastid genomes are highly rearranged, and each of the four genera already sequenced in the family has a distinct genome organization. This study reports plastid genome sequences of six additional species, Francoa sonchifolia, Melianthus villosus, and Viviania marifolia from Geraniales, and Pelargonium alternans, California macrophylla, and Hypseocharis bilobata from Geraniaceae. These genome sequences, combined with previously published species, provide sufficient taxon sampling to reconstruct the ancestral plastid genome organization of Geraniaceae and the rearrangements unique to each genus. The ancestral plastid genome of Geraniaceae has a 4 kb inversion and a reduced, Pelargonium-like small single copy region. Our ancestral genome reconstruction suggests that a few minor rearrangements occurred in the stem branch of Geraniaceae followed by independent rearrangements in each genus. The genomic comparison demonstrates that a series of inverted repeat boundary shifts and inversions played a major role in shaping genome organization in the family. The distribution of repeats is strongly associated with breakpoints in the rearranged genomes, and the proportion and the number of large repeats (>20 bp and >60 bp) are significantly correlated with the degree of genome rearrangements. Increases in the degree of plastid genome rearrangements are correlated with the acceleration in nonsynonymous substitution rates (dN) but not with synonymous substitution rates (dS). Possible mechanisms that might contribute to this correlation, including DNA repair system and selection, are discussed. PMID:24336877

  7. Two-Photon Correlation Spectroscopy in Single Dendritic Spines Reveals Fast Actin Filament Reorganization during Activity-Dependent Growth.

    Directory of Open Access Journals (Sweden)

    Jian-Hua Chen

    Full Text Available Two-photon fluorescence correlation spectroscopy (2P-FCS within single dendritic spines of living hippocampal pyramidal neurons was used to resolve various subpopulations of mobile F-actin during activity-dependent structural changes such as potentiation induced spine head growth. Two major classes of mobile F-actin were discovered: very dynamic and about a hundred times less dynamic F-actin. Spine head enlargement upon application of Tetraethylammonium (TEA, a protocol previously used for the chemical induction of long-term potentiation (cLTP strictly correlated to changes in the dynamics and filament numbers in the different actin filament fractions. Our observations suggest that spine enlargement is governed by a mechanism in which longer filaments are first cut into smaller filaments that cooperate with the second, increasingly dynamic shorter actin filament population to quickly reorganize and expand the actin cytoskeleton within the spine head. This process would allow a fast and efficient spine head enlargement using a major fraction of the actin filament population that was already present before spine head growth.

  8. Nonlinear optical method for the investigation of spectral properties of biomolecular complexes: second harmonic generation in ordered structures of bacteriorhodopsin

    Science.gov (United States)

    Aktsipetrov, Oleg A.; Fedyanin, Andrew A.; Murzina, Tatyana V.; Borisevich, G. P.; Kononenko, A. A.

    1995-02-01

    For the first time the method of the second harmonic generation was used to study the photo- and electrically induced nonlinear optical transformations in thin oriented films of purple membranes (PM). Variations of the film nonlinear susceptibility were investigated as the bacteriorhodopsin (bR) molecule underwent the cycle of photoinduced transformations for both dry electrically oriented films and bR molecules embedded into poly(vinyl alcohol) matrix. The electrically induced changes of the nonlinear optical properties were studied for the electrostatic field strength up to the values 4 (DOT) 104 V/cm. Nonlinear susceptibilities of oriented and nonoriented dried PM films are compared.

  9. Acidic Properties and Structure-Activity Correlations of Solid Acid Catalysts Revealed by Solid-State NMR Spectroscopy.

    Science.gov (United States)

    Zheng, Anmin; Li, Shenhui; Liu, Shang-Bin; Deng, Feng

    2016-04-19

    Solid acid materials with tunable structural and acidic properties are promising heterogeneous catalysts for manipulating and/or emulating the activity and selectivity of industrially important catalytic reactions. On the other hand, the performances of acid-catalyzed reactions are mostly dictated by the acidic features, namely, type (Brønsted vs Lewis acidity), amount, strength, and local environment of acid sites. The latter is relevant to their location (intra- vs extracrystalline), and possible confinement and Brønsted-Lewis acid synergy effects that may strongly affect the host-guest interactions, reaction mechanism, and shape selectivity of the catalytic system. This account aims to highlight some important applications of state-of-the-art solid-state NMR (SSNMR) techniques for exploring the structural and acidic properties of solid acid catalysts as well as their catalytic performances and relevant reaction pathway invoked. In addition, density functional theory (DFT) calculations may be exploited in conjunction with experimental SSNMR studies to verify the structure-activity correlations of the catalytic system at a microscopic scale. We describe in this Account the developments and applications of advanced ex situ and/or in situ SSNMR techniques, such as two-dimensional (2D) double-quantum magic-angle spinning (DQ MAS) homonuclear correlation spectroscopy for structural investigation of solid acids as well as study of their acidic properties. Moreover, the energies and electronic structures of the catalysts and detailed catalytic reaction processes, including the identification of reaction species, elucidation of reaction mechanism, and verification of structure-activity correlations, made available by DFT theoretical calculations were also discussed. Relevant discussions will focus primarily on results obtained from our laboratories in the past decade, including (i) quantitative and qualitative acidity characterization utilizing assorted probe molecules

  10. Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission.

    Science.gov (United States)

    Hapuarachchi, Hapuarachchige Chanditha; Koo, Carmen; Kek, Relus; Xu, Helen; Lai, Yee Ling; Liu, Lilac; Kok, Suet Yheng; Shi, Yuan; Chuen, Raphael Lee Tze; Lee, Kim-Sung; Maurer-Stroh, Sebastian; Ng, Lee Ching

    2016-01-01

    Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013-2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design.

  11. Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission.

    Science.gov (United States)

    Hapuarachchi, Hapuarachchige Chanditha; Koo, Carmen; Kek, Relus; Xu, Helen; Lai, Yee Ling; Liu, Lilac; Kok, Suet Yheng; Shi, Yuan; Chuen, Raphael Lee Tze; Lee, Kim-Sung; Maurer-Stroh, Sebastian; Ng, Lee Ching

    2016-01-01

    Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013-2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design. PMID:26940650

  12. Phylogenetic analysis reveals positive correlations between adaptations to diverse hosts in a group of pathogen-like herbivores.

    Science.gov (United States)

    Peterson, Daniel A; Hardy, Nate B; Morse, Geoffrey E; Stocks, Ian C; Okusu, Akiko; Normark, Benjamin B

    2015-10-01

    A jack of all trades can be master of none-this intuitive idea underlies most theoretical models of host-use evolution in plant-feeding insects, yet empirical support for trade-offs in performance on distinct host plants is weak. Trade-offs may influence the long-term evolution of host use while being difficult to detect in extant populations, but host-use evolution may also be driven by adaptations for generalism. Here we used host-use data from insect collection records to parameterize a phylogenetic model of host-use evolution in armored scale insects, a large family of plant-feeding insects with a simple, pathogen-like life history. We found that a model incorporating positive correlations between evolutionary changes in host performance best fit the observed patterns of diaspidid presence and absence on nearly all focal host taxa, suggesting that adaptations to particular hosts also enhance performance on other hosts. In contrast to the widely invoked trade-off model, we advocate a "toolbox" model of host-use evolution in which armored scale insects accumulate a set of independent genetic tools, each of which is under selection for a single function but may be useful on multiple hosts. PMID:26374400

  13. High resolution electron diffraction analysis of structural changes associated with the photocycle of bacteriorhodopsin

    Energy Technology Data Exchange (ETDEWEB)

    Han, B. -G. [Lawrence Berkeley Lab., CA (United States). Life Sciences Div.; Univ. of California, Berkeley, CA (United States). Dept. of Biophysics

    1994-04-01

    Changes in protein structure that occur during the formation of the M photointermediate of bacteriorhodopsin can be directly visualized by electron diffraction techniques. Samples containing a high percentage of the M intermediate were trapped by rapidly cooling the crystals with liquid nitrogen following illumination with filtered green light at 240K and 260K respectively. Difference Fourier projection maps for M minus bR at two temperatures and for M{sub 260K} minus M{sub 240K} are presented. While it is likely that a unique M-substate is trapped when illuminated at 260K produces a mixture of the M{sub 240K} substate and a second M-substate which may have a protein structure similar to the N-intermediate. The diffraction data clearly show that statistically significant structural changes occur upon formation of the M{sub 240K} specimen and then further upon formation of the second substate which is present in the mixture that is produced at 260K. A preliminary 3-D difference map, based on data collected with samples tilted up to 30{degree}, has been constructed at a resolution of 3.5{angstrom} parallel to the membrane plane and a resolution of 8.5{angstrom} perpendicular to the membrane. The data have been analyzed by a number of different criteria to ensure that the differences seen reflect real conformation changes at a level which is significantly above the noise in the map. Furthermore, a comparison of the positions of specific backbone and side-chain groups relative to significant difference peaks suggests that it will be necessary to further refine the atomic resolution model before it will be possible to interpret the changes in chemical structure that occur in the protein at this stage of the photocycle.

  14. Optical Fourier and Holographic Techniques for Medical Image Processing with Bacteriorhodopsin

    Science.gov (United States)

    Yelleswarapu, Chandra

    2008-03-01

    The biological photochrome bacteriorhodopsin (bR) shows many intrinsic optical and physical properties. The active chromophore in bR is a retinal group which absorbs light and goes through a photocycle. The unique feature of the system is its flexibility -- the photocycle can be optically controllable since the process of photoisomerization can go in both directions depending on wavelength, intensity and polarization of the incident light, opening a variety of possibilities for manipulating amplitude, phase, polarization and index of refraction of the incident light. Over the years we studied the basic nonlinear optics and successfully exploited the unique properties for several optical spatial filtering techniques with applications in medical image processing. For nonlinear Fourier filtering, the photo-controlled light modulating characteristics of bR films are exploited. At the Fourier plane, the spatial frequency information carried by a blue probe beam at 442 nm is selectively manipulated in the bR film by changing the position and intensity of a yellow control beam at 568 nm. In transient Fourier holography, photoisomerizative gratings are recorded and reconstructed in bR films. Desired spatial frequencies are obtained by matching the reference beam intensity to that of the particular frequency band in object beam. A novel feature of the technique is the ability to transient display of selected spatial frequencies in the reconstructing process which enables radiologists to study the features of interest in time scale. The results offer useful information to radiologists for early detection of breast cancer. Some of the highlights will be presented.

  15. All-Optical Switching in Bacteriorhodopsin Based on Excited-State Absorption

    Science.gov (United States)

    Roy, Sukhdev

    2008-03-01

    Switching light with light is of tremendous importance for both fundamental and applied science. The advent of nano-bio-photonics has led to the design, synthesis and characterization of novel biomolecules that exhibit an efficient nonlinear optical response, which can be utilized for designing all-optical biomolecular switches. Bacteriorhodopsin (bR) protein found in the purple membrane of Halobacterium halobium has been the focus of intense research due to its unique properties that can also be tailored by physical, chemical and genetic engineering techniques to suit desired applications. The talk would focus on our recent results on all-optical switching in bR and its mutants, based on excited-state absorption, using the pump-probe technique. We would discuss the all-optical control of various features of the switching characteristics such as switching contrast, switching time, switching pump intensity, switched probe profile and phase, and relative phase-shift. Optimized conditions for all-optical switching that include optimized values of the small-signal absorption coefficient (for cw case), the pump pulse width and concentration for maximum switching contrast (for pulsed case), would be presented. We would discuss the desired optimal spectral and kinetic properties for device applications. We would also discuss the application of all-optical switching to design low power all-optical computing devices, such as, spatial light modulators, logic gates and multiplexers and compare their performance with other natural photoreceptors such as pharaonis phoborhodopsin, proteorhodopsin, photoactive yellow protein and the blue light plant photoreceptor phototropin.

  16. Simultaneous fNIRS and thermal infrared imaging during cognitive task reveal autonomic correlates of prefrontal cortex activity

    Science.gov (United States)

    Pinti, Paola; Cardone, Daniela; Merla, Arcangelo

    2015-12-01

    Functional Near Infrared-Spectroscopy (fNIRS) represents a powerful tool to non-invasively study task-evoked brain activity. fNIRS assessment of cortical activity may suffer for contamination by physiological noises of different origin (e.g. heart beat, respiration, blood pressure, skin blood flow), both task-evoked and spontaneous. Spontaneous changes occur at different time scales and, even if they are not directly elicited by tasks, their amplitude may result task-modulated. In this study, concentration changes of hemoglobin were recorded over the prefrontal cortex while simultaneously recording the facial temperature variations of the participants through functional infrared thermal (fIR) imaging. fIR imaging provides touch-less estimation of the thermal expression of peripheral autonomic. Wavelet analysis revealed task-modulation of the very low frequency (VLF) components of both fNIRS and fIR signals and strong coherence between them. Our results indicate that subjective cognitive and autonomic activities are intimately linked and that the VLF component of the fNIRS signal is affected by the autonomic activity elicited by the cognitive task. Moreover, we showed that task-modulated changes in vascular tone occur both at a superficial and at larger depth in the brain. Combined use of fNIRS and fIR imaging can effectively quantify the impact of VLF autonomic activity on the fNIRS signals.

  17. Application of nonlinear absorption properties and light adaptation process in the polymer films based on bacteriorhodopsin for the low-power optical signal processing

    Science.gov (United States)

    Korchemskaya, Elena Y.; Soskin, Marat S.

    1994-01-01

    Experimental and theoretical investigations were made of the characteristics of nonlinear transmission and light adaptation processes of polymer films based on bacteriorhodopsin (BR). It was found that media containing BR can be used to enhance the contrast of low-power signals for realization of the connection structure of the neural network.

  18. Tissue microarray analysis reveals a tight correlation between protein expression pattern and progression of esophageal squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    He Zu-gen

    2006-12-01

    Full Text Available Abstract Background The development of esophageal squamous cell carcinoma (ESCC progresses a multistage process, collectively known as precursor lesions, also called dysplasia (DYS and carcinoma in situ (CIS, subsequent invasive lesions and final metastasis. In this study, we are interested in investigating the expression of a variety of functional classes of proteins in ESCC and its precursor lesions and characterizing the correlation of these proteins with ESCC malignant progression. Methods Fas, FADD, caspase 8, CDC25B, fascin, CK14, CK4, annexin I, laminin-5γ2 and SPARC were analyzed using immunohistochemistry on tissue microarray containing 205 ESCC and 173 adjacent precursor lesions as well as corresponding normal mucosa. To confirm the immunohistochemical results, three proteins, fascin, CK14 and laminin-5γ2, which were overexpressed in ESCC on tissue microarray, were detected in 12 ESCC cell lines by Western blot assay. Results In ESCC and its precursor lesions, FADD, CDC25B, fascin, CK14, laminin-5γ2 and SPARC were overexpressed, while Fas, caspase 8, CK4 and annexin I were underexpressed. The abnormalities of these proteins could be classified into different groups in relation to the stages of ESCC development. They were "early" corresponding to mild and moderate DYS with overexpression of fascin, FADD and CDC25B and underexpression of Fas, caspase 8, CK4 and annexin I, "intermediate" to severe DYS and CIS with overexpression of FADD and CK14, and "late" to invasive lesions (ESCC and to advanced pTNM stage ESCC lesions with overexpression of CK14, laminin-5γ2 and SPARC. Conclusion Analyzing the protein expression patterns of Fas, FADD, caspase 8, CDC25B, fascin, CK14, CK4, annexin I, laminin-5γ2 and SPARC would be valuable to develop rational strategies for early detection of lesions at risk in advance as well as for prevention and treatment of ESCC.

  19. Studying the Mechanism of Phototransformation of Light Signal by Various Mammal and Bacterial Photoreceptor Pigments  Rhodopsin, Iodopsin and Bacteriorhodopsin

    Directory of Open Access Journals (Sweden)

    Ignat Ignatov

    2015-06-01

    Full Text Available This review article outlines the structure and function of mammal and bacterial photoreceptor pigments (rhodopsin, iodopsin, bacteriorhodopsin and their aspects of bio-nanotechnological usage. On an example of bacteriorhodopsin is described the method of its isolation from purple membranes of photo-organotrophic halobacterium Halobacterium halobium ET 1001 by cellular autolysis by distilled water, processing of bacterial biomass by ultrasound at 22 KHz, alcohol extraction of low and high-weight molecular impurities, cellular RNA, carotenoids and lipids, the solubilization with 0,5 % (w/v SDS-Na and subsequent fractionation by methanol and gel filtration chromatography on Sephadex G-200 Column balanced with 0,09 M Tris-buffer (pH = 8,35 with 0,1 % (w/v SDS-Na and 2,5 mM EDTA. Within the framework of the research the mechanism of color perception by the visual retina analyzer having the ability to analyze certain ranges of the optical spectrum as colors, was studied along with an analysis of the additive mixing of two or more colors. It was shown that at the mixing of electromagnetic waves with different wavelengths, the visual analyzer perceives them as the separate or average wave length corresponding to the mixing color.

  20. A residue substitution near the beta-ionone ring of the retinal affects the M substates of bacteriorhodopsin

    Science.gov (United States)

    Varo, G.; Zimanyi, L.; Chang, M.; Ni, B.; Needleman, R.; Lanyi, J. K.

    1992-01-01

    The switch in the bacteriorhodopsin photocycle, which reorients access of the retinal Schiff base from the extracellular to the cytoplasmic side, was suggested to be an M1----M2 reaction (Varo and Lanyi. 1991. Biochemistry. 30:5008-5015, 5016-5022). Thus, in this light-driven proton pump it is the interconversion of proposed M substates that gives direction to the transport. We find that in monomeric, although not purple membrane-lattice immobilized, D115N bacteriorhodopsin, the absorption maximum of M changes during the photocycle: in the time domain between its rise and decay it shifts 15 nm to the blue relative to the spectrum at earlier times. This large shift strongly supports the existence of two M substates. Since D115 is located near the beta-ionone ring of the retinal, the result raises questions about the possible involvement of the retinal chain or protein residues as far away as 10 A from the Schiff base in the mechanism of the switching reaction.

  1. Time-resolved step-scan Fourier transform infrared spectroscopy reveals differences between early and late M intermediates of bacteriorhodopsin.

    Science.gov (United States)

    Rödig, C; Chizhov, I; Weidlich, O; Siebert, F

    1999-05-01

    In this report, from time-resolved step-scan Fourier transform infrared investigations from 15 ns to 160 ms, we provide evidence for the subsequent rise of three different M states that differ in their structures. The first state rises with approximately 3 microseconds to only a small percentage. Its structure as judged from amide I/II bands differs in small but well-defined aspects from the L state. The next M state, which appears in approximately 40 microseconds, has almost all of the characteristics of the "late" M state, i.e., it differs considerably from the first one. Here, the L left arrow over right arrow M equilibrium is shifted toward M, although some percentage of L still persists. In the last M state (rise time approximately 130 microseconds), the equilibrium is shifted toward full deprotonation of the Schiff base, and only small additional structural changes take place. In addition to these results obtained for unbuffered conditions or at pH 7, experiments performed at lower and higher pH are presented. These results are discussed in terms of the molecular changes postulated to occur in the M intermediate to allow the shift of the L/M equilibrium toward M and possibly to regulate the change of the accessibility of the Schiff base necessary for effective proton pumping. PMID:10233083

  2. Synthesis of 13C and 2H labelled retinals: spectroscopic investigations on isotopically labelled rhodopsin and bacteriorhodopsin

    International Nuclear Information System (INIS)

    In order to develop probes of the structure of chromophores, the author introduces isotopic modifications at specific chromophoric positions as structural probes. To obtain bacteriorhodopsin, rhodopsin and their photoproducts labelled in the chromophore at selected positions, bacterioopsin and opsin were reacted with the appropriate labelled a11-trans and 11-cis retinals. The author describes the synthesis of a11-trans retinal selectively 13C labelled at different positions. The characterization of these labelled a11-trans retinals by mass spectrometry, 300 MHz 1H NMR and 75 MHz 13C NMR spectroscopy is given. The photochemical preparation and isolation of the pure 9-, 11- and 13-cis forms is described in the experimental part. (Auth.)

  3. Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal.

    Science.gov (United States)

    Schobert, Brigitte; Cupp-Vickery, Jill; Hornak, Viktor; Smith, Steven; Lanyi, Janos

    2002-08-23

    The K state, an early intermediate of the bacteriorhodopsin photocycle, contains the excess free energy used for light-driven proton transport. The energy gain must reside in or near the photoisomerized retinal, but in what form has long been an open question. We produced the K intermediate in bacteriorhodopsin crystals in a photostationary state at 100K, with 40% yield, and determined its X-ray diffraction structure to 1.43 A resolution. In independent refinements of data from four crystals, the changes are confined mainly to the photoisomerized retinal. The retinal is 13-cis,15-anti, as known from vibrational spectroscopy. The C13=C14 bond is rotated nearly fully to cis from the initial trans configuration, but the C14-C15 and C15=NZ bonds are partially counter-rotated. This strained geometry keeps the direction of the Schiff base N-H bond vector roughly in the extracellular direction, but the angle of its hydrogen bond with water 402, that connects it to the anionic Asp85 and Asp212, is not optimal. Weakening of this hydrogen bond may account for many of the reported features of the infrared spectrum of K, and for its photoelectric signal, as well as the deprotonation of the Schiff base later in the cycle. Importantly, although 13-cis, the retinal does not assume the expected bent shape of this configuration. Comparison of the calculated energy of the increased angle of C12-C13=C14, that allows this distortion, with the earlier reported calorimetric measurement of the enthalpy gain of the K state indicates that a significant part of the excess energy is conserved in the bond strain at C13.

  4. Point correlation dimension can reveal functional changes caused by gap junction blockers in the 4-aminopyridine in vivo rat epilepsy model

    Energy Technology Data Exchange (ETDEWEB)

    Jardanhazy, Anett [Department of Neurology, University of Szeged, Semmelweis u. 6, Szeged H-6725 (Hungary); Molnar, Mark [Department of Psychophysiology, Institute for Psychology of the Hungarian Academy of Sciences, P.O. Box 398, Budapest H-1394 (Hungary)], E-mail: molnar@cogpsyphy.hu; Jardanhazy, Tamas [Department of Neurology, University of Szeged, Semmelweis u. 6, Szeged H-6725 (Hungary)], E-mail: jt@nepsy.szote.u-szeged.hu

    2009-04-15

    The contribution of gap junction (GJ) blockers to seizure initiation was reexamined by means of an analysis on nonlinear dynamics with point correlation dimension (PD2i) at as well as around the primary focus, and mirror focus in an already active 4-aminopyridine-induced in vivo epilepsy model. From the data base of the ECoGs of anesthetized adult rats treated with quinine, a selective blocker of Cx36, and in combination with an additional broad-spectrum GJ blocker, carbenoxolone, 14 cases of each condition were reexamined with a stationarity insensitive nonlinear PD2i method. The blockade of the Cx36 channels decreased the usual drop of the point correlation dimension at the beginning of the seizures, and this was enhanced by the additional use of the global blocker carbenoxolone. The so-called characteristic DC shift just prior to seizure onset denotes a low dimensional seizure event and the recognizable seizures display very variable, rapidly changing dynamics, as revealed by the PD2i analysis. This nonlinear PD2i analysis demonstrated that the different GJ blockers in the already active epileptic model helped seizure initiation, but exerted inhibitory effects on the seizure onset itself, acting differently on the local components of the network organization generating seizure discharges, possibly changing the coupling strengths and time delays in the GJ-s.

  5. The influence of a transmembrane pH gradient on protonation probabilities of bacteriorhodopsin: the structural basis of the back-pressure effect.

    Science.gov (United States)

    Calimet, Nicolas; Ullmann, G Matthias

    2004-06-01

    Bacteriorhodopsin pumps protons across a membrane using the energy of light. The proton pumping is inhibited when the transmembrane proton gradient that the protein generates becomes larger than four pH units. This phenomenon is known as the back-pressure effect. Here, we investigate the structural basis of this effect by predicting the influence of a transmembrane pH gradient on the titration behavior of bacteriorhodopsin. For this purpose we introduce a method that accounts for a pH gradient in protonation probability calculations. The method considers that in a transmembrane protein, which is exposed to two different aqueous phases, each titratable residue is accessible for protons from one side of the membrane depending on its hydrogen-bond pattern. This method is applied to several ground-state structures of bacteriorhodopsin, which residues already present complicated titration behaviors in the absence of a proton gradient. Our calculations show that a pH gradient across the membrane influences in a non-trivial manner the protonation probabilities of six titratable residues which are known to participate in the proton transfer: D85, D96, D115, E194, E204, and the Schiff base. The residues connected to one side of the membrane are influenced by the pH on the other side because of their long-range electrostatic interactions within the protein. In particular, D115 senses the pH at the cytoplasmic side of the membrane and transmits this information to D85 and the Schiff base. We propose that the strong electrostatic interactions found between D85, D115, and the Schiff base as well as the interplay of their respective protonation states under the influence of a transmembrane pH gradient are responsible for the back-pressure effect on bacteriorhodopsin.

  6. Multivariate imaging-genetics study of MRI gray matter volume and SNPs reveals biological pathways correlated with brain structural differences in Attention Deficit Hyperactivity Disorder

    Directory of Open Access Journals (Sweden)

    Sabin Khadka

    2016-07-01

    Full Text Available Background: Attention Deficit Hyperactivity Disorder (ADHD is a prevalent neurodevelopmental disorder affecting children, adolescents, and adults. Its etiology is not well-understood, but it is increasingly believed to result from diverse pathophysiologies that affect the structure and function of specific brain circuits. Although one of the best-studied neurobiological abnormalities in ADHD is reduced fronto-striatal-cerebellar gray matter volume, its specific genetic correlates are largely unknown. Methods: In this study, T1-weighted MR images of brain structure were collected from 198 adolescents (63 ADHD-diagnosed. A multivariate parallel independent component analysis technique (Para-ICA identified imaging-genetic relationships between regional gray matter volume and single nucleotide polymorphism data. Results: Para-ICA analyses extracted 14 components from genetic data and 9 from MR data. An iterative cross-validation using randomly-chosen sub-samples indicated acceptable stability of these ICA solutions. A series of partial correlation analyses controlling for age, sex, and ethnicity revealed two genotype-phenotype component pairs significantly differed between ADHD and non-ADHD groups, after a Bonferroni correction for multiple comparisons. The brain phenotype component not only included structures frequently found to have abnormally low volume in previous ADHD studies, but was also significantly associated with ADHD differences in symptom severity and performance on cognitive tests frequently found to be impaired in patients diagnosed with the disorder. Pathway analysis of the genotype component identified several different biological pathways linked to these structural abnormalities in ADHD. Conclusions: Some of these pathways implicate well-known dopaminergic neurotransmission and neurodevelopment hypothesized to be abnormal in ADHD. Other more recently implicated pathways included glutamatergic and GABA-eric physiological systems

  7. Correlation-Based Network Analysis of Metabolite and Enzyme Profiles Reveals a Role of Citrate Biosynthesis in Modulating N and C Metabolism in Zea mays.

    Science.gov (United States)

    Toubiana, David; Xue, Wentao; Zhang, Nengyi; Kremling, Karl; Gur, Amit; Pilosof, Shai; Gibon, Yves; Stitt, Mark; Buckler, Edward S; Fernie, Alisdair R; Fait, Aaron

    2016-01-01

    To investigate the natural variability of leaf metabolism and enzymatic activity in a maize inbred population, statistical and network analyses were employed on metabolite and enzyme profiles. The test of coefficient of variation showed that sugars and amino acids displayed opposite trends in their variance within the population, consistently with their related enzymes. The overall higher CV values for metabolites as compared to the tested enzymes are indicative for their greater phenotypic plasticity. H(2) tests revealed galactinol (1) and asparagine (0.91) as the highest scorers among metabolites and nitrate reductase (0.73), NAD-glutamate dehydrogenase (0.52), and phosphoglucomutase (0.51) among enzymes. The overall low H(2) scores for metabolites and enzymes are suggestive for a great environmental impact or gene-environment interaction. Correlation-based network generation followed by community detection analysis, partitioned the network into three main communities and one dyad, (i) reflecting the different levels of phenotypic plasticity of the two molecular classes as observed for the CV values and (ii) highlighting the concerted changes between classes of chemically related metabolites. Community 1 is composed mainly of enzymes and specialized metabolites, community 2' is enriched in N-containing compounds and phosphorylated-intermediates. The third community contains mainly organic acids and sugars. Cross-community linkages are supported by aspartate, by the photorespiration amino acids glycine and serine, by the metabolically related GABA and putrescine, and by citrate. The latter displayed the strongest node-betweenness value (185.25) of all nodes highlighting its fundamental structural role in the connectivity of the network by linking between different communities and to the also strongly connected enzyme aldolase. PMID:27462343

  8. Recent Advances in the Field of Bionanotechnology: An Insight into Optoelectric Bacteriorhodopsin, Quantum Dots, and Noble Metal Nanoclusters

    Directory of Open Access Journals (Sweden)

    Christopher Knoblauch

    2014-10-01

    Full Text Available Molecular sensors and molecular electronics are a major component of a recent research area known as bionanotechnology, which merges biology with nanotechnology. This new class of biosensors and bioelectronics has been a subject of intense research over the past decade and has found application in a wide variety of fields. The unique characteristics of these biomolecular transduction systems has been utilized in applications ranging from solar cells and single-electron transistors (SETs to fluorescent sensors capable of sensitive and selective detection of a wide variety of targets, both organic and inorganic. This review will discuss three major systems in the area of molecular sensors and electronics and their application in unique technological innovations. Firstly, the synthesis of optoelectric bacteriorhodopsin (bR and its application in the field of molecular sensors and electronics will be discussed. Next, this article will discuss recent advances in the synthesis and application of semiconductor quantum dots (QDs. Finally, this article will conclude with a review of the new and exciting field of noble metal nanoclusters and their application in the creation of a new class of fluorescent sensors.

  9. Topological change and impedance spectrum of rat olfactory receptor I7: A comparative analysis with bovine rhodopsin and bacteriorhodopsin

    Science.gov (United States)

    Alfinito, Eleonora; Pennetta, Cecilia; Reggiani, Lino

    2009-04-01

    We present a theoretical investigation on possible selection of olfactory receptors (ORs) as sensing components of nanobiosensors. Accordingly, we generate the impedance spectra of the rat OR I7 in the native and activated states and analyze their differences. In this way, we connect the protein morphological transformation, caused by the sensing action, with its change in electrical impedance. The results are compared with those obtained by studying the best known protein of the G protein coupled receptor (GPCR) family: bovine rhodopsin. Our investigations indicate that a change in morphology goes with a change in impedance spectrum mostly associated with a decrease in the static impedance up to about 60% of the initial value, in qualitative agreement with existing experiments on rat OR I7. The predictiveness of the model is tested successfully for the case of recent experiments on bacteriorhodopsin. The present results point to a promising development of a new class of nanobiosensors based on the electrical properties of GPCR and other sensing proteins.

  10. Application of polymer films based on bacteriorhodopsin and its analogs for low-light-level imaging systems

    Science.gov (United States)

    Korchemskaya, Elena Y.; Soskin, Marat S.; Stepanchikov, Dmitriy A.; Djukova, T. V.; Druzhko, Anna B.; Vsevolodov, Nicolai N.

    1995-03-01

    In recent years polymer films based on bacteriorhodopsin (BR) have attracted a lot of attention in the area of optical imaging systems. The high photosensitivity of these films allows the processing of low-power optical signals (several mW/cm2 CW gas laser irradiation). Spatial resolution does not fall below 5000 lines/mm, photoresponse time is 50 microsecond(s) and images can be recorded and erased over million cycles. Polymer film with BR combine a dynamic recording with optical image processing. The characteristics of anisotropically-saturating nonlinearity of polymer films with BR allow a suppression of the background with greater intensity than usable signal intensity of be performed. Low saturation intensity of the polymer films with BR allows the operation of the polarization of low-intensity signals to be realized. Nonlinear photoresponse of the high photosensitivity BR genetic variant Asp96-Glu is studied in this work too. We hope that the polymer films based on BR and its analogs will find potential use precisely in the medical low- light-level imaging systems.

  11. All-optical switching in bacteriorhodopsin based on M state dynamics and its application to photonic logic gates

    Science.gov (United States)

    Singh, Chandra Pal; Roy, Sukhdev

    2003-03-01

    All-optical switching has been theoretically analyzed in bacteriorhodopsin (bR) based on nonlinear intensity induced excited state absorption of the M state. The transmission of a cw probe laser beam at 410 nm corresponding to the peak absorption of M state through a bR film is switched by a pulsed pump laser beam at 570 nm that corresponds to the maximum initial B state absorption. The switching characteristics have been numerically simulated using the rate equation approach considering all the six intermediate states (B, K, L, M, N and O) in the bR photocycle. The switching characteristics are shown to be sensitive to various parameters such as the pump pulse width, pump intensity, life time of the M state, thickness of the film and absorption cross-section of the B-state at probe wavelength ( σBp). It has been shown that the probe laser beam can be completely switched off (100% modulation) by the pump laser beam at relatively low pump powers, for σBp=0. The switching characteristics have also been used to theoretically design all-optical NOT, OR, AND and the universal NOR and NAND logic gates with two pulsed pump laser beams using the six state model.

  12. Dynamic behavior of solar wind as revealed by a correlation study of magnetic fields observed at the Venus and Earth orbits

    Science.gov (United States)

    Marubashi, K.

    1995-01-01

    Correlations between interplanetary magnetic fields (IMFs) at 0.72 AU and 1.0 AU have been examined using data sets obtained from the Pioneer Venus orbiter and Earth-orbiting spacecraft. While the two-sector structures are evident in long-term variations at these two heliocentric distances, the corresponding auto-correlation coefficients are consistently smaller at 1.0 AU than at 0.72 AU. This suggests that the IMF structures become less persistent at 1.0 AU due to the effects of changing solar wind dynamics between the Venus and Earth orbits. Short-term variations exhibit generally poor correlations between IMFs near Venus and those near Earth, though good correlations are sometimes obtained for well-defined structures when the Sun, Venus, and Earth are closely aligned. The rather poor correlations in the background streams indicate that the IMFs are still changing between the Venus and Earth orbits under the strong influence of solar wind dynamics.

  13. Revealing discriminating power of the elements in edible sea salts: Line-intensity correlation analysis from laser-induced plasma emission spectra

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Yonghoon, E-mail: yhlee@mokpo.ac.kr [Department of Chemistry, Mokpo National University, Jeonnam 534-729 (Korea, Republic of); Ham, Kyung-Sik [Department of Food Engineering, Mokpo National University, Jeonnam 534-729 (Korea, Republic of); Han, Song-Hee [Division of Maritime Transportation System, Mokpo National Maritime University, Jeonnam 530-729 (Korea, Republic of); Yoo, Jonghyun, E-mail: jyoo@appliedspectra.com [Applied Spectra, Inc., 46665 Fremont Boulevard, Fremont, CA 94538 (United States); Jeong, Sungho [School of Mechatronics, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of)

    2014-11-01

    We have investigated the discriminating power of the elements in edible sea salts using Laser-Induced Breakdown Spectroscopy (LIBS). For the ten different sea salts from South Korea, China, Japan, France, Mexico and New Zealand, LIBS spectra were recorded in the spectral range between 190 and 1040 nm, identifying the presence of Na, Cl, K, Ca, Mg, Li, Sr, Al, Si, Ti, Fe, C, O, N, and H. Intensity correlation analysis of the observed emission lines provided a valuable insight into the discriminating power of the different elements in the sea salts. The correlation analysis suggests that the elements with independent discrimination power can be categorized into three groups; those that represent dissolved ions in seawater (K, Li, and Mg), those that are associated with calcified particles (Ca and Sr), and those that are present in soils contained in the sea salts (Al, Si, Ti, and Fe). Classification models using a few emission lines selected based on the results from intensity correlation analysis and full broadband LIBS spectra were developed based on Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) and their performances were compared. Our results indicate that effective combination of a few emission lines can provide a dependable model for discriminating the edible sea salts and the performance is not much degraded from that based on the full broadband spectra. This can be rationalized by the intensity correlation results. - Highlights: • Broadband LIBS spectra of various edible sea salts were obtained. • Intensity correlation of emission lines of the elements in edible sea salts was analyzed. • The elements were categorized into three groups with independent discriminating power. • The effective combination of a few lines can provide dependable classification models.

  14. Revealing discriminating power of the elements in edible sea salts: Line-intensity correlation analysis from laser-induced plasma emission spectra

    International Nuclear Information System (INIS)

    We have investigated the discriminating power of the elements in edible sea salts using Laser-Induced Breakdown Spectroscopy (LIBS). For the ten different sea salts from South Korea, China, Japan, France, Mexico and New Zealand, LIBS spectra were recorded in the spectral range between 190 and 1040 nm, identifying the presence of Na, Cl, K, Ca, Mg, Li, Sr, Al, Si, Ti, Fe, C, O, N, and H. Intensity correlation analysis of the observed emission lines provided a valuable insight into the discriminating power of the different elements in the sea salts. The correlation analysis suggests that the elements with independent discrimination power can be categorized into three groups; those that represent dissolved ions in seawater (K, Li, and Mg), those that are associated with calcified particles (Ca and Sr), and those that are present in soils contained in the sea salts (Al, Si, Ti, and Fe). Classification models using a few emission lines selected based on the results from intensity correlation analysis and full broadband LIBS spectra were developed based on Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) and their performances were compared. Our results indicate that effective combination of a few emission lines can provide a dependable model for discriminating the edible sea salts and the performance is not much degraded from that based on the full broadband spectra. This can be rationalized by the intensity correlation results. - Highlights: • Broadband LIBS spectra of various edible sea salts were obtained. • Intensity correlation of emission lines of the elements in edible sea salts was analyzed. • The elements were categorized into three groups with independent discriminating power. • The effective combination of a few lines can provide dependable classification models

  15. Laser-diode-based joint transform correlator for fingerprint identification

    Science.gov (United States)

    Lal, Amit K.; Zang, De Yu; Millerd, James E.

    1999-01-01

    A laser-diode-based joint transform correlator (JTC) is reported here for the identification and discrimination of fingerprints. The system employs compact and inexpensive laser diodes as the light sources and a bacteriorhodopsin (BR) film in the Fourier plane, which can record the joint power spectrum without the need for expensive spatial light modulators or CCD cameras. The BR film also introduces nonlinearities in the Fourier plane which can improve JTC performance. In addition, real-time, all-optical programmable spatial filtering is demonstrated to improve the discrimination of the system. We present computer modeling and experimental results of this optical correlator, which shows excellent potential for the identification and discrimination of fingerprints.

  16. Shared and distinct anatomical correlates of semantic and phonemic fluency revealed by lesion-symptom mapping in patients with ischemic stroke.

    Science.gov (United States)

    Biesbroek, J Matthijs; van Zandvoort, Martine J E; Kappelle, L Jaap; Velthuis, Birgitta K; Biessels, Geert Jan; Postma, Albert

    2016-05-01

    Semantic and phonemic fluency tasks are frequently used to test executive functioning, speed and attention, and access to the mental lexicon. In semantic fluency tasks, subjects are required to generate words belonging to a category (e.g., animals) within a limited time window, whereas in phonemic fluency tasks subjects have to generate words starting with a given letter. Anatomical correlates of semantic and phonemic fluency are currently assumed to overlap in left frontal structures, reflecting shared executive processes, and to be distinct in left temporal and right frontal structures, reflecting involvement of distinct memory processes and search strategies. Definite evidence for this assumption is lacking. To further establish the anatomical correlates of semantic and phonemic fluency, we applied assumption-free voxel-based and region-of-interest-based lesion-symptom mapping in 93 patients with ischemic stroke. Fluency was assessed by asking patients to name animals (semantic), and words starting with the letter N and A (phonemic). Our findings indicate that anatomical correlates of semantic and phonemic fluency overlap in the left inferior frontal gyrus and insula, reflecting shared underlying cognitive processes. Phonemic fluency additionally draws on the left rolandic operculum, which might reflect a search through phonological memory, and the middle frontal gyrus. Semantic fluency additionally draws on left medial temporal regions, probably reflecting a search through semantic memory, and the right inferior frontal gyrus, which might reflect the application of a visuospatial mental imagery strategy in semantic fluency. These findings establish shared and distinct anatomical correlates of semantic and phonemic fluency.

  17. Shared and distinct anatomical correlates of semantic and phonemic fluency revealed by lesion-symptom mapping in patients with ischemic stroke.

    Science.gov (United States)

    Biesbroek, J Matthijs; van Zandvoort, Martine J E; Kappelle, L Jaap; Velthuis, Birgitta K; Biessels, Geert Jan; Postma, Albert

    2016-05-01

    Semantic and phonemic fluency tasks are frequently used to test executive functioning, speed and attention, and access to the mental lexicon. In semantic fluency tasks, subjects are required to generate words belonging to a category (e.g., animals) within a limited time window, whereas in phonemic fluency tasks subjects have to generate words starting with a given letter. Anatomical correlates of semantic and phonemic fluency are currently assumed to overlap in left frontal structures, reflecting shared executive processes, and to be distinct in left temporal and right frontal structures, reflecting involvement of distinct memory processes and search strategies. Definite evidence for this assumption is lacking. To further establish the anatomical correlates of semantic and phonemic fluency, we applied assumption-free voxel-based and region-of-interest-based lesion-symptom mapping in 93 patients with ischemic stroke. Fluency was assessed by asking patients to name animals (semantic), and words starting with the letter N and A (phonemic). Our findings indicate that anatomical correlates of semantic and phonemic fluency overlap in the left inferior frontal gyrus and insula, reflecting shared underlying cognitive processes. Phonemic fluency additionally draws on the left rolandic operculum, which might reflect a search through phonological memory, and the middle frontal gyrus. Semantic fluency additionally draws on left medial temporal regions, probably reflecting a search through semantic memory, and the right inferior frontal gyrus, which might reflect the application of a visuospatial mental imagery strategy in semantic fluency. These findings establish shared and distinct anatomical correlates of semantic and phonemic fluency. PMID:25939335

  18. Charge transport in bacteriorhodopsin monolayers: The contribution of conformational change to current-voltage characteristics

    Science.gov (United States)

    Alfinito, E.; Reggiani, L.

    2009-03-01

    When moving from native to light-activated bacteriorhodospin, modification of charge transport consisting of an increase of conductance is correlated to the protein conformational change. A theoretical model based on a map of the protein tertiary structure into a resistor network is implemented to account for a sequential tunneling mechanism of charge transfer through neighbouring amino acids. The model is validated by comparison with current-voltage experiments. The predictability of the model is further tested on bovine rhodopsin, a G-protein coupled receptor (GPCR) also sensitive to light. In this case, results show an opposite behaviour with a decrease of conductance in the presence of light.

  19. The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: higher-order correlations revealed by germ-grain Minkowski Functionals

    CERN Document Server

    Wiegand, Alexander

    2016-01-01

    We probe the higher-order clustering of the galaxies in the final data release (DR12) of the Sloan Digital Sky Survey Baryon Oscillation Spectroscopic Survey (BOSS) using the method of germ-grain Minkowski Functionals (MFs). Our sample consists of 410,615 BOSS galaxies from the northern Galactic cap in the redshift range 0.450--0.595. We show the MFs to be sensitive to contributions up to the six-point correlation function for this data set. We ensure with a custom angular mask that the results are more independent of boundary effects than in previous analyses of this type. We extract the higher-order part of the MFs and quantify the difference to the case without higher-order correlations. The resulting $\\chi^{2}$ value of over 10,000 for a modest number of degrees of freedom, O(200), indicates a 100-sigma deviation and demonstrates that we have a highly significant signal of the non-Gaussian contributions to the galaxy distribution. This statistical power can be useful in testing models with differing highe...

  20. P64QUANTITATIVE MGMT METHYLATION ANALYSIS BY PYROSEQUENCING REVEALS A STRONG CORRELATION BETWEEN 1P/19Q CO-DELETION AND HIGH LEVEL METHYLATION IN HIGH GRADE GLIOMAS

    Science.gov (United States)

    Laxton, R.; Doey, L.; Aizpurua, M.; Bodi, I.; King, A.; Chandler, C.; Bhangoo, R.; Beaney, R.; Brazil, L.; Ashkan, K.; Al-Sarraj, S.

    2014-01-01

    INTRODUCTION: Pyrosequencing is a method that allows MGMT methylation to be measured in a quantitative manner. MGMT methylation, along with 1p/19q co-deletion and IDH1 mutation, is an important biomarker in high grade gliomas. MGMT methylation indicates an improved response to temozolomide chemotherapy; patients with 1p/19q co-deleted anaplastic oligodendrogliomas benefit from the addition of chemotherapy to radiotherapy. Aim: To compare the average MGMT promoter methylation level of high grade gliomas and correlate it with other clinical parameters and markers including IDH1&2 mutation and 1p/19q co-deletion. METHOD: For 171 high grade gliomas MGMT methylation analysis was performed by pyrosequencing, mutations to IDH1 and IDH2 genes were also detected by pyrosequencing, or immunohistochemistry (n = 166). Screening for 1p/19q deletion was by fluorescence in situ hybridisation (n = 46). Statistical analysis was performed using R-Stats v2.15.2. RESULTS: The results show that higher methylation was correlated with lower grade and mutation to either IDH1 or IDH2 (27.0% vs. 16.6% p = 0.008; and 27.5 vs. 16.1 p = 0.002 respectively). Interestingly 1p/19q co-deletion versus non co-deletion was associated with a particularly high level of methylation (42.2% vs. 17.7% p = 0.001). No significant differences were seen for age or gender. CONCLUSION: The results offer a potential explanation for the improved prognosis seen in glioma patients with 1p/19q co-deletion and when combined with IDH mutation status may provide an extra control to confirm true 1p/19q co-deletion.

  1. Rab11 and Lysotracker Markers Reveal Correlation between Endosomal Pathways and Transfection Efficiency of Surface-Functionalized Cationic Liposome-DNA Nanoparticles.

    Science.gov (United States)

    Majzoub, Ramsey N; Wonder, Emily; Ewert, Kai K; Kotamraju, Venkata Ramana; Teesalu, Tambet; Safinya, Cyrus R

    2016-07-01

    Cationic liposomes (CLs) are widely studied as carriers of DNA and short-interfering RNA for gene delivery and silencing, and related clinical trials are ongoing. Optimization of transfection efficiency (TE) requires understanding of CL-nucleic acid nanoparticle (NP) interactions with cells, NP endosomal pathways, endosomal escape, and events leading to release of active nucleic acid from the lipid carrier. Here, we studied endosomal pathways and TE of surface-functionalized CL-DNA NPs in PC-3 prostate cancer cells displaying overexpressed integrin and neuropilin-1 receptors. The NPs contained RGD-PEG-lipid or RPARPAR-PEG-lipid, targeting integrin, and neuropilin-1 receptors, respectively, or control PEG-lipid. Fluorescence colocalization using Rab11-GFP and Lysotracker enabled simultaneous colocalization of NPs with recycling endosome (Rab11) and late endosome/lysosome (Rab7/Lysotracker) pathways at increasing mole fractions of pentavalent MVL5 (+5 e) at low (10 mol %), high (50 mol %), and very high (70 mol %) membrane charge density (σM). For these cationic NPs (lipid/DNA molar charge ratio, ρchg = 5), the influence of membrane charge density on pathway selection and transfection efficiency is similar for both peptide-PEG NPs, although, quantitatively, the effect is larger for RGD-PEG compared to RPARPAR-PEG NPs. At low σM, peptide-PEG NPs show preference for the recycling endosome over the late endosome/lysosome pathway. Increases in σM, from low to high, lead to decreases in colocalization with recycling endosomes and simultaneous increases in colocalization with the late endosome/lysosome pathway. Combining colocalization and functional TE data at low and high σM shows that higher TE correlates with a larger fraction of NPs colocalized with the late endosome/lysosome pathway while lower TE correlates with a larger fraction of NPs colocalized with the Rab11 recycling pathway. The findings lead to a hypothesis that increases in σM, leading to enhanced

  2. Orbital character and electron correlation effects on two- and three-dimensional Fermi surfaces in KFe2As2 revealed by angle-resolved photoemission spectroscopy

    Directory of Open Access Journals (Sweden)

    Teppei eYoshida

    2014-04-01

    Full Text Available We have investigated orbital character and electron correlation effects on Fermi surfaces in the hole-overdoped iron pnictide superconductor KFe2As2, which shows a low Tc of ~4 K, by angle-resolved photoemission spectroscopy. From the polarization-dependence of the ARPES spectra, we have determined the orbital character of each Fermi surface. Electron mass renormalization of each band is quantitatively consistent with de Haas-van Alphen results. The outer beta and middle zeta Fermi surfaces show large renormalization factor of m*/mb ~6-7, while the inner Fermi surface has a smaller factor m*/mb ~2. Middle hole Fermi surface zeta has strong three-dimensionality compared to other Fermi surfaces, indicating the d3z2-r2 orbital character, which may be related to the octet-line nodes recently observed by laser ARPES. The observed orbital-dependent mass renormalization would give constraints on the pairing mechanism with line nodes of this system.

  3. A Genome-Wide Transcription An alysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids

    Institute of Scientific and Technical Information of China (English)

    Hui-Yong Zhang; Li-Geng Ma; Xing Wang Deng; Hang He; Liang-Bi Chen; Lei Li; Man-Zhong Liang; Xiang-Feng Wang; Xi-Gang Liu; Guang-Ming He; Run-Sheng Chen

    2008-01-01

    Heterosis,or hybrid vigor,refers to the phenomenon in which hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance.Although a century-long history of research has generated several hypotheses regarding the genetic basis of heterosis,the molecular mechanisms underlying heterosis and heterotic gene expression remain elusive.Here,we report a genome-wide gene expression analysis of two heterotic crosses in rice,taking advantage of its fully sequenced genomes.Approximately 7-9%of the genes were differentially expressed in the seedling shoots from two sets of heterotic crosses,including many transcription factor genes,and exhibited multiple modes of gene action.Comparison of the putative promoter regions of the ortholog genes between inbred parents revealed extensive sequence variation,particularly smallinsertions/deletions(INDELs),many of which result in the formation/disruption of putative cis-regulatory elements.Together,these results suggest that a combinatoriaI interplay between expression of transcription factors and polymorphic promoter cis-regulatory elements in the hybrids is one plausible molecular mechanism underlying heterotic gene action and thus heterosis in rice.

  4. Diffusion tensor imaging reveals adolescent binge ethanol-induced brain structural integrity alterations in adult rats that correlate with behavioral dysfunction.

    Science.gov (United States)

    Vetreno, Ryan P; Yaxley, Richard; Paniagua, Beatriz; Crews, Fulton T

    2016-07-01

    Adolescence is characterized by considerable brain maturation that coincides with the development of adult behavior. Binge drinking is common during adolescence and can have deleterious effects on brain maturation because of the heightened neuroplasticity of the adolescent brain. Using an animal model of adolescent intermittent ethanol [AIE; 5.0 g/kg, intragastric, 20 percent EtOH w/v; 2 days on/2 days off from postnatal day (P)25 to P55], we assessed the adult brain structural volumes and integrity on P80 and P220 using diffusion tensor imaging (DTI). While we did not observe a long-term effect of AIE on structural volumes, AIE did reduce axial diffusivity (AD) in the cerebellum, hippocampus and neocortex. Radial diffusivity (RD) was reduced in the hippocampus and neocortex of AIE-treated animals. Prior AIE treatment did not affect fractional anisotropy (FA), but did lead to long-term reductions of mean diffusivity (MD) in both the cerebellum and corpus callosum. AIE resulted in increased anxiety-like behavior and diminished object recognition memory, the latter of which was positively correlated with DTI measures. Across aging, whole brain volumes increased, as did volumes of the corpus callosum and neocortex. This was accompanied by age-associated AD reductions in the cerebellum and neocortex as well as RD and MD reductions in the cerebellum. Further, we found that FA increased in both the cerebellum and corpus callosum as rats aged from P80 to P220. Thus, both age and AIE treatment caused long-term changes to brain structural integrity that could contribute to cognitive dysfunction. PMID:25678360

  5. Expression profiles of key phenylpropanoid genes during Vanilla planifolia pod development reveal a positive correlation between PAL gene expression and vanillin biosynthesis.

    Science.gov (United States)

    Fock-Bastide, Isabelle; Palama, Tony Lionel; Bory, Séverine; Lécolier, Aurélie; Noirot, Michel; Joët, Thierry

    2014-01-01

    In Vanilla planifolia pods, development of flavor precursors is dependent on the phenylpropanoid pathway. The distinctive vanilla aroma is produced by numerous phenolic compounds of which vanillin is the most important. Because of the economic importance of vanilla, vanillin biosynthetic pathways have been extensively studied but agreement has not yet been reached on the processes leading to its accumulation. In order to explore the transcriptional control exerted on these pathways, five key phenylpropanoid genes expressed during pod development were identified and their mRNA accumulation profiles were evaluated during pod development and maturation using quantitative real-time PCR. As a prerequisite for expression analysis using qRT-PCR, five potential reference genes were tested, and two genes encoding Actin and EF1 were shown to be the most stable reference genes for accurate normalization during pod development. For the first time, genes encoding a phenylalanine ammonia-lyase (VpPAL1) and a cinnamate 4-hydroxylase (VpC4H1) were identified in vanilla pods and studied during maturation. Among phenylpropanoid genes, differential regulation was observed from 3 to 8 months after pollination. VpPAL1 was gradually up-regulated, reaching the maximum expression level at maturity. In contrast, genes encoding 4HBS, C4H, OMT2 and OMT3 did not show significant increase in expression levels after the fourth month post-pollination. Expression profiling of these key phenylpropanoid genes is also discussed in light of accumulation patterns for key phenolic compounds. Interestingly, VpPAL1 gene expression was shown to be positively correlated to maturation and vanillin accumulation.

  6. Generalized Two-Dimensional Perturbation Correlation Infrared Spectroscopy reveals Mechanisms for the Development of Surface Charge and Recalcitrance in Plant-derived Biochars

    Energy Technology Data Exchange (ETDEWEB)

    Harvey, Omar R.; Herbert, Bruce; Kuo, Li-Jung; Louchouarn, Patrick

    2012-09-05

    Fundamental knowledge of how biochars develop surface-charge and resistance to environmental degradation (or recalcitrance) is crucial to their production for customized applications or, understanding their functions in the environment. Two-dimensional perturbation-based correlation infrared spectroscopy (2D-PCIS) was used to study the biochar formation process in three taxonomically-different plant biomass, under oxygen-limited conditions along a heat-treatment-temperature gradient (HTT; 200-650 oC). Results from 2D-PCIS pointed to the systematic, HTT-induced defragmenting of lignocellulose H-bonding network, and demethylenation/demethylation, oxidation or dehydroxylation/dehydrogenation of lignocellulose fragments as the primary reactions controlling biochar properties along the HTT gradient. The cleavage of OH O-type H-bonds, oxidation of free primary hydroxyls (HTT≤500 oC), and their subsequent dehydrogenation/dehydroxylation (HTT>500 oC) controlled surface charge on the biochars; while the dehydrogenation of methylene groups, which yielded increasingly condensed structures (R-CH2-R →R=CH-R →R=C=R), controlled biochar recalcitrance. Variations in biochar properties across plant biomass type were attributable to taxa-specific transformations. For example, apparent inefficiencies in the cleavage of wood-specific H-bonds, and their subsequent oxidation to carboxyls, lead to lower surface charge in wood biochars (compared to grass biochars). Both non-taxa and taxa-specific transformations highlighted by 2D-PCIS could have significant implications for biochar functioning in fire-impacted or biochar-amended systems.

  7. Changes in fluorescent dissolved organic matter upon interaction with anionic surfactant as revealed by EEM-PARAFAC and two dimensional correlation spectroscopy.

    Science.gov (United States)

    Maqbool, Tahir; Hur, Jin

    2016-10-01

    Surfactants are present in significant amounts in both domestic and industrial wastewater, which may interact with dissolved organic matter (DOM). The present study investigated the interactions of sodium dodecyl sulfate (SDS) with three different DOM solutions, including bovine serum albumin (BSA), humic acid (HA), and the mixture of the two (BSA-HA), based on two advanced spectroscopic tools: excitation emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC) and two dimensional correlation spectroscopy (2D-COS). The responses of two protein-like components to the addition of SDS differed depending the presence and the absence of HA. A decreasing and an increasing trend was observed for tryptophan-like (C1) and tyrosine-like (C2) components, respectively, in the BSA solution, while the BSA-HA mixture exhibited increasing fluorescence trends for both protein-like components. The conflicting results suggest that HA plays a secondary role in the protein-SDS interactions. No interaction between the SDS and humic-like component was found. 2D-COS combined with fluorescence spectra demonstrated that the protein-SDS interaction occurred on the order of C2 > C1 for the BSA solution but C1 > C2 for the BSA-HA mixture. Analyses of Scatchard plots confirmed the sequential order interpreted from 2D-COS, showing consistent trends in the binding constants. However, the presence of HA affected the protein-SDS interactions in different manners for C1 and C2, enhancing and reducing the binding constants, respectively. Circular dichroism spectra confirmed the occurrence of conformational changes in BSA with SDS. EEM-PARAFAC and 2D-COS successfully explained different interactions of surfactant with protein-like components in the presence of HA. PMID:27427776

  8. High sensitivity detection of Plasmodium species reveals positive correlations between infections of different species, shifts in age distribution and reduced local variation in Papua New Guinea

    Directory of Open Access Journals (Sweden)

    Smith Thomas A

    2009-03-01

    demonstrates that application of molecular diagnosis reveals patterns of malaria risk that are significantly different from those obtained by standard LM. Results provide insight relevant to design of malaria control and eradication strategies.

  9. Steric interaction between the 9-methyl group of the retinal and tryptophan 182 controls 13-cis to all-trans reisomerization and proton uptake in the bacteriorhodopsin photocycle

    Energy Technology Data Exchange (ETDEWEB)

    Weidlich, O.; Schalt, B.; Siebert, F. [Albert-Ludwigs-Universitaet, Freiburg (Germany)] [and others

    1996-08-20

    The hypothesis was tested whether in bacteriorhodopsin (BR) the reduction of the steric interaction between the 9-methyl group of the chromophore all-trans-retinal and the tryptophan at position 182 causes the same changes as observed in the photocycle of 9-demethyl-BR. For this, the photocycle of the mutant W182F was investigated by time-resolved UV-vis and pH measurements and by static and time-resolved FT-IR difference spectroscopy. We found that the second half of the photocycle was similarly distorted in the two modified systems: based on the amide-I band, the protonation state of D96, and the kinetics of proton uptake, four N intermediates could be identified, the last one having a lifetime of several seconds; no O intermediate could be detected; the proton uptake showed a pronounced biphasic time course; and the pK{sub a} of group(s) on the cytoplasmic side in N was reduced from 11 in wild type BR to around 7.5. In contrast to 9-demethyl-BR, in the W182F mutant the first part of the photocycle does not drastically deviate from that of wild type BR. The results demonstrate the importance of the steric interaction between W182 and the 9-methyl group of the retinal in providing tight coupling between chromophore isomerization and the late proton transfer steps. 51 refs., 7 figs.

  10. Second-harmonic generation of biological interfaces: probing the membrane protein bacteriorhodopsin and imaging membrane potential around GFP molecules at specific sites in neuronal cells of C. elegans

    Science.gov (United States)

    Lewis, Aaron; Khatchatouriants, Artium; Treinin, Millet; Chen, Zhongping; Peleg, Gadi; Friedman, Noga; Bouevitch, Oleg; Rothman, Zvi; Loew, Leslie; Sheres, Mordechai

    1999-07-01

    Second-harmonic generation (SHG) is applied to problems of probing membrane proteins and functionally imaging around selective sites and at single molecules in biological membranes. The membrane protein bacteriorhodopsin (bR) has been shown to have large second-harmonic (SH) intensities that are modulated by protein/retinylidene chromophore interactions. The nonlinear optical properties of model compounds, which simulate these protein chromophore interactions in retinal proteins, are studied in this work by surface SHG and by hyper-Rayleigh scattering. Our results indicate that non-conjugated charges and hydrogen bonding effects have a large effect on the molecular hyperpolarizability of the retinal chromophore. However, mbR, the model system studies suggest that polarizable amino acids strongly affect the vertically excited state of the retinylidene chromophore and appear to play the major role in the observed protein enhancement (>50%) of the retinylidene chromophore molecular hyperpolarizability and associated induced dipole. Furthermore, the data provide insights on emulating these interactions for the design of organic nonlinear optical materials. Our studies have also led to the development of dyes with large SH intensities that can be embedded in cell membranes and can functionally image membrane potential. Single molecules of such dyes in selected single molecular regions of a cell membrane have been detected. SHG from green fluorescent protein (GFP) selectively expressed in concert with a specific protein in neuronal cells in a transgenic form of the worm C. elegans is also reported. The membrane potential around the GFP molecules expressed in these cells has been imaged with SHG in live animals.

  11. Nonlinear Optical Characteristic Measurement of Chemically Enhanced Bacteriorhodopsin Film Using Z-scan Technology%利用Z扫描技术测量菌紫质膜的非线性光学参数

    Institute of Scientific and Technical Information of China (English)

    徐军; 何俊发; 侯素霞; 胡坤生; 张亦南

    2000-01-01

    本文讨论一种有发展前景的光敏生物材料-细菌视紫红质(菌紫质),采用化学增强法制备菌紫质膜,利用Z扫描技术测量了菌紫质膜的非线性光学参数,结果表明菌紫质具有大的非线性光学系数,在光信息处理领域有十分广泛的应用.%We present a unique biological material that exhibits interesting photochromic characteristics and important optoelectric properties. This distinctive material is related to the visual pigment rhodopsin and is called bacteriorhodopsin (bR). In this paper the films of the chemically enhanced bacteriorhodopsin are prepared and the effective nonlinearity n2 of the film is measured with the Z-scan Technology. Anomalous absorption at three wavelengths is observed. Large optical nonlinearities of bR should be useful for both information storage and compulation.

  12. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  13. Revealed Attention

    OpenAIRE

    Masatlioglu, Yusufcan; NAKAJIMA, Daisuke; Ozbay, Erkut Y

    2012-01-01

    The standard revealed preference argument relies on an implicit assumption that a decision maker considers all feasible alternatives. The marketing and psychology literatures, however, provide wellestablished evidence that consumers do not consider all brands in a given market before making a purchase (Limited Attention). In this paper, we illustrate how one can deduce both the decision maker's preference and the alternatives to which she pays attention and inattention from the observed behav...

  14. Revealed Attention

    OpenAIRE

    Yusufcan Masatlioglu; Daisuke Nakajima; Ozbay, Erkut Y

    2012-01-01

    The standard revealed preference argument relies on an implicit assumption that a decision maker considers all feasible alternatives. The marketing and psychology literatures, however, provide well-established evidence that consumers do not consider all brands in a given market before making a purchase (Limited Attention). In this paper, we illustrate how one can deduce both the decision maker's preference and the alternatives to which she pays attention and inattention from the observed beha...

  15. Quadratic electro-optic effects in bacteriorhodopsin: Measurement of γ(-ω;0,0,ω) in dried gelatin thin films

    Science.gov (United States)

    Yamazaki, Mikio; Goodisman, Jerry; Birge, Robert R.

    1998-04-01

    Quadratic electro-optic effects (dc or low frequency Kerr effect) of bacteriorhodopsin dispersed in dried gelatin thin films are examined in the near resonance region at three wavelengths: 633, 647, and 676 nm. The films show relatively large quadratic electro-optic effects compared to other molecular dispersed systems. The purple membrane is fixed within the polymerized gelatin matrix, and we show that the electronic contribution to γ dominates over possible orientational contributions. At 676 nm, the quadratic electro-optic coefficient s1133(-ω;0,0,ω) is 6.7×10-20m2/V2 and the third order nonlinear susceptibility χ1133(3)(-ω;0,0,ω) is 7.0×10-13cm4 statCoulomb-2, with both values obtained for a protein concentration of 6.9×1018cm-3. The orientationally averaged second molecular hyperpolarizability determined from the quadratic electro-optic coefficients at 676 nm assuming an Onsager ellipsoidal local field factor is (10.8±5.1)×10-32 cm7 statCoulomb-2 [(1.34±0.63)×10-56 F3 m4 C-2]. The value increases roughly tenfold when the probe wavelength is decreased to 633 nm. The behavior of γ(-ω;0,0,ω), when fit to a two-state model, predicts that γ(-ω;0,0,ω) is strongly enhanced via type III processes. Thus, the magnitude of γ(-ω;0,0,ω) is dominated by a term (Δμ102×μ102)/(ω10-ω)3, where Δμ10 is the change in dipole moment, μ10 is the transition moment, and ω10 is the transition energy of the lowest-lying allowed 1Bu*+-like π,π* state. We calculate that Δμ10 is 12.8±1.2 D, in good agreement with previous Stark and two-photon experimental values. Time-dependent Hartree-Fock methods based on the MNDO Hamiltonian yield reasonable agreement with experiment, underestimating γ(-ω;0,0,ω) by factors of only 2-4, with the error increasing as the frequency approaches resonance.

  16. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  17. Incorporation of the dopamine D2L receptor and bacteriorhodopsin within bicontinuous cubic lipid phases. 2. Relevance to in meso crystallization of integral membrane proteins in novel lipid systems

    Energy Technology Data Exchange (ETDEWEB)

    Conn, Charlotte E.; Darmanin, Connie; Sagnella, Sharon M.; Mulet, Xavier; Greaves, Tamar L.; Varghese, Joseph N.; Drummond, Calum J.

    2014-09-24

    The dopamine D2 long (D2L) receptor and bacteriorhodopsin (bR), which are integral membraneproteins, have been incorporated within bicontinuous cubic mesophases formed by the lipids anandamide and H-farnesoyl monoethanolamide, which have been specifically investigated by us for use as in mesocrystallization media. We show that the incorporated membraneprotein affects the structure of the cubic phases with the particular effect observed dependent on the geometry of the underlying cubic phase. The results are complementary to those obtained in Part 1 of this series, where we demonstrated that the structural effects observed depend on the structure of the membraneprotein. Importantly protein concentrations commonly used for crystallization can destroy the cubic phase matrix, particularly where there is a large discrepancy between the hydrophilic and the hydrophobic spans of the membraneprotein, and the hydrophilic and hydrophobic domain sizes of the cubic phase.

  18. Determination of the Waist Position of a Gaussian Beam by Bacteriorhodopsin Film%由细菌视紫红质测定高斯光束的束腰位置

    Institute of Scientific and Technical Information of China (English)

    陈桂英; 郭宗霞; 张春平; 田建国; Q.W.Song; Mingchien Huang

    2004-01-01

    Relation between transmitted intensity of bacteriorhodopsin(bR) film and the incident intensity was tested.A new method of determining waist position of a Gaussian beam passing an optical system was proposed by the nonlinear transmission of the bR film.The measured results are in agreement with the calculated results based on the parameters of the Guassian beam.%介绍并测量了细菌视紫红质(bR)的透过光强随入射光强的变化特性,并提出利用bR的非线性透过特性测定高斯光束的束腰位置,测量结果与利用已知的高斯光束参数所计算的结果相一致.

  19. Revealing Cosmic Rotation

    CERN Document Server

    Yadav, Amit P S; Keating, Brian G

    2012-01-01

    Cosmological Birefringence (CB), a rotation of the polarization plane of radiation coming to us from distant astrophysical sources, may reveal parity violation in either the electromagnetic or gravitational sectors of the fundamental interactions in nature. Until only recently this phenomenon could be probed with only radio observations or observations at UV wavelengths. Recently, there is a substantial effort to constrain such non-standard models using observations of the rotation of the polarization plane of cosmic microwave background (CMB) radiation. This can be done via measurements of the $B$-modes of the CMB or by measuring its TB and EB correlations which vanish in the standard model. In this paper we show that $EB$ correlations-based estimator is the best for upcoming polarization experiments. The $EB$ based estimator surpasses other estimators because it has the smallest noise and of all the estimators is least affected by systematics. Current polarimeters are optimized for the detection of $B$-mode...

  20. Analysis of 6912 unselected somatic hypermutations in human VDJ rearrangements reveals lack of strand specificity and correlation between phase II substitution rates and distance to the nearest 3' activation-induced cytidine deaminase target

    DEFF Research Database (Denmark)

    Ohm-Laursen, Line; Barington, Torben

    2007-01-01

    -23*01) from blood B lymphocytes enriched for CD27-positive memory cells. Analyses of 6,912 unique, unselected substitutions showed that in vivo hot and cold spots for the SHM of C and G residues corresponded closely to the target preferences reported for AID in vitro. A detailed analysis of all possible four......-nucleotide motifs present on both strands of the V(H) gene showed significant correlations between the substitution frequencies in reverse complementary motifs, suggesting that the SHM machinery targets both strands equally well. An analysis of individual J(H) and D gene segments showed that the substitution...... rates in G and T residues correlated inversely with the distance to the nearest 3' WRC AID hot spot motif on both the nontranscribed and transcribed strands. This suggests that phase II SHM takes place 5' of the initial AID deamination target and primarily targets T and G residues or, alternatively, the...

  1. Deterioration of abstract reasoning ability in mild cognitive impairment and Alzheimer's disease: correlation with regional grey matter volume loss revealed by diffeomorphic anatomical registration through exponentiated lie algebra analysis

    Energy Technology Data Exchange (ETDEWEB)

    Yoshiura, Takashi; Hiwatashi, Akio; Yamashita, Koji; Takayama, Yukihisa; Kamano, Norihiro; Honda, Hiroshi [Kyushu University, Department of Clinical Radiology, Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka (Japan); Ohyagi, Yasumasa; Kira, Jun-ichi [Kyushu University, Department of Neurology, Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka (Japan); Monji, Akira; Kawashima, Toshiro [Kyushu University, Department of Neuropsychiatry, Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka (Japan)

    2011-02-15

    To determine which brain regions are relevant to deterioration in abstract reasoning as measured by Raven's Colored Progressive Matrices (CPM) in the context of dementia. MR images of 37 consecutive patients including 19 with Alzheimer's disease (AD) and 18 with amnestic mild cognitive impairment (aMCI) were retrospectively analyzed. All patients were administered the CPM. Regional grey matter (GM) volume was evaluated according to the regimens of voxel-based morphometry, during which a non-linear registration algorithm called Diffeomorphic Anatomical Registration Through Exponentiated Lie algebra was employed. Multiple regression analyses were used to map the regions where GM volumes were correlated with CPM scores. The strongest correlation with CPM scores was seen in the left middle frontal gyrus while a region with the largest volume was identified in the left superior temporal gyrus. Significant correlations were seen in 14 additional regions in the bilateral cerebral hemispheres and right cerebellum. Deterioration of abstract reasoning ability in AD and aMCI measured by CPM is related to GM loss in multiple regions, which is in close agreement with the results of previous activation studies. (orig.)

  2. Superadditive correlation.

    Science.gov (United States)

    Giraud, B G; Heumann, J M; Lapedes, A S

    1999-05-01

    The fact that correlation does not imply causation is well known. Correlation between variables at two sites does not imply that the two sites directly interact, because, e.g., correlation between distant sites may be induced by chaining of correlation between a set of intervening, directly interacting sites. Such "noncausal correlation" is well understood in statistical physics: an example is long-range order in spin systems, where spins which have only short-range direct interactions, e.g., the Ising model, display correlation at a distance. It is less well recognized that such long-range "noncausal" correlations can in fact be stronger than the magnitude of any causal correlation induced by direct interactions. We call this phenomenon superadditive correlation (SAC). We demonstrate this counterintuitive phenomenon by explicit examples in (i) a model spin system and (ii) a model continuous variable system, where both models are such that two variables have multiple intervening pathways of indirect interaction. We apply the technique known as decimation to explain SAC as an additive, constructive interference phenomenon between the multiple pathways of indirect interaction. We also explain the effect using a definition of the collective mode describing the intervening spin variables. Finally, we show that the SAC effect is mirrored in information theory, and is true for mutual information measures in addition to correlation measures. Generic complex systems typically exhibit multiple pathways of indirect interaction, making SAC a potentially widespread phenomenon. This affects, e.g., attempts to deduce interactions by examination of correlations, as well as, e.g., hierarchical approximation methods for multivariate probability distributions, which introduce parameters based on successive orders of correlation. PMID:11969452

  3. Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes

    DEFF Research Database (Denmark)

    Kool, Jaap; Uren, Anthony G; Martins, Carla P;

    2010-01-01

    genetic context of predisposing germline and somatic mutations. We also found associations between these loci with gender, age of tumor onset, and lymphocyte lineage (B or T cell). Comparison of retroviral insertion sites with single nucleotide polymorphisms associated with chronic lymphocytic leukemia...... revealed a significant overlap between the datasets. Together, our findings highlight the importance of genetic context within large-scale mutation detection studies, and they show a novel use for insertional mutagenesis data in prioritizing disease-associated genes that emerge from genome-wide association...

  4. Score Correlation

    OpenAIRE

    Fabián, Z. (Zdeněk)

    2010-01-01

    In this paper, we study a distribution-dependent correlation coefficient based on the concept of scalar score. This new measure of association of continuous random variables is compared by means of simulation experiments with the Pearson, Kendall and Spearman correlation coefficients.

  5. Cross-correlation and time-lag analysis of high frequency monitoring data of the Vallcebre landslide (Eastern Pyrenees, Spain) to reveal cause-effect relationships between variables governing slope instability

    Science.gov (United States)

    Mulas, Marco; Moya, Jose; Corsini, Alessandro; Corominas, Jordi

    2015-04-01

    The Vallcebre landslide is a slow moving large landslide located 140 km north of Barcelona in the Eastern Pyrenees. Monitoring data of the Vallcebre landslide represent a singular case of multi parameter high-frequency monitoring system set up in 1996 and still ongoing. Data of movements and groundwater levels are measured and recorded with a frequency of 20 minutes in 6 boreholes distributed in the landslide, each one equipped with a wire extensometer and a piezometer, while rainfall is recorded by a specific gauge at the site. Data from 3 boreholes recorded during three full years of measurements (from 1999 to 2001) have been analyzed by means of a cross-correlation function in order to determine the reciprocal interdependency and the relative time lag between rainfall, groundwater and movement rate maxima and, ultimately, to evidence cause-effect processes occurring along the slope. It should be pinpointed that, in this specific case, rainfall is also a proxy for the discharge level of the stream eroding the toe of the landslide, that is believed to be one of the main instability factors. The cross-correlation function is a quite simple signal processing tool for measuring similarities of waveforms as function of an applied time-lag. Specifically, it was applied to study: i) the relations between rainfall and movement rate, so to highlight the relative time lag for rainfall to produce an effect in different points of the landslide; ii) the inter-dependencies between different movement rates in the three boreholes in order to determine the pattern of mobilization of the landslide (from up to down slope and vice-versa); iii) the response of groundwater with respect to rainfall, which reflects the local permeability; iv) the evolution of groundwater levels in the three monitoring points. Altogether, results confirm and constrain in time the retrogressive trend of movements in the landslide (in agreement with a 2D numerical model previously developed by Ferrari et

  6. MIBG scans in patients with stage 4 neuroblastoma reveal two metastatic patterns, one is associated with MYCN amplification and in MYCN-amplified tumours correlates with a better prognosis

    Energy Technology Data Exchange (ETDEWEB)

    Bleeker, Gitta [Academic Medical Centre/Emma Children' s Hospital, Department of Paediatric Oncology, Amsterdam (Netherlands); Academic Medical Centre, Department of Oncogenomics, Amsterdam (Netherlands); Eck-Smit, Berthe L. van [Academic Medical Centre, Department of Nuclear Medicine, Amsterdam (Netherlands); Zwinderman, Koos H. [Academic Medical Centre, Department of Biostatistics, Amsterdam (Netherlands); Versteeg, Rogier [Academic Medical Centre, Department of Oncogenomics, Amsterdam (Netherlands); Noesel, Max M. van [Erasmus Medical Centre/Sophia Children' s Hospital, Department of Paediatric Oncology/Haematology, Rotterdam (Netherlands); Kam, Boen L. [Erasmus Medical Centre, Department of Nuclear Medicine, Rotterdam (Netherlands); Kaspers, Gertjan J. [VU University Medical Centre, Department of Paediatric Oncology, Amsterdam (Netherlands); Schie, Annelies van [VU University Medical Centre, Department of Nuclear Medicine, Amsterdam (Netherlands); Kreissman, Susan G. [Duke University Medical Centre, Durham, NC (United States); University of Florida, Children' s Oncology Group (COG), Gainesville, FL (United States); Yanik, Gregory [University of Florida, Children' s Oncology Group (COG), Gainesville, FL (United States); University of Michigan, Department of Paediatrics, Division of Haematology and Oncology, Ann Arbor, MI (United States); Hero, Barbara [University Hospital of Cologne, Children' s Hospital, Cologne (Germany); Schmidt, Matthias [University Hospital of Cologne, Department of Nuclear Medicine, Cologne (Germany); Laureys, Genevieve [Ghent University Hospital, Department of Paediatric Haematology and Oncology, Ghent (Belgium); Lambert, Bieke [Ghent University Hospital, Department of Nuclear Medicine, Ghent (Belgium); Oera, Ingrid [Academic Medical Centre, Department of Oncogenomics, Amsterdam (Netherlands); Lund University Hospital, Department of Paediatric Oncology, Lund (Sweden); Schulte, Johannes H. [University Children' s Hospital Essen, Essen (Germany); Caron, Huib N.; Tytgat, Godelieve A. [Academic Medical Centre/Emma Children' s Hospital, Department of Paediatric Oncology, Amsterdam (Netherlands); Dutch Childhood Oncology Group (DCOG), The Hague (Netherlands)

    2014-09-30

    The aim of this study was to find clinically relevant MIBG-avid metastatic patterns in patients with newly diagnosed stage 4 neuroblastoma. Diagnostic {sup 123}I-MIBG scans from 249 patients (123 from a European and 126 from the COG cohort) were assessed for metastatic spread in 14 body segments and the form of the lesions: ''focal'' (clear margins distinguishable from adjacent background) or ''diffuse'' (indistinct margins, dispersed throughout the body segment). The total numbers of diffuse and focal lesions were recorded. Patients were then categorized as having lesions exclusively focal, lesions more focal than diffuse, lesions more diffuse than focal, or lesions exclusively diffuse. Diffuse lesions affected a median of seven body segments and focal lesions a median of two body segments (P < 0.001, both cohorts). Patients with a focal pattern had a median of 2 affected body segments and those with a diffuse pattern a median of 11 affected body segments (P < 0.001, both cohorts). Thus, two MIBG-avid metastatic patterns emerged: ''limited-focal'' and ''extensive-diffuse''. The median numbers of affected body segments in MYCN-amplified (MNA) tumours were 5 (European cohort) and 4 (COG cohort) compared to 9 and 11, respectively, in single-copy MYCN (MYCNsc) tumours (P < 0.001). Patients with exclusively focal metastases were more likely to have a MNA tumour (60 % and 70 %, respectively) than patients with the other types of metastases (23 % and 28 %, respectively; P < 0.001). In a multivariate Cox regression analysis, focal metastases were associated with a better event-free and overall survival than the other types of metastases in patients with MNA tumours in the COG cohort (P < 0.01). Two metastatic patterns were found: a ''limited and focal'' pattern found mainly in patients with MNA neuroblastoma that correlated with prognosis, and an ''extensive and

  7. Immune-correlates analysis of an HIV-1 vaccine efficacy trial reveals an association of nonspecific interferon-γ secretion with increased HIV-1 infection risk: a cohort-based modeling study.

    Directory of Open Access Journals (Sweden)

    Yunda Huang

    Full Text Available BACKGROUND: Elevated risk of HIV-1 infection among recipients of an adenovirus serotype 5 (Ad5-vectored HIV-1 vaccine was previously reported in the Step HIV-1 vaccine efficacy trial. We assessed pre-infection cellular immune responses measured at 4 weeks after the second vaccination to determine their roles in HIV-1 infection susceptibility among Step study male participants. METHODS: We examined ex vivo interferon-γ (IFN-γ secretion from peripheral blood mononuclear cells (PBMC using an ELISpot assay in 112 HIV-infected and 962 uninfected participants. In addition, we performed flow cytometric assays to examine T-cell activation, and ex vivo IFN-γ and interleukin-2 secretion from CD4(+ and CD8(+ T cells. We accounted for the sub-sampling design in Cox proportional hazards models to estimate hazard ratios (HRs of HIV-1 infection per 1-log(e increase of the immune responses. FINDINGS: We found that HIV-specific immune responses were not associated with risk of HIV-1 infection. However, each 1-log(e increase of mock responses measured by the ELISpot assay (i.e., IFN-γ secretion in the absence of antigen-specific stimulation was associated with a 62% increase of HIV-1 infection risk among vaccine recipients (HR = 1.62, 95% CI: (1.28, 2.04, p<0.001. This association remains after accounting for CD4(+ or CD8(+ T-cell activation. We observed a moderate correlation between ELISpot mock responses and CD4(+ T-cells secreting IFN-γ (ρ = 0.33, p = 0.007. In addition, the effect of the Step vaccine on infection risk appeared to vary with ELISpot mock response levels, especially among participants who had pre-existing anti-Ad5 antibodies (interaction p = 0.04. CONCLUSIONS: The proportion of cells, likely CD4(+ T-cells, producing IFN-γ without stimulation by exogenous antigen appears to carry information beyond T-cell activation and baseline characteristics that predict risk of HIV-1 infection. These results motivate additional investigation to

  8. Robust correlators

    CERN Document Server

    Fridman, P A

    2010-01-01

    Radio frequency interference (RFI) already limits the sensitivity of existing radio telescopes in several frequency bands and may prove to be an even greater obstacle for future generation instruments to overcome. I aim to create a structure of radio astronomy correlators which will be statistically stable (robust) in the presence of interference. A statistical analysis of the mixture of system noise + signal noise + RFI is proposed here which could be incorporated into the block diagram of a correlator. Order and rank statistics are especially useful when calculated in both temporal and frequency domains. Several new algorithms of robust correlators are proposed and investigated here. Computer simulations and processing of real data demonstrate the efficacy of the proposed algorithms.

  9. Nanoscale Electric Characteristics and Oriented Assembly of Halobacterium salinarum Membrane Revealed by Electric Force Microscopy

    Directory of Open Access Journals (Sweden)

    Denghua Li

    2016-11-01

    Full Text Available Purple membranes (PM of the bacteria Halobacterium salinarum are a unique natural membrane where bacteriorhodopsin (BR can convert photon energy and pump protons. Elucidating the electronic properties of biomembranes is critical for revealing biological mechanisms and developing new devices. We report here the electric properties of PMs studied by using multi-functional electric force microscopy (EFM at the nanoscale. The topography, surface potential, and dielectric capacity of PMs were imaged and quantitatively measured in parallel. Two orientations of PMs were identified by EFM because of its high resolution in differentiating electrical characteristics. The extracellular (EC sides were more negative than the cytoplasmic (CP side by 8 mV. The direction of potential difference may facilitate movement of protons across the membrane and thus play important roles in proton pumping. Unlike the side-dependent surface potentials observed in PM, the EFM capacitive response was independent of the side and was measured to be at a dC/dz value of ~5.25 nF/m. Furthermore, by modification of PM with de novo peptides based on peptide-protein interaction, directional oriented PM assembly on silicon substrate was obtained for technical devices. This work develops a new method for studying membrane nanoelectronics and exploring the bioelectric application at the nanoscale.

  10. Revealing advantage in a quantum network

    Science.gov (United States)

    Mukherjee, Kaushiki; Paul, Biswajit; Sarkar, Debasis

    2016-07-01

    The assumption of source independence was used to reveal nonlocal (apart from standard Bell-CHSH scenario) nature of correlations generated in entanglement swapping experiments. In this work, we have discussed the various utilities of this assumption to reveal nonlocality (via generation of nonbilocal correlations) and thereby exploiting quantumness under lesser requirements compared to some standard means of doing the same. We have also provided with a set of sufficient criteria, imposed on the states (produced by the sources) under which source independence can reveal nonbilocal nature of correlations in a quantum network.

  11. Correlator technology

    NARCIS (Netherlands)

    Schooneveld, C. van

    1968-01-01

    The paper reviews a number of designs of cross-correlation receivers for the detection of active underwater transmissions. Particular attention is given to the various structures of phase insensitive receivers, and to the problems concerned with clipping of the input signal and the reference functio

  12. 细菌视紫红质激子的饱和密度及激子长度的研究%Study on Saturation Density and Length of Excitons in Bacteriorhodopsin

    Institute of Scientific and Technical Information of China (English)

    黄燕萍; 陈树德; 王祖赓; 李庆国

    2001-01-01

    The three-energy model simulated with photocycle characteristicsis used to explain bacteriorhodopsin’s 3-order nonlinear susceptibility and its time response, which was measured with four-wave mixing technique. The saturation density and length of excitons in bacteriorhodopsin are obtained with fitting to the phase-space filling model. The possible mechanism for generating the 3rd nonlinear optical susceptibility χ(3) and response time are discussed.%对光能转换生物分子细菌视紫红质(bR)作前向立体简并四波混频实验所测得的三阶非线性电极化率和它们的时间响应,用光循环结构模拟的三能级模型予以解释,并用位相空间充满理论模拟得到激子饱和密度和激子长度。

  13. Correlative microscopy.

    Science.gov (United States)

    Loussert Fonta, Céline; Humbel, Bruno M

    2015-09-01

    In recent years correlative microscopy, combining the power and advantages of different imaging system, e.g., light, electrons, X-ray, NMR, etc., has become an important tool for biomedical research. Among all the possible combinations of techniques, light and electron microscopy, have made an especially big step forward and are being implemented in more and more research labs. Electron microscopy profits from the high spatial resolution, the direct recognition of the cellular ultrastructure and identification of the organelles. It, however, has two severe limitations: the restricted field of view and the fact that no live imaging can be done. On the other hand light microscopy has the advantage of live imaging, following a fluorescently tagged molecule in real time and at lower magnifications the large field of view facilitates the identification and location of sparse individual cells in a large context, e.g., tissue. The combination of these two imaging techniques appears to be a valuable approach to dissect biological events at a submicrometer level. Light microscopy can be used to follow a labelled protein of interest, or a visible organelle such as mitochondria, in time, then the sample is fixed and the exactly same region is investigated by electron microscopy. The time resolution is dependent on the speed of penetration and fixation when chemical fixatives are used and on the reaction time of the operator for cryo-fixation. Light microscopy can also be used to identify cells of interest, e.g., a special cell type in tissue or cells that have been modified by either transfections or RNAi, in a large population of non-modified cells. A further application is to find fluorescence labels in cells on a large section to reduce searching time in the electron microscope. Multiple fluorescence labelling of a series of sections can be correlated with the ultrastructure of the individual sections to get 3D information of the distribution of the marked proteins: array

  14. Correlation measurement of squeezed light

    DEFF Research Database (Denmark)

    Krivitsky, Leonid; Andersen, Ulrik Lund; Dong, R.;

    2009-01-01

    We study the implementation of a correlation measurement technique for the characterization of squeezed light which is nearly free of electronic noise. With two different sources of squeezed light, we show that the sign of the covariance coefficient, revealed from the time-resolved correlation data......, is witnessing the presence of squeezing in the system. Furthermore, we estimate the degree of squeezing using the correlation method and compare it to the standard homodyne measurement scheme. We show that the role of electronic detector noise is minimized using the correlation approach as opposed to homodyning...

  15. Novel implementation of nonlinear joint transform correlators in optical security and validation

    Science.gov (United States)

    Weber, David C.; Trolinger, James D.

    1999-01-01

    Emblems using holograms or other diffractive devices have long been used to mark cards and other objects as a means of authentication. The effectiveness of such emblems as security devices is ultimately determined by the inspection system. Due to the expense and highly variable performance of the human inspector, automated machine reading devices are an attractive alternative for performing the verification task. An additional advantage of the machine reactor is that information regarding the card or its holder can be stored covertly. A security verification system is presented consisting of a holographic security emblem in which information is covertly stored and an automated reader based on a joint transform correlator. A holographic encoding method is used to produce an emblem that stores the required phase and/or amplitude information in the form of a complex, 3D diffraction pattern that can be interpreted only through the use of a second `key' hologram. The reader incorporates the use of the nonlinear material, bacteriorhodopsin, as a means of miniaturizing the system, reducing system cost, and improving system performance. Experimental results are presented that demonstrate the feasibility of the approach for security applications.

  16. Variable angle correlation spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y K [Univ. of California, Berkeley, CA (United States)

    1994-05-01

    In this dissertation, a novel nuclear magnetic resonance (NMR) technique, variable angle correlation spectroscopy (VACSY) is described and demonstrated with {sup 13}C nuclei in rapidly rotating samples. These experiments focus on one of the basic problems in solid state NMR: how to extract the wealth of information contained in the anisotropic component of the NMR signal while still maintaining spectral resolution. Analysis of the anisotropic spectral patterns from poly-crystalline systems reveal information concerning molecular structure and dynamics, yet in all but the simplest of systems, the overlap of spectral patterns from chemically distinct sites renders the spectral analysis difficult if not impossible. One solution to this problem is to perform multi-dimensional experiments where the high-resolution, isotropic spectrum in one dimension is correlated with the anisotropic spectral patterns in the other dimensions. The VACSY technique incorporates the angle between the spinner axis and the static magnetic field as an experimental parameter that may be incremented during the course of the experiment to help correlate the isotropic and anisotropic components of the spectrum. The two-dimensional version of the VACSY experiments is used to extract the chemical shift anisotropy tensor values from multi-site organic molecules, study molecular dynamics in the intermediate time regime, and to examine the ordering properties of partially oriented samples. The VACSY technique is then extended to three-dimensional experiments to study slow molecular reorientations in a multi-site polymer system.

  17. Neural Correlates of Gratitude

    Directory of Open Access Journals (Sweden)

    Glenn Ryan Fox

    2015-09-01

    Full Text Available Gratitude is an important aspect of human sociality, and is valued by religions and moral philosophies. It has been established that gratitude leads to benefits for both mental health and interpersonal relationships. It is thus important to elucidate the neurobiological correlates of gratitude, which are only now beginning to be investigated. To this end, we conducted an experiment during which we induced gratitude in participants while they underwent functional magnetic resonance imaging. We hypothesized that gratitude ratings would correlate with activity in brain regions associated with moral cognition, value judgment and theory of mind. The stimuli used to elicit gratitude were drawn from stories of survivors of the Holocaust, as many survivors report being sheltered by strangers or receiving lifesaving food and clothing, and having strong feelings of gratitude for such gifts. The participants were asked to place themselves in the context of the Holocaust and imagine what their own experience would feel like if they received such gifts. For each gift, they rated how grateful they felt. The results revealed that ratings of gratitude correlated with brain activity in the anterior cingulate cortex and medial prefrontal cortex, in support of our hypotheses. The results provide a window into the brain circuitry for moral cognition and positive emotion that accompanies the experience of benefitting from the goodwill of others.

  18. Spatiotermporal correlations of earthquakes

    International Nuclear Information System (INIS)

    Complete text of publication follows. An earthquake is the result of a sudden release of energy in the Earth's crust that creates seismic waves. At the present technological level, earthquakes of magnitude larger than three can be recorded all over the world. In spite of the apparent randomness of earthquake occurrence, long term measurements have revealed interesting scaling laws of earthquake characteristics: the rate of aftershocks following major earthquakes has a power law decay (Omori law); the magnitude distribution of earthquakes exhibits a power law behavior (Gutenberg-Richter law), furthermore, it has recently been pointed out that epicenters form fractal networks in fault zones (Kagan law). The theoretical explanation of earthquakes is based on plate tectonics: the earth's crust has been broken into plates which slowly move under the action of the flowing magma. Neighboring plates touch each other along ridges (fault zones) where a large amount of energy is stored in deformation. Earthquakes occur when the stored energy exceeds a material dependent threshold value and gets released in a sudden jump of the plate. The Burridge-Knopoff (BK) model of earthquakes represents earth's crust as a coupled system of driven oscillators where nonlinearity occurs through a stick-slip frictional instability. Laboratory experiments have revealed that under a high pressure the friction of rock interfaces exhibits a weakening with increasing velocity. In the present project we extend recent theoretical studies of the BK model by taking into account a realistic velocity weakening friction force between tectonic plates. Varying the strength of weakening a broad spectrum of interesting phenomena is obtained: the model reproduces the Omori and Gutenberg-Richter laws of earthquakes, furthermore, it provides information on the correlation of earthquake sequences. We showed by computer simulations that the spatial and temporal correlations of consecutive earthquakes are very

  19. Antiferromagnetic noise correlations in optical lattices

    DEFF Research Database (Denmark)

    Bruun, Niels Bohr International Academy, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark, Georg Morten; Syljuåsen, F. T.; Pedersen, K. G. L.;

    2009-01-01

    We analyze how noise correlations probed by time-of-flight experiments reveal antiferromagnetic (AF) correlations of fermionic atoms in two-dimensional and three-dimensional optical lattices. Combining analytical and quantum Monte Carlo calculations using experimentally realistic parameters, we...... show that AF correlations can be detected for temperatures above and below the critical temperature for AF ordering. It is demonstrated that spin-resolved noise correlations yield important information about the spin ordering. Finally, we show how to extract the spin correlation length and the related...

  20. Structure of quantum and broadcasting nonlocal correlations

    Science.gov (United States)

    Saha, Debashis; Pawłowski, Marcin

    2015-12-01

    The multipartite setting offers much more complexity of nonlocality than the bipartite one. We analyze the structure of tripartite nonlocal correlations by proposing inequalities satisfied by each of type bilocal, broadcasting, and quantum but violated by the other two. One of the inequalities satisfied by broadcasting correlations is generalized for multipartite systems. The study of its quantum mechanical violation reveals that Greenberger-Horne-Zeilinger-like states exhibit new, powerful correlations.

  1. Heat reveals faults

    Energy Technology Data Exchange (ETDEWEB)

    Weinreich, Bernhard [Solarschmiede GmbH, Muenchen (Germany). Engineering Dept.

    2010-07-01

    Gremlins cannot hide from the all-revealing view of a thermographic camera, whereby it makes no difference whether it is a roof-mounted system or a megawatt-sized farm. Just as diverse are the range of faults that, with the growing level of expertise, can now be detected and differentiated with even greater detail. (orig.)

  2. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    in which case an android robot like the Geminoid|DK –a duplicate of an Original person- reveals emotions convincingly; when following an empirical perspective, or when following a theoretical one. The methodology includes the processes of acquiring the empirical data, and gathering feedback on them. Our...

  3. Correlation and Entanglement

    Institute of Scientific and Technical Information of China (English)

    Shun-long Luo; You-feng Luo

    2003-01-01

    In quantum mechanics, it is long recognized that there exist correlations between observables which are much stronger than the classical ones. These correlations are usually called entanglement, and cannot be accounted for by classical theory. In this paper, we will study correlations between observables in terms of covariance and the Wigner-Yanase correlation, and compare their merits in characterizing entanglement. We will show that the Wigner-Yanase correlation has some advantages over the conventional covariance.

  4. Nonlinear phase contrast using a bacteriorhodopsin film

    Science.gov (United States)

    Iturbe Castillo, Marcelo D.; Sanchez-de-la-Llave, J. D.; Ramos Garcia, Ruben; Tepichin-Rodriguez, Eduardo; Olivos-Perez, L. I.

    2002-11-01

    In this paper we demonstrate a novel phase contrast system that employs a BR film. Since the filter is optically induced by the Fourier transform of the phase object, no alignment is necessary at the filter plane making it extremely robust. Due to the optical properties of BR films the phase filter can be induced with low light intensity levels. The material response allows operation at video frame rates, processing of high spatial resolution objects, and the use of relatively inexpensive laser sources. Such characteristics and the fact that BR films can be produced at a low cost makes the system simple to implement, relatively inexpensive and extremely robust. The effects of varying the illuminating area beyond the phase object area and filter saturation are also analyzed.

  5. Holographic particle image velocimetry using Bacteriorhodopsin

    NARCIS (Netherlands)

    Koek, W.D.

    2006-01-01

    To gain better insight into the behaviour of turbulent flow there is a demand for a practical measurement instrument to perform three-dimensional flow measurements. Holography is a three-dimensional imaging technique, and as such is ideally suited for this purpose. Because flow media (such as water

  6. TypeScript revealed

    CERN Document Server

    Maharry, Dan

    2013-01-01

    TypeScript Revealed is a quick 100-page guide to Anders Hejlsberg's new take on JavaScript. With this brief, fast-paced introduction to TypeScript, .NET, Web and Windows 8 application developers who are already familiar with JavaScript will easily get up to speed with TypeScript and decide whether or not to start incorporating it into their own development. TypeScript is 'JavaScript for Application-scale development'; a superset of JavaScript that brings to it an additional object-oriented-like syntax familiar to .NET programmers that compiles down into simple, clean JavaScript that any browse

  7. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because the textb......One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...... process for which process recordings are a valuable communication media in order to enhance the learning process. Student feedback indicates both high learning outcome and superior learning potential compared to traditional classroom teaching....

  8. Fracture toughness correlations

    International Nuclear Information System (INIS)

    In this study existing fracture parameter correlations are reviewed. Their applicability and reliability are discussed in detail. A new KIC-CVN-correlation, based on a theoretical brittle fracture model, is presented

  9. Teager Correlation Function

    DEFF Research Database (Denmark)

    Bysted, Tommy Kristensen; Hamila, R.; Gabbouj, M.;

    1998-01-01

    A new correlation function called the Teager correlation function is introduced in this paper. The connection between this function, the Teager energy operator and the conventional correlation function is established. Two applications are presented. The first is the minimization of the Teager err...... norm and the second one is the use of the instantaneous Teager correlation function for simultaneous estimation of TDOA and FDOA (Time and Frequency Difference of Arrivals)....

  10. Complementarity and correlations

    OpenAIRE

    Maccone, Lorenzo; Bruss, Dagmar; Macchiavello, Chiara

    2014-01-01

    We provide an interpretation of entanglement based on classical correlations between measurement outcomes of complementary properties: states that have correlations beyond a certain threshold are entangled. The reverse is not true, however. We also show that, surprisingly, all separable nonclassical states exhibit smaller correlations for complementary observables than some strictly classical states. We use mutual information as a measure of classical correlations, but we conjecture that the ...

  11. Chemistry of plutonium revealed

    International Nuclear Information System (INIS)

    In 1941 one goal of the Manhattan Project was to unravel the chemistry of the synthetic element plutonium as rapidly as possible. In this paper the work carried out at Berkeley from the spring of 1942 to the summer of 1945 is described briefly. The aqueous chemistry of plutonium is quite remarkable. Important insights were obtained from tracer experiments, but the full complexity was not revealed until macroscopic amounts (milligrams) became available. Because processes for separation from fission products were based on aqueous solutions, such solution chemistry was emphasized, particularly precipitation and oxidation-reduction behavior. The latter turned out to be unusually intricate when it was discovered that two more oxidation states existed in aqueous solution than had previously been suspected. Further, an equilibrium was rapidly established among the four aqueous oxidation states, while at the same time any three were not in equilibrium. These and other observations made while doing a crash study of a previously unknown element are reported

  12. Echoes in correlated neural systems

    Science.gov (United States)

    Helias, M.; Tetzlaff, T.; Diesmann, M.

    2013-02-01

    Correlations are employed in modern physics to explain microscopic and macroscopic phenomena, like the fractional quantum Hall effect and the Mott insulator state in high temperature superconductors and ultracold atoms. Simultaneously probed neurons in the intact brain reveal correlations between their activity, an important measure to study information processing in the brain that also influences the macroscopic signals of neural activity, like the electroencephalogram (EEG). Networks of spiking neurons differ from most physical systems: the interaction between elements is directed, time delayed, mediated by short pulses and each neuron receives events from thousands of neurons. Even the stationary state of the network cannot be described by equilibrium statistical mechanics. Here we develop a quantitative theory of pairwise correlations in finite-sized random networks of spiking neurons. We derive explicit analytic expressions for the population-averaged cross correlation functions. Our theory explains why the intuitive mean field description fails, how the echo of single action potentials causes an apparent lag of inhibition with respect to excitation and how the size of the network can be scaled while maintaining its dynamical state. Finally, we derive a new criterion for the emergence of collective oscillations from the spectrum of the time-evolution propagator.

  13. Integral and Multidimensional Linear Distinguishers with Correlation Zero

    DEFF Research Database (Denmark)

    Bogdanov, Andrey; Leander, Gregor; Nyberg, Kaisa;

    2012-01-01

    Zero-correlation cryptanalysis uses linear approximations holding with probability exactly 1/2. In this paper, we reveal fundamental links of zero-correlation distinguishers to integral distinguishers and multidimensional linear distinguishers. We show that an integral implies zero-correlation li...

  14. The Dynamic Correlation Between Growth and Unemployment

    OpenAIRE

    Fabien Tripier

    2002-01-01

    We apply the measure of dynamic correlation developed by Croux, Forni and Reichlin (2001) [A measure of comovement for economic variables: theory and empirics. Review of Economics and Statistics 83, 232-241] to the relation between the quarterly rates of unemployment and labor productivity growth for the post-war United-States economy. The application of the dynamic correlation reveals that these variables are strongly related, but in a different manner according to the frequencies considered...

  15. Emergent spatial correlations in stochastically evolving populations

    CERN Document Server

    Grabowski, M; Grabowski, Marek

    1997-01-01

    We study the spatial pattern formation and emerging long range correlations in a model of three species coevolving in space and time according to stochastic contact rules. Analytical results for the pair correlation functions, based on a truncation approximation and supported by computer simulations, reveal emergent strategies of survival for minority agents based on selection of patterns. Minority agents exhibit defensive clustering and cooperative behavior close to phase transitions.

  16. Experimentally witnessing the quantumness of correlations

    CERN Document Server

    Auccaise, R; Celeri, L C; Soares-Pinto, D O; deAzevedo, E R; Bonagamba, T J; Sarthour, R S; Oliveira, I S; Serra, R M

    2011-01-01

    The quantification of quantum correlations (other than entanglement) usually entails laboured numerical optimization procedures demanding quantum state tomographic methods. Thus it is interesting to have a laboratory friendly witness for the nature of correlations. In this article we report a direct experimental implementation of such a witness in a room temperature system by using a nuclear magnetic resonance setup. In our experiment the nature of correlations is revealed by performing only few local magnetization measurements. We also compare the witness results with those for the quantum discord and we obtained a fairly good agreement.

  17. Almost quantum correlations.

    Science.gov (United States)

    Navascués, Miguel; Guryanova, Yelena; Hoban, Matty J; Acín, Antonio

    2015-01-01

    Quantum theory is not only successfully tested in laboratories every day but also constitutes a robust theoretical framework: small variations usually lead to implausible consequences, such as faster-than-light communication. It has even been argued that quantum theory may be special among possible theories. Here we report that, at the level of correlations among different systems, quantum theory is not so special. We define a set of correlations, dubbed 'almost quantum', and prove that it strictly contains the set of quantum correlations but satisfies all-but-one of the proposed principles to capture quantum correlations. We present numerical evidence that the remaining principle is satisfied too. PMID:25697645

  18. Learning efficient correlated equilibria

    KAUST Repository

    Borowski, Holly P.

    2014-12-15

    The majority of distributed learning literature focuses on convergence to Nash equilibria. Correlated equilibria, on the other hand, can often characterize more efficient collective behavior than even the best Nash equilibrium. However, there are no existing distributed learning algorithms that converge to specific correlated equilibria. In this paper, we provide one such algorithm which guarantees that the agents\\' collective joint strategy will constitute an efficient correlated equilibrium with high probability. The key to attaining efficient correlated behavior through distributed learning involves incorporating a common random signal into the learning environment.

  19. Puerto Rico Revealed Preference data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Revealed preference models provide insights into recreational angler behavior and the economic value of recreational fishing trips. Revealed preference data is...

  20. Correlates of Academic Procrastination.

    Science.gov (United States)

    Milgram, Norman A.; And Others

    1993-01-01

    Investigated concurrent correlates of academic procrastination in Israeli college preparatory students (n=113). Procrastination in one course of study was found to be moderately correlated with procrastination in another but not to procrastination in routine tasks of daily living. Procrastination was weakly related to emotional upset about it and…

  1. ALMA correlator computer systems

    Science.gov (United States)

    Pisano, Jim; Amestica, Rodrigo; Perez, Jesus

    2004-09-01

    We present a design for the computer systems which control, configure, and monitor the Atacama Large Millimeter Array (ALMA) correlator and process its output. Two distinct computer systems implement this functionality: a rack- mounted PC controls and monitors the correlator, and a cluster of 17 PCs process the correlator output into raw spectral results. The correlator computer systems interface to other ALMA computers via gigabit Ethernet networks utilizing CORBA and raw socket connections. ALMA Common Software provides the software infrastructure for this distributed computer environment. The control computer interfaces to the correlator via multiple CAN busses and the data processing computer cluster interfaces to the correlator via sixteen dedicated high speed data ports. An independent array-wide hardware timing bus connects to the computer systems and the correlator hardware ensuring synchronous behavior and imposing hard deadlines on the control and data processor computers. An aggregate correlator output of 1 gigabyte per second with 16 millisecond periods and computational data rates of approximately 1 billion floating point operations per second define other hard deadlines for the data processing computer cluster.

  2. Higher-spin correlators

    CERN Document Server

    Alday, Luis F

    2013-01-01

    We analyze the properly normalized three-point correlator of two protected scalar operators and one higher spin twist-two operator in N=4 super Yang-Mills, in the limit of large spin j. The relevant structure constant can be extracted from the OPE of the four-point correlator of protected scalar operators. We show that crossing symmetry of the four point correlator plus a judicious guess for the perturbative structure of the three-point correlator, allow to make a prediction for the structure constant at all loops in perturbation theory, up to terms that remain finite as the spin becomes large. Furthermore, the expression for the structure constant allows to propose an expression for the all loops four-point correlator G(u,v), in the limit u,v -> 0. Our predictions are in perfect agreement with the large j expansion of results available in the literature.

  3. Revealing the Beast Within

    Science.gov (United States)

    2003-07-01

    Deeply Embedded Massive Stellar Clusters Discovered in Milky Way Powerhouse Summary Peering into a giant molecular cloud in the Milky Way galaxy - known as W49 - astronomers from the European Southern Observatory (ESO) have discovered a whole new population of very massive newborn stars . This research is being presented today at the International Astronomical Union's 25th General Assembly held in Sydney, Australia, by ESO-scientist João Alves. With the help of infrared images obtained during a period of excellent observing conditions with the ESO 3.5-m New Technology Telescope (NTT) at the La Silla Observatory (Chile), the astronomers looked deep into this molecular cloud and discovered four massive stellar clusters, with hot and energetic stars as massive as 120 solar masses. The exceedingly strong radiation from the stars in the largest of these clusters is "powering" a 20 light-year diameter region of mostly ionized hydrogen gas (a "giant HII region"). W49 is one of the most energetic regions of star formation in the Milky Way. With the present discovery, the true sources of the enormous energy have now been revealed for the first time, finally bringing to an end some decades of astronomical speculations and hypotheses. PR Photo 21a/03 : Colour Composite of W49A (NTT+SOFI). PR Photo 21b/03 : Radio and Near-Infrared Composite of W49A Giant molecular clouds Stars form predominantly inside Giant Molecular Clouds which populate our Galaxy, the Milky Way. One of the most prominent of these is W49 , which has a mass of a million solar masses. It is located some 37,000 light-years away and is the most luminous star-forming region known in our home galaxy: its luminosity is several million times the luminosity of our Sun. A smaller region within this cloud is denoted W49A - this is one of the strongest radio-emitting areas known in the Galaxy . Massive stars are excessive in all ways. Compared to their smaller and ligther brethren, they form at an Olympic speed and

  4. Hadronic Correlations and Fluctuations

    Energy Technology Data Exchange (ETDEWEB)

    Koch, Volker

    2008-10-09

    We will provide a review of some of the physics which can be addressed by studying fluctuations and correlations in heavy ion collisions. We will discuss Lattice QCD results on fluctuations and correlations and will put them into context with observables which have been measured in heavy-ion collisions. Special attention will be given to the QCD critical point and the first order co-existence region, and we will discuss how the measurement of fluctuations and correlations can help in an experimental search for non-trivial structures in the QCD phase diagram.

  5. Electron correlation in molecules

    CERN Document Server

    Wilson, S

    2007-01-01

    Electron correlation effects are of vital significance to the calculation of potential energy curves and surfaces, the study of molecular excitation processes, and in the theory of electron-molecule scattering. This text describes methods for addressing one of theoretical chemistry's central problems, the study of electron correlation effects in molecules.Although the energy associated with electron correlation is a small fraction of the total energy of an atom or molecule, it is of the same order of magnitude as most energies of chemical interest. If the solution of quantum mechanical equatio

  6. Asymmetric matrices in an analysis of financial correlations

    CERN Document Server

    Kwapien, J; Górski, A Z; Oswiecimka, P

    2006-01-01

    Financial markets are highly correlated systems that reveal both the inter-market dependencies and the correlations among their different components. Standard analyzing techniques include correlation coefficients for pairs of signals and correlation matrices for rich multivariate data. In the latter case one constructs a real symmetric matrix with real non-negative eigenvalues describing the correlation structure of the data. However, if one performs a correlation-function-like analysis of multivariate data, when a stress is put on investigation of delayed dependencies among different types of signals, one can calculate an asymmetric correlation matrix with complex eigenspectrum. From the Random Matrix Theory point of view this kind of matrices is closely related to Ginibre Orthogonal Ensemble (GinOE). We present an example of practical application of such matrices in correlation analyses of empirical data. By introducing the time lag, we are able to identify temporal structure of the inter-market correlation...

  7. Optically fixed photorefractive correlator

    Institute of Scientific and Technical Information of China (English)

    刘友文; 刘立人; 周常河; 徐良瑛

    2002-01-01

    An optically fixed photorefractive correlator is presented, where two-centre non-volatile holographic recording isemployed to write and fix the matched filter in doubly doped LiNbO3 crystals. This correlator shows good correlationcharacteristics and insensitivity to the writing beam during readout. It can be used in cases requiring stability and notrequiring modification for a long period, and it is refreshed optically when new information needs to be registered.

  8. Emerging Correlation Optics

    DEFF Research Database (Denmark)

    Angelsky, Oleg V.; Gbur, Gregory J.; Polyanskii, Peter;

    2012-01-01

    This feature issue of Applied Optics contains a series of selected papers reflecting the state-of-the-art of correlation optics and showing synergetics between the theoretical background and experimental techniques.......This feature issue of Applied Optics contains a series of selected papers reflecting the state-of-the-art of correlation optics and showing synergetics between the theoretical background and experimental techniques....

  9. Correlation Degree and Correlation Coefficient of Multi- Output Functions

    Institute of Scientific and Technical Information of China (English)

    JU Gui-zhi; ZHAO Ya-qun

    2005-01-01

    We present definitions of the correlation degree and correlation coefficient of multi-output functions. Two relationships about the correlation degree of multi-output functions are proved. One is between the correlation degree and independency,the other is between the correlation degree and balance. Especially the paper discusses the correlation degree of affine multioutput functions. We demonstrate properties of the correlation coefficient of multi-output functions. One is the value range of the correlation coefficient, one is the relationship between the correlation coefficient and independency, and another is the sufficient and necessary condition that two multi-output functions are equivalent to each other.

  10. Correlational Neural Networks.

    Science.gov (United States)

    Chandar, Sarath; Khapra, Mitesh M; Larochelle, Hugo; Ravindran, Balaraman

    2016-02-01

    Common representation learning (CRL), wherein different descriptions (or views) of the data are embedded in a common subspace, has been receiving a lot of attention recently. Two popular paradigms here are canonical correlation analysis (CCA)-based approaches and autoencoder (AE)-based approaches. CCA-based approaches learn a joint representation by maximizing correlation of the views when projected to the common subspace. AE-based methods learn a common representation by minimizing the error of reconstructing the two views. Each of these approaches has its own advantages and disadvantages. For example, while CCA-based approaches outperform AE-based approaches for the task of transfer learning, they are not as scalable as the latter. In this work, we propose an AE-based approach, correlational neural network (CorrNet), that explicitly maximizes correlation among the views when projected to the common subspace. Through a series of experiments, we demonstrate that the proposed CorrNet is better than AE and CCA with respect to its ability to learn correlated common representations. We employ CorrNet for several cross-language tasks and show that the representations learned using it perform better than the ones learned using other state-of-the-art approaches. PMID:26654210

  11. Correlation-induced spectral changes

    Science.gov (United States)

    Wolf, Emil; James, Daniel F. V.

    1996-06-01

    This paper presents a review of research, both theoretical and experimental, concerning the influence of coherence properties of fluctuating light sources and of correlation properties of scattering media on the spectra of radiated and scattered fields. Much of this research followed a discovery made in 1986, that the spectrum of light may change on propagation, even in free space. More than 100 papers on this topic have been published to date and many of them are reviewed, or at least mentioned, in this article. After an introduction and a summary of some of the main mathematical results relating to second-order coherence theory of statistically stationary optical fields, spectral changes that may take place on superposing fields produced by two partially correlated sources are discussed. Spectral effects in fields produced by two-dimensional secondary sources and by three-dimensional primary sources are then considered. The section which follows describes spectral changes that may arise when polychromatic light is scattered on media whose physical properties vary randomly either in space and/or in time. A review is also presented of recent research, which has revealed that under certain circumstances the changes in the spectrum of light scattered on random media may imitate the Doppler effect, even though the source, the medium and the observer are all at rest with respect to one another. In the final section a brief review is given of a new emerging technique sometimes called spatial-coherence spectroscopy. It is based on the discovery that it is possible, under certain circumstances, to determine field correlations from spectral measurements.

  12. Correlation-induced spectral changes

    International Nuclear Information System (INIS)

    This paper presents a review of research, both theoretical and experimental, concerning the influence of coherence properties of fluctuating light sources and of correlation properties of scattering media on the spectra of radiated and scattered fields. Much of this research followed a discovery made in 1986, that the spectrum of light may change on propagation, even in free space. More than 100 papers on this topic have been published to date and many of them are reviewed, or at least mentioned, in this article. After an introduction and a summary of some of the main mathematical results relating to second-order coherence theory of statistically stationary optical fields, spectral changes that may take place on superposing fields produced by two partially correlated sources are discussed. Spectral effects in fields produced by two-dimensional secondary sources and by three-dimensional primary sources are then considered. The section which follows describes spectral changes that may arise when polychromatic light is scattered on media whose physical properties vary randomly either in space and/or in time. A review is also presented of recent research, which has revealed that under certain circumstances the changes in the spectrum of light scattered on random media may imitate the Doppler effect, even though the source, the medium and the observer are all at rest with respect to one another. In the final section a brief review is given of a new emerging technique sometimes called spatial-coherence spectroscopy. It is based on the discovery that it is possible, under certain circumstances, to determine field correlations from spectral measurements. (author)

  13. Correlation-Peak Imaging

    Science.gov (United States)

    Ziegler, A.; Metzler, A.; Köckenberger, W.; Izquierdo, M.; Komor, E.; Haase, A.; Décorps, M.; von Kienlin, M.

    1996-08-01

    Identification and quantitation in conventional1H spectroscopic imagingin vivois often hampered by the small chemical-shift range. To improve the spectral resolution of spectroscopic imaging, homonuclear two-dimensional correlation spectroscopy has been combined with phase encoding of the spatial dimensions. From the theoretical description of the coherence-transfer signal in the Fourier-transform domain, a comprehensive acquisition and processing strategy is presented that includes optimization of the width and the position of the acquisition windows, matched filtering of the signal envelope, and graphical presentation of the cross peak of interest. The procedure has been applied to image the spatial distribution of the correlation peaks from specific spin systems in the hypocotyl of castor bean (Ricinus communis) seedlings. Despite the overlap of many resonances, correlation-peak imaging made it possible to observe a number of proton resonances, such as those of sucrose, β-glucose, glutamine/glutamate, lysine, and arginine.

  14. Pair Correlation Function Integrals

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; O'Connell, John P.; Peters, Günther H.J.;

    2011-01-01

    -distance behavior of radial distribution functions is determined by requiring that the corresponding direct correlation functions follow certain approximations at long distances. We have briefly described the method and tested its performance in previous communications [R. Wedberg, J. P. O’Connell, G. H. Peters......, and J. Abildskov, Mol. Simul. 36, 1243 (2010); Fluid Phase Equilib. 302, 32 (2011)], but describe here its theoretical basis more thoroughly and derive long-distance approximations for the direct correlation functions. We describe the numerical implementation of the method in detail, and report...... numerical tests complementing previous results. Pure molecular fluids are here studied in the isothermal-isobaric ensemble with isothermal compressibilities evaluated from the total correlation function integrals and compared with values derived from volume fluctuations. For systems where the radial...

  15. Structure correlation and chemistry

    International Nuclear Information System (INIS)

    The main goal of crystal and molecular structure determination is to provide a starting point for understanding the physical, chemical and biological properties of matter. At present, results from nearly 300000 crystal structure studies are available in computer-readable form. Structure correlation attempts to extract knowledge and understanding from this body of information, which is not available from its parts. This article reviews some typical examples: libraries of prototypal molecular dimensions, mappings of chemical reaction pathways, correlations between structure on one hand and energy, reaction rate, catalytic activity or magnetism on the other. The knowledge gained from structure-correlation studies, together with quantum-chemical and other modeling techniques, provides conceptual and practical tools for designing molecules and materials with tailor-made properties. (orig.)

  16. Nonlocality of quantum correlations

    CERN Document Server

    Streltsov, A; Roga, W; Bruß, D; Illuminati, F

    2012-01-01

    We show that only those composite quantum systems possessing nonvanishing quantum correlations have the property that any nontrivial local unitary evolution changes their global state. This type of nonlocality occurs also for states that do not violate a Bell inequality, such as, for instance, Werner states with a low degree of entanglement. We derive the exact relation between the global state change induced by local unitary evolutions and the amount of quantum correlations. We prove that the minimal change coincides with the geometric measure of discord, thus providing the latter with an operational interpretation in terms of the capability of a local unitary dynamics to modify a global state. We establish rigorously that Werner states are the maximally quantum correlated two-qubit states, and thus are the ones that maximize this novel type of nonlocality.

  17. Correlation ion mobility spectroscopy

    Science.gov (United States)

    Pfeifer, Kent B.; Rohde, Steven B.

    2008-08-26

    Correlation ion mobility spectrometry (CIMS) uses gating modulation and correlation signal processing to improve IMS instrument performance. Closely spaced ion peaks can be resolved by adding discriminating codes to the gate and matched filtering for the received ion current signal, thereby improving sensitivity and resolution of an ion mobility spectrometer. CIMS can be used to improve the signal-to-noise ratio even for transient chemical samples. CIMS is especially advantageous for small geometry IMS drift tubes that can otherwise have poor resolution due to their small size.

  18. Robust correlation tracker

    Indian Academy of Sciences (India)

    M Sankar Kishore; K Veerabhadra Rao

    2001-06-01

    Correlation tracking plays an important role in the automation of weapon systems. Area correlation is an effective technique for tracking targets that have neither prominent features nor high contrast with the background and the ‘target’ can even be an area or a scene of interest. Even though this technique is robust under varying conditions of target background and light conditions, it has some problems like target drift and false registration. When the tracker or target is moving, the registration point drifts due to the discrete pixel size and aspect angle change. In this research work, an attempt has been made to improve the performance of a correlation tracker for tracking ground targets with very poor contrast. In the present work only the CCD visible images with very poor target to background contrast are considered. Applying novel linear and nonlinear filters, the problems present in the correlation tracker are overcome. Confidence and redundancy measures have been proposed to improve the performance by detecting misregistration. The proposed algorithm is tested on different sequences of images and its performance is satisfactory.

  19. HIM Correlational Study

    Science.gov (United States)

    Powell, Evan R.

    1977-01-01

    This study uses two methods of analysis to examine the degree to which items within the cells of the Hill Interaction Matrix correlate. It is found that the table of specifications does not hold up. But the author recommends caution in interpreting this finding. (Author/BP)

  20. Quantum correlations induced by multiple scattering of quadrature squeezed light

    DEFF Research Database (Denmark)

    Lodahl, Peter

    2006-01-01

    Propagating quadrature squeezed light through a multiple scattering random medium is found to induce pronounced spatial quantum correlations that have no classical analogue. The correlations are revealed in the number of photons transported through the sample that can be measured from the intensity...... fluctuations of the total transmission or reflection. In contrast, no pronounced spatial quantum correlations appear in the quadrature amplitudes where excess noise above the shot noise level is found....

  1. From micro-correlations to macro-correlations

    Science.gov (United States)

    Eliazar, Iddo

    2016-11-01

    Random vectors with a symmetric correlation structure share a common value of pair-wise correlation between their different components. The symmetric correlation structure appears in a multitude of settings, e.g. mixture models. In a mixture model the components of the random vector are drawn independently from a general probability distribution that is determined by an underlying parameter, and the parameter itself is randomized. In this paper we study the overall correlation of high-dimensional random vectors with a symmetric correlation structure. Considering such a random vector, and terming its pair-wise correlation "micro-correlation", we use an asymptotic analysis to derive the random vector's "macro-correlation" : a score that takes values in the unit interval, and that quantifies the random vector's overall correlation. The method of obtaining macro-correlations from micro-correlations is then applied to a diverse collection of frameworks that demonstrate the method's wide applicability.

  2. Effect of noise correlations on randomized benchmarking

    Science.gov (United States)

    Ball, Harrison; Stace, Thomas M.; Flammia, Steven T.; Biercuk, Michael J.

    2016-02-01

    Among the most popular and well-studied quantum characterization, verification, and validation techniques is randomized benchmarking (RB), an important statistical tool used to characterize the performance of physical logic operations useful in quantum information processing. In this work we provide a detailed mathematical treatment of the effect of temporal noise correlations on the outcomes of RB protocols. We provide a fully analytic framework capturing the accumulation of error in RB expressed in terms of a three-dimensional random walk in "Pauli space." Using this framework we derive the probability density function describing RB outcomes (averaged over noise) for both Markovian and correlated errors, which we show is generally described by a Γ distribution with shape and scale parameters depending on the correlation structure. Long temporal correlations impart large nonvanishing variance and skew in the distribution towards high-fidelity outcomes—consistent with existing experimental data—highlighting potential finite-sampling pitfalls and the divergence of the mean RB outcome from worst-case errors in the presence of noise correlations. We use the filter-transfer function formalism to reveal the underlying reason for these differences in terms of effective coherent averaging of correlated errors in certain random sequences. We conclude by commenting on the impact of these calculations on the utility of single-metric approaches to quantum characterization, verification, and validation.

  3. Fluorescence correlation spectroscopy in laser gradient field

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Fluorescence correlation spectroscopy (FCS) is capable of probing dynamic processes in living biological systems. From photon fluctuation of fluorescing particles which diffuse through a small detection volume, FCS reveals information on the concentration and the structure of the particles, as well as information on microscopic environment.In this note, we study the radiation forces experienced by Rayleigh particles in a laser field in details, and analyze the effects of gradient field on FCS measurements.

  4. Correlates of Suicidal Behaviors Among Asian Americans

    OpenAIRE

    Duldulao, Aileen Alfonso; Takeuchi, David T.; Hong, Seunghye

    2009-01-01

    This study examines the correlates of suicidal ideation, suicide plan and suicide attempt among Asian Americans focusing on nativity and gender. Analyses are performed on data from the National Latino and Asian American Study (N=2095), the first ever study conducted on the mental health of a national sample of Asian Americans. The sample is comprised of adults with 998 men (47%) and 1,097 (53%) women. Weighted logistic regression analyses reveal that US-born women have a higher percentage tha...

  5. Multiplicities and correlations at LEP

    CERN Document Server

    Sarkisyan-Grinbaum, E

    2002-01-01

    A brief review on recent charge multiplicity and correlation measurements at LEP is given. The measurements of unbiased gluon jet multiplicity are discussed. Recent results on charged particle Bose- Einstein and Fermi-Dirac correlations at LEP1. are reported. New results on two-particle correlations of neutral pions are given. Correlations of more than two particles (high-order correlations) obtained using different methods are performed. Recent Bose-Einstein correlation measurements at LEP2 are discussed. (13 refs).

  6. MR-pathologic correlation of lung specimens

    International Nuclear Information System (INIS)

    The aim of this study was to assess the feasibility of a new MR-pathologic correlation method utilizing a high-resolution MR technique with a 3-inch surface coil and elimination of susceptibility by replacing air in the pulmonary alveoli of lung specimens with water. Inflated cadaver lung specimens of various lung disorders were imaged using a conventional spin echo (SE) sequence in a clinical 1.5T MR scanner. The MR images were correlated with pathologic specimens. In six out of seven specimens, MR revealed detailed images corresponding to pathological changes. MR may provide a non-invasive and non-destructive method for examining lung specimens and for image-pathologic correlation

  7. Strong diquark correlations inside the proton

    Directory of Open Access Journals (Sweden)

    Segovia Jorge

    2016-01-01

    Full Text Available Quantum Chromodynamics is thought to be the relativistic quantum field theory that describes the strong interaction of the Standard Model. This interaction produces mesons but it is also able to generate quark-quark (diquark correlations inside baryons. In this work, we employ a continuum approach to QCD based on Dyson-Schwinger equations to calculate the electromagnetic form factors of the proton and analyze in a deeper way the consequences of having strong diquark correlations. Comparison with the experimental data reveals that the presence of strong diquark correlations within the proton is sufficient to understand empirical extractions of the flavour-separated form factors. The explained reduction of the ratios F1d/F1u and F2d/F2u at high Q2 in the quark-diquark picture are responsible of the precocious scaling of the F2p/F1p observed experimentally.

  8. Correlations and Ostwald ripening

    Science.gov (United States)

    Marder, M.

    1987-01-01

    A previously developed model (Weins and Cahn, 1973) describing the growth of spheres of a second phase in metal alloys (Ostwald coarsening) is slightly modified to make it possible to study the complete time evolution of the system rather than simply the late-stage scaling behavior. Closed equations are obtained which describe the time evolution of two-particle correlations in the system. The development of the correlations is analyzed, and simpler expressions are found and solved numerically. The results are compared with experimental data for different systems (e.g., Ni-Al, Ni-Cr-Al, Co-Ni-Cr-Ti, Cu-Co, and MgO-Fe), alternate methods, and existing theories.

  9. Correlation radio range finder

    Directory of Open Access Journals (Sweden)

    A. Sorochan

    2012-10-01

    Full Text Available In work widely known methods of range measuring are short characterized. The basic attention is given features of signal processing in a correlation method of range measuring. The signal with angular modulation with one-voice-frequency fluctuation is used as a probing signal. The absence of Doppler effect on the formation of the correlation integral, the frequency instability of the transmitter, the phase change on reflection from the target is presented. It is noticed that the result of signal processing in the range measuring instrument is reduced to formation on an exit one-voice-frequency harmonious fluctuation equal to modulating frequency that provides high characteristics of a radio range finder.

  10. Quantum correlations and measurements

    International Nuclear Information System (INIS)

    It is demonstrated that the collapse of the wavefunction in the quantum measurement process is reflected in the two-particle correlation function for the electron spin, which can in principle be studied by a triple Stern-Gerlach experiment. The change in momentum of a Stern-Gerlach magnet is itself sufficient to allow the determination of the electron spin, subject to the uncertainty principle, if the coherence of the two components of the spin is destroyed by the magnetic field. Similar considerations apply to the two-particle correlation function for the photon polarisation, and two-photon atomic cascades can be used in practice to investigate the measurement process and determine the extension of a photon wavepacket. The irreversibility of quantum mechanical measurements and its relation to the uncertainty principle is briefly considered. (author)

  11. Quantum correlations and measurements

    Energy Technology Data Exchange (ETDEWEB)

    Sperling, Jan

    2015-07-16

    The present thesis is a state of the art report on the characterization techniques and measurement strategies to verify quantum correlations. I mainly focus on research which has been performed in the theoretical quantum optics group at the University of Rostock during the last few years. The results include theoretical findings and analysis of experimental studies of radiation fields. We investigate the verification of quantum properties, the quantification of these quantum effects, and the characterization of quantum optical detector systems.

  12. Correlation Algorithm Library

    Energy Technology Data Exchange (ETDEWEB)

    2013-08-02

    CorAL is a software Library designed to aid in the analysis of femtoscipic data. Femtoscopic data are a class of measured quantities used in heavy-ion collisions to characterize particle emitting source sizes. The most common type of this data is two-particle correleations induced by the Hanbury-Brown/Twiss (HBT) Effect, but can also include correlations induced by final-state interactions between pairs of emitted particles in a heavy-ion collision. Because heavy-ion collisions are complex many particle systems, modeling hydrodynamical models or hybrid techniques. Using the CRAB module, CorAL can turn the output from these models into something that can be directley compared to experimental data. CorAL can also take the raw experimentally measured correlation functions and image them by inverting the Koonin-Pratt equation to extract the space-time emission profile of the particle emitting source. This source function can be further analyzed or directly compared to theoretical calculations.

  13. Can Clustering in Genotype Space Reveal "Niches"?

    Science.gov (United States)

    D'Andrea, Rafael; Ostling, Annette

    2016-01-01

    Community ecology lacks the success enjoyed by population genetics to quantify the relative roles played by deterministic and stochastic processes. It has been proposed that clustered patterns of abundance in genotype space provide evidence of selection in microbial communities, since no such clustering would arise in the absence of selection. We critique this test for its unrealistic null hypothesis. We show mathematically and with simulations that point mutations alone lead to clustering in genotype space by causing correlations between abundances of similar genotypes. We also show potential deviations from the mutation-only pattern caused by immigration from a source pool. Clustered patterns in genotype space may still be revealing of selection if analyzed quantitatively but only if neutral and selective regimes can be distinguished once mutation and immigration are included in the null model.

  14. Quantum Correlations Reduce Classical Correlations with Ancillary Systems

    Institute of Scientific and Technical Information of China (English)

    LUO Shun-Long; LI Nan

    2010-01-01

    @@ We illustrate the dichotomy of classical/quantum correlations by virtue of monogamy.More precisely,we show that correlations in a bipartite state are classical if and only if each party of the state can be perfectly correlated with other ancillary systems.In particular,this means that if there are quantum correlations between two parties,then the classical(as well as quantum)correlating capabilities of the two parties with other systems have to be strictly reduced.

  15. Bell correlations in a Bose-Einstein condensate.

    Science.gov (United States)

    Schmied, Roman; Bancal, Jean-Daniel; Allard, Baptiste; Fadel, Matteo; Scarani, Valerio; Treutlein, Philipp; Sangouard, Nicolas

    2016-04-22

    Characterizing many-body systems through the quantum correlations between their constituent particles is a major goal of quantum physics. Although entanglement is routinely observed in many systems, we report here the detection of stronger correlations--Bell correlations--between the spins of about 480 atoms in a Bose-Einstein condensate. We derive a Bell correlation witness from a many-particle Bell inequality involving only one- and two-body correlation functions. Our measurement on a spin-squeezed state exceeds the threshold for Bell correlations by 3.8 standard deviations. Our work shows that the strongest possible nonclassical correlations are experimentally accessible in many-body systems and that they can be revealed by collective measurements. PMID:27102479

  16. Bell correlations in a Bose-Einstein condensate.

    Science.gov (United States)

    Schmied, Roman; Bancal, Jean-Daniel; Allard, Baptiste; Fadel, Matteo; Scarani, Valerio; Treutlein, Philipp; Sangouard, Nicolas

    2016-04-22

    Characterizing many-body systems through the quantum correlations between their constituent particles is a major goal of quantum physics. Although entanglement is routinely observed in many systems, we report here the detection of stronger correlations--Bell correlations--between the spins of about 480 atoms in a Bose-Einstein condensate. We derive a Bell correlation witness from a many-particle Bell inequality involving only one- and two-body correlation functions. Our measurement on a spin-squeezed state exceeds the threshold for Bell correlations by 3.8 standard deviations. Our work shows that the strongest possible nonclassical correlations are experimentally accessible in many-body systems and that they can be revealed by collective measurements.

  17. Quantum correlations; quantum probability approach

    OpenAIRE

    Majewski, W A

    2014-01-01

    This survey gives a comprehensive account of quantum correlations understood as a phenomenon stemming from the rules of quantization. Centered on quantum probability it describes the physical concepts related to correlations (both classical and quantum), mathematical structures, and their consequences. These include the canonical form of classical correlation functionals, general definitions of separable (entangled) states, definition and analysis of quantumness of correlations, description o...

  18. Bootstrapped Deattenuated Correlation: Nonnormal Distributions

    Science.gov (United States)

    Padilla, Miguel A.; Veprinsky, Anna

    2014-01-01

    Correlation attenuation due to measurement error and a corresponding correction, the deattenuated correlation, have been known for over a century. Nevertheless, the deattenuated correlation remains underutilized. A few studies in recent years have investigated factors affecting the deattenuated correlation, and a couple of them provide alternative…

  19. Biological Correlates of Empathy

    Directory of Open Access Journals (Sweden)

    E. Timucin Oral

    2010-04-01

    Full Text Available Empathy can be defined as the capacity to know emotionally what another is experiencing from within the frame of reference of that other person and the capacity to sample the feelings of another or it can be metaphorized as to put oneself in another’s shoes. Although the concept of empathy was firstly described in psychological theories, researches studying the biological correlates of psychological theories have been increasing recently. Not suprisingly, dinamically oriented psychotherapists Freud, Kohut, Basch and Fenichel had suggested theories about the biological correlates of empathy concept and established the basis of this modality decades ago. Some other theorists emphasized the importance of empathy in the early years of lifetime regarding mother-child attachment in terms of developmental psychology and investigated its role in explanation of psychopathology. The data coming from some of the recent brain imaging and animal model studies also seem to support these theories. Although increased activity in different brain regions was shown in many of the brain imaging studies, the role of cingulate cortex for understanding mother-child relationship was constantly emphasized in nearly all of the studies. In addition to these studies, a group of Italian scientists has defined a group of neurons as “mirror neurons” in their studies observing rhesus macaque monkeys. Later, they also defined mirror neurons in human studies, and suggested them as “empathy neurons”. After the discovery of mirror neurons, the hopes of finding the missing part of the puzzle for understanding the biological correlates of empathy raised again. Although the roles of different biological parameters such as skin conductance and pupil diameter for defining empathy have not been certain yet, they are going to give us the opportunity to revise the inconsistent basis of structural validity in psychiatry and to stabilize descriptive validity. In this review, the

  20. The isotope correlation experiment

    International Nuclear Information System (INIS)

    The ESARDA working group on Isotopic Correlation Techniques, ICT and Reprocessing Input Analysis performed an Isotope Correlation Experiment, ICE with the aim to check the feasibility of the new technique. Ten input batches of the reprocessing of the KWO fuel at the WAK plant were analysed by 4 laboratories. All information to compare ICT with the gravimetric and volumetric methods was available. ICT combined with simplified reactor physics calculation was included. The main objectives of the statistical data evaluation were detection of outliers, the estimation of random errors and of systematic errors of the measurements performed by the 4 laboratories. Different methods for outlier detection, analysis of variances, Grubbs' analysis for the constant-bias model and Jaech's non-constant-bias model were applied. Some of the results of the statistical analysis may seem inconsistent which is due to the following reasons. For the statistical evaluations isotope abundance data (weight percent) as well as nuclear concentration data (atoms/initial metal atoms) were subjected to different outlier criteria before being used for further statistical evaluations. None of the four data evaluation groups performed a complete statistical data analysis which would render possible a comparison of the different methods applied since no commonly agreed statistical evaluation procedure existed. The results prove that ICT is as accurate as conventional techniques which have to rely on costly mass spectrometric isotope dilution analysis. The potential of outlier detection by ICT on the basis of the results from a single laboratory is as good as outlier detection by costly interlaboratory comparison. The application of fission product or Cm-244 correlations would be more timely than remeasurements at safeguards laboratories

  1. Strongly correlated Bose gases

    Science.gov (United States)

    Chevy, F.; Salomon, C.

    2016-10-01

    The strongly interacting Bose gas is one of the most fundamental paradigms of quantum many-body physics and the subject of many experimental and theoretical investigations. We review recent progress on strongly correlated Bose gases, starting with a description of beyond mean-field corrections. We show that the Efimov effect leads to non universal phenomena and to a metastability of the low temperature Bose gas through three-body recombination to deeply bound molecular states. We outline differences and similarities with ultracold Fermi gases, discuss recent experiments on the unitary Bose gas, and finally present a few perspectives for future research.

  2. Multiparticle azimuthal correlations

    Indian Academy of Sciences (India)

    N Borghini; P M Dinh; J-Y Ollitrault

    2003-04-01

    First observations of elliptic flow in Au–Au collisions at RHIC have been interpreted as evidence that the colliding system reaches thermal equilibrium. We discuss some of the arguments leading to this conclusion and show that a more accurate analysis is needed, which the standard flow analysis may not provide. We then present a new method of flow analysis, based on a systematic study of multiparticle azimuthal correlations. This method allows one to test quantitatively the collective behaviour of the interacting system. It has recently been applied by the STAR Collaboration at RHIC.

  3. Jet-quenching and correlations

    Indian Academy of Sciences (India)

    Fuqiang Wang

    2015-05-01

    This article reviews recent advances in our understanding of the experimental aspects of jet-quenching and correlations in relativistic heavy-ion collisions at RHIC and LHC. Emphasis is put on correlation measurements, namely jet-like correlations with anisotropic flow subtraction in heavy-ion collisions and long-range pseudorapidity correlations in small systems. Future path on correlation studies is envisioned which may elucidate jet–medium interactions and the properties of the hot dense medium in QCD.

  4. Nonlinear Correlations of Protein Sequences and Symmetries of Their Structures

    Institute of Scientific and Technical Information of China (English)

    LI Ming-Feng; HUANG Yan-Zhao; XIAO Yi

    2005-01-01

    @@ We investigate the nonlinear correlations of protein sequences by using the nonlinear prediction method developed in nonlinear dynamical theory.It is found that a lot of protein sequences show strong nonlinear correlations and have deterministic structures.Further investigations show that the strong nonlinear correlations of these protein sequences are due to the symmetries of their tertiary structures.Furthermore, the correlation lengths of the sequences are related to the degrees of the symmetries.These results support the duplication mechanism of protein evolution and also reveal one aspect how amino acid sequences encode their spatial structures.

  5. Revealing and Concealing in Antiquity

    DEFF Research Database (Denmark)

    implications in Antiquity, Late Antiquity and the Renaissance in eleven cross-disciplinary contributions using both textual and archaeological sources. By exploring the revealing and concealing of knowledge across different social contexts, time frames and geographical locations, the book provides insight...

  6. Decision Making and Revealed Preference

    DEFF Research Database (Denmark)

    de la Rosa, Leonidas Enrique

    If our decision-making processes are to some extent shaped by evolutionary pressures and our environment is different from that to which we adapted, some of our choices will not be in our best interest. But revealed preference is the only tool that we have so far to conduct a normative analysis...

  7. Neural correlates of mystical experience.

    Science.gov (United States)

    Cristofori, Irene; Bulbulia, Joseph; Shaver, John H; Wilson, Marc; Krueger, Frank; Grafman, Jordan

    2016-01-01

    Mystical experiences, or subjectively believed encounters with a supernatural world, are widely reported across cultures and throughout human history. Previous theories speculate that executive brain functions underpin mystical experiences. To evaluate causal hypotheses, structural studies of brain lesion are required. Previous studies suffer from small samples or do not have valid measures of cognitive functioning prior to injury. We investigated mystical experience among participants from the Vietnam Head Injury Study and compared those who suffered penetrating traumatic brain injury (pTBI; n=116) with matched healthy controls (HC; n=32). Voxel-based lesion-symptom mapping analysis showed that lesions to frontal and temporal brain regions were linked with greater mystical experiences. Such regions included the dorsolateral prefrontal cortex (dlPFC) and middle/superior temporal cortex (TC). In a confirmatory analysis, we grouped pTBI patients by lesion location and compared mysticism experiences with the HC group. The dlPFC group presented markedly increased mysticism. Notably, longitudinal analysis of pre-injury data (correlating with general intelligence and executive performance) excludes explanations from individual differences. Our findings support previous speculation linking executive brain functions to mystical experiences, and reveal that executive functioning (dlPFC) causally contributes to the down-regulation of mystical experiences. PMID:26631541

  8. Energy calibration via correlation

    CERN Document Server

    Maier, Daniel

    2015-01-01

    The main task of an energy calibration is to find a relation between pulse-height values and the corresponding energies. Doing this for each pulse-height channel individually requires an elaborated input spectrum with an excellent counting statistics and a sophisticated data analysis. This work presents an easy to handle energy calibration process which can operate reliably on calibration measurements with low counting statistics. The method uses a parameter based model for the energy calibration and concludes on the optimal parameters of the model by finding the best correlation between the measured pulse-height spectrum and multiple synthetic pulse-height spectra which are constructed with different sets of calibration parameters. A CdTe-based semiconductor detector and the line emissions of an 241 Am source were used to test the performance of the correlation method in terms of systematic calibration errors for different counting statistics. Up to energies of 60 keV systematic errors were measured to be le...

  9. Correlation networks visualization

    Directory of Open Access Journals (Sweden)

    Nicholas J. Provart

    2012-10-01

    Full Text Available New, in silico ways of generating hypotheses based on large data sets have emerged in the past decade. These data sets have been used to investigate different aspects of plant biology, especially at the level of transcriptome, from tissue-specific expression patterns to patterns in as little as a few cells. Such publicly-available data are a boon to researchers for hypothesis generation by providing a guide for experimental work such as phenotyping or genetic analysis. More advanced computational methods can leverage these data via gene coexpression analysis, the results of which can be visualized and refined using network analysis. Other kinds of networks of e.g. protein-protein interactions, can also be used to inform biology. These networks can be visualized and analyzed with additional information on gene expression levels, subcellular localization, etc., or with other emerging kinds information. Finally, cross-level correlation is an area that will become increasingly important. Visualizing these cross-level correlations will require new data visualization tools.

  10. PREFACE: Correlated Electrons (Japan)

    Science.gov (United States)

    Miyake, Kazumasa

    2007-03-01

    This issue of Journal of Physics: Condensed Matter is dedicated to results in the field of strongly correlated electron systems under multiple-environment. The physics of strongly correlated electron systems (SCES) has attracted much attention since the discovery of superconductivity in CeCu_2 Si_2 by Steglich and his co-workers a quater-century ago. Its interest has been intensified by the discovery of high-Tc superconductivity in a series of cuprates with layered perovskite structure which are still under active debate. The present issue of Journal of Physics: Condensed Matter present some aspects of SCES physics on the basis of activities of a late project "Centre-Of-Excellence" supported by MEXT (Ministry of Education, Sports, Science, Culture and Technology of the Japanese Government). This project has been performed by a condensed matter physics group in the faculties of science and engineering science of Osaka University. Although this project also covers correlated phenomena in optics and nano-scale systems, we focus here on the issues of SCES related to superconductivity, mainly unconventional. The present issue covers the discussions on a new mechanism of superconductivity with electronic origin (critical valence fluctuation mechanism), interplay and unification of magnetism and superconductivity in SCES based on a systematic study of NQR under pressure, varieties of Fermi surface of Ce- and U-based SCES probed by the de Haas-van Alphen effect, electronic states probed by a bulk sensitive photoemission spectroscopy with soft X-ray, pressure induced superconductivity of heavy electron materials, pressure dependence of superconducting transition temperature based on a first-principle calculation, and new superconductors under very high-pressure. Some papers offer readers' reviews of the relevant fields and/or include new developments of this intriguing research field of SCES. Altogether, the papers within this issue outline some aspects of electronic states

  11. Flatbands under correlated perturbations.

    Science.gov (United States)

    Bodyfelt, Joshua D; Leykam, Daniel; Danieli, Carlo; Yu, Xiaoquan; Flach, Sergej

    2014-12-01

    Flatband networks are characterized by the coexistence of dispersive and flatbands. Flatbands (FBs) are generated by compact localized eigenstates (CLSs) with local network symmetries, based on destructive interference. Correlated disorder and quasiperiodic potentials hybridize CLSs without additional renormalization, yet with surprising consequences: (i) states are expelled from the FB energy E_{FB}, (ii) the localization length of eigenstates vanishes as ξ∼1/ln(E-E_{FB}), (iii) the density of states diverges logarithmically (particle-hole symmetry) and algebraically (no particle-hole symmetry), and (iv) mobility edge curves show algebraic singularities at E_{FB}. Our analytical results are based on perturbative expansions of the CLSs and supported by numerical data in one and two lattice dimensions. PMID:25526142

  12. Some correlates of trust.

    Science.gov (United States)

    Frost, T; Stimpson, D V; Maughan, M R

    1978-05-01

    Trust has been variously defined by behavioral scientists and not very thoroughly investigated. In this study trust was defined as an expectancy held by an individual that the behavior of another person or a group would be altruistic and personally beneficial. An attempt was made, using this conceptual definition, to identify some personality and behavioral correlates of trust. Seven interpersonal relations groups with approximately 10 male and female undergraduates per group were studied with use of the Janis and Field self-esteem inventory, Schutz's FIRO-B scale, and the Rotter internal-external scale. It was discovered that a trusted person is one who is highly influential, has an internal locus of control, a low need to control others, high self-esteem, and is open to being influenced by others.

  13. Forward central jets correlations

    International Nuclear Information System (INIS)

    The azimuthal correlation between forward and central jets has been measured in pp collisions with the CMS detector at the LHC at the centre-of-mass energy of 7 TeV. The forward jet is required to be reconstructed in the hadronic forward calorimeter, within the pseudo-rapidity 3.2t>35 GeV. The measurement of the azimuthal angle between the jets is performed for different separations in pseudo-rapidity between the jets, with the largest separation being 7.5 units. The measurement is repeated for two subsamples of events, one in which an additional jet is required between the forward and the central jet, and one where the additional jet is vetoed. The measurement is compared to several different Monte Carlo models and tunes.

  14. Flatbands under Correlated Perturbations

    Science.gov (United States)

    Bodyfelt, Joshua D.; Leykam, Daniel; Danieli, Carlo; Yu, Xiaoquan; Flach, Sergej

    2014-12-01

    Flatband networks are characterized by the coexistence of dispersive and flatbands. Flatbands (FBs) are generated by compact localized eigenstates (CLSs) with local network symmetries, based on destructive interference. Correlated disorder and quasiperiodic potentials hybridize CLSs without additional renormalization, yet with surprising consequences: (i) states are expelled from the FB energy EFB, (ii) the localization length of eigenstates vanishes as ξ ˜1 /ln (E -EFB) , (iii) the density of states diverges logarithmically (particle-hole symmetry) and algebraically (no particle-hole symmetry), and (iv) mobility edge curves show algebraic singularities at EFB . Our analytical results are based on perturbative expansions of the CLSs and supported by numerical data in one and two lattice dimensions.

  15. Urticarial vasculitis reveals unsuspected thyroiditis.

    Science.gov (United States)

    Ferreira, Olga; Mota, Alberto; Baudrier, Teresa; Azevedo, Filomena

    2012-01-01

    A 38-year-old woman presented with erythematous, violaceous plaques with a serpiginous and unusual appearance located on the left shoulder, left thigh, and right buttock, evolving for 5 days, which eventually became generalized. A skin biopsy revealed leukocytoclastic vasculitis and a diagnosis of urticarial vasculitis was made. The complete blood count, biochemistry, complement levels, and other immunological test results were unremarkable. However, antithyroid antibody titers were increased. Despite having normal thyroid function tests and an absence of specific symptoms, the patient underwent a thyroid ultrasound, which revealed features of thyroiditis, and was subsequently referred to an endocrinologist. Several diseases can be associated with urticarial vasculitis, namely infections and autoimmune connective-tissue disorders such as systemic lupus erythematosus and Sjögren syndrome. Thyroiditis is an uncommon association. PMID:23000939

  16. Correlated signals and causal transport in ocean circulation

    Science.gov (United States)

    Jeffress, Stephen

    2014-05-01

    This paper presents a framework for interpreting the time-lagged correlation of oceanographic data in terms of physical transport mechanisms. Previous studies have inferred aspects of ocean circulation by correlating fluctuations in temperature and salinity measurements at distant stations. Typically, the time-lag of greatest correlation is interpreted as an advective transit time and hence the advective speed of the current. In this paper we relate correlation functions directly to the underlying equations of fluid transport. This is accomplished by expressing the correlation functions in terms of the Green's function of the transport equation. Two types of correlation functions are distinguished: field-forcing correlation and field-field correlation. Their unique relationships to the Green's function are illustrated in two idealized models of geophysical transport: a leaky pipe model and an advective-diffusive model. Both models show that the field-forcing correlation function converges to the Green's function as the characteristic (time or length) scale of forcing autocorrelation decreases. The leaky pipe model provides an explanation for why advective speeds inferred from time-lagged correlations are often less than the speed of the main current. The advective-diffusive model reveals a structural bias in the field-field correlation function when used to estimate transit times.

  17. Neuroanatomical correlates of tinnitus revealed by cortical thickness analysis and diffusion tensor imaging

    International Nuclear Information System (INIS)

    Tinnitus is a poorly understood auditory perception of sound in the absence of external stimuli. Convergent evidence proposes that tinnitus perception involves brain structural alterations as part of its pathophysiology. The aim of this study is to investigate the structural brain changes that might be associated with tinnitus-related stress and negative emotions. Using high-resolution magnetic resonance imaging and diffusion tensor imaging, we investigated grey matter and white matter (WM) alterations by estimating cortical thickness measures, fractional anisotropy and mean diffusivity in 14 tinnitus subjects and 14 age- and sex-matched non-tinnitus subjects. Significant cortical thickness reductions were found in the prefrontal cortex (PFC), temporal lobe and limbic system in tinnitus subjects compared to non-tinnitus subjects. Tinnitus sufferers were found to have disrupted WM integrity in tracts involving connectivity of the PFC, temporal lobe, thalamus and limbic system. Our results suggest that such neural changes may represent neural origins for tinnitus or consequences of tinnitus and its associations. (orig.)

  18. Neuroanatomical correlates of tinnitus revealed by cortical thickness analysis and diffusion tensor imaging

    Energy Technology Data Exchange (ETDEWEB)

    Aldhafeeri, Faten M. [The University of Liverpool, Department of Medical Imaging, School of Health Sciences, Liverpool (United Kingdom); King Khalid General Hospital, Ministry of Health, Radiology Department, Hafral-batin (Saudi Arabia); Mackenzie, Ian; Kay, Tony [Aintree University Hospitals NHS Foundation Trust, Liverpool (United Kingdom); Alghamdi, Jamaan [The University of Liverpool, Department of Medical Imaging, School of Health Sciences, Liverpool (United Kingdom); King Abdul Aziz University, Physics Department, Faculty of Sciences, Jeddah (Saudi Arabia); Sluming, Vanessa [The University of Liverpool, Department of Medical Imaging, School of Health Sciences, Liverpool (United Kingdom); Magnetic Resonance and Image Analysis Research Centre, Liverpool (United Kingdom)

    2012-08-15

    Tinnitus is a poorly understood auditory perception of sound in the absence of external stimuli. Convergent evidence proposes that tinnitus perception involves brain structural alterations as part of its pathophysiology. The aim of this study is to investigate the structural brain changes that might be associated with tinnitus-related stress and negative emotions. Using high-resolution magnetic resonance imaging and diffusion tensor imaging, we investigated grey matter and white matter (WM) alterations by estimating cortical thickness measures, fractional anisotropy and mean diffusivity in 14 tinnitus subjects and 14 age- and sex-matched non-tinnitus subjects. Significant cortical thickness reductions were found in the prefrontal cortex (PFC), temporal lobe and limbic system in tinnitus subjects compared to non-tinnitus subjects. Tinnitus sufferers were found to have disrupted WM integrity in tracts involving connectivity of the PFC, temporal lobe, thalamus and limbic system. Our results suggest that such neural changes may represent neural origins for tinnitus or consequences of tinnitus and its associations. (orig.)

  19. Contribution of psychoacoustics and neuroaudiology in revealing correlation of mental disorders with central auditory processing disorders

    OpenAIRE

    Iliadou, V; Iakovides, S

    2003-01-01

    Background Psychoacoustics is a fascinating developing field concerned with the evaluation of the hearing sensation as an outcome of a sound or speech stimulus. Neuroaudiology with electrophysiologic testing, records the electrical activity of the auditory pathways, extending from the 8th cranial nerve up to the cortical auditory centers as a result of external auditory stimuli. Central Auditory Processing Disorders may co-exist with mental disorders and complicate diagnosis and outcome. Desi...

  20. Multipion correlations induced by isospin conservation of coherent emission

    CERN Document Server

    Gangadharan, Dhevan

    2016-01-01

    Recent measurements have revealed a significant suppression of multipion Bose-Einstein correlations in heavy-ion collisions at the LHC. The suppression may be explained by postulating coherent pion emission. Typically, the suppression of Bose-Einstein correlations due to coherence is taken into account with the coherent state formalism in quantum optics. However, since charged pion correlations are most often measured, the additional constraint of isospin conservation, which is absent in quantum optics, needs to be taken into account. As a consequence, correlations emerge between pions of opposite charge. A calculation of the correlations induced by isospin conservation of coherent emission is made for two, three- and four-pion correlation functions and compared to the data from the LHC.

  1. Robust Statistical Detection of Power-Law Cross-Correlation

    Science.gov (United States)

    Blythe, Duncan A. J.; Nikulin, Vadim V.; Müller, Klaus-Robert

    2016-06-01

    We show that widely used approaches in statistical physics incorrectly indicate the existence of power-law cross-correlations between financial stock market fluctuations measured over several years and the neuronal activity of the human brain lasting for only a few minutes. While such cross-correlations are nonsensical, no current methodology allows them to be reliably discarded, leaving researchers at greater risk when the spurious nature of cross-correlations is not clear from the unrelated origin of the time series and rather requires careful statistical estimation. Here we propose a theory and method (PLCC-test) which allows us to rigorously and robustly test for power-law cross-correlations, correctly detecting genuine and discarding spurious cross-correlations, thus establishing meaningful relationships between processes in complex physical systems. Our method reveals for the first time the presence of power-law cross-correlations between amplitudes of the alpha and beta frequency ranges of the human electroencephalogram.

  2. Cross-correlation laser scattering.

    OpenAIRE

    Kam, Z; Rigler, R

    1982-01-01

    Cross-correlation between two detectors was applied to analyze laser light-scattering fluctuations. Laser scattering from random concentration fluctuations is spatially coherent over small angular areas that are inversely proportional in size to the dimension of the scattering volume. By cross-correlating scattering intensity fluctuations in different angles, the correlation due to relaxation of concentration fluctuations is practically eliminated, and correlations reflecting changes in the s...

  3. A Note on Intrinsic Correlation

    OpenAIRE

    Du, Songzi

    2008-01-01

    In this note we characterize the strategic implication of intrinsic correlation, introduced by Brandenburger and Friedenberg (2008), in the subjective correlated equilibrium setting of a complete information game. Intrinsic correlation restricts correlation devices to variables within the game, i.e. players's beliefs (and higher order beliefs) about each other's strategies, in contrast to signals or sunspots from the "outside." The characterization is a strengthening of best-response set wi...

  4. On the Kendall Correlation Coefficient

    OpenAIRE

    Stepanov, Alexei

    2015-01-01

    In the present paper, we first discuss the Kendall rank correlation coefficient. In continuous case, we define the Kendall rank correlation coefficient in terms of the concomitants of order statistics, find the expected value of the Kendall rank correlation coefficient and show that the later is free of n. We also prove that in continuous case the Kendall correlation coefficient converges in probability to its expected value. We then propose to consider the expected value of the Kendall rank ...

  5. Lagged correlation networks

    Science.gov (United States)

    Curme, Chester

    Technological advances have provided scientists with large high-dimensional datasets that describe the behaviors of complex systems: from the statistics of energy levels in complex quantum systems, to the time-dependent transcription of genes, to price fluctuations among assets in a financial market. In this environment, where it may be difficult to infer the joint distribution of the data, network science has flourished as a way to gain insight into the structure and organization of such systems by focusing on pairwise interactions. This work focuses on a particular setting, in which a system is described by multivariate time series data. We consider time-lagged correlations among elements in this system, in such a way that the measured interactions among elements are asymmetric. Finally, we allow these interactions to be characteristically weak, so that statistical uncertainties may be important to consider when inferring the structure of the system. We introduce a methodology for constructing statistically validated networks to describe such a system, extend the methodology to accommodate interactions with a periodic component, and show how consideration of bipartite community structures in these networks can aid in the construction of robust statistical models. An example of such a system is a financial market, in which high frequency returns data may be used to describe contagion, or the spreading of shocks in price among assets. These data provide the experimental testing ground for our methodology. We study NYSE data from both the present day and one decade ago, examine the time scales over which the validated lagged correlation networks exist, and relate differences in the topological properties of the networks to an increasing economic efficiency. We uncover daily periodicities in the validated interactions, and relate our findings to explanations of the Epps Effect, an empirical phenomenon of financial time series. We also study bipartite community

  6. Estimating the Polyserial Correlation Coefficient.

    Science.gov (United States)

    Bedrick, Edward J.; Breslin, Frederick C.

    1996-01-01

    Simple noniterative estimators of the polyserial correlation coefficient are developed by exploiting a general relationship between the polyserial correlation and the point polyserial correlation to give extensions of the biserial estimators of K. Pearson (1909), H. E. Brogden (1949), and F. M. Lord (1963) to the multicategory setting. (SLD)

  7. Model validation: Correlation for updating

    Indian Academy of Sciences (India)

    D J Ewins

    2000-06-01

    In this paper, a review is presented of the various methods which are available for the purpose of performing a systematic comparison and correlation between two sets of vibration data. In the present case, the application of interest is in conducting this correlation process as a prelude to model correlation or updating activity.

  8. Correlates of Sensitive Technologies

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Paul [Texas A & M Univ., College Station, TX (United States)

    2016-04-22

    By “Quantitative Empirical Analysis” (QEA) is intended the use of statistical methods to infer, from data that often tend to be of a historical nature, the characteristics of states that correlate with some designated dependent variable (e.g. proliferation of nuclear weapons). QEA is a well-established approach in the social sciences, but is not notably well-known among physical scientists, who tend to think of the social sciences as inherently qualitative. This article attempts to provide a snapshot of research, most of which has evolved over the past decade, involving the application of QEA to issues in which the dependent variable of interest is intended as some measure of nuclear proliferation. Standard practices in QEA are described, especially as they relate to data collection. The QEA approach is compared and contrasted to other quantitative approaches to studying proliferation-related issues, including a “figure of merit” approach that has largely been developed within the DOE complex, and two distinct methodologies termed in a recent US National Academy of Sciences study as “case by case” and “predefined framework.” Sample results from QEA applied to proliferation are indicated, as are doubts about such quantitative approaches. A simplistic decision-theoretic model of the optimal time for the international community to intervene in a possible proliferation scenario is used to illustrate the possibility of synergies between different approaches

  9. Spectral correlates lexical prosody

    Science.gov (United States)

    Okobi, Anthony

    2005-09-01

    The purpose of this study is to derive a quantitative acoustic model of lexical-prosodic characteristics of stressed vowels by looking at several spectral properties associated with the articulatory mechanisms used in speech production. Native speakers of American English were asked to name disyllabic visualizable nouns. Words containing liquids or glides were not used in this study because of their effect on the spectra of adjacent vowels. Subjects uttered short phrases in which the target word was pitch accent half of the time and unaccented the other half. Results show that within the category of full vowels, unstressed and stressed vowels can be distinguished by syllable/vowel durations and spectral tilt. Spectral tilt (SpT) is an acoustic measure related to the degree of glottal spreading. Stressed full vowels had longer duration and less SpT. Distinction between unaccented and accented stressed vowels can be made by amplitude of voicing (AV), F0 (pitch), and intensity contour differences. Accented stressed vowels have higher pitch, and greater AV and intensity. These results suggest that there are acoustic correlates to lexical stress that can be used to determine the stressed syllable of a word, regardless of whether or not it is pitch accented. [Work supported by NIH T32-DC00038.

  10. Transparency masters for mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1980-01-01

    Transparency Masters for Mathematics Revealed focuses on master diagrams that can be used for transparencies for an overhead projector or duplicator masters for worksheets. The book offers information on a compilation of master diagrams prepared by John R. Stafford, Jr., audiovisual supervisor at the University of Missouri at Kansas City. Some of the transparencies are designed to be shown horizontally. The initial three masters are number lines and grids that can be used in a mathematics course, while the others are adaptations of text figures which are slightly altered in some instances. The

  11. Harvesting correlations from the quantum vacuum

    CERN Document Server

    Pozas-Kerstjens, Alejandro

    2015-01-01

    We analyze the harvesting of entanglement and classical correlations from the quantum vacuum to particle detectors. We assess the impact on the detectors' harvesting ability of the spacetime dimensionality, the suddenness of the detectors' switching, their physical size and their internal energy structure. Our study reveals several interesting dependences on these parameters that can be used to optimize the harvesting of classical and quantum correlations. Furthermore, we find that, contrary to previous belief, smooth switching is much more efficient than sudden switching in order to harvest vacuum entanglement, especially when the detectors remain spacelike separated. Additionally, we show that the reported phenomenology of spacelike entanglement harvesting is not altered by subleading order perturbative corrections.

  12. Surface-Bulk Vibrational Correlation Spectroscopy.

    Science.gov (United States)

    Roy, Sandra; Covert, Paul A; Jarisz, Tasha A; Chan, Chantelle; Hore, Dennis K

    2016-05-01

    Homo- and heterospectral correlation analysis are powerful methods for investigating the effects of external influences on the spectra acquired using distinct and complementary techniques. Nonlinear vibrational spectroscopy is a selective and sensitive probe of surface structure changes, as bulk molecules are excluded on the basis of symmetry. However, as a result of this exquisite specificity, it is blind to changes that may be occurring in the solution. We demonstrate that correlation analysis between surface-specific techniques and bulk probes such as infrared absorption or Raman scattering may be used to reveal additional details of the adsorption process. Using the adsorption of water and ethanol binary mixtures as an example, we illustrate that this provides support for a competitive binding model and adds new insight into a dimer-to-bilayer transition proposed from previous experiments and simulations. PMID:27058265

  13. Monofractal nature of air temperature signals reveals their climate variability

    CERN Document Server

    Deliège, Adrien

    2014-01-01

    We use the discrete "wavelet transform microscope" to show that the surface air temperature signals of weather stations selected in Europe are monofractal. This study reveals that the information obtained in this way are richer than previous works studying long range correlations in meteorological stations. The approach presented here allows to bind the H\\"older exponents with the climate variability. We also establish that such a link does not exist with methods previously carried out.

  14. DSN Beowulf Cluster-Based VLBI Correlator

    Science.gov (United States)

    Rogstad, Stephen P.; Jongeling, Andre P.; Finley, Susan G.; White, Leslie A.; Lanyi, Gabor E.; Clark, John E.; Goodhart, Charles E.

    2009-01-01

    used to delegate parallel tasks between nodes and storage areas (see Figure 2). This script forks into three processes: extract, translate, and correlate. Each of these processes iterates on available scan data and updates the status database as the work for each scan is completed. The extract process coordinates and monitors the transfer of data from each of the Mark5s to the Beowulf RAID storage systems. The translate process monitors and executes the data conversion processes on available scan files, and writes the translated files to the slave nodes. The correlate process monitors the execution of SoftC correlation processes on the slave nodes for scans that have completed translation. A comparison of the JVC and the legacy Block II correlator outputs reveals they are well within a formal error, and that the data are comparable with respect to their use in flight navigation. The processing speed of the JVC is improved over the Block II correlator by a factor of 4, largely due to the elimination of the reel-to-reel tape drives used in the Block II correlator.

  15. Quotient correlation: A sample based alternative to Pearson's correlation

    OpenAIRE

    Zhang, Zhengjun

    2008-01-01

    The quotient correlation is defined here as an alternative to Pearson’s correlation that is more intuitive and flexible in cases where the tail behavior of data is important. It measures nonlinear dependence where the regular correlation coefficient is generally not applicable. One of its most useful features is a test statistic that has high power when testing nonlinear dependence in cases where the Fisher’s Z-transformation test may fail to reach a right conclusion. Unlike most asymptotic t...

  16. Plan competitions reveal entrepreneurial talent

    Energy Technology Data Exchange (ETDEWEB)

    Madison, Alison L.

    2011-05-15

    Monthly economic diversity column for Tri-City Herald business section. Excerpt below: There’s something to be said for gaining valuable real-world experience in a structured, nurturing environment. Take for instance learning to scuba dive in the comfort of my resort pool rather than immediately hanging out with sharks while I figure out little things like oxygen tanks and avoiding underwater panic attacks. Likewise, graduate students are getting some excellent, supportive real-world training through university business plan competitions. These competitions are places where smart minds, new technologies, months of preparation and coaching, and some healthy pre-presentation jitters collide to reveal not only solid new business ideas, but also some promising entrepreneurial talent. In fact, professionals from around our region descend upon college campuses every spring to judge these events, which help to bridge the gap between academics and the real technology and business-driven economy.

  17. The Murchison Widefield Array Correlator

    CERN Document Server

    Ord, S M; Emrich, D; Pallot, D; Wayth, R B; Clark, M A; Tremblay, S E; Arcus, W; Barnes, D; Bell, M; Bernardi, G; Bhat, N D R; Bowman, J D; Briggs, F; Bunton, J D; Cappallo, R J; Corey, B E; Deshpande, A A; deSouza, L; Ewell-Wice, A; Feng, L; Goeke, R; Greenhill, L J; Hazelton, B J; Herne, D; Hewitt, J N; Hindson, L; Hurley-Walker, H; Jacobs, D; Johnston-Hollitt, M; Kaplan, D L; Kasper, J C; Kincaid, B B; Koenig, R; Kratzenberg, E; Kudryavtseva, N; Lenc, E; Lonsdale, C J; Lynch, M J; McKinley, B; McWhirter, S R; Mitchell, D A; Morales, M F; Morgan, E; Oberoi, D; Offringa, A; Pathikulangara, J; Pindor, B; Prabu, T; Procopio, P; Remillard, R A; Riding, J; Rogers, A E E; Roshi, A; Salah, J E; Sault, R J; Shankar, N Udaya; Srivani, K S; Stevens, J; Subrahmanyan, R; Tingay, S J; Waterson, M; Webster, R L; Whitney, A R; Williams, A; Williams, C L; Wyithe, J S B

    2015-01-01

    The Murchison Widefield Array (MWA) is a Square Kilometre Array (SKA) Precursor. The telescope is located at the Murchison Radio--astronomy Observatory (MRO) in Western Australia (WA). The MWA consists of 4096 dipoles arranged into 128 dual polarisation aperture arrays forming a connected element interferometer that cross-correlates signals from all 256 inputs. A hybrid approach to the correlation task is employed, with some processing stages being performed by bespoke hardware, based on Field Programmable Gate Arrays (FPGAs), and others by Graphics Processing Units (GPUs) housed in general purpose rack mounted servers. The correlation capability required is approximately 8 TFLOPS (Tera FLoating point Operations Per Second). The MWA has commenced operations and the correlator is generating 8.3 TB/day of correlation products, that are subsequently transferred 700 km from the MRO to Perth (WA) in real-time for storage and offline processing. In this paper we outline the correlator design, signal path, and proce...

  18. Analysis and perturbation of degree correlation in complex networks

    CERN Document Server

    Xiang, Ju; Hu, Tao; Zhang, Yan

    2015-01-01

    Degree correlation is an important topological property common to many real-world networks. In this paper, the statistical measures for characterizing the degree correlation in networks are investigated analytically. We give an exact proof of the consistency for the statistical measures, reveal the general linear relation in the degree correlation, which provide a simple and interesting perspective on the analysis of the degree correlation in complex networks. By using the general linear analysis, we investigate the perturbation of the degree correlation in complex networks caused by the addition of few nodes and the rich club. The results show that the assortativity of homogeneous networks such as the ER graphs is easily to be affected strongly by the simple structural changes, while it has only slight variation for heterogeneous networks with broad degree distribution such as the scale-free networks. Clearly, the homogeneous networks are more sensitive for the perturbation than the heterogeneous networks.

  19. Correlations between large prime numbers

    OpenAIRE

    Bershadskii, A.

    2011-01-01

    It is shown that short-range correlations between large prime numbers (~10^5 and larger) have a Poissonian nature. Correlation length \\zeta = 4.5 for the primes ~10^5 and it is increasing logarithmically according to the prime number theorem. For moderate prime numbers (~10^4) the Poissonian distribution is not applicable while the correlation length surprisingly continues to follow to the logarithmical law. A chaotic (deterministic) hypothesis has been suggested to explain the moderate prime...

  20. State estimation on correlated copies

    OpenAIRE

    Demkowicz-Dobrzanski, Rafal

    2004-01-01

    State estimation is usually analyzed in the situation when copies are in a product state, either mixed or pure. We investigate here the concept of state estimation on correlated copies. We analyze state estimation on correlated N qubit states, which are permutationally invariant. Using a correlated state we try to estimate as good as possible the direction of the Bloch vector of a single particle reduced density matrix. We derive the optimal fidelity for all permutation invariant states. We f...

  1. Are Bose-Einstein Correlations emerging from correlations of fluctuations?

    OpenAIRE

    Rybczynski, M.; Utyuzh, O. V.; Wilk, G.(National Centre for Nuclear Studies, Warsaw, Poland); Wlodarczyk, Z

    2002-01-01

    We demonstrate how Bose-Einstein correlations emerge from the correlations of fluctuations allowing for their extremely simple and fast numerical modelling. Both the advantages and limitations of this new method of implementation of BEC in the numerical modelling of high energy multiparticle processes are outlined and discussed. First applications to description of $e^+e^-$ data are given.

  2. Quantum and semiclassical polarization correlations

    CERN Document Server

    Banaszek, Konrad; Karpinski, Michal; Migdal, Piotr; Radzewicz, Czeslaw

    2009-01-01

    We analyze the strength of polarization correlations between two light beams that can be achieved in the semiclassical regime using statistical mixtures of coherent states and binary on/off detectors. Under certain symmetry assumptions, the visibility of polarization correlations is shown to be bounded by 1/3, which is in a striking contrast with perfect 100% correlations exhibited by photon pairs prepared in the singlet state. The semiclassical limit is demonstrated in a measurement performed on a pair of laser beams undergoing correlated depolarization. This result illustrates the dramatic difference between predictions of quantum mechanics and the semiclassical theory of electromagnetic radiation for the polarization degree of freedom.

  3. CORRELATION STUDIES BETWEEN PHYSICO-CHEMICAL, CHEMICAL AND NUTRIENT UPTAKES OF PADDY IN PHOSPHORUS RICH VERTISOLS

    OpenAIRE

    V Siva Jyothi; T Giridhara Krishna; P.KAVITHA; Srinivasa Reddy, M.

    2014-01-01

    A field experiment was conducted in paddy having high soil available P vertisols under K.C. Canal ayacut at Regional Agricultural Research Station, Nandyal, Andhra Pradesh. The correlation studies revealed that there exist a positive strong correlation between agronomic characters at different stages with the yield. pH and EC was positively correlate with yield except pH at panicle initiation stage is non significantly correlate with yield. The available nitrogen at tillering (r= 0.446), pani...

  4. Correlated Energy Exchange in Drifting Sea Ice

    Directory of Open Access Journals (Sweden)

    A. Chmel

    2011-01-01

    Full Text Available The ice floe speed variations were monitored at the research camp North Pole 35 established on the Arctic ice pack in 2008. A three-month time series of measured speed values was used for determining changes in the kinetic energy of the drifting ice floe. The constructed energy distributions were analyzed by methods of nonextensive statistical mechanics based on the Tsallis statistics for open nonequilibrium systems, such as tectonic formations and drifting sea ice. The nonextensivity means the nonadditivity of externally induced energy changes in multicomponent systems due to dynamic interrelation of components having no structural links. The Tsallis formalism gives one an opportunity to assess the correlation between ice floe motions through a specific parameter, the so-called parameter of nonextensivity. This formalistic assessment of the actual state of drifting pack allows one to forecast some important trends in sea ice behavior, because the level of correlated dynamics determines conditions for extended mechanical perturbations in ice pack. In this work, we revealed temporal fluctuations of the parameter of nonextensivity and observed its maximum value before a large-scale sea ice fragmentation (faulting of consolidated sea ice. The correlation was not detected in fragmented sea ice where long-range interactions are weakened.

  5. Real-time software correlation

    NARCIS (Netherlands)

    N.G.H. Kruithof; D.C.P.M. Marchal

    2008-01-01

    In this chapter we present the progress of the SCARIe project, where we investigate the capabilities of a next generation grid-based software correlator for VLBI. We will mostly focus on the current design of our software correlator and on the challenges of running real-time scientific experiments o

  6. Correlation Functions and Power Spectra

    DEFF Research Database (Denmark)

    Larsen, Jan

    2006-01-01

    The present lecture note is a supplement to the textbook Digital Signal Processing by J. Proakis and D.G. Manolakis used in the IMM/DTU course 02451 Digital Signal Processing and provides an extended discussion of correlation functions and power spectra. The definitions of correlation functions...

  7. Electronic Correlation Strength of Pu

    DEFF Research Database (Denmark)

    Svane, A.; C. Albers, R.; E. Christensen, N.;

    2013-01-01

    A new electronic quantity, the correlation strength, is defined as a necessary step for understanding the properties and trends in strongly correlated electronic materials. As a test case, this is applied to the different phases of elemental Pu. Within the GW approximation we have surprisingly...

  8. Analysis of Negative Correlation Learning

    Institute of Scientific and Technical Information of China (English)

    Liu Yong; Zou Xiu-fen

    2003-01-01

    This paper describes negative correlation learning for designing neural network ensembles. Negative correlation learning has been firstly analysed in terms of minimising mutual information on a regression task. By ninimising the mutual information between variables extracted by two neural networks, they are forced to convey different information about some features of their input. Based on the decision boundaries and correct response sets, negative correlation learning has been further studied on two pattern classification problems. The purpose of examining the decision boundaries and the correct response sets is not only to illustrate the learning behavior of negative correlation learning, but also to cast light on how to design more effective neural network ensembles. The experimental results showed the decision boundary of the trained neural network ensemble by negative correlation learning is almost as good as the optimum decision boundary.

  9. Quantum correlations for the metric

    CERN Document Server

    Wetterich, C

    2016-01-01

    We discuss the correlation function for the metric for homogeneous and isotropic cosmologies. The exact propagator equation determines the correlation function as the inverse of the second functional derivative of the quantum effective action, for which we take the Einstein-Hilbert approximation. This formulation relates the metric correlation function employed in quantum gravity computations to cosmological observables as the graviton power spectrum. While the graviton correlation function can be obtained equivalently as a solution of the linearized Einstein equations, this does not hold for the vector and scalar components of the metric. We project the metric fluctuations on the subspace of "physical fluctuations", which couple to a conserved energy momentum tensor. On the subspace of physical metric fluctuations the relation to physical sources becomes invertible, such that the effective action and its relation to correlation functions does not need gauge fixing. The physical metric fluctuations have a sim...

  10. Multiview Bayesian Correlated Component Analysis

    DEFF Research Database (Denmark)

    Kamronn, Simon Due; Poulsen, Andreas Trier; Hansen, Lars Kai

    2015-01-01

    Correlated component analysis as proposed by Dmochowski, Sajda, Dias, and Parra (2012) is a tool for investigating brain process similarity in the responses to multiple views of a given stimulus. Correlated components are identified under the assumption that the involved spatial networks...... are identical. Here we propose a hierarchical probabilistic model that can infer the level of universality in such multiview data, from completely unrelated representations, corresponding to canonical correlation analysis, to identical representations as in correlated component analysis. This new model, which...... we denote Bayesian correlated component analysis, evaluates favorably against three relevant algorithms in simulated data. A well-established benchmark EEG data set is used to further validate the new model and infer the variability of spatial representations across multiple subjects....

  11. Different Luminosity Correlation of GRBs

    Indian Academy of Sciences (India)

    Z. B. Zhang; H. C. Liu; L. Y. Jiang; D. Y. Chen

    2014-09-01

    We report our recent understanding about a tight correlation between relative spectral lag and luminosity (or redshift) for -ray bursts. The latest investigations indicate that the empirical correlations got from BATSE bursts also exist for Swift/BAT ones. The special luminosity-lag correlation is much similar to that of the luminosity with pulse number proposed by Schaefer (2003), but largely different from most others ever discovered. Note that our newly built luminosity-lag correlation predicts that luminosity should evolve with cosmological redshift as p ∝ (1 + )2.4 ± 0.7 that is excellently confirmed by Salvaterra et al. (2012) and Geng & Huang (2013). In addition, it is also surprisingly found that the luminosity-lag correlation can account for both long and short Swift/BAT bursts, which might be an evidence of the same radiation mechanism for diverse burst groups.

  12. Focus groups reveal consumer ambivalence.

    Science.gov (United States)

    1983-01-01

    According to qualitative research, Salvadoreans are ambivalent about the use of contraceptives. Since complete responsibility for management of the CSM project was accepted by the Association Demografica Salvadorena (ADS), the agency which operates the contraceptive social marketing project in El Salvador, in November 1980, the need for decisions in such areas as product price increases, introduction of new condom brands, promotion of the vaginal foaming tablet, and assessment of product sales performance had arisen. The ICSMP funded market research, completed during 1983, was intended to provide the data on which such decisions by ADS could be based. The qualitative research involved 8 focus groups, comprised of men and women, aged 18-45, contraceptive users and nonusers, from the middle and lower socioeconomic strata of the city of San Salvador and other suburban areas. In each group a moderator led discussion of family planning and probed respondents for specific attitudes, knowledge, and behavior regarding the use of contraceptives. To assess attitudes at a more emotional level, moderators asked respondents to "draw" their ideas on certain issues. A marked discrepancy was revealed between respondents' intellectual responses to the issues raised in group discussion, as opposed to their feelings expressed in the drawings. Intellectually, participants responded very positively to family planning practice, but when they were asked to draw their perceptions, ambivalent feelings emerged. Drawings of both the user and the nonuser convey primarily negative aspects for either choice. The user is tense and moody toward her children; the nonuser loses her attractiveness and "dies." Figures also show drawings of some of the attitudes of single and married male participants. 1 drawing shows an incomplete and a complete circle, symbolizing a sterilized man (incomplete) and a nonsterilized man (complete). Another picture depicts a chained man who has lost his freedom

  13. Correlation between Correlations Process and Time in Quantum Networks

    CERN Document Server

    Mahler, G; Kim, Ilki

    1998-01-01

    We study a special inhomogeneous quantum network consisting of a ring of M pseudospins (here M = 4) sequentially coupled to one and the same central spin under the influence of given pulse sequences (quantum gate operations). This architecture could be visualized as a quantum Turing machine with a cyclic ``tape''. Rather than input-output-relations we investigate the resulting process, i.e. the correlation between one- and two-point expectation values (``correlations'') over various time-steps. The resulting spatio-temporal pattern exhibits many non-classical features including Zeno-effects, violation of temporal Bell-inequalities, and quantum parallelism. Due to the strange web of correlations being built-up, specific measurement outcomes for the tape may refer to one or several preparation histories of the head. Specific families of correlation functions are more stable with respect to dissipation than the total wavefunction.

  14. Superconductivity, Antiferromagnetism, and Kinetic Correlation in Strongly Correlated Electron Systems

    Directory of Open Access Journals (Sweden)

    Takashi Yanagisawa

    2015-01-01

    Full Text Available We investigate the ground state of two-dimensional Hubbard model on the basis of the variational Monte Carlo method. We use wave functions that include kinetic correlation and doublon-holon correlation beyond the Gutzwiller ansatz. It is still not clear whether the Hubbard model accounts for high-temperature superconductivity. The antiferromagnetic correlation plays a key role in the study of pairing mechanism because the superconductive phase exists usually close to the antiferromagnetic phase. We investigate the stability of the antiferromagnetic state when holes are doped as a function of the Coulomb repulsion U. We show that the antiferromagnetic correlation is suppressed as U is increased exceeding the bandwidth. High-temperature superconductivity is possible in this region with enhanced antiferromagnetic spin fluctuation and pairing interaction.

  15. 25 ns software correlator for photon and fluorescence correlation spectroscopy

    Science.gov (United States)

    Magatti, Davide; Ferri, Fabio

    2003-02-01

    A 25 ns time resolution, multi-tau software correlator developed in LABVIEW based on the use of a standard photon counting unit, a fast timer/counter board (6602-PCI National Instrument) and a personal computer (PC) (1.5 GHz Pentium 4) is presented and quantitatively discussed. The correlator works by processing the stream of incoming data in parallel according to two different algorithms: For large lag times (τ⩾100 μs), a classical time-mode (TM) scheme, based on the measure of the number of pulses per time interval, is used; differently, for τ⩽100 μs a photon-mode (PM) scheme is adopted and the time sequence of the arrival times of the photon pulses is measured. By combining the two methods, we developed a system capable of working out correlation functions on line, in full real time for the TM correlator and partially in batch processing for the PM correlator. For the latter one, the duty cycle depends on the count rate of the incoming pulses, being ˜100% for count rates ⩽3×104 Hz, ˜15% at 105 Hz, and ˜1% at 106 Hz. For limitations imposed by the fairly small first-in, first-out (FIFO) buffer available on the counter board, the maximum count rate permissible for a proper functioning of the PM correlator is limited to ˜105 Hz. However, this limit can be removed by using a board with a deeper FIFO. Similarly, the 25 ns time resolution is only limited by maximum clock frequency available on the 6602-PCI and can be easily improved by using a faster clock. When tested on dilute solutions of calibrated latex spheres, the overall performances of the correlator appear to be comparable with those of commercial hardware correlators, but with several nontrivial advantages related to its flexibility, low cost, and easy adaptability to future developments of PC and data acquisition technology.

  16. Dynamic holography in optical pattern recognition

    Science.gov (United States)

    Rajbenbach, Henri J.

    1994-03-01

    This paper reviews the basic principles, physical processes, and most recent demonstrations of optical correlators using dynamic holographic techniques in nonlinear media such as bulk photorefractives (PR), thin multiple quantum wells (MQW), and bacteriorhodopsin (BR) films.

  17. Cluster identification based on correlations

    Science.gov (United States)

    Schulman, L. S.

    2012-04-01

    The problem addressed is the identification of cooperating agents based on correlations created as a result of the joint action of these and other agents. A systematic method for using correlations beyond second moments is developed. The technique is applied to a didactic example, the identification of alphabet letters based on correlations among the pixels used in an image of the letter. As in this example, agents can belong to more than one cluster. Moreover, the identification scheme does not require that the patterns be known ahead of time.

  18. Atomic structure and electron correlations

    International Nuclear Information System (INIS)

    Synchrotron experiments combined with theoretical calculations have already given much information on atomic structure and the effects of electron correlations, and this combination of theory and experiment is expected to yield much new information in coming years. In the calculations of photoabsorption cross sections, it is almost always necessary to include electron correlations in both initial and final states to obtain good agreement with experiment. The main theoretical approaches which include effects of electron correlations have been R-matrix theory, random phase approximation with exchange (RPAE), relativistic random phase approximation with exchange, and many-body perturbation theory

  19. Unveiling linearly and nonlinearly correlated signals between gravitational wave detectors and environmental monitors

    Science.gov (United States)

    Yuzurihara, Hirotaka; Hayama, Kazuhiro; Mano, Shuhei; Verkindt, Didier; Kanda, Nobuyuki

    2016-08-01

    Noise hunting is a critical requirement for realizing design sensitivity of a detector, and consequently, noise origins and its features have been revealed partially. Among the noise sources to be hunted, sources of nonlinearly correlated noise, such up-conversion noise, are hard to find and can limit the sensitivity of gravitational wave searches with advanced detectors. We propose using a correlation analysis method called maximal information coefficient (MIC) to find both nonlinear and linear correlations. We apply MIC to the scattered light noise correlated between the seismic activity and the strain signal, which limited the sensitivity of the Virgo detector during the first science run. The results show that MIC can find nonlinearly correlated noise more efficiently than the Pearson correlation method. When the data is linearly correlated, the efficiency of the Pearson method and MIC is comparable. On the other hand, when the data is known to be nonlinearly correlated, MIC finds the correlation while the Pearson method fails completely.

  20. Modernizing the JPL VLBI Correlator

    Science.gov (United States)

    Rogstad, S.; Goodhart, C. E.; Clark, J. E.; Finley, S.; Lanyi, G. E.; White, L. A.; Jacobs, Christopher S.>

    This poster will present the current capabilities of the JPL VLBI Correlator (JVC) and the general architecture of the equipment. In addition, the scientific and navigation uses of the JVC will be enumerated for background purposes. The JVC is a software correlator based on a Beowulf cluster of computers. It replaces a thirty year old correlator based on custom designed digital hardware. General comparisons between the old and new equipment will be made. The JVC makes use of a separate program, SoftC, to do the actual correlations. The JVC manages the sending of data to multiple machines in a Beowulf cluster each running SoftC in parallel on small chunks of the data. The basic architecture of SoftC will also be described.

  1. Correlations and Neuronal Population Information.

    Science.gov (United States)

    Kohn, Adam; Coen-Cagli, Ruben; Kanitscheider, Ingmar; Pouget, Alexandre

    2016-07-01

    Brain function involves the activity of neuronal populations. Much recent effort has been devoted to measuring the activity of neuronal populations in different parts of the brain under various experimental conditions. Population activity patterns contain rich structure, yet many studies have focused on measuring pairwise relationships between members of a larger population-termed noise correlations. Here we review recent progress in understanding how these correlations affect population information, how information should be quantified, and what mechanisms may give rise to correlations. As population coding theory has improved, it has made clear that some forms of correlation are more important for information than others. We argue that this is a critical lesson for those interested in neuronal population responses more generally: Descriptions of population responses should be motivated by and linked to well-specified function. Within this context, we offer suggestions of where current theoretical frameworks fall short.

  2. Totality of Subquantum Nonlocal Correlations

    CERN Document Server

    Khrennikov, Andrei

    2011-01-01

    In a series of previous papers we developed a purely field model of microphenomena, so called prequantum classical statistical field theory (PCSFT). This model not only reproduces important probabilistic predictions of QM including correlations for entangled systems, but it also gives a possibility to go beyond quantum mechanics (QM), i.e., to make predictions of phenomena which could be observed at the subquantum level. In this paper we discuss one of such predictions - existence of nonlocal correlations between prequantum random fields corresponding to {\\it all} quantum systems. (And by PCSFT quantum systems are represented by classical Gaussian random fields and quantum observables by quadratic forms of these fields.) The source of these correlations is the common background field. Thus all prequantum random fields are "entangled", but in the sense of classical signal theory. On one hand, PCSFT demystifies quantum nonlocality by reducing it to nonlocal classical correlations based on the common random back...

  3. The Murchison Widefield Array Correlator

    OpenAIRE

    Ord, S. M.; Crosse, B.; Emrich, D.; Pallot, D.; Wayth, R. B.; Clark, M. A.; Tremblay, S. E.; Arcus, W.; Barnes, D; Bell, M.; Bernardi, G.; Bhat, N. D. R.; Bowman, J.D.; Briggs, F.; Bunton, J. D.

    2014-01-01

    The Murchison Widefield Array (MWA) is a Square Kilometre Array (SKA) Precursor. The telescope is located at the Murchison Radio--astronomy Observatory (MRO) in Western Australia (WA). The MWA consists of 4096 dipoles arranged into 128 dual polarisation aperture arrays forming a connected element interferometer that cross-correlates signals from all 256 inputs. A hybrid approach to the correlation task is employed, with some processing stages being performed by bespoke hardware, based on Fiel...

  4. Connected Correlators in Quantum Gravity

    OpenAIRE

    Ambjorn, J.; Bialas, P.; Jurkiewicz, J.(Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, ul. prof. Stanislawa Lojasiewicza 11, Krakow, PL 30-348, Poland)

    1998-01-01

    We discuss the concept of connected, reparameterization invariant matter correlators in quantum gravity. We analyze the effect of discretization in two solvable cases: branched polymers and two-dimensional simplicial gravity. In both cases the naively defined connected correlators for a fixed volume display an anomalous behavior, which could be interpreted as a long-range order. We suggest that this is in fact only a highly non-trivial finite-size effect and propose an improved definition of ...

  5. Quantum correlation via quantum coherence

    OpenAIRE

    Yu, Chang-shui; Zhang, Yang; Zhao, Haiqing

    2014-01-01

    Quantum correlation includes quantum entanglement and quantum discord. Both entanglement and discord have a common necessary condition--------quantum coherence or quantum superposition. In this paper, we attempt to give an alternative understanding of how quantum correlation is related to quantum coherence. We divide the coherence of a quantum state into several classes and find the complete coincidence between geometric (symmetric and asymmetric) quantum discords and some particular classes ...

  6. Default probabilities and default correlations

    OpenAIRE

    Erlenmaier, Ulrich; Gersbach, Hans

    2001-01-01

    Starting from the Merton framework for firm defaults, we provide the analytics and robustness of the relationship between default correlations. We show that loans with higher default probabilities will not only have higher variances but also higher correlations between loans. As a consequence, portfolio standard deviation can increase substantially when loan default probabilities rise. This result has two important implications. First, relative prices of loans with different default probabili...

  7. Why Waveform Correlation Sometimes Fails

    Science.gov (United States)

    Carmichael, J.

    2015-12-01

    Waveform correlation detectors used in explosion monitoring scan noisy geophysical data to test two competing hypotheses: either (1) an amplitude-scaled version of a template waveform is present, or, (2) no signal is present at all. In reality, geophysical wavefields that are monitored for explosion signatures include waveforms produced by non-target sources that are partially correlated with the waveform template. Such signals can falsely trigger correlation detectors, particularly at low thresholds required to monitor for smaller target explosions. This challenge is particularly formidable when monitoring known test sites for seismic disturbances, since uncatalogued natural seismicity is (generally) more prevalent at lower magnitudes, and could be mistaken for small explosions. To address these challenges, we identify real examples in which correlation detectors targeting explosions falsely trigger on both site-proximal earthquakes (Figure 1, below) and microseismic "noise". Motivated by these examples, we quantify performance loss when applying these detectors, and re-evaluate the correlation-detector's hypothesis test. We thereby derive new detectors from more general hypotheses that admit unknown background seismicity, and apply these to real data. From our treatment, we derive "rules of thumb'' for proper template and threshold selection in heavily cluttered signal environments. Last, we answer the question "what is the probability of falsely detecting an earthquake collocated at a test site?", using correlation detectors that include explosion-triggered templates. Figure Top: An eight-channel data stream (black) recorded from an earthquake near a mine. Red markers indicate a detection. Middle: The correlation statistic computed by scanning the template against the data stream at top. The red line indicates the threshold for event declaration, determined by a false-alarm on noise probability constraint, as computed from the signal-absent distribution using

  8. Correlation properties of quantum measurements

    OpenAIRE

    Busch, Paul; Lahti, Pekka

    1996-01-01

    The kind of information provided by a measurement is determined in terms of the correlation established between observables of the apparatus and the measured system. Using the framework of quantum measurement theory, necessary and sufficient conditions for a measurement interaction to produce strong correlations are given and are found to be related to properties of the final object and apparatus states. These general results are illustrated with reference to the standard model of the quantum...

  9. Conductivity of epitaxial and CVD graphene with correlated line defects

    DEFF Research Database (Denmark)

    Radchenko, T. M.; Shylau, Artsem; Zozoulenko, I. V.

    2014-01-01

    -type scattering potential. The dc conductivity is calculated numerically for different cases of distribution of line defects. This includes a random (uncorrelated) and a correlated distribution with a prevailing direction in the orientation of lines. The anisotropy of the conductivity along and across the line...... defects is revealed, which agrees with experimental measurements for epitaxial graphene grown on SiC. We performed a detailed study of the conductivity for different defect correlations, introducing the correlation angle αmax-the maximum possible angle between any two lines. We find that for a given...... electron density, the relative enhancement of the conductivity for the case of fully correlated line defects in comparison to the case of uncorrelatecl ones is larger for a higher defect density. Finally, we, for the first time, study the conductivity of realistic samples where both extended line defects...

  10. Correlation and path coefficient analysis in coconut (Cocos nucifera L.

    Directory of Open Access Journals (Sweden)

    S. Geethanjali, D. Rajkumar and N.Shoba

    2014-12-01

    Full Text Available A total of 43 coconut germplasm accessions were characterized for nut yield and fruit component traits. Correlation analysis showed that most of the fruit traits viz., fruit length, fruit breadth, fruit weight, nut weight, kernel weight and copra weight per nut were positively correlated with each other but showed significant negative correlation with the number of nuts produced per palm per annum. Shell thickness and husk thickness were not correlated with any of the fruit component traits. Path analysis revealed that nut yield and copra content per nut had positive direct effect on the total copra yield per palm. The results of this study showed that equal consideration should be given for both nut yield and copra content per nut while selecting elite genotypes for dual purpose viz., tender nut or culinary use and copra for oil extraction.

  11. Quaternion correlation for tracking crystal motions

    Science.gov (United States)

    Shi, Qiwei; Latourte, Félix; Hild, François; Roux, Stéphane

    2016-09-01

    During in situ mechanical tests performed on polycrystalline materials in a scanning electron microscope, crystal orientation maps may be recorded at different stages of deformation from electron backscattered diffraction (EBSD). The present study introduces a novel correlation technique that exploits the crystallographic orientation field as a surface pattern to measure crystal motions. Introducing a quaternion-based formalism reveals crystal symmetry that is very convenient to handle and orientation extraction. Spatial regularization is provided by a penalty to deviation of displacement fields from being the solution to a homogeneous linear elastic problem. This procedure allows the large scale features of the displacement field to be captured, mostly from grain boundaries, and a fair interpolation of the displacement to be obtained within the grains. From these data, crystal rotations can be estimated very accurately. Both synthetic and real experimental cases are considered to illustrate the method.

  12. Quantifying Fluctuations/Correlations in Polymer Brushes

    Science.gov (United States)

    Wang, Qiang; Zhang, Xinghua; Zhang, Pengfei; Li, Baohui

    2011-03-01

    Fast lattice Monte Carlo (FLMC) simulations with multiple occupancy of lattice sites and Kronecker δ -function interactions give orders of magnitude faster/better sampling of the configurational space of multi-chain systems than conventional lattice MC simulations with self- and mutual- avoiding walks and nearest-neighbor interactions. Using FLMC simulations with Wang-Landau -- Transition-Matrix sampling, we have studied polymer brushes in both an implicit and explicit solvent. The various quantities obtained from simulations (including the internal energy, Helmholtz free energy, constant-volume heat capacity, segmental distribution, and chain sizes) are compared with predictions from the corresponding lattice self-consistent field theory and Gaussian fluctuation theory that are based on the same Hamiltonian as in FLMC simulations (thus without any parameter-fitting) to unambiguously and quantitatively reveal the effects of system fluctuations and correlations neglected or treated only approximately in the theories. Q. Wang, Soft Matter, 5, 4564 (2009).

  13. Photon correlation spectroscopy investigations of proteins.

    Science.gov (United States)

    Gun'ko, Vladimir M; Klyueva, Alla V; Levchuk, Yuri N; Leboda, Roman

    2003-09-18

    Physical principles of photon correlation spectroscopy (PCS), mathematical treatment of the PCS data (converting autocorrelation functions to distribution functions or average characteristics), and PCS applications to study proteins and other biomacromolecules in aqueous media are described and analysed. The PCS investigations of conformational changes in protein molecules, their aggregation itself or in consequence of interaction with other molecules or organic (polymers) and inorganic (e.g. fumed silica) fine particles as well as the influence of low molecular compounds (surfactants, drugs, salts, metal ions, etc.) reveal unique capability of the PCS techniques for elucidation of important native functions of proteins and other biomacromolecules (DNA, RNA, etc.) or microorganisms (Escherichia coli, Pseudomonas putida, Dunaliella viridis, etc.). Special attention is paid to the interaction of proteins with fumed oxides and the impact of polymers and fine oxide particles on the motion of living flagellar microorganisms analysed by means of PCS. PMID:12969646

  14. Data mining of VDJ genes reveals interesting clues.

    Science.gov (United States)

    Joshi, Rajani R; Gupta, Vinay K

    2006-01-01

    Hypervariability of the complementary determining regions in characteristic structure of Immunoglobulins and the distinct, cell-specific expressions of the genes coding for this important class of proteins pose intriguing problems in experimental and computational/informatics research requiring a special approach different from those for the other proteins. We present here an Average Linkage Hierarchical Clustering of the Homosapien VDJ genes and the Immunoglobulin polypeptides generated by them using special kind of data structures and correlation matrices in place of the microarray data. The results reveal interesting clues on the heterogeneity of exon - intron locations in these gene-families and its possible role in hypervariability of the Immunoglobulins. PMID:16842114

  15. Integrated optical devices using bacteriorhodopsin as active nonlinear optical material

    OpenAIRE

    Dér, A; Fábián, L.; Valkai, S.; Wolff, E.; Ramsden, Jeremy J.; Ormos, P.

    2006-01-01

    Coupling of optical data-processing devices with microelectronics, telecocommunication and sensory functions, is among the biggest challenges in molecular electronics. Intensive research is going on to find suitable nonlinear optical materials that could meet the demanding requirements of optoelectronic applications, especially regarding high sensitivity and stability. In addition to inorganic and organic crystals, biological molecules have also been considered for use in in...

  16. First hyperpolarizability of bacteriorhodopsin, retinal and related molecules revisited

    Science.gov (United States)

    Ghosh, Sampa; Ranjini, Arumugam Sri; Pandey, Ravindra; Das, Puspendu Kumar

    2009-06-01

    The previously reported β values of BR and retinal based chromophores were very high but subsequent measurements found them to be much less. We have found that the β values of these compounds do not vary so much with experimental conditions as with the method of analysis. Hyper-Rayleigh scattering measurements at 1543 and 1907 nm produce more realistic β values close to the intrinsic (static) hyperpolarizability, β0 which for BR is still very high (275 × 10 -30 esu). The optical nonlinearity of BR arises entirely due to the protonated retinal Schiff Base (PRSB) which in its isolated form has the same intrinsic hyperpolarizability as that of the protein.

  17. Real-time holography on bacteriorhodopsin-based materials

    Science.gov (United States)

    Taranenko, Victor B.

    1998-09-01

    The main properties and mechanisms of photoresponse of the bacteriohodopsin-based materials are presented. Fields of their potential applications in the real-time holography and nonlinear optics are discussed.

  18. Reusable holographic velocimetry system based on polarization multiplexing in Bacteriorhodopsin

    NARCIS (Netherlands)

    Koek, W.D.; Chan, V.S.S.; Ooms, T.A.; Bhattacharya, N.; Westerweel, J.; Braat, J.J.M.

    2005-01-01

    We present a novel holographic particle image velocimetry (HPIV) system using a reversible holographic material as the recording medium. In HPIV the three-dimensional flow field throughout a volume is detected by adding small tracer particles to a normally transparent medium. By recording the partic

  19. A scalable correlator for multichannel diffuse correlation spectroscopy

    Science.gov (United States)

    Stapels, Christopher J.; Kolodziejski, Noah J.; McAdams, Daniel; Podolsky, Matthew J.; Fernandez, Daniel E.; Farkas, Dana; Christian, James F.

    2016-03-01

    Diffuse correlation spectroscopy (DCS) is a technique which enables powerful and robust non-invasive optical studies of tissue micro-circulation and vascular blood flow. The technique amounts to autocorrelation analysis of coherent photons after their migration through moving scatterers and subsequent collection by single-mode optical fibers. A primary cost driver of DCS instruments are the commercial hardware-based correlators, limiting the proliferation of multi-channel instruments for validation of perfusion analysis as a clinical diagnostic metric. We present the development of a low-cost scalable correlator enabled by microchip-based time-tagging, and a software-based multi-tau data analysis method. We will discuss the capabilities of the instrument as well as the implementation and validation of 2- and 8-channel systems built for live animal and pre-clinical settings.

  20. Estimating correlations of neighbouring frequencies in ambient seismic noise

    Science.gov (United States)

    Liu, Xin; Ben-Zion, Yehuda

    2016-08-01

    Extracting accurate empirical Green's functions from the ambient seismic noise field requires the noise to be fully diffuse and that different frequency components are not correlated. Calculating a matrix of correlation coefficients of power spectral samples can be used to estimate deviations from a fully diffuse random noise field in the analysed frequency range. A fully diffuse field has correlations only in a narrow region around the diagonal of the matrix, with frequency resolution inversely proportional to length of the used time window. Analysis of low-frequency data (0.005-0.6 Hz) recorded by three broad-band stations of the southern California seismic network reveals three common types of correlations, manifested in the correlation coefficient matrix as square, diagonal halo and correlated stripes. Synthetic calculations show that these types of signatures in the correlation coefficient matrix can result from certain combinations of cross-frequency correlated random components and diffuse field. The analysis of observed data indicates that the secondary microseismic peak around 0.15 Hz is correlated with its neighbouring frequencies, while the primary peak around 0.06 Hz is more diffuse. This suggests that the primary and secondary peaks may be associated with somewhat different physical origins. In addition, significant correlation of frequencies below that of the primary microseismic peak suggests that the very low frequencies noise is less scattered during propagation. The power spectra recorded by a station close to the edge of the Los Angeles basin is higher compared to data recorded by stations outside the basin perhaps because of enhanced basin reverberations and/or closer proximity to the ocean. This and other regional variations should be tested further using data from many more stations.

  1. Segmentation of time series with long-range fractal correlations

    Science.gov (United States)

    Bernaola-Galván, P.; Oliver, J.L.; Hackenberg, M.; Coronado, A.V.; Ivanov, P.Ch.; Carpena, P.

    2012-01-01

    Segmentation is a standard method of data analysis to identify change-points dividing a nonstationary time series into homogeneous segments. However, for long-range fractal correlated series, most of the segmentation techniques detect spurious change-points which are simply due to the heterogeneities induced by the correlations and not to real nonstationarities. To avoid this oversegmentation, we present a segmentation algorithm which takes as a reference for homogeneity, instead of a random i.i.d. series, a correlated series modeled by a fractional noise with the same degree of correlations as the series to be segmented. We apply our algorithm to artificial series with long-range correlations and show that it systematically detects only the change-points produced by real nonstationarities and not those created by the correlations of the signal. Further, we apply the method to the sequence of the long arm of human chromosome 21, which is known to have long-range fractal correlations. We obtain only three segments that clearly correspond to the three regions of different G + C composition revealed by means of a multi-scale wavelet plot. Similar results have been obtained when segmenting all human chromosome sequences, showing the existence of previously unknown huge compositional superstructures in the human genome. PMID:23645997

  2. Image correlates of crowding in natural scenes.

    Science.gov (United States)

    Wallis, Thomas S A; Bex, Peter J

    2012-07-13

    Visual crowding is the inability to identify visible features when they are surrounded by other structure in the peripheral field. Since natural environments are replete with structure and most of our visual field is peripheral, crowding represents the primary limit on vision in the real world. However, little is known about the characteristics of crowding under natural conditions. Here we examine where crowding occurs in natural images. Observers were required to identify which of four locations contained a patch of "dead leaves'' (synthetic, naturalistic contour structure) embedded into natural images. Threshold size for the dead leaves patch scaled with eccentricity in a manner consistent with crowding. Reverse correlation at multiple scales was used to determine local image statistics that correlated with task performance. Stepwise model selection revealed that local RMS contrast and edge density at the site of the dead leaves patch were of primary importance in predicting the occurrence of crowding once patch size and eccentricity had been considered. The absolute magnitudes of the regression weights for RMS contrast at different spatial scales varied in a manner consistent with receptive field sizes measured in striate cortex of primate brains. Our results are consistent with crowding models that are based on spatial averaging of features in the early stages of the visual system, and allow the prediction of where crowding is likely to occur in natural images.

  3. Neurophysiological correlates of musical creativity: The example of improvisation.

    Directory of Open Access Journals (Sweden)

    Skirtach I.A.

    2015-07-01

    Full Text Available Since the turn of this century, a substantial body of research has been published on the neuroscience of creativity. Now, it is necessary to study the neurophysiological correlates in true-to-life, professionally specific situations. The aim of our empirical research was to study the neurophysiological correlates of musical improvisation, a spontaneous creative activity. The participants were 136 right-handed practicing musicians aged 19 to 36 (102 males and 34 females, divided into two groups—professionals (56 people and amateurs (80 people. EEG signals were recorded in a resting state (eyes closed and during three types of internal musical activity (perceiving, mentally reproducing, and mentally improvising from 21 scalp electrodes according to the International 10-20 System. For statistical analysis, we used ANOVA and post hoc analysis. For the main neurophysiological correlates of musical creativity, we revealed higher values of EEG spectral power in the delta band and the dominance of long-distance functional cortical connections in the high-frequency bands. Variable neurophysiological correlates were differentiated according to emotions and the professional level of the musicians. The distinguishing EEG pattern in the professional musicians during improvisation was the predominant activation of the left- hemisphere cortical regions simultaneously with high interhemispheric integration in the high-frequency band along the “creativity axis.” The revealed neurophysiological correlates of musical creativity during improvisation included basic and variable components and were characterized by a specific frequency-spatial organization of bioelectric cortical activity in the musicians.

  4. Abrasive supply for ancient Egypt revealed

    International Nuclear Information System (INIS)

    In the framework of the major research scheme 'Synchronization of Civilizations in the Eastern Mediterranean Region in the 2nd Millennium B.C' instrumental neutron activation analysis (INAA) was used to determine 30 elements in pumice from archaeological excavations to reveal their specific volcanic origin. In ancient time, the widespread pumiceous products of several eruptions in the Aegean region have been used as abrasive tools and were therefore popular trade objects. The correlation of such archaeological findings to a specific eruption of known age would therefore allow to certify a maximum age of the respective stratum ('dating by first appearance'). Pumices from the Aegean region can easily be distinguished by their trace element distribution patterns. This has been shown by previous studies of the group. The elements Al, Ba, Ca, Ce, Co, Cr, Cs, Dy, Eu, Fe, Hf, K, La, Lu, Mn, Na, Nd, Rb, Sb, Sc, Sm, Ta, Tb, Th, Ti, U, V, Yb, Zr and Zn were determined in 16 samples of pumice lumps from excavations in Tell-el-Dab'a and Tell-el-Herr (Egypt). Two irradiation cycles and five measurement runs were applied. To show the accuracy of the results obtained, typical samples of the most important pumice sources in the Aegean region, particularly from Milos, Nisyros, Kos and Thera were analyzed together with the Egyptian samples of unknown origin. A reliable identification of the samples is achieved by comparing these results to the database compiled in previous studies. The geographical positions of these islands are shown. Within the error range, most of the elements determined in typical representatives of Milos, Nisyros, Kos and Santorini were in perfect agreement with values from the literature. On the basis of the Cluster graphics presented, it is possible to relate unknown pumice to its primary source, just by comparing the relation of a few elements, like Ta-Eu and Th-Hf. One concludes that all samples except one can be related to the Minoan eruption of Thera

  5. Volume-Energy Correlations in the Slow Degrees of Freedom of Computer-Simulated Phospholipid Membranes

    DEFF Research Database (Denmark)

    Pedersen, U.R.; Peters, Günther H.j.; Schröder, T.B.;

    2008-01-01

    by Heimburg from experiments focusing on the phase transition between the Lα and the Lβ phases. The correlations, which are reported here for three different membranes (DMPC, DMPS-Na, and DMPSH), have volume-energy correlation coefficients ranging from 0.81 to 0.89. The DMPC membrane was studied at two...... temperatures showing that the correlation coefficient increases as the phase transition is approached.......Constant-pressure molecular-dynamics simulations of phospholipid membranes in the fluid Lα phase reveal strong correlations between equilibrium fluctuations of volume and energy on the nanosecond time-scale. The existence of strong volume-energy correlations was previously deduced indirectly...

  6. Volume-energy correlations in the slow degrees of freedom of computer-simulated phospholipid membranes

    DEFF Research Database (Denmark)

    Pedersen, Ulf Rørbæk; Peters, Günther H.; Schrøder, Thomas;

    by Heimburg from experiments focusing on the phase transition between the fluid and the ordered gel phases. The correlations, which are reported here for three different membranes (DMPC, DMPS-Na, and DMPSH), have volume-energy correlation coefficients ranging from 0.81 to 0.89. The DMPC membrane was studied...... at two temperatures showing that the correlation coefficient increases as the phase transition is approached......Constant-pressure molecular-dynamics simulations of phospholipid membranes in the fluid phase reveal strong correlations between equilibrium fluctuations of volume and energy on the nanosecond time-scale. The existence of strong volume-energy correlations was previously deduced indirectly...

  7. Correlates of suicide and violence risk: III. A two-stage model of countervailing forces.

    Science.gov (United States)

    Plutchik, R; van Praag, H M; Conte, H R

    1989-05-01

    Questionnaires and self-report scales were administered to 100 psychiatric inpatients. The scales measured such variables as depression, hopelessness, impulsivity, mental and life problems, family violence, personality characteristics, and dyscontrol tendencies. These were correlated with indices of suicide risk and violence risk. Most variables were found to correlate significantly with both suicide and violence risk. Partial correlation analyses revealed that 10 variables correlated significantly with suicide risk but not violence risk, while four variables correlated significantly with violence risk but not suicide risk. A two-stage model of countervailing forces, incorporating concepts from both psychoanalysis and ethology, is presented as a way of interpreting the results. PMID:2748772

  8. Effect of Electronic Correlations on Magnetotransport through a Parallel Double Quantum Dot

    Institute of Scientific and Technical Information of China (English)

    FANG Dong-Kai; WU Shao-Quan; ZOU Cheng-Yi; ZHAO Guo-Ping

    2012-01-01

    We theoretically investigate the effect of electronic correlations (including spin and Coulomb correlations) on magnetotransport through a parallel double quantum dot coupled to ferromagnetic leads.Within the framework of the generalized master equation,we analyze the current,differential conductance and tunnel magnetoresistance versus bias for different electron correlations.Our results reveal that spin correlations can induce a giant tunnel magnetoresistance,while Coulomb correlations can lead to the occurrence of negative tunnel magetoresistance and negative differential conductance,and the relevant underlying physics of this problem is discussed.

  9. Correlation of Numerical Anxiety and Mathematics Performance

    Directory of Open Access Journals (Sweden)

    Michael Howard D. Morada

    2015-12-01

    Full Text Available It has been observed that most students had negative view towards mathematics and as a result, they also performed poorly.As such, it is imperative for every math teacher to understand the reasons behind this negative view to improve their student’s performance. This observation led the researcher to conduct a study on Correlation of Mathematics Performance and Anxiety of third and fourth year students for school year 2012-2013 across the different programs.This study determined the numerical anxiety level and mathematics performance of the respondents along age, gender and programs. The study revealed that students, regardless of age had passing performance. However, female and male students had fair and passing mathematics performance, respectively. Students from College of Business Education, Teacher Education and Computer Studies had fair performance while those from Marine Transportation, Criminal Justice Education and Engineering had passing performance. The study also revealed that students across different variables had moderate numerical anxiety level. Furthermore, it was found out that mathematics performance is significantly related to numerical anxiety. However, the relationship was inverse and small.

  10. Correlative fluorescence and electron microscopy.

    Science.gov (United States)

    Schirra, Randall T; Zhang, Peijun

    2014-10-01

    Correlative fluorescence and electron microscopy (CFEM) is a multimodal technique that combines dynamic and localization information from fluorescence methods with ultrastructural data from electron microscopy, to give new information about how cellular components change relative to the spatiotemporal dynamics within their environment. In this review, we will discuss some of the basic techniques and tools of the trade for utilizing this attractive research method, which is becoming a very powerful tool for biology labs. The information obtained from correlative methods has proven to be invaluable in creating consensus between the two types of microscopy, extending the capability of each, and cutting the time and expense associated with using each method separately for comparative analysis. The realization of the advantages of these methods in cell biology has led to rapid improvement in the protocols and has ushered in a new generation of instruments to reach the next level of correlation--integration.

  11. Hadron Correlations Measured with ALICE

    CERN Document Server

    Grosse-Oetringhaus, Jan Fiete

    2013-01-01

    Angular particle correlations are a powerful tool to study collective effects and in-medium jet modification as well as their interplay in the hot and dense medium produced in central heavy-ion collisions. We present measurements of two-particle angular correlations of inclusive charged and identified particles performed with the ALICE detector. The near-side peak in the short-range correlation region is quantitatively analyzed: while the rms of the peak in $\\phi$-direction is independent of centrality within uncertainties, we find a significant broadening in $\\eta$-direction from peripheral to central collisions. The particle content of the near-side peak is studied finding that the $p/\\pi$ ratio of particles associated to a trigger particle is much smaller than the one in the bulk of the particles and consistent with fragmentation of a parton in vacuum.

  12. Electron correlations in quantum dots

    CERN Document Server

    Tipton, D L J

    2001-01-01

    Quantum dot structures confine electrons in a small region of space. Some properties of semiconductor quantum dots, such as the discrete energy levels and shell filling effects visible in addition spectra, have analogies to those of atoms and indeed dots are sometimes referred to as 'artificial atoms'. However, atoms and dots show some fundamental differences due to electron correlations. For real atoms, the kinetic energy of electrons dominates over their mutual Coulomb repulsion energy and for this reason the independent electron approximation works well. For quantum dots the confining potential may be shallower than that of real atoms leading to lower electron densities and a dominance of mutual Coulomb repulsion over kinetic energy. In this strongly correlated regime the independent electron picture leads to qualitatively incorrect results. This thesis concentrates on few-electron quantum dots in the strongly correlated regime both for quasi-one-dimensional and two-dimensional dots in a square confining p...

  13. Softc: An Operational Software Correlator

    Science.gov (United States)

    Lowe, Stephen T.

    2004-01-01

    Softc has been used operationally for spacecraft navigation at JPL for over 2 years and will be JPL's Mark 5 correlator next year. Softc was written to be as close to an ideal correlator as possible, making approximations only below 10(exp -13) seconds. The program can correlate real USB, real LSB, or complex I/Q data sampled with 1, 2, 4. or 8-bit resolution, and was developed with strong debugging tools that made final debugging relatively quick. Softc's algorithms and program structure are fully documented. Timing tests on a recent Intel CPU show Softc processes 8 lags of 1-bit sampled data at 10 MSamples/sec, independent of sample rate.

  14. Connected correlators in quantum gravity

    International Nuclear Information System (INIS)

    We discuss the concept of connected, reparameterization invariant matter correlators in quantum gravity. We analyze the effect of discretization in two solvable cases: branched polymers and two-dimensional simplicial gravity. In both cases the naively defined connected correlators for a fixed volume display an anomalous behavior, which could be interpreted as a long-range order. We suggest that this is in fact only a highly non-trivial finite-size effect and propose an improved definition of the connected correlator, which reduces the effect. Using this definition we illustrate the appearance of a long-range spin order in the Ising model on a two-dimensional random lattice in an external magnetic field H, when H to 0 and β=βC. (author)

  15. State estimation on correlated copies

    International Nuclear Information System (INIS)

    State estimation is usually analyzed in the situation when copies are in a product state, either mixed or pure. We investigate here the concept of state estimation on correlated copies. We analyze state estimation on correlated N-qubit states, which are permutationally invariant. Using a correlated state we try to estimate as good as possible the direction of the Bloch vector of a single-particle reduced density matrix. We derive the optimal fidelity for all permutation invariant states. We find the optimal state, which yields the highest estimation fidelity among the states with the same reduced density matrix. Interestingly, this state is not a product state. We also point out that states produced by optimal universal cloning machines are the worst, from the point of view of estimating the reduced density matrix

  16. Quantumness of correlations and entanglement

    CERN Document Server

    Devi, A R Usha; Sudha,

    2011-01-01

    Generalized measurement schemes on one part of bipartite states, which would leave the set of all separable states insensitive are explored here to understand quantumness of correlations in a more general perspecitve. This is done by employing linear maps associated with generalized projective measurements. A generalized measurement corresponds to a quantum operation mapping a density matrix to another density matrix, preserving its positivity, hermiticity and traceclass. The Positive Operator Valued Measure (POVM) -- employed earlier in the literature to optimize the measures of classical/quatnum correlations -- correspond to completely positive (CP) maps. The other class, the not completely positive (NCP) maps, are investigated here, in the context of measurements, for the first time. It is shown that that such NCP projective maps provide a new clue to the understanding the quantumness of correlations in a general setting. Especially, the separability-classicality dichotomy gets resolved only when both the ...

  17. Spatiotemporal correlations of aftershock sequences

    CERN Document Server

    Peixoto, Tiago P; Davidsen, Jörn

    2010-01-01

    Aftershock sequences are of particular interest in seismic research since they may condition seismic activity in a given region over long time spans. While they are typically identified with periods of enhanced seismic activity after a large earthquake as characterized by the Omori law, our knowledge of the spatiotemporal correlations between events in an aftershock sequence is limited. Here, we study the spatiotemporal correlations of two aftershock sequences form California (Parkfield and Hector Mine) using the recently introduced concept of "recurrent" events. We find that both sequences have very similar properties and that most of them are captured by the space-time epidemic-type aftershock sequence (ETAS) model if one takes into account catalog incompleteness. However, the stochastic model does not capture the spatiotemporal correlations leading to the observed structure of seismicity on small spatial scales.

  18. Correlations between black holes formed in cosmic string breaking

    OpenAIRE

    Emparan García de Salazar, Roberto A.

    1995-01-01

    An analysis of cosmic string breaking with the formation of black holes attached to the ends reveals a remarkable feature: the black holes can be correlated or uncorrelated. We find that, as a consequence, the number-of-states enhancement factor in the action governing the formation of uncorrelated black holes is twice the one for a correlated pair. We argue that when an uncorrelated pair forms at the ends of the string, the physics involved is more analogous to thermal nucleation than to par...

  19. Scalings of field correlations and heat transport in turbulent convection.

    Science.gov (United States)

    Verma, Mahendra K; Mishra, Pankaj K; Pandey, Ambrish; Paul, Supriyo

    2012-01-01

    Using direct numerical simulations of Rayleigh-Bénard convection under free-slip boundary condition, we show that the normalized correlation function between the vertical velocity field and the temperature field, as well as the normalized viscous dissipation rate, scales as Ra-0.22 for moderately large Rayleigh number Ra. This scaling accounts for the Nusselt number Nu exponent of approximately 0.3, as observed in experiments. Numerical simulations also reveal that the aforementioned normalized correlation functions are constants for the convection simulation under periodic boundary conditions.

  20. Anti-correlation and subsector structure in financial systems

    Science.gov (United States)

    Jiang, X. F.; Zheng, B.

    2012-02-01

    With the random matrix theory, we study the spatial structure of the Chinese stock market, the American stock market and global market indices. After taking into account the signs of the components in the eigenvectors of the cross-correlation matrix, we detect the subsector structure of the financial systems. The positive and negative subsectors are anti-correlated with respect to each other in the corresponding eigenmode. The subsector structure is strong in the Chinese stock market, while somewhat weaker in the American stock market and global market indices. Characteristics of the subsector structures in different markets are revealed.

  1. CORRELATION AND PATH COEFFICIENT ANALYSIS IN GROUNDNUT (ARACHIS HYPOGAEA L.

    Directory of Open Access Journals (Sweden)

    C. Pavan Kumar

    2014-02-01

    Full Text Available Sixty six genotypes of groundnut were used to study the correlation and path analysis for yield and yield contributing characters. Correlation studies revealed that kernel yield was significantly and positively associated with pod yield per plant, number of mature pods per plant, shelling percentage, harvest index, sound mature kernel percentage, specific leaf weight at 60 DAS, protein content and oil content. Path coefficient analysis indicated that pod yield per plant and shelling percentage had high positive direct effect on kernel yield signifying the importance of these traits in the improvement of seed yield.

  2. Probing Spatial Spin Correlations of Ultracold Gases by Quantum Noise Spectroscopy

    OpenAIRE

    Bruun, G.; Andersen, Brian; Sørensen, Anders; Demler, Eugene A.

    2009-01-01

    Spin noise spectroscopy with a single laser beam is demonstrated theoretically to provide a direct probe of the spatial correlations of cold fermionic gases. We show how the generic many-body phenomena of anti-bunching, pairing, antiferromagnetic, and algebraic spin liquid correlations can be revealed by measuring the spin noise as a function of laser width, temperature, and frequency.

  3. Psycholinguistic Correlates of Progress in Literature of Students of Russian Vocational Training School

    Science.gov (United States)

    Nuriakhmetov, Aidar

    2012-01-01

    The article describes psycholinguistic correlates of progress in literature, discovered on the basis of correlation analysis of grades, and results of several psychological and psycholinguistic tests were taken in the context of comprehensive psycholinguistic research based on one of Russian vocational training schools. Analysis revealed a list of…

  4. Correlation between the abundance of cellulolitic fungi and selected soil properties

    Directory of Open Access Journals (Sweden)

    Teresa Korniłłowicz-Kowalska

    2014-08-01

    Full Text Available The study conducted has revealed the general abundance of cellulolytic fungi in the soil is significantly correlated only with the phosphors content. The correlation with specific soil properties was found in the case of the genera Humicola, Penicillium, Fusarium and Chrysosporium of the 10 genera of these fungi isolated most often.

  5. Pairing correlations in exotic nuclei

    CERN Document Server

    Sagawa, H

    2012-01-01

    The BCS and HFB theories which can accommodate the pairing correlations in the ground states of atomic nuclei are presented. As an application of the pairing theories, we investigate the spatial extension of weakly bound Ne and C isotopes by taking into account the pairing correlation with the Hartree-Fock-Bogoliubov (HFB) method and a 3-body model, respectively. We show that the odd-even staggering in the reaction cross sections of $^{30,31,32}$Ne and $^{14,15,16}$C are successfully reproduced, and thus the staggering can be attributed to the unique role of pairing correlations in nuclei far from the stability line. A correlation between a one-neutron separation energy and the anti-halo effect is demonstrated for $s$- and p-waves using the HFB wave functions. We also propose effective density-dependent pairing interactions which reproduce both the neutron-neutron ($nn$) scattering length at zero density and the neutron pairing gap in uniform matter. Then, we apply these interactions to study pairing gaps in ...

  6. The Seduction of Correlational Data.

    Science.gov (United States)

    Cochran, Nancy

    1979-01-01

    A dependency on correlational data allows one to avoid theory building and even to avoid defining terms. The social science community is being seduced by data and would do well to resist what is available simply because of its ease of tabulation and redundancy. (RL)

  7. Correlations among alfalfa yield components

    Directory of Open Access Journals (Sweden)

    Ilić Olivera

    2006-01-01

    Full Text Available Presented in this paper are the results of our study of correlations among yield components in ten alfalfa genotypes under open pollination (polycross conditions. The study was conducted between 2000 and 2002 at the Rimski Sancevi Experiment Field of the Institute of Field and Vegetable Crops in Novi Sad. Highly significant correlations were found between pod number per inflorescence and seed number per inflorescence (r= 0.645 as well as between seed number per pod and seed number per inflorescence (r= 0.685. Similarly, the correlation between inflorescence number per stem and seed yield was significant and positive (r= 0.589. Negative correlations existed between ovule number per ovary on the one hand and seed yield and inflorescence number per stem on the other (r= -0.617 and r= -0.598, respectively. The highest seed yield was achieved with the cultivar Europe (651.4 kg ha-1 and the lowest with the genotype Le-6 (426.25 kg ha-1. The difference was highly significant (CV= 14,93%.

  8. Time correlators from deferred measurements

    Science.gov (United States)

    Oehri, D.; Lebedev, A. V.; Lesovik, G. B.; Blatter, G.

    2016-01-01

    Repeated measurements that typically occur in two-time or multitime correlators rely on von Neumann's projection postulate, telling how to restart the system after an intermediate measurement. We invoke the principle of deferred measurement to describe an alternative procedure in which coevolving quantum memories extract system information through entanglement, combined with a final readout of the memories described by Born's rule. Our approach to repeated quantum measurements respects the unitary evolution of quantum mechanics during intermediate times, unifies the treatment of strong and weak measurements, and reproduces the projected and (anti)symmetrized correlators in the two limits. As an illustration, we apply our formalism to the calculation of the electron charge correlator in a mesoscopic physics setting, where single electron pulses assume the role of flying memory qubits. We propose an experimental setup that reduces the measurement of the time correlator to the measurement of currents and noise, exploiting the (pulsed) injection of electrons to cope with the challenge of performing short-time measurements.

  9. Programming services with correlation sets

    DEFF Research Database (Denmark)

    Montesi, Fabrizio; Carbone, Marco

    2011-01-01

    -oriented systems, such as distribution, loose coupling, open-endedness and integration. Distinguishing features of our approach are the notion of correlation aliases and an asynchronous communication model. Our language is equipped with formal syntax, semantics, and a typing system for ensuring desirable...

  10. Correlation in the lanthanide series

    International Nuclear Information System (INIS)

    The correlations lgK vs. lgK', V vs. V' (K - stability constant of the complex, V - unit cell volume of compound) within the lanthanide tetrads were reviewed. Ligands with - C = N-group were found to show a positive deviation from the lgK vs. lgK' plot. (Author)

  11. Octupole correlation effects in nuclei

    International Nuclear Information System (INIS)

    Octupole correlation effects in nuclei are discussed from the point of view of many-body wavefunctions as well as mean-field methods. The light actinides, where octupole effects are largest, are considered in detail. Comparisons of theory and experiment are made for energy splittings of parity doublets; E1 transition matrix elements and one-nucleon transfer reactions

  12. Quantum and classical correlations of intense beams of light via joint photodetection

    OpenAIRE

    Agliati, A.; Bondani, M.; Andreoni, A.; De Cillis, G.; Paris, M. G. A.

    2005-01-01

    We address joint photodetection as a method to discriminate between the classical correlations of a thermal beam divided by a beam splitter and the quantum entanglement of a twin-beam obtained by parametric downconversion. We show that for intense beams of light the detection of the difference photocurrent may be used, in principle, in order to reveal entanglement, while the simple measurement of the correlation coefficient is not sufficient. We have experimentally measured the correlation co...

  13. Spatial quantum correlations induced by random multiple scattering of quadrature squeezed light

    DEFF Research Database (Denmark)

    Lodahl, Peter

    2007-01-01

    The authors demonstrates that spatial quantum correlations are induced by multiple scattering of quadrature squeezed light through a random medium. As a consequence, light scattered along two different directions by the random medium will not be independent, but be correlated to an extent that can...... only be described by a quantum mechanical theory for multiple scattering. The spatial quantum correlation is revealed in the fluctuations of the total intensity transmission or reflection through the multiple scattering medium....

  14. Return of the Volcano: PHENIX Azimuthal Correlations 62.4 GeV Au+Au

    CERN Document Server

    McCumber, M; Cumber, Michael Mc; Frantz, Justin

    2005-01-01

    As in previous analyses at sqrt(s_NN) 200 GeV, correlations in azimuthal angles between inclusive charge particles at intermediate transverse momentum (p_T = 1.0-4.0) GeV/c are studied at sqrt(s_NN) 62.4 GeV. The jet correlations reveal similar modification as in 200 GeV. Specifically large modification, including the "volcano" or "cone" structure, persists in the awayside correlation.

  15. Correlation between glycemic excursion by CGMS and diabetic retinopathy among Type 2 diabetes mellitus

    International Nuclear Information System (INIS)

    Objective: To investigate correlation between glycemic excursion by CGMS and diabetic retinopathy among type 2 diabetes mellitus. Methods: Used continuous glucose monitoring system (CGMS) to monitoring glycemic excursion within a day of twenty four patients with type 2 diabetes mellitus, and inspect fundus photography, correlation was analyzed. Results: Glycemic excursion might reveal the risk for diabetic retinopathy better than HbA1c does. Conclusion: Diabetic retinopathy may correlate with glycemic excursion. (authors)

  16. Correlated Electron Phenomena in 2D Materials

    Science.gov (United States)

    Lambert, Joseph G.

    In this thesis, I present experimental results on coherent electron phenomena in layered two-dimensional materials: single layer graphene and van der Waals coupled 2D TiSe2. Graphene is a two-dimensional single-atom thick sheet of carbon atoms first derived from bulk graphite by the mechanical exfoliation technique in 2004. Low-energy charge carriers in graphene behave like massless Dirac fermions, and their density can be easily tuned between electron-rich and hole-rich quasiparticles with electrostatic gating techniques. The sharp interfaces between regions of different carrier densities form barriers with selective transmission, making them behave as partially reflecting mirrors. When two of these interfaces are set at a separation distance within the phase coherence length of the carriers, they form an electronic version of a Fabry-Perot cavity. I present measurements and analysis of multiple Fabry-Perot modes in graphene with parallel electrodes spaced a few hundred nanometers apart. Transition metal dichalcogenide (TMD) TiSe2 is part of the family of materials that coined the term "materials beyond graphene". It contains van der Waals coupled trilayer stacks of Se-Ti-Se. Many TMD materials exhibit a host of interesting correlated electronic phases. In particular, TiSe2 exhibits chiral charge density waves (CDW) below TCDW ˜ 200 K. Upon doping with copper, the CDW state gets suppressed with Cu concentration, and CuxTiSe2 becomes superconducting with critical temperature of T c = 4.15 K. There is still much debate over the mechanisms governing the coexistence of the two correlated electronic phases---CDW and superconductivity. I will present some of the first conductance spectroscopy measurements of proximity coupled superconductor-CDW systems. Measurements reveal a proximity-induced critical current at the Nb-TiSe2 interfaces, suggesting pair correlations in the pure TiSe2. The results indicate that superconducting order is present concurrently with CDW in

  17. Is Utility Transferable? A Revealed Preference Analysis

    NARCIS (Netherlands)

    Cherchye, L.J.H.; Demuynck, T.; de Rock, B.

    2011-01-01

    We provide a revealed preference analysis of the transferable utility hypothesis, which is widely used in economic models. First, we establish revealed preference conditions that must be satisfied for observed group behavior to be consistent with Pareto efficiency under transferable utility. Next, w

  18. Robust Statistical Detection of Power-Law Cross-Correlation.

    Science.gov (United States)

    Blythe, Duncan A J; Nikulin, Vadim V; Müller, Klaus-Robert

    2016-01-01

    We show that widely used approaches in statistical physics incorrectly indicate the existence of power-law cross-correlations between financial stock market fluctuations measured over several years and the neuronal activity of the human brain lasting for only a few minutes. While such cross-correlations are nonsensical, no current methodology allows them to be reliably discarded, leaving researchers at greater risk when the spurious nature of cross-correlations is not clear from the unrelated origin of the time series and rather requires careful statistical estimation. Here we propose a theory and method (PLCC-test) which allows us to rigorously and robustly test for power-law cross-correlations, correctly detecting genuine and discarding spurious cross-correlations, thus establishing meaningful relationships between processes in complex physical systems. Our method reveals for the first time the presence of power-law cross-correlations between amplitudes of the alpha and beta frequency ranges of the human electroencephalogram. PMID:27250630

  19. Structure of a financial cross-correlation matrix under attack

    Science.gov (United States)

    Lim, Gyuchang; Kim, SooYong; Kim, Junghwan; Kim, Pyungsoo; Kang, Yoonjong; Park, Sanghoon; Park, Inho; Park, Sang-Bum; Kim, Kyungsik

    2009-09-01

    We investigate the structure of a perturbed stock market in terms of correlation matrices. For the purpose of perturbing a stock market, two distinct methods are used, namely local and global perturbation. The former involves replacing a correlation coefficient of the cross-correlation matrix with one calculated from two Gaussian-distributed time series while the latter reconstructs the cross-correlation matrix just after replacing the original return series with Gaussian-distributed time series. Concerning the local case, it is a technical study only and there is no attempt to model reality. The term ‘global’ means the overall effect of the replacement on other untouched returns. Through statistical analyses such as random matrix theory (RMT), network theory, and the correlation coefficient distributions, we show that the global structure of a stock market is vulnerable to perturbation. However, apart from in the analysis of inverse participation ratios (IPRs), the vulnerability becomes dull under a small-scale perturbation. This means that these analysis tools are inappropriate for monitoring the whole stock market due to the low sensitivity of a stock market to a small-scale perturbation. In contrast, when going down to the structure of business sectors, we confirm that correlation-based business sectors are regrouped in terms of IPRs. This result gives a clue about monitoring the effect of hidden intentions, which are revealed via portfolios taken mostly by large investors.

  20. Electrophysiological correlates of non-stationary BOLD functional connectivity fluctuations

    OpenAIRE

    Tagliazucchi, Enzo; von Wegner, Frederic; Morzelewski, Astrid; Brodbeck, Verena; Laufs, Helmut

    2012-01-01

    Spontaneous fluctuations of the BOLD (Blood Oxygen Level-Dependent) signal, measured with fMRI (functional Magnetic Resonance Imaging), display a rich and neurobiologically relevant functional connectivity structure. This structure is usually revealed using time averaging methods, which prevent the detection of functional connectivity changes over time. In this work we studied the electrophysiological correlates of dynamical BOLD functional connectivity fluctuations, by means of long (approx....

  1. Resonant matter: pattern correlates of process-in-formation

    OpenAIRE

    Báez, Manuel Antonio

    2013-01-01

    Through the aid of ever advancing technology, the analysis of complex phenomena offers us more comprehensive insights regarding the intricate inner workings of Nature’s dynamic processes. Through such digital simulations (i.e., of fluid, aero, neuro and vibratory dynamics), the operations and flow of energy are revealed as highly patterned process-structures of activity. These vivid configurations often resemble and correlate with the patterns and motifs found at different scales throughout N...

  2. Alien Hand Syndrome: Neural Correlates of Movements without Conscious Will

    OpenAIRE

    Schaefer, Michael,; Heinze, Hans-Jochen; Galazky, Imke

    2010-01-01

    Background The alien hand syndrome is a striking phenomenon characterized by purposeful and autonomous movements that are not voluntarily initiated. This study aimed to examine neural correlates of this rare neurological disorder in a patient with corticobasal degeneration and alien hand syndrome of the left hand. Methodology/Principal Findings We employed functional magnetic resonance imaging to investigate brain responses associated with unwanted movements in a case study. Results revealed ...

  3. Copula-based dynamic conditional correlation multiplicative error processes

    OpenAIRE

    Bodnar, Taras; Hautsch, Nikolaus

    2013-01-01

    We introduce a copula-based dynamic model for multivariate processes of (non-negative) high-frequency trading variables revealing time-varying conditional variances and correlations. Modeling the variables’ conditional mean processes using a multiplicative error model we map the resulting residuals into a Gaussian domain using a Gaussian copula. Based on high-frequency volatility, cumulative trading volumes, trade counts and market depth of various stocks traded at the NYSE, we show that the ...

  4. Substance Use Correlates of Depression among African American Male Inmates

    OpenAIRE

    Holliday, Rhonda Conerly; Braithwaite, Ronald L.; Yancey, Elleen; Akintobi, Tabia; Stevens-Watkins, Danielle; Smith, Selina; Powell, C. Lamonte

    2016-01-01

    Substance use correlates of depressive symptoms among incarcerated adult male African American substance users were examined in the current study. Frequency of drug use was assessed with 12 items specific to an individual’s substance use. The Patient Depression Questionnaire (PHQ-9) was used to assess symptoms of depression. Approximately 90% of the sample displayed symptoms of depression ranging from minimal to severe. Regression models revealed that three substance use variables demonstrate...

  5. Parametric Spectral Correlations of Disordered Systems in the Fourier Domain

    OpenAIRE

    Guarneri, I.; Zyczkowski, K.; Zakrzewski, J.; Molinari, L.; Casati, G.

    1995-01-01

    A Fourier analysis of parametric level dynamics for random matrices periodically depending on a phase is developed. We demonstrate both theoretically and numerically that under very general conditions the correlation $C(\\varphi )$ of level velocities is singular at $\\varphi =0$ for any symmetry class; the singularity is revealed by algebraic tails in Fourier transforms, and is milder, the stronger the level repulsion in the chosen ensemble. The singularity is strictly connected with the diver...

  6. Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory

    DEFF Research Database (Denmark)

    Kutty, Sujatha Narayanan; Pont, Adrian C.; Meier, Rudolf;

    2014-01-01

    of the number of larval instars from three (ancestral) to two and one. The genus Achanthiptera which was previously in its own subfamily is shown to be closely related to Azeliini. However, it appears that Azeliinae is paraphyletic because Muscinae is sister-group to the Azeliini while the azeliine...

  7. Revealing Hidden Coherence in Partially Coherent Light

    CERN Document Server

    Svozilík, Jiří; Peřina, Jan; Torres, Juan P

    2015-01-01

    The coherence of a system can be ultimately related to the nature of its correlations with the surroundings (outside world). The system can be, for instance, the polarization of a photon, which forms part of a polarization-entangled two-photon state, or the spatial shape of a coherent beam, where each spatial mode bears different polarizations. Whereas a local unitary transformation of the system do not affect its coherence, global unitary transformations modifying both the system and its surroundings can enhance its coherence transforming mutual correlations into coherence. The question naturally arises of what is the best measure that quantifies the correlations that can be turned into coherence, and how much coherence can be extracted. We answer both questions, and illustrate its application for some typical simple systems, with the aim at illuminating the general concept of enhancing coherence by modifying correlations.

  8. Using metabarcoding to reveal and quantify plant-pollinator interactions.

    Science.gov (United States)

    Pornon, André; Escaravage, Nathalie; Burrus, Monique; Holota, Hélène; Khimoun, Aurélie; Mariette, Jérome; Pellizzari, Charlène; Iribar, Amaia; Etienne, Roselyne; Taberlet, Pierre; Vidal, Marie; Winterton, Peter; Zinger, Lucie; Andalo, Christophe

    2016-01-01

    Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole. PMID:27255732

  9. Correlations of Abelian monopoles in quark-gluon plasma

    CERN Document Server

    Braguta, V V

    2012-01-01

    In this paper the properties of thermal Abelian monopoles in the deconfinement phase of the SU(2) gluodynamics are considered. In particular, to study the properties of the Abelian monopole component of QGP we calculate three-point correlation functions of monopoles for different temperatures from the region $T/T_c \\in (1.5, 6.8)$. The results of the calculation show that the three-point correlation functions can be described by independent pair correlations of monopoles. From this one can conclude that the system of Abelian monopoles in QGP reveals the properties of a dilute gas. In addition, one can assert that the interaction between Abelian monopoles is a pair interaction and there are no three-particle forces acting between monopoles.

  10. Temporal Correlations of the Running Maximum of a Brownian Trajectory

    Science.gov (United States)

    Bénichou, Olivier; Krapivsky, P. L.; Mejía-Monasterio, Carlos; Oshanin, Gleb

    2016-08-01

    We study the correlations between the maxima m and M of a Brownian motion (BM) on the time intervals [0 ,t1] and [0 ,t2], with t2>t1. We determine the exact forms of the distribution functions P (m ,M ) and P (G =M -m ), and calculate the moments E {(M-m ) k} and the cross-moments E {mlMk} with arbitrary integers l and k . We show that correlations between m and M decay as √{t1/t2 } when t2/t1→∞ , revealing strong memory effects in the statistics of the BM maxima. We also compute the Pearson correlation coefficient ρ (m ,M ) and the power spectrum of Mt, and we discuss a possibility of extracting the ensemble-averaged diffusion coefficient in single-trajectory experiments using a single realization of the maximum process.

  11. Effective capacity of multiple antenna channels: Correlation and keyhole

    KAUST Repository

    Zhong, Caijun

    2012-01-01

    In this study, the authors derive the effective capacity limits for multiple antenna channels which quantify the maximum achievable rate with consideration of link-layer delay-bound violation probability. Both correlated multiple-input single-output and multiple-input multiple-output keyhole channels are studied. Based on the closed-form exact expressions for the effective capacity of both channels, the authors look into the asymptotic high and low signal-to-noise ratio regimes, and derive simple expressions to gain more insights. The impact of spatial correlation on effective capacity is also characterised with the aid of a majorisation theory result. It is revealed that antenna correlation reduces the effective capacity of the channels and a stringent quality-of-service requirement causes a severe reduction in the effective capacity but can be alleviated by increasing the number of antennas. © 2012 The Institution of Engineering and Technology.

  12. Correlation effects in focused transmission through disordered media

    CERN Document Server

    Hsu, Chia Wei; Goetschy, Arthur; Cao, Hui; Stone, A Douglas

    2016-01-01

    By controlling the many degrees of freedom in the incident wavefront, one can manipulate wave propagation in complex structures. Such wavefront-shaping methods have been used extensively for controlling light transmitted into wavelength-scale regions (speckles), a property that is insensitive to correlations in the speckle pattern. Extending coherent control to larger regions should reveal correlation effects and is of great interest for several applications. Here we show with optical wavefront-shaping experiments that long-range correlations substantially increase the dynamic range of control over light transmitted onto larger target regions, when the number of targeted speckles, $M_2$, exceeds the dimensionless conductance $g$. Using a filtered random matrix ensemble appropriate for describing coherent diffusion in an open geometry, we show analytically that $M_2/g$ appears as the controlling parameter in universal scaling laws for several statistical properties of interest--predictions that we quantitative...

  13. Pruning Redundant Alarm Correlation Patterns

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Efficient methods exist for discovering association rules from large collections of data. The number of discovered rules can, however, be so large. At the same time it is well known that many discovered associations are redundant or minor variations of others. Their existence may simply be due to chance rather than true correlation. Thus, those spurious and insignificant rules should be removed. In this paper, we propose a novel technique to overcome this problem. The technique firstly introduces the new concept -- structure rule cover, and then present a quantitative method to prune redundant correlation patterns. The user can now obtain a complete picture of the domain without being overwhelmed by a huge number of rules.

  14. The dynamics of correlated novelties

    CERN Document Server

    Tria, F; Servedio, V D P; Strogatz, S H

    2013-01-01

    One new thing often leads to another. Such correlated novelties are a familiar part of daily life. They are also thought to be fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called "expanding the adjacent possible". The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (analogous to Heaps' law) and for the probability distribution on the space explored (analogous to Zipf's law), as well as signatures of the hypothesized process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit ev...

  15. Bootstrapping N=2 chiral correlators

    Energy Technology Data Exchange (ETDEWEB)

    Lemos, Madalena [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Liendo, Pedro [Humboldt-Univ. Berlin (Germany). IMIP

    2015-12-15

    We apply the numerical bootstrap program to chiral operators in four-dimensional N=2 SCFTs. In the first part of this work we study four-point functions in which all fields have the same conformal dimension. We give special emphasis to bootstrapping a specific theory: the simplest Argyres-Douglas fixed point with no flavor symmetry. In the second part we generalize our setup and consider correlators of fields with unequal dimension. This is an example of a mixed correlator and allows us to probe new regions in the parameter space of N=2 SCFTs. In particular, our results put constraints on relations in the Coulomb branch chiral ring and on the curvature of the Zamolodchikov metric.

  16. Multiparticle Bose-Einstein Correlations

    CERN Document Server

    Wiedemann, Urs Achim

    1998-01-01

    Multiparticle symmetrization effects are contributions to the spectra of Bose-symmetrized states which are not the product of pairwise correlations. Usually they are neglected in particle interferometric calculations which aim at determining the geometry of the boson emitting source from the measured momentum distributions. Based on a method introduced by Zajc and Pratt, we give a calculation of all multiparticle symmetrization effects to the one- and two-particle momentum spectra for a Gaussian phase space distribution of emission points. Our starting point is an ensemble of N-particle Bose-symmetrized wavefunctions with specified phase space localization. In scenarios typical for relativistic heavy ion collisions, multiparticle effects steepen the slope of the one-particle spectrum for realistic particle phase space densities by up to 20 MeV, and they broaden the relative momentum dependence of the two-particle correlations. We discuss these modifications and their consequences in quantitative detail. Also,...

  17. Correlated electrons in quantum matter

    CERN Document Server

    Fulde, Peter

    2012-01-01

    An understanding of the effects of electronic correlations in quantum systems is one of the most challenging problems in physics, partly due to the relevance in modern high technology. Yet there exist hardly any books on the subject which try to give a comprehensive overview on the field covering insulators, semiconductors, as well as metals. The present book tries to fill that gap. It intends to provide graduate students and researchers a comprehensive survey of electron correlations, weak and strong, in insulators, semiconductors and metals. This topic is a central one in condensed matter and beyond that in theoretical physics. The reader will have a better understanding of the great progress which has been made in the field over the past few decades.

  18. Correlated Electrons in Reduced Dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Bonesteel, Nicholas E [Florida State Univ., Tallahassee, FL (United States)

    2015-01-31

    This report summarizes the work accomplished under the support of US DOE grant # DE-FG02-97ER45639, "Correlated Electrons in Reduced Dimensions." The underlying hypothesis of the research supported by this grant has been that studying the unique behavior of correlated electrons in reduced dimensions can lead to new ways of understanding how matter can order and how it can potentially be used. The systems under study have included i) fractional quantum Hall matter, which is realized when electrons are confined to two-dimensions and placed in a strong magnetic field at low temperature, ii) one-dimensional chains of spins and exotic quasiparticle excitations of topologically ordered matter, and iii) electrons confined in effectively ``zero-dimensional" semiconductor quantum dots.

  19. Strongly correlated systems experimental techniques

    CERN Document Server

    Mancini, Ferdinando

    2015-01-01

    The continuous evolution and development of experimental techniques is at the basis of any fundamental achievement in modern physics. Strongly correlated systems (SCS), more than any other, need to be investigated through the greatest variety of experimental techniques in order to unveil and crosscheck the numerous and puzzling anomalous behaviors characterizing them. The study of SCS fostered the improvement of many old experimental techniques, but also the advent of many new ones just invented in order to analyze the complex behaviors of these systems. Many novel materials, with functional properties emerging from macroscopic quantum behaviors at the frontier of modern research in physics, chemistry and materials science, belong to this class of systems. The volume presents a representative collection of the modern experimental techniques specifically tailored for the analysis of strongly correlated systems. Any technique is presented in great detail by its own inventor or by one of the world-wide recognize...

  20. Flat Bands Under Correlated Perturbations

    OpenAIRE

    Bodyfelt, Joshua D.; Leykam, Daniel; Danieli, Carlo; Yu, Xiaoquan; Flach, Sergej

    2014-01-01

    Flat band networks are characterized by coexistence of dispersive and flat bands. Flat bands (FB) are generated by compact localized eigenstates (CLS) with local network symmetries, based on destructive interference. Correlated disorder and quasiperiodic potentials hybridize CLS without additional renormalization, yet with surprising consequencies: (i) states are expelled from the FB energy $E_{FB}$, (ii) the localization length of eigenstates vanishes as $\\xi \\sim 1 / \\ln (E- E_{FB})$, (iii)...

  1. Boundary Anomalies and Correlation Functions

    OpenAIRE

    Huang, Kuo-Wei(C.N. Yang Institute for Theoretical Physics, Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, 11794, U.S.A.)

    2016-01-01

    It was shown recently that boundary terms of conformal anomalies recover the universal contribution to the entanglement entropy and also play an important role in the boundary monotonicity theorem of odd-dimensional quantum field theories. Motivated by these results, we investigate relationships between boundary anomalies and the stress tensor correlation functions in conformal field theories. In particular, we focus on how the conformal Ward identity and the renormalization group equation ar...

  2. Universality in quantum parametric correlations

    OpenAIRE

    Leboeuf, P.; Sieber, M.

    1999-01-01

    We investigate the universality of correlation functions of chaotic and disordered quantum systems as an external parameter is varied. A new, general scaling procedure is introduced which makes the theory invariant under reparametrizations. Under certain general conditions we show that this procedure is unique. The approach is illustrated with the particular case of the distribution of eigenvalue curvatures. We also derive a semiclassical formula for the non-universal scaling factor, and give...

  3. Strictly correlated uniform electron droplets

    OpenAIRE

    Rasanen, E.; Seidl, M.; Gori Giorgi, P.

    2011-01-01

    We study the energetic properties of finite but internally homogeneous D-dimensional electron droplets in the strict-correlation limit. The indirect Coulomb interaction is found to increase as a function of the electron number, approaching the tighter forms of the Lieb-Oxford bound recently proposed by Rasanen et al. [Phys. Rev. Lett. 102, 206406 (2009)]. The bound is satisfied in three-, two-, and one-dimensional droplets, and in the latter case it is reached exactly - regardless of the type...

  4. Correlation effects on topological insulator

    OpenAIRE

    Liu, Xiong-Jun; Liu, Yang; Liu, Xin

    2010-01-01

    The strong correlation effects on topological insulator are studied in a two-sublattice system with an onsite single-particle energy difference $\\Delta$ between two sublattices. At $\\Delta=0$, increasing the onsite interaction strength $U$ drives the transition from the quantum spin Hall insulating state to the non-topological antiferromagnetic Mott-insulating (AFMI) state. When $\\Delta$ is larger than a certain value, a topologically trivial band insulator or AFMI at small values of $U$ may ...

  5. New burnout correlation for annuli

    Energy Technology Data Exchange (ETDEWEB)

    Towell, R.H.

    1964-03-26

    A number of burnout tests have been run subsequent to the publication of the burnout equations in DP-355 and DP-725. The range of variables was extended in these tests and the burnout heat flux was measured. This memorandum presents a modified empirical equation, which correlates the new data, for use in the design of fuel assemblies for the HWCTR. We expect to submit this material for a journal publication within the next quarter.

  6. Observed Correlations in Minkowski Space

    OpenAIRE

    Mould, Richard A

    2003-01-01

    The author has proposed five rules that permit conscious observers to be included in quantum mechanics. In the present paper, these rules are applied to the observation of a non-local pair of correlated particles. Rule (4) again prevents an anomalous result. Two different kinds of relativistic state reduction are considered, where these differ in the way that they impose boundary conditions in Minkowski space. In response to a problem that arises in this context, we require the Lorentz invari...

  7. Spatial correlations in attribute communities.

    Directory of Open Access Journals (Sweden)

    Federica Cerina

    Full Text Available Community detection is an important tool for exploring and classifying the properties of large complex networks and should be of great help for spatial networks. Indeed, in addition to their location, nodes in spatial networks can have attributes such as the language for individuals, or any other socio-economical feature that we would like to identify in communities. We discuss in this paper a crucial aspect which was not considered in previous studies which is the possible existence of correlations between space and attributes. Introducing a simple toy model in which both space and node attributes are considered, we discuss the effect of space-attribute correlations on the results of various community detection methods proposed for spatial networks in this paper and in previous studies. When space is irrelevant, our model is equivalent to the stochastic block model which has been shown to display a detectability-non detectability transition. In the regime where space dominates the link formation process, most methods can fail to recover the communities, an effect which is particularly marked when space-attributes correlations are strong. In this latter case, community detection methods which remove the spatial component of the network can miss a large part of the community structure and can lead to incorrect results.

  8. Neuropsychological correlates of domestic violence.

    Science.gov (United States)

    Cohen, R A; Rosenbaum, A; Kane, R L; Warnken, W J; Benjamin, S

    1999-01-01

    Neuropsychological functioning was assessed in 39 males who had committed domestic violence (batterers) and compared to 63 nonviolent (both maritally discordant and satisfied) subjects recruited by advertisement. Subjects were subsequently divided into two groups (head injured, nonhead injured) and these groups were also contrasted as a function of batterer status. Tests were administered to assess for cognitive and behavioral functions, including executive dysfunction, hypothesized to be a factor contributing to propensity for violence. Questionnaires and structured clinical interviews were used to assess marital discord, emotional distress, and violent behaviors. Batterers differed from nonbatterers across several cognitive domains: executive, learning, memory, and verbal functioning. Batterers were reliably discriminated from nonbatterers based on three neuropsychological tasks: Digit Symbol, Recognition Memory Test-Words, Wisconsin Card Sorting Test. Neuropsychological performance was the strongest correlate of domestic violence of all clinical variables measured. However, the inclusion of two other variables, severity of emotional distress and history of head injury, together with the neuropsychological indices provided the strongest correlation with batterers status. Among batterers, neuropsychological performance did not vary as a function of head injury status, indicating that while prior head injury was correlated with batterer status, it was not the sole basis for their impairments. The findings suggest that current cognitive status, prior brain injury, childhood academic problems, as well as psychosocial influences, contribute along with coexisting emotional distress to a propensity for domestic violence. PMID:10751047

  9. Intersubject information mapping: revealing canonical representations of complex natural stimuli

    Directory of Open Access Journals (Sweden)

    Nikolaus Kriegeskorte

    2015-03-01

    Full Text Available Real-world time-continuous stimuli such as video promise greater naturalism for studies of brain function. However, modeling the stimulus variation is challenging and introduces a bias in favor of particular descriptive dimensions. Alternatively, we can look for brain regions whose signal is correlated between subjects, essentially using one subject to model another. Intersubject correlation mapping (ICM allows us to find brain regions driven in a canonical manner across subjects by a complex natural stimulus. However, it requires a direct voxel-to-voxel match between the spatiotemporal activity patterns and is thus only sensitive to common activations sufficiently extended to match up in Talairach space (or in an alternative, e.g. cortical-surface-based, common brain space. Here we introduce the more general approach of intersubject information mapping (IIM. For each brain region, IIM determines how much information is shared between the subjects' local spatiotemporal activity patterns. We estimate the intersubject mutual information using canonical correlation analysis applied to voxels within a spherical searchlight centered on each voxel in turn. The intersubject information estimate is invariant to linear transforms including spatial rearrangement of the voxels within the searchlight. This invariance to local encoding will be crucial in exploring fine-grained brain representations, which cannot be matched up in a common space and, more fundamentally, might be unique to each individual – like fingerprints. IIM yields a continuous brain map, which reflects intersubject information in fine-grained patterns. Performed on data from functional magnetic resonance imaging (fMRI of subjects viewing the same television show, IIM and ICM both highlighted sensory representations, including primary visual and auditory cortices. However, IIM revealed additional regions in higher association cortices, namely temporal pole and orbitofrontal cortex. These

  10. Detecting temporal and spatial correlations in pseudoperiodic time series

    Science.gov (United States)

    Zhang, Jie; Luo, Xiaodong; Nakamura, Tomomichi; Sun, Junfeng; Small, Michael

    2007-01-01

    Recently there has been much attention devoted to exploring the complicated possibly chaotic dynamics in pseudoperiodic time series. Two methods [Zhang , Phys. Rev. E 73, 016216 (2006); Zhang and Small, Phys. Rev. Lett. 96, 238701 (2006)] have been forwarded to reveal the chaotic temporal and spatial correlations, respectively, among the cycles in the time series. Both these methods treat the cycle as the basic unit and design specific statistics that indicate the presence of chaotic dynamics. In this paper, we verify the validity of these statistics to capture the chaotic correlation among cycles by using the surrogate data method. In particular, the statistics computed for the original time series are compared with those from its surrogates. The surrogate data we generate is pseudoperiodic type (PPS), which preserves the inherent periodic components while destroying the subtle nonlinear (chaotic) structure. Since the inherent chaotic correlations among cycles, either spatial or temporal (which are suitably characterized by the proposed statistics), are eliminated through the surrogate generation process, we expect the statistics from the surrogate to take significantly different values than those from the original time series. Hence the ability of the statistics to capture the chaotic correlation in the time series can be validated. Application of this procedure to both chaotic time series and real world data clearly demonstrates the effectiveness of the statistics. We have found clear evidence of chaotic correlations among cycles in human electrocardiogram and vowel time series. Furthermore, we show that this framework is more sensitive to examine the subtle changes in the dynamics of the time series due to the match between PPS surrogate and the statistics adopted. It offers a more reliable tool to reveal the possible correlations among cycles intrinsic to the chaotic nature of the pseudoperiodic time series.

  11. Saturn's Rings Reveal Unexpected Phenomena

    Institute of Scientific and Technical Information of China (English)

    李颖

    2004-01-01

    Safely in orbit around Saturn, NASA's Cassini spacecraft sent back its first close-up images of the massive planet's rings on July 1, revealing an unexpectedly varied terrain featuring surprisingly sharp edges, braids and delicate ridges.

  12. Iterative Method for Generating Correlated Binary Sequences

    CERN Document Server

    Usatenko, O V; Apostolov, S S; Makarov, N M; Krokhin, A A

    2014-01-01

    We propose a new efficient iterative method for generating random correlated binary sequences with prescribed correlation function. The method is based on consecutive linear modulations of initially uncorrelated sequence into a correlated one. Each step of modulation increases the correlations until the desired level has been reached. Robustness and efficiency for the proposed algorithm are tested by generating sequences with inverse power-law correlations. The substantial increase in the strength of correlation in the iterative method with respect to the single-step filtering generation is shown for all studied correlation functions. Our results can be used for design of disordered superlattices, waveguides, and surfaces with selective transport properties.

  13. The crystallography of correlated disorder.

    Science.gov (United States)

    Keen, David A; Goodwin, Andrew L

    2015-05-21

    Classical crystallography can determine structures as complicated as multi-component ribosomal assemblies with atomic resolution, but is inadequate for disordered systems--even those as simple as water ice--that occupy the complex middle ground between liquid-like randomness and crystalline periodic order. Correlated disorder nevertheless has clear crystallographic signatures that map to the type of disorder, irrespective of the underlying physical or chemical interactions and material involved. This mapping hints at a common language for disordered states that will help us to understand, control and exploit the disorder responsible for many interesting physical properties.

  14. Correlations for the Novak process

    CERN Document Server

    Nordenstam, Eric

    2012-01-01

    We study random lozenge tilings of a certain shape in the plane called the Novak half-hexagon, and compute the correlation functions for this process. This model was introduced by Nordenstam and Young (2011) and has many intriguing similarities with a more well-studied model, domino tilings of the Aztec diamond. The most difficult step in the present paper is to compute the inverse of the matrix whose (i,j) entry is the binomial coefficient C(A, B_j - i) for indeterminate variables A and B_1, ..., B_n.

  15. Pairing Correlations at High Spins

    Science.gov (United States)

    Ma, Hai-Liang; Dong, Bao-Guo; Zhang, Yan; Fan, Ping; Yuan, Da-Qing; Zhu, Shen-Yun; Zhang, Huan-Qiao; Petrache, C. M.; Ragnarsson, I.; Carlsson, B. G.

    The pairing correcting energies at high spins in 161Lu and 138Nd are studied by comparing the results of the cranked-Nilsson-Strutinsky (CNS) and cranked-Nilsson-Strutinsky-Bogoliubov (CNSB) models. It is concluded that the Coriolis effect rather than the rotational alignment effect plays a major role in the reduction of the pairing correlations in the high spin region. Then we proposed an average pairing correction method which not only better reproduces the experimental data comparing with the CNS model but also enables a clean-cut tracing of the configurations thus the full-spin-range discussion on the various rotating bands.

  16. Boundary anomalies and correlation functions

    Science.gov (United States)

    Huang, Kuo-Wei

    2016-08-01

    It was shown recently that boundary terms of conformal anomalies recover the universal contribution to the entanglement entropy and also play an important role in the boundary monotonicity theorem of odd-dimensional quantum field theories. Motivated by these results, we investigate relationships between boundary anomalies and the stress tensor correlation functions in conformal field theories. In particular, we focus on how the conformal Ward identity and the renormalization group equation are modified by boundary central charges. Renormalized stress tensors induced by boundary Weyl invariants are also discussed, with examples in spherical and cylindrical geometries.

  17. Correlation dimension of complex networks

    CERN Document Server

    Lacasa, Lucas

    2012-01-01

    We propose a new measure to characterize the dimension of complex networks based on the ergodic theory of dynamical systems. This measure is derived from the correlation sum of a trajectory generated by a random walker navigating the network, and extends the classical Grassberger-Procaccia algorithm to the context of complex networks. The method is validated with reliable results for both synthetic networks and real-world networks such as the world air-transportation network or urban networks, and provides a computationally fast way for estimating the dimensionality of networks which only relies on the local information provided by the walkers.

  18. Spin squeezing and quantum correlations

    Indian Academy of Sciences (India)

    K S Mallesh; Swarnamala Sirsi; Mahmoud A A Sbaih; P N Deepak; G Ramachandran

    2002-08-01

    We discuss the notion of spin squeezing considering two mutually exclusive classes of spin- states, namely, oriented and non-oriented states. Our analysis shows that the oriented states are not squeezed while non-oriented states exhibit squeezing. We also present a new scheme for construction of spin- states using 2 spinors oriented along different axes. Taking the case of = 1, we show that the `non-oriented’ nature and hence squeezing arise from the intrinsic quantum correlations that exist among the spinors in the coupled state.

  19. Boundary Anomalies and Correlation Functions

    CERN Document Server

    Huang, Kuo-Wei

    2016-01-01

    It was shown recently that boundary terms of conformal anomalies recover the universal contribution to the entanglement entropy and also play an important role in the boundary monotonicity theorem of odd-dimensional quantum field theories. Motivated by these results, we investigate relationships between boundary anomalies and the stress tensor correlation functions in conformal field theories. In particular, we focus on how the conformal Ward identity and the renormalization group equation are modified by boundary central charges. Renormalized stress tensors induced by boundary Weyl invariants are also discussed, with examples in spherical and cylindrical geometries.

  20. Preselected Sub-Poissonian Correlations

    Science.gov (United States)

    Pavicic, Mladen

    1996-01-01

    The simplest possible photon-number-squeezed states containing only two photons and exhibiting sub-poissonian statistics with the Fano factor approaching 0.5 have been used for a proposal of a loophole-free Bell experiment requiring only 67 percent of detection efficiency. The states are obtained by the fourth order interference first of two downconverted photons at an asymmetrical beam splitter and thereupon of two photons from two independent singlets at an asymmetrical beam splitter. In the latter set-up, the other two photons which nowhere interacted and whose paths never crossed appear entangled in a singlet-like correlated state.

  1. Slow dynamics and correlation functions

    OpenAIRE

    Halpern, V.

    2006-01-01

    The slow dynamics of a system as it approaches a phase transition, associated with the slowing down in the decay of a correlation function, can be caused by a sharp increase in the probability of a particle's returning to its original state following a transition, rather than to a slowing down in the transition rates as is usually assumed. The results of our calculations show that this is the case for the ferromagnetic Potts model. The implications of this result for various theories of the g...

  2. BMN correlators by loop equations

    International Nuclear Information System (INIS)

    In the BMN approach to N=4 SYM a large class of correlators of interest are expressible in terms of expectation values of traces of words in a zero-dimensional gaussian complex matrix model. We develop a loop-equation based, analytic strategy for evaluating such expectation values to any order in the genus expansion. We reproduce the expectation values which were needed for the calculation of the one-loop, genus one correction to the anomalous dimension of BMN-operators and which were earlier obtained by combinatorial means. Furthermore, we present the expectation values needed for the calculation of the one-loop, genus two correction. (author)

  3. EDITORIAL: Strongly correlated electron systems Strongly correlated electron systems

    Science.gov (United States)

    Ronning, Filip; Batista, Cristian

    2011-03-01

    Strongly correlated electrons is an exciting and diverse field in condensed matter physics. This special issue aims to capture some of that excitement and recent developments in the field. Given that this issue was inspired by the 2010 International Conference on Strongly Correlated Electron Systems (SCES 2010), we briefly give some history in order to place this issue in context. The 2010 International Conference on Strongly Correlated Electron Systems was held in Santa Fe, New Mexico, a reunion of sorts from the 1989 International Conference on the Physics of Highly Correlated Electron Systems that also convened in Santa Fe. SCES 2010—co-chaired by John Sarrao and Joe Thompson—followed the tradition of earlier conferences, in this century, hosted by Buzios (2008), Houston (2007), Vienna (2005), Karlsruhe (2004), Krakow (2002) and Ann Arbor (2001). Every three years since 1997, SCES has joined the International Conference on Magnetism (ICM), held in Recife (2000), Rome (2003), Kyoto (2006) and Karlsruhe (2009). Like its predecessors, SCES 2010 topics included strongly correlated f- and d-electron systems, heavy-fermion behaviors, quantum-phase transitions, non-Fermi liquid phenomena, unconventional superconductivity, and emergent states that arise from electronic correlations. Recent developments from studies of quantum magnetism and cold atoms complemented the traditional subjects and were included in SCES 2010. 2010 celebrated the 400th anniversary of Santa Fe as well as the birth of astronomy. So what's the connection to SCES? The Dutch invention of the first practical telescope and its use by Galileo in 1610 and subsequent years overturned dogma that the sun revolved about the earth. This revolutionary, and at the time heretical, conclusion required innovative combinations of new instrumentation, observation and mathematics. These same combinations are just as important 400 years later and are the foundation of scientific discoveries that were discussed

  4. Plane correlations in small colliding systems

    CERN Document Server

    Yan, Li

    2015-01-01

    I propose event-plane correlations as a test of collectivity in small colliding systems: In d-Au and $^3$He-Au collisions, I predict a strong anti-correlation between elliptic and triangular flow, generated by the geometry of the light projectile. A significant anti-correlation is also predicted in central p-Pb collisions at the LHC, which is solely generated by fluctuations. Similar, but stronger correlation patterns are predicted in correlations involving dipolar flow.

  5. Measures of Linear Correlation for Multiple Variables

    OpenAIRE

    Wang, Jianji; Zheng, Nanning

    2014-01-01

    Multivariate linear correlation analysis plays an important role in various fields such as statistics, economics, and big data analytics. However, there was no compact formulation to define and measure multivariate linear correlation. In this paper, we propose a pair of coupling coefficients, the multivariate linear correlation coefficient (LCC) and linear incorrelation coefficient (LIC), to measure the strength of multivariate linear correlation and linear irrelevance. Pearson's correlation ...

  6. Accurate estimator of correlations between asynchronous signals

    OpenAIRE

    Toth, Bence; Kertesz, Janos

    2008-01-01

    The estimation of the correlation between time series is often hampered by the asynchronicity of the signals. Cumulating data within a time window suppresses this source of noise but weakens the statistics. We present a method to estimate correlations without applying long time windows. We decompose the correlations of data cumulated over a long window using decay of lagged correlations as calculated from short window data. This increases the accuracy of the estimated correlation significantl...

  7. Adaptation improves neural coding efficiency despite increasing correlations in variability.

    Science.gov (United States)

    Adibi, Mehdi; McDonald, James S; Clifford, Colin W G; Arabzadeh, Ehsan

    2013-01-30

    Exposure of cortical cells to sustained sensory stimuli results in changes in the neuronal response function. This phenomenon, known as adaptation, is a common feature across sensory modalities. Here, we quantified the functional effect of adaptation on the ensemble activity of cortical neurons in the rat whisker-barrel system. A multishank array of electrodes was used to allow simultaneous sampling of neuronal activity. We characterized the response of neurons to sinusoidal whisker vibrations of varying amplitude in three states of adaptation. The adaptors produced a systematic rightward shift in the neuronal response function. Consistently, mutual information revealed that peak discrimination performance was not aligned to the adaptor but to test amplitudes 3-9 μm higher. Stimulus presentation reduced single neuron trial-to-trial response variability (captured by Fano factor) and correlations in the population response variability (noise correlation). We found that these two types of variability were inversely proportional to the average firing rate regardless of the adaptation state. Adaptation transferred the neuronal operating regime to lower rates with higher Fano factor and noise correlations. Noise correlations were positive and in the direction of signal, and thus detrimental to coding efficiency. Interestingly, across all population sizes, the net effect of adaptation was to increase the total information despite increasing the noise correlation between neurons. PMID:23365247

  8. Contributed Review: Review of integrated correlative light and electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Timmermans, F. J.; Otto, C. [Medical Cell Biophysics Group, MIRA Institute, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)

    2015-01-15

    New developments in the field of microscopy enable to acquire increasing amounts of information from large sample areas and at an increased resolution. Depending on the nature of the technique, the information may reveal morphological, structural, chemical, and still other sample characteristics. In research fields, such as cell biology and materials science, there is an increasing demand to correlate these individual levels of information and in this way to obtain a better understanding of sample preparation and specific sample properties. To address this need, integrated systems were developed that combine nanometer resolution electron microscopes with optical microscopes, which produce chemically or label specific information through spectroscopy. The complementary information from electron microscopy and light microscopy presents an opportunity to investigate a broad range of sample properties in a correlated fashion. An important part of correlating the differences in information lies in bridging the different resolution and image contrast features. The trend to analyse samples using multiple correlated microscopes has resulted in a new research field. Current research is focused, for instance, on (a) the investigation of samples with nanometer scale distribution of inorganic and organic materials, (b) live cell analysis combined with electron microscopy, and (c) in situ spectroscopic and electron microscopy analysis of catalytic materials, but more areas will benefit from integrated correlative microscopy.

  9. Strongly correlated perovskite fuel cells.

    Science.gov (United States)

    Zhou, You; Guan, Xiaofei; Zhou, Hua; Ramadoss, Koushik; Adam, Suhare; Liu, Huajun; Lee, Sungsik; Shi, Jian; Tsuchiya, Masaru; Fong, Dillon D; Ramanathan, Shriram

    2016-05-16

    Fuel cells convert chemical energy directly into electrical energy with high efficiencies and environmental benefits, as compared with traditional heat engines. Yttria-stabilized zirconia is perhaps the material with the most potential as an electrolyte in solid oxide fuel cells (SOFCs), owing to its stability and near-unity ionic transference number. Although there exist materials with superior ionic conductivity, they are often limited by their ability to suppress electronic leakage when exposed to the reducing environment at the fuel interface. Such electronic leakage reduces fuel cell power output and the associated chemo-mechanical stresses can also lead to catastrophic fracture of electrolyte membranes. Here we depart from traditional electrolyte design that relies on cation substitution to sustain ionic conduction. Instead, we use a perovskite nickelate as an electrolyte with high initial ionic and electronic conductivity. Since many such oxides are also correlated electron systems, we can suppress the electronic conduction through a filling-controlled Mott transition induced by spontaneous hydrogen incorporation. Using such a nickelate as the electrolyte in free-standing membrane geometry, we demonstrate a low-temperature micro-fabricated SOFC with high performance. The ionic conductivity of the nickelate perovskite is comparable to the best-performing solid electrolytes in the same temperature range, with a very low activation energy. The results present a design strategy for high-performance materials exhibiting emergent properties arising from strong electron correlations.

  10. The dynamics of correlated novelties

    Science.gov (United States)

    Tria, F.; Loreto, V.; Servedio, V. D. P.; Strogatz, S. H.

    2014-07-01

    Novelties are a familiar part of daily life. They are also fundamental to the evolution of biological systems, human society, and technology. By opening new possibilities, one novelty can pave the way for others in a process that Kauffman has called ``expanding the adjacent possible''. The dynamics of correlated novelties, however, have yet to be quantified empirically or modeled mathematically. Here we propose a simple mathematical model that mimics the process of exploring a physical, biological, or conceptual space that enlarges whenever a novelty occurs. The model, a generalization of Polya's urn, predicts statistical laws for the rate at which novelties happen (Heaps' law) and for the probability distribution on the space explored (Zipf's law), as well as signatures of the process by which one novelty sets the stage for another. We test these predictions on four data sets of human activity: the edit events of Wikipedia pages, the emergence of tags in annotation systems, the sequence of words in texts, and listening to new songs in online music catalogues. By quantifying the dynamics of correlated novelties, our results provide a starting point for a deeper understanding of the adjacent possible and its role in biological, cultural, and technological evolution.

  11. PREFACE: Correlation Dynamics in Nuclei

    Science.gov (United States)

    Suzuki, Toshio; Otsuka, Takaharu; Ichimura, Munetake

    2005-01-01

    The International Symposium on `Correlation Dynamics in Nuclei' was held at the Sanjo Kaikan, the University of Tokyo, from the 31 January to 4 February 2005. This symposium was organized on the occasion of the 50th anniversary of the Configuration Mixing theory of Arima and Horie. The symposium was hosted by the University of Tokyo, and supported by the Inoue Foundation for Science, the Japan Atomic Energy Research Institute and the Ministry of Education, Culture, Sports, Science and Technology. The purpose of the symposium was to discuss theoretical and experimental developments and future prospects in physics of correlation dynamics in nuclei, including topics such as effective interactions, shell model studies of configuration mixing and spin-isospin modes in nuclei. It was shown in many ways and angles that the Arima-Horie theory has been a starting point of a variety of developments of the studies in these fields over many decades. The developments have been enhanced by the expansion of computational capabilities and the progress in accelerators, detectors and radioactive beam facilities. We enjoyed 28 excellent and lively invited talks and 30 oral presentations in the symposium with about 90 participants. A special session was dedicated to celebrate the 80th birthday of Professor Igal Talmi, who made invaluable and pioneering works in the shell model theory. Finally, we would like to thank all the speakers and the participants as well as the other organizers for their contributions which made the symposium very successful.

  12. Oral health correlates of captivity.

    Science.gov (United States)

    Kapoor, Varsha; Antonelli, Tyler; Parkinson, Jennifer A; Hartstone-Rose, Adam

    2016-08-01

    The predominant diet fed to captive carnivores in North America consists of ground meat formulated to provide full nutritional requirements. However, this ground meat diet completely lacks the mechanical properties (i.e., toughness and hardness) of the foods these animals would consume in the wild. The goal of this study is to evaluate the effect of captivity on oral health by comparing the prevalence of periodontal disease and dental calculus accumulation in wild and captive lions and tigers (Panthera leo and Panthera tigris), and to also correlate oral health with cranial morphology in these specimens. To achieve this, 34 adult lion and 29 adult tiger skulls were scored for the presence and extent of dental calculus and periodontal disease. These oral health scores were also compared to cranial deformations examined in a previous study. We found that the occurrence and severity of calculus buildup and periodontal disease was significantly higher in captive felids compared to their wild counterparts. Further, higher calculus accumulation occurred on the posterior teeth when compared to the anterior teeth, while an opposite trend for periodontal disease was observed. We also found a significant correlation between oral health and cranial morphology of lions and tigers. The results suggest that food mechanical properties are significant factors contributing to oral health in felids.

  13. Astrochemical Correlations in Molecular Clouds

    CERN Document Server

    Gaches, Brandt A L; Rosolowsky, Erik W; Bisbas, Thomas G

    2014-01-01

    We investigate the spectral correlations between different species used to observe molecular clouds. We use hydrodynamic simulations and a full chemical network to study the abundances of over 150 species in typical Milky Way molecular clouds. We perform synthetic observations in order to produce emission maps of a subset of these tracers. We study the effects of different lines of sight and spatial resolution on the emission distribution and perform a robust quantitative comparison of the species to each other. We use the Spectral Correlation Function (SCF), which quantifies the root mean squared difference between spectra separated by some length scale, to characterize the structure of the simulated cloud in position-position-velocity (PPV) space. We predict the observed SCF for a broad range of observational tracers, and thus, identify homologous species. In particular, we show that the pairs C and CO, C$^{+}$ and CN, NH$_3$ and H$_2$CS have very similar SCFs. We measure the SCF slope variation as a functi...

  14. ASTROCHEMICAL CORRELATIONS IN MOLECULAR CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Gaches, Brandt A. L.; Offner, Stella S. R. [Department of Astronomy, University of Massachusetts—Amherst, Amherst, MA (United States); Rosolowsky, Erik W. [Department of Physics, University of Alberta, Alberta, CA (Canada); Bisbas, Thomas G., E-mail: bgaches@astro.umass.edu, E-mail: soffner@astro.umass.edu, E-mail: erosolow@ualberta.ca, E-mail: tb@star.ucl.ac.uk [Department of Physics and Astronomy, University College London, London (United Kingdom)

    2015-02-01

    We investigate the spectral correlations between different species used to observe molecular clouds. We use hydrodynamic simulations and a full chemical network to study the abundances of over 150 species in typical Milky Way molecular clouds. We perform synthetic observations in order to produce emission maps of a subset of these tracers. We study the effects of different lines of sight and spatial resolution on the emission distribution and perform a robust quantitative comparison of the species to each other. We use the Spectral Correlation Function (SCF), which quantifies the root mean squared difference between spectra separated by some length scale, to characterize the structure of the simulated cloud in position-position-velocity (PPV) space. We predict the observed SCF for a broad range of observational tracers, and thus identify homologous species. In particular, we show that the pairs C and CO, C{sup +} and CN, and NH{sub 3} and H{sub 2}CS have very similar SCFs. We measure the SCF slope variation as a function of beam size for all species and demonstrate that the beam size has a distinct effect on different species emission. However, for beams of up to 10'', placing the cloud at 1 kpc, the change is not large enough to move the SCF slopes into different regions of parameter space. The results from this study provide observational guidance for choosing the best tracer to probe various cloud length scales.

  15. Strongly correlated perovskite fuel cells

    Science.gov (United States)

    Zhou, You; Guan, Xiaofei; Zhou, Hua; Ramadoss, Koushik; Adam, Suhare; Liu, Huajun; Lee, Sungsik; Shi, Jian; Tsuchiya, Masaru; Fong, Dillon D.; Ramanathan, Shriram

    2016-06-01

    Fuel cells convert chemical energy directly into electrical energy with high efficiencies and environmental benefits, as compared with traditional heat engines. Yttria-stabilized zirconia is perhaps the material with the most potential as an electrolyte in solid oxide fuel cells (SOFCs), owing to its stability and near-unity ionic transference number. Although there exist materials with superior ionic conductivity, they are often limited by their ability to suppress electronic leakage when exposed to the reducing environment at the fuel interface. Such electronic leakage reduces fuel cell power output and the associated chemo-mechanical stresses can also lead to catastrophic fracture of electrolyte membranes. Here we depart from traditional electrolyte design that relies on cation substitution to sustain ionic conduction. Instead, we use a perovskite nickelate as an electrolyte with high initial ionic and electronic conductivity. Since many such oxides are also correlated electron systems, we can suppress the electronic conduction through a filling-controlled Mott transition induced by spontaneous hydrogen incorporation. Using such a nickelate as the electrolyte in free-standing membrane geometry, we demonstrate a low-temperature micro-fabricated SOFC with high performance. The ionic conductivity of the nickelate perovskite is comparable to the best-performing solid electrolytes in the same temperature range, with a very low activation energy. The results present a design strategy for high-performance materials exhibiting emergent properties arising from strong electron correlations.

  16. Metabolomics reveals metabolic biomarkers of Crohn's disease

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, J.K.; Willing, B.; Lucio, M.; Fekete, A.; Dicksved, J.; Halfvarson, J.; Tysk, C.; Schmitt-Kopplin, P.

    2009-06-01

    The causes and etiology of Crohn's disease (CD) are currently unknown although both host genetics and environmental factors play a role. Here we used non-targeted metabolic profiling to determine the contribution of metabolites produced by the gut microbiota towards disease status of the host. Ion Cyclotron Resonance Fourier Transform Mass Spectrometry (ICR-FT/MS) was used to discern the masses of thousands of metabolites in fecal samples collected from 17 identical twin pairs, including healthy individuals and those with CD. Pathways with differentiating metabolites included those involved in the metabolism and or synthesis of amino acids, fatty acids, bile acids and arachidonic acid. Several metabolites were positively or negatively correlated to the disease phenotype and to specific microbes previously characterized in the same samples. Our data reveal novel differentiating metabolites for CD that may provide diagnostic biomarkers and/or monitoring tools as well as insight into potential targets for disease therapy and prevention.

  17. Spring-block model reveals region-like structures.

    Directory of Open Access Journals (Sweden)

    Gabriell Máté

    Full Text Available A mechanical spring-block model is used for realizing an objective space partition of settlements from a geographic territory in region-like structures. The method is based on the relaxation-dynamics of the spring-block system and reveals in a hierarchical manner region-like entities at different spatial scales. It takes into account in an elegant manner both the spatiality of the elements and the connectivity relations among them. Spatiality is taken into account by using the geographic coordinates of the settlements, and by detecting the neighbors with the help of a Delaunay triangulation. Connectivity between neighboring settlements are quantified using a Pearson-like correlation for the relative variation of a relevant socio-economic parameter (population size, GDP, tax payed per inhabitant, etc.. The method is implemented in an interactive JAVA application and it is applied with success for an artificially generated society and for the case of USA, Hungary and Transylvania.

  18. Improved Estimation and Interpretation of Correlations in Neural Circuits

    Science.gov (United States)

    Yatsenko, Dimitri; Josić, Krešimir; Ecker, Alexander S.; Froudarakis, Emmanouil; Cotton, R. James; Tolias, Andreas S.

    2015-01-01

    Ambitious projects aim to record the activity of ever larger and denser neuronal populations in vivo. Correlations in neural activity measured in such recordings can reveal important aspects of neural circuit organization. However, estimating and interpreting large correlation matrices is statistically challenging. Estimation can be improved by regularization, i.e. by imposing a structure on the estimate. The amount of improvement depends on how closely the assumed structure represents dependencies in the data. Therefore, the selection of the most efficient correlation matrix estimator for a given neural circuit must be determined empirically. Importantly, the identity and structure of the most efficient estimator informs about the types of dominant dependencies governing the system. We sought statistically efficient estimators of neural correlation matrices in recordings from large, dense groups of cortical neurons. Using fast 3D random-access laser scanning microscopy of calcium signals, we recorded the activity of nearly every neuron in volumes 200 μm wide and 100 μm deep (150–350 cells) in mouse visual cortex. We hypothesized that in these densely sampled recordings, the correlation matrix should be best modeled as the combination of a sparse graph of pairwise partial correlations representing local interactions and a low-rank component representing common fluctuations and external inputs. Indeed, in cross-validation tests, the covariance matrix estimator with this structure consistently outperformed other regularized estimators. The sparse component of the estimate defined a graph of interactions. These interactions reflected the physical distances and orientation tuning properties of cells: The density of positive ‘excitatory’ interactions decreased rapidly with geometric distances and with differences in orientation preference whereas negative ‘inhibitory’ interactions were less selective. Because of its superior performance, this

  19. REVEAL: Software Documentation and Platform Migration

    Science.gov (United States)

    Wilson, Michael A.; Veibell, Victoir T.

    2011-01-01

    The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA's Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This presentation specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as an overview of the content of the final report for that internship.

  20. The neural correlates of desire.

    Directory of Open Access Journals (Sweden)

    Hideaki Kawabata

    Full Text Available In an event-related fMRI study, we scanned eighteen normal human subjects while they viewed three categories of pictures (events, objects and persons which they classified according to desirability (desirable, indifferent or undesirable. Each category produced activity in a distinct part of the visual brain, thus reflecting its functional specialization. We used conjunction analysis to learn whether there is a brain area which is always active when a desirable picture is viewed, regardless of the category to which it belongs. The conjunction analysis of the contrast desirable > undesirable revealed activity in the superior orbito-frontal cortex. This activity bore a positive linear relationship to the declared level of desirability. The conjunction analysis of desirable > indifferent revealed activity in the mid-cingulate cortex and in the anterior cingulate cortex. In the former, activity was greater for desirable and undesirable stimuli than for stimuli classed as indifferent. Other conjunction analyses produced no significant effects. These results show that categorizing any stimulus according to its desirability activates three different brain areas: the superior orbito-frontal, the mid-cingulate, and the anterior cingulate cortices.

  1. Initiation process of a thrust fault revealed by analog experiments

    Science.gov (United States)

    Yamada, Yasuhiro; Dotare, Tatsuya; Adam, Juergen; Hori, Takane; Sakaguchi, Hide

    2016-04-01

    We conducted 2D (cross-sectional) analog experiments with dry sand using a high resolution digital image correlation (DIC) technique to reveal initiation process of a thrust fault in detail, and identified a number of "weak shear bands" and minor uplift prior to the thrust initiation. The observations suggest that the process can be divided into three stages. Stage 1: characterized by a series of abrupt and short-lived weak shear bands at the location where the thrust will be generated later. Before initiation of the fault, the area to be the hanging wall starts to uplift. Stage 2: defined by the generation of the new thrust and its active displacement. The location of the new thrust seems to be constrained by its associated back-thrust, produced at the foot of the surface slope (by the previous thrust). The activity of the previous thrust turns to zero once the new thrust is generated, but the timing of these two events is not the same. Stage 3: characterized by a constant displacement along the (new) thrust. Similar minor shear bands can be seen in the toe area of the Nankai accretionary prism, SW Japan and we can correlate the along-strike variations in seismic profiles to the model results that show the characteristic features in each thrust development stage.

  2. Organizational Design Correlates of Entrepreneurship

    DEFF Research Database (Denmark)

    Foss, Nicolai Juul; Lyngsie, Jacob; Zahra, Shaker A.

    2015-01-01

    structures are associated with opportunity realization as well discovery, and this effect is reinforced by formalization. Decentralization gives managers the discretion and autonomy needed to recognize and realize opportunities, while formalization enables the standardization and codification of actions......Extant research offers relatively little insight into the organizational design correlates of entrepreneurship in established firms. We argue on theoretical grounds that the same organizational designs support the realization as well as the discovery of opportunities. Specifically, decentralized...... and processes. To test these ideas, we use a data-set based on paired responses from 474 Danish firms operating in several industries for our analyses. We find that decentralization and formalization have direct, positive, and significant associations with opportunity realization. We also address how...

  3. Correlating thalamocortical connectivity and activity

    Science.gov (United States)

    da Fontoura Costa, Luciano; Sporns, Olaf

    2006-07-01

    The segregated regions of the mammalian cerebral cortex and thalamus form an extensive and complex network, whose structure and function are still only incompletely understood. The present letter describes an application of the concepts of complex networks and random walks that allows the identification of nonrandom, highly structured features of thalamocortical connections and their potential effects on dynamic interactions between cortical areas in the cat brain. Utilizing large-scale anatomical data sets of this thalamocortical system, we investigate uniform random walks in such a network by considering the steady state eigenvector of the respective stochastic matrix. It is shown that thalamocortical connections are organized in such a way as to guarantee strong correlation between the outdegree and occupancy rate (a stochastic measure potentially related to activation) of each cortical area. Possible organizational principles underlying this effect are identified and discussed.

  4. CORRELATIONS IN CONFINED QUANTUM PLASMAS

    Energy Technology Data Exchange (ETDEWEB)

    DUFTY J W

    2012-01-11

    This is the final report for the project 'Correlations in Confined Quantum Plasmas', NSF-DOE Partnership Grant DE FG02 07ER54946, 8/1/2007 - 7/30/2010. The research was performed in collaboration with a group at Christian Albrechts University (CAU), Kiel, Germany. That collaboration, almost 15 years old, was formalized during the past four years under this NSF-DOE Partnership Grant to support graduate students at the two institutions and to facilitate frequent exchange visits. The research was focused on exploring the frontiers of charged particle physics evolving from new experimental access to unusual states associated with confinement. Particular attention was paid to combined effects of quantum mechanics and confinement. A suite of analytical and numerical tools tailored to the specific inquiry has been developed and employed

  5. CORRELATION BETWEEN ASO AND AAO

    Institute of Scientific and Technical Information of China (English)

    LIU Na; ZHANG Qing-hua; CHEN Hong-xia

    2004-01-01

    Using a 34 years database consisting of sea level pressure and sea ice concentration,the relationship between Antarctic Oscillation(AAO)and Antarctic Sea-ice Oscillation(ASO)was investigated.Firstly,Empirical Orthogonal Function(EOF)analysis depicts the spatial variability of AAO and ASO and Antarctic Sea-ice Oscillation Index(ASOI)was defined for the first time.Secondly,power spectrum and head-lag correlation analysis show that ASO and AAO have the same periods of quasi-three years,quasi-one year and quasi-half a year.Corresponding to AAO,ASO has an evident anti-oscillation after one and half a year.

  6. Are quantum correlations genuinely quantum?

    CERN Document Server

    Di Lorenzo, Antonio

    2012-01-01

    It is shown that the probabilities for the spin singlet can be reproduced through classical resources, with no communication between the distant parties, by using merely shared (pseudo-)randomness. If the parties are conscious beings aware of both the hidden-variables and the random mechanism, then one has a conspiracy. If the parties are aware of only the random variables, they may be induced to believe that they are able to send instantaneous information to one another. It is also possible to reproduce the correlations at the price of reducing the detection efficiency. It is further demonstrated that the same probability decomposition could be realized through action-at-a-distance, provided it existed.

  7. Observed Correlations in Minkowski Space

    CERN Document Server

    Mould, R A

    2003-01-01

    The author has proposed five rules that permit conscious observers to be included in quantum mechanics. In the present paper, these rules are applied to the observation of a non-local pair of correlated particles. Rule (4) again prevents an anomalous result. Two different kinds of relativistic state reduction are considered, where these differ in the way that they impose boundary conditions in Minkowski space. In response to a problem that arises in this context, we require the Lorentz invariance of stochastic hits. And finally, it is claimed that the rules proposed by the author are themselves relativistically covariant with some qualification. Key Words: brain states, boundary conditions, consciousness, decoherence, macroscopic superposition, probability current, von Neumann, wave collapse.

  8. Health correlates of workplace bullying

    DEFF Research Database (Denmark)

    Bonde, Jens Peter; Gullander, Maria; Hansen, Åse Marie;

    2016-01-01

    OBJECTIVE: This study aimed to examine the course of workplace bullying and health correlates among Danish employees across a four-year period. METHODS: In total, 7502 public service and private sector employees participated in a 3-wave study from 2006 through 2011. Workplace bullying over the past......-labelled bullying at baseline using logistic regression. RESULTS: Reports of bullying were persistent across four years in 22.2% (57/257) of employees who initially reported bullying. Baseline associations between self-labelled bullying and sick-listing, poor self-rated health, poor sleep, and depressive symptoms...... were significant with adjusted odds ratios (OR) ranging from 1.8 [95% confidence interval (95% CI) 1.5-2.4] for poor sleep quality among those bullied "now and then" to 6.9 (95% CI 3.9-12.3) for depression among those reporting being bullied on a daily to monthly basis. In longitudinal analyses...

  9. Correlation between Voronoi volumes in disc packings

    OpenAIRE

    Zhao, Song-Chuan; Sidle, Stacy; Swinney, Harry L.; Schröter, Matthias

    2011-01-01

    We measure the two-point correlation of free Voronoi volumes in binary disc packings, where the packing fraction $\\phi_{\\rm avg}$ ranges from 0.8175 to 0.8380. We observe short-ranged correlations over the whole range of $\\phi_{\\rm avg}$ and anti-correlations for $\\phi_{\\rm avg}>0.8277$. The spatial extent of the anti-correlation increases with $\\phi_{\\rm avg}$ while the position of the maximum of the anti-correlation and the extent of the positive correlation shrink with $\\phi_{\\rm avg}$. We...

  10. Time-resolved metabolomics reveals metabolic modulation in rice foliage

    Directory of Open Access Journals (Sweden)

    Arita Masanori

    2008-06-01

    Full Text Available Abstract Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed. Results Using capillary electrophoresis mass spectrometry (CE-MS and capillary electrophoresis diode-array detection (CE-DAD, we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks. Conclusion Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the

  11. Clinicoradiological correlation in birth asphyxia

    Directory of Open Access Journals (Sweden)

    Basavaraj Patil

    2015-06-01

    Full Text Available Background: Hypoxic Ischemic Encephalopathy (HIE is the most dreaded neurological disease of the new-born. Assessment of severity of HIE would help proper parent counseling and early institution of stimulation therapy for better development of the infant. Methods: This study was conducted between December 2012 and May 2014. 37 term neonates with perinatal asphyxia were the subjects. The cranial ultrasound, EEG and MRI findings of these babies are analysed and correlated with each other and with clinical staging and the neurological condition of the babies at discharge. Results: Among the 37 neonates, 21 were of HIE stage 2 and 16 were of stage 3. Sensitivity of EEG in detecting abnormality in the neurological condition according to our study is 76.9%, specificity 87.5%, positive predictive value 76.9%, negative predictive value 87.5%. Sensitivity of severe pattern of injury in MRI brain in detecting abnormality in neurological condition according to our study is 76.9%, specificity 91.6%, positive predictive value 83.3%, negative predictive value 88%. Involvement of both basal ganglia and cortex in MRI brain had statistically significant correlation with abnormal neurological condition at discharge in our study (P = 0.04. Conclusion: An abnormal EEG and MRI brain in a term new-born with Hypoxic Ischemic Encephalopathy (HIE is associated with poor neurological outcome. Involvement of basal ganglia/thalamus and cortex together in the MRI are predictors of abnormal outcome. [Int J Res Med Sci 2015; 3(3.000: 560-567

  12. Electron correlations in copper oxides

    Science.gov (United States)

    Jefferson, J. H.

    A model which explicitly takes into account the hybridization of copper and oxygen orbitals and Coulomb correlations in copper-oxide chains and layers is considered. Degenerate perturbation theory is used to derive various effective Hamiltonians and shown to give rise to effective interactions which would be absent from a model that did not account for the oxygen states explicitly. In particular, there are hole-hole repulsion terms which mitigate against pairing. Exact solutions of the single hole problem and numerical solutions of the two-hole case for CuO chains confirm that the holes repel in the large correlation limit. Nous considérons un modèle dans lequel l'hybridation des orbitales de cuivre et d'oxygène et les corrélations de Coulomb en chaînes et en couches sont données explicitement. Les Hamiltoniens effectifs sont dérivés en utilisant la théorie de la perturbation dégénérée. On trouve les interactions effectives qui sont absentes d'un modèle dans lequel les états de l'oxygène ne sont pas considérés explicitement. Notamment, les forces répulsives entre les trous produisent une diminution de la probabilité d'association. Les solutions précises du problème pour un trou simple, et les solutions numériques du cas de deux trous dans les chaînes de CuO, confirment que dans la limite pour les corrélations fortes, les trous subissent une force répulsive.

  13. Optimal measurements for nonlocal correlations

    Science.gov (United States)

    Schwarz, Sacha; Stefanov, André; Wolf, Stefan; Montina, Alberto

    2016-08-01

    A problem in quantum information theory is to find the experimental setup that maximizes the nonlocality of correlations with respect to some suitable measure such as the violation of Bell inequalities. There are however some complications with Bell inequalities. First and foremost it is unfeasible to determine the whole set of Bell inequalities already for a few measurements and thus unfeasible to find the experimental setup maximizing their violation. Second, the Bell violation suffers from an ambiguity stemming from the choice of the normalization of the Bell coefficients. An alternative measure of nonlocality with a direct information-theoretic interpretation is the minimal amount of classical communication required for simulating nonlocal correlations. In the case of many instances simulated in parallel, the minimal communication cost per instance is called nonlocal capacity, and its computation can be reduced to a convex-optimization problem. This quantity can be computed for a higher number of measurements and turns out to be useful for finding the optimal experimental setup. Focusing on the bipartite case, we present a simple method for maximizing the nonlocal capacity over a given configuration space and, in particular, over a set of possible measurements, yielding the corresponding optimal setup. Furthermore, we show that there is a functional relationship between Bell violation and nonlocal capacity. The method is illustrated with numerical tests and compared with the maximization of the violation of CGLMP-type Bell inequalities on the basis of entangled two-qubit as well as two-qutrit states. Remarkably, the anomaly of nonlocality displayed by qutrits turns out to be even stronger if the nonlocal capacity is employed as a measure of nonlocality.

  14. Aberrant activity in degenerated retinas revealed by electrical imaging

    Directory of Open Access Journals (Sweden)

    Günther eZeck

    2016-02-01

    Full Text Available In this review I present and discuss the current understanding of aberrant electrical activity found in the ganglion cell layer (GCL of rod-degenerated (rd mouse retinas. The reported electrophysiological properties revealed by electrical imaging using high-density microelectrode arrays can be subdivided between spiking activity originating from retinal ganglion cells (RGCs and local field potentials reflecting strong trans-membrane currents within the GCL. RGCs in rod-degenerated retinas show increased and rhythmic spiking compared to age-matched wild-type retinas. Fundamental spiking frequencies range from 5 to 15 Hz in various mouse models. The rhythmic RGC spiking is driven by a presynaptic network comprising AII amacrine and bipolar cells. In the healthy retina this rhythm-generating circuit is inhibited by photoreceptor input. A unique physiological feature of rd retinas is rhythmic local field potentials (LFP manifested as spatially-restricted low-frequency (5–15 Hz voltage changes. Their spatiotemporal characterization revealed propagation and correlation with RGC spiking. LFPs rely on gap-junctional coupling and are shaped by glycinergic and by GABAergic transmission. The aberrant RGC spiking and LFPs provide a simple readout of the functionality of the remaining retinal circuitry which can be used in the development of improved vision restoration strategies.

  15. Dynamic evolution of cross-correlations in the Chinese stock market.

    Science.gov (United States)

    Ren, Fei; Zhou, Wei-Xing

    2014-01-01

    The analysis of cross-correlations is extensively applied for the understanding of interconnections in stock markets and the portfolio risk estimation. Current studies of correlations in Chinese market mainly focus on the static correlations between return series, and this calls for an urgent need to investigate their dynamic correlations. Our study aims to reveal the dynamic evolution of cross-correlations in the Chinese stock market, and offer an exact interpretation for the evolution behavior. The correlation matrices constructed from the return series of 367 A-share stocks traded on the Shanghai Stock Exchange from January 4, 1999 to December 30, 2011 are calculated over a moving window with a size of 400 days. The evolutions of the statistical properties of the correlation coefficients, eigenvalues, and eigenvectors of the correlation matrices are carefully analyzed. We find that the stock correlations are significantly increased in the periods of two market crashes in 2001 and 2008, during which only five eigenvalues significantly deviate from the random correlation matrix, and the systemic risk is higher in these volatile periods than calm periods. By investigating the significant contributors of the deviating eigenvectors in different time periods, we observe a dynamic evolution behavior in business sectors such as IT, electronics, and real estate, which lead the rise (drop) before (after) the crashes. Our results provide new perspectives for the understanding of the dynamic evolution of cross-correlations in the Chines stock markets, and the result of risk estimation is valuable for the application of risk management. PMID:24867071

  16. Cardiac hydatid cyst revealed by ventricular tachycardia

    OpenAIRE

    Ibn Elhadj, Zied; Boukhris, Marouane; Kammoun, Ikram; Halima, Afef Ben; Addad, Faouzi; Kachboura, Salem

    2013-01-01

    Hydatid disease is a human parasitic infestation caused by the larval stage of Echinococcus Granulosus. The liver and the lungs are the most common locations. Cardiac involvement is rare and accounts for 0.5–2% of all hydatid disease. We report an unusual presentation of cardiac hydatid cyst revealed by ventricular tachycardia in a patient with a history of cerebral hydatid cyst.

  17. Consumer choice and revealed bounded rationality

    OpenAIRE

    Manzini, Paola; Mariotti, Marco

    2006-01-01

    We study two boundedly rational procedures in consumer behavior. We show that these procedures can be detected by conditions on observable demand data of the same type as standard revealed preference axioms. This provides the basis for a non-parametric analysis of boundedly rational consumer behavior mirroring the classical one for utility maximization.

  18. Eye Movements Reveal Dynamics of Task Control

    Science.gov (United States)

    Mayr, Ulrich; Kuhns, David; Rieter, Miranda

    2013-01-01

    With the goal to determine the cognitive architecture that underlies flexible changes of control settings, we assessed within-trial and across-trial dynamics of attentional selection by tracking of eye movements in the context of a cued task-switching paradigm. Within-trial dynamics revealed a switch-induced, discrete delay in onset of…

  19. Towards a comprehensive understanding of brain machinery by correlative microscopy

    Science.gov (United States)

    Allegra Mascaro, Anna Letizia; Silvestri, Ludovico; Sacconi, Leonardo; Pavone, Francesco S.

    2015-06-01

    Unraveling the complexity of brain structure and function is the biggest challenge of contemporary science. Due to their flexibility, optical techniques are the key to exploring this intricate network. However, a single imaging technique can reveal only a small part of this machinery due to its inherent multilevel organization. To obtain a more comprehensive view of brain functionality, complementary approaches have been combined. For instance, brain activity was monitored simultaneously on different spatiotemporal scales with functional magnetic resonance imaging and calcium imaging. On the other hand, dynamic information on the structural plasticity of neuronal networks has been contextualized in a wider framework combining two-photon and light-sheet microscopy. Finally, synaptic features have been revealed on previously in vivo imaged samples by correlative light-electron microscopy. Although these approaches have revealed important features of brain machinery, they provided small bridges between specific spatiotemporal scales, lacking an omni-comprehensive view. In this perspective, we briefly review the state of the art of correlative techniques and propose a wider methodological framework fusing multiple levels of brain investigation.

  20. Genes but not genomes reveal bacterial domestication of Lactococcus lactis.

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    Delphine Passerini

    Full Text Available BACKGROUND: The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE. METHODOLOGY/PRINCIPAL FINDINGS: The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST differing by up to 230 kb in genome size. CONCLUSION/SIGNIFICANCE: The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between "environmental" strains, the main contributors to the genetic diversity within the subspecies, and "domesticated" strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the "domesticated" strains essentially arose through substantial genomic flux within the dispensable