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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. Fractal morphological analysis of Bacteriorhodopsin (bR) layers deposited onto Indium Tin Oxide (ITO) electrodes

    International Nuclear Information System (INIS)

    Uniform Bacteriorhodopsin layers for the purpose of fabricating Bacteriorhodopsin-based biosensors were prepared by allowing drying of the layers under a constant electric field. To properly observe and understand the 'electric field effect' on the protein Bacteriorhodopsin, the electric and non-electric field influenced Bacteriorhodopsin layers prepared using a manual syringe-deposition method applied onto Indium Tin Oxide electrodes were structurally investigated using Scanning Electron Microscopy and Atomic Force Microscopy. The results yield obvious morphological differences between the electric and non-electric field assisted Bacteriorhodopsin layers and brings to attention the occurrence of the so-called 'coffee-ring' effect in the latter case. We applied stochastic fractal method based on the generalized Cauchy process to describe the morphological features surrounding the void. Fractal dimension is used to characterize the local regularity of the Bacteriorhodopsin clusters and the correlation exponent is used to describe the long-range correlation between the clusters. It is found that the Bacteriorhodopsin protein tends to exhibit with strong spatial correlation in the presence of external electric field compared to in absence of the electric field. Long-range correlation in the morphological feature may be associated to the enhancement of aggregation process of Bacteriorhodopsin protein in the presence of electric field, thereby inhibiting the formation of the so-called 'coffee-ring' effect. As such, the observations discussed in this work suggest some amount of control of surface uniformity when forming layers.

  3. 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.

  4. 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.

  5. 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.

  6. Three electronic state model of the primary phototransformation of bacteriorhodopsin.

    OpenAIRE

    Humphrey, W; H. Lu; Logunov, I; Werner, H.J.; Schulten, K

    1998-01-01

    The primary all-trans --> 13-cis photoisomerization of retinal in bacteriorhodopsin has been investigated by means of quantum chemical and combined classical/quantum mechanical simulations employing the density matrix evolution method. Ab initio calculations on an analog of a protonated Schiff base of retinal in vacuo reveal two excited states S1 and S2, the potential surfaces of which intersect along the reaction coordinate through an avoided crossing, and then exhibit a second, weakly avoid...

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Multiplexed Holographic Data Storage in Bacteriorhodopsin

    Science.gov (United States)

    Mehrl, David J.; Krile, Thomas F.

    1999-01-01

    Biochrome photosensitive films in particular Bacteriorhodopsin exhibit features which make these materials an attractive recording medium for optical data storage and processing. Bacteriorhodopsin films find numerous applications in a wide range of optical data processing applications; however the short-term memory characteristics of BR limits their applications for holographic data storage. The life-time of the BR can be extended using cryogenic temperatures [1], although this method makes the system overly complicated and unstable. Longer life-times can be provided in one modification of BR - the "blue" membrane BR [2], however currently available films are characterized by both low diffraction efficiency and difficulties in providing photoreversible recording. In addition, as a dynamic recording material, the BR requires different wavelengths for recording and reconstructing of optical data in order to prevent the information erasure during its readout. This fact also put constraints on a BR-based Optical Memory, due to information loss in holographic memory systems employing the two-lambda technique for reading-writing thick multiplexed holograms.

  1. Multiplexed Holographic Optical Data Storage In Thick Bacteriorhodopsin Films

    Science.gov (United States)

    Downie, John D.; Timucin, Dogan A.; Gary, Charles K.; Ozcan, Meric; Smithey, Daniel T.; Crew, Marshall

    1998-01-01

    The optical data storage capacity of photochromic bacteriorhodopsin films is investigated by means of theoretical calculations, numerical simulations, and experimental measurements on sequential recording of angularly multiplexed diffraction gratings inside a thick D85N BR film.

  2. 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...

  3. Linear-Angle correlation plots: New graphs for revealing correlation structure

    OpenAIRE

    Graffelman, Jan

    2013-01-01

    In multivariate graphics, correlations between variables are often approximated by the cosines of the angles between vectors. In practice, it is difficult to reliably estimate correlations from such displays by eye. In this article, we therefore develop new graphs, called linear-angle correlation plots, that have a linear relationship between correlation and angle, and from which correlation coefficients are read off more easily. Several multivariate datasets are used to illust...

  4. Voices of athletes reveal only modest acoustic correlates of stature

    Science.gov (United States)

    Owren, Michael J.; Anderson, John D.

    2005-04-01

    Recent studies of acoustic cues to body-size in nonhuman primate and human vocalizations have produced results varying from very strong relationships between formant frequencies and length/weight in rhesus monkeys to weak correlations between formants and stature in humans. The current work attempted to address these discrepancies by compiling a database of naturally occurring speech with a large number of vocalizers of maximally varying size. To that end, fundamental frequency (F0) and formant frequencies were measured in both running speech and filled pauses (i.e., ``ah'' and ``um'') produced by male athletes during televised same-day interviews. Multiple-regression analysis of data from 100 male athletes showed that these acoustic measures accounted for at most 17% of variance in height over a 37-cm range. Analyses of filled speech pauses produced by a subset of 48 athletes could account for up to 36%. These outcomes fall within the range of previously reported outcomes, indicating that while speech acoustics are correlated with body-size in human adult males, the cues provided are quite modest.

  5. 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. PMID:26487684

  6. 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.

  7. 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.

  8. 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.

  9. Bacteriorhodopsin-based photochromic pigments for optical security applications

    Science.gov (United States)

    Hampp, Norbert A.; Fischer, Thorsten; Neebe, Martin

    2002-04-01

    Bacteriorhodopsin is a two-dimensional crystalline photochromic protein which is astonishingly stable towards chemical and thermal degradation. This is one of the reasons why this is one of the very few proteins which may be used as a biological pigment in printing inks. Variants of the naturally occurring bacteriorhodopsin have been developed which show a distinguished color change even with low light intensities and without the requirement of UV-light. Several pigments with different color changes are available right now. In addition to this visual detectable feature, the photochromism, the proteins amino acid sequence can be genetically altered in order to code and identify specific production lots. For advanced applications the data storage capability of bacteriorhodopsin will be useful. Write-once-read-many (WORM) recording of digital data is accomplished by laser excitation of printed bacteriorhodopsin inks. A density of 1 MBit per square inch is currently achieved. Several application examples for this biological molecule are described where low and high level features are used in combination. Bacteriorhodopsin-based inks are a new class of optical security pigments.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Optical CDMA system using bacteriorhodopsin for optical data storage

    Science.gov (United States)

    Bae; Yang; Jin; Lee; Park

    1999-11-01

    An optical CDMA (code division multiple access) system for the optical data storage using bacteriorhodopsin (BR) is reported as an application of the BR materials. The desired signal of multiple input can be recorded and reconstructed by use of orthogonal codes. An experimental setup is proposed and demonstrated. PMID:10585180

  17. Application of chemical modification and spin-labeling techniques to the study of energy conversion by bacteriorhodopsin

    Energy Technology Data Exchange (ETDEWEB)

    Packer, L.; Quintanilha, A.T.; Mehlhorn, R.J.

    1983-03-01

    Light generates a pH gradient and an electrical potential across the purple membrane of Halobacterium halobium. We are investigating the time-resolved changes in protonation of the side chains of specific amino-acid residues and the correlation of these changes with photon absorption and the ensuing photo-reaction cycle. We seek to determine the precise molecular description of the photocycle and of the time dependent steps in the uptake, translocation, and release of protons by the retinal proton catalyst in this membrane, bacteriorhodopsin (BR). 14 references, 3 figures, 1 table.

  18. Studies on light transduction by bacteriorhodopsin and rhodopsin

    International Nuclear Information System (INIS)

    The visual photoreceptor pigments in vertebrates and invertebrates all use retinal (vitamin A aldehyde) as the light-absorbing molecule. Recently, Stoeckenius et al. discovered bacteriorhodopsin (bR) in the purple membrane of the extreme halophile, Halobacterium halobium, which also contains all-trans retinal as the chromophore, bR carries out light-dependent proton translocation from the inside to the outside of the H. halobium cell. Since the discovery of bR, H. halobium has been found to elaborate three more retinal-based light-transducing proteins. These are halorhodopsin, a chloride ion pump, and sensory rhodopsins I and II. The authors are carrying out structure-function studies of bacteriorhodopsin, bovine rhodopsin, and related proteins primarily by the technique of recombinant DNA; they summarize below the results they have obtained recently

  19. 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.

  20. 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.

  1. Bacteriorhodopsin as a Possible Element of Membrane Bioreactors

    Science.gov (United States)

    Maksimychev, A. V.; Chamorovskii, S. K.

    1988-06-01

    Certain approaches to the creation of membrane bioreactors, representing an example of integrated membrane systems, are examined. The characteristic features of the use of organised molecular assemblies in such systems as sensor and regulatory elements are discussed. The properties of the retinal-protein complex of bacteriorhodopsin as a promising component of integrated membrane systems, capable of carrying out regulatory functions, are examined. The bibliography includes 139 references.

  2. 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.

  3. 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.

  4. 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.

  5. High production of bacteriorhodopsin from wild type Halobacterium salinarum.

    Science.gov (United States)

    Seyedkarimi, Mansooreh-Sadat; Aramvash, Asieh; Ramezani, Rohollah

    2015-09-01

    Bacteriorhodopsin (bR) is a trans-membrane proton pump found in the purple membrane of Halobacterium salinarum. This protein has high photochemical and photoelectric conversion efficiency and thermal stability, allowing it to withstand high temperatures, high salinity, and nutritionally-limited environments. The ability of this protein to convert light energy into chemical energy has applications that are mainly therapeutic/diagnostic and research-oriented. There is increasing demand for bacteriorhodopsin production in different fields. The present study maximized bacteriorhodopsin production using H. salinarum. The physical parameters of illumination, agitation speed, temperature, and nitrogen source were studied using a fractional factorial design to determine the optimal levels of each. The most suitable nitrogen source was determined to be peptone from meat. The optimal temperature was 39 °C, agitation speed was 150 rpm, and light intensity was 6300 lux for bR production. Under these conditions, the maximum bR yield was 196 mg/l, which is about 4.23 fold greater than those obtained with basal medium. The proposed strategies could be used for bR production using this archaeobacterium; the results are the highest reported thus far from a batch culture of H. salinarum. PMID:26254806

  6. 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

  7. On the mechanism of weak-field coherent control of retinal isomerization in bacteriorhodopsin

    International Nuclear Information System (INIS)

    Experimental studies of the short time reaction dynamics controlling the chemical branching ratio provide direct evidence for the mechanism of coherent control of the retinal photoisomerization in bacteriorhodopsin in the weak-field limit with respect to the previous report [V. Prokhorenko, A. Nagy, S. Waschuk, L. Brown, R. Birge, R. Miller, Science 313 (2006) 1257]. The phase sensitivity of the reaction dynamics is directly revealed using time- and frequency-resolved pump-probe measurements. The high degree of control of the reaction branching ratio is theoretically explained through a combination of spectral amplitude shaping and phase-dependent coupling to selectively excite vibrations most strongly coupled to the reaction coordinate. Coherent control in this context must involve reaction dynamics that occur on time scales comparable to electronic and vibrational decoherence time scales

  8. 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. PMID:27215321

  9. 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.

  10. Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2

    Science.gov (United States)

    Spellmon, Nicholas; Sun, Xiaonan; Sirinupong, Nualpun; Edwards, Brian; Li, Chunying; Yang, Zhe

    2015-01-01

    SMYD proteins are an exciting field of study as they are linked to many types of cancer-related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open–closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative correlated inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to by a twisting motion of the C-lobe with respect to the N-lobe and a clamshell-like motion between the lobes. Dynamical network analysis defines possible allosteric paths for the correlated dynamics. There are nine communities in the dynamical network with six in the N-lobe and three in the C-lobe, and the communication between the lobes is mediated by a lobe-bridging β hairpin. This study provides insight into the dynamical nature of SMYD2 and could facilitate better understanding of SMYD2 substrate specificity. PMID:26717235

  11. A Simple Geotracer Compositional Correlation Analysis Reveals Oil Charge and Migration Pathways

    Science.gov (United States)

    Yang, Yunlai; Arouri, Khaled

    2016-03-01

    A novel approach, based on geotracer compositional correlation analysis is reported, which reveals the oil charge sequence and migration pathways for five oil fields in Saudi Arabia. The geotracers utilised are carbazoles, a family of neutral pyrrolic nitrogen compounds known to occur naturally in crude oils. The approach is based on the concept that closely related fields, with respect to filling sequence, will show a higher carbazole compositional correlation, than those fields that are less related. That is, carbazole compositional correlation coefficients can quantify the charge and filling relationships among different fields. Consequently, oil migration pathways can be defined based on the established filling relationships. The compositional correlation coefficients of isomers of C1 and C2 carbazoles, and benzo[a]carbazole for all different combination pairs of the five fields were found to vary extremely widely (0.28 to 0.94). A wide range of compositional correlation coefficients allows adequate differentiation of separate filling relationships. Based on the established filling relationships, three distinct migration pathways were inferred, with each apparently being charged from a different part of a common source kitchen. The recognition of these charge and migration pathways will greatly aid the search for new accumulations.

  12. 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.

  13. 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

  14. 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.

  15. Bacteriorhodopsin protein hybrids for chemical and biological sensing

    Science.gov (United States)

    Winder, Eric Michael

    Bacteriorhodopsin (bR), an optoelectric protein found in Halobacterium salinarum, has the potential for use in protein hybrid sensing systems. Bacteriorhodopsin has no intrinsic sensing properties, however molecular and chemical tools permit production of bR protein hybrids with transducing and sensing properties. As a proof of concept, a maltose binding protein-bacteriorhodopsin ([MBP]-bR) hybrid was developed. It was proposed that the energy associated with target molecule binding, maltose, to the hybrid sensor protein would provide a means to directly modulate the electrical output from the MBP-bR bio-nanosensor platform. The bR protein hybrid is produced by linkage between bR (principal component of purified purple membrane [PM]) and MBP, which was produced by use of a plasmid expression vector system in Escherichia coli and purified utilizing an amylose affinity column. These proteins were chemically linked using 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS), which facilitates formation of an amide bond between a primary carboxylic acid and a primary amine. The presence of novel protein hybrids after chemical linkage was analyzed by SDS-PAGE. Soluble proteins (MBP-only derivatives and unlinked MBP) were separated from insoluble proteins (PM derivatives and unlinked PM) using size exclusion chromatography. The putatively identified MBP-bR protein hybrid, in addition to unlinked bR, was collected. This sample was normalized for bR concentration to native PM and both were deposited onto indium tin oxide (ITO) coated glass slides by electrophoretic sedimentation. The photoresponse of both samples, activated using 100 Watt tungsten lamp at 10 cm distance, were equal at 175 mV. Testing of deposited PM with 1 mM sucrose or 1 mM maltose showed no change in the photoresponse of the material, however addition of 1 mM maltose to the deposited MBP-bR linked hybrid material elicited a 57% decrease in photoresponse

  16. 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.

  17. 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) ...

  18. 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.

  19. 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.

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

    International Nuclear Information System (INIS)

    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 (RP ⩾ 4 RE); 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 RE

  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. 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.

  3. Correlative Light and Electron Microscopy Reveals the HAS3-Induced Dorsal Plasma Membrane Ruffles

    Directory of Open Access Journals (Sweden)

    Kirsi Rilla

    2015-01-01

    Full Text Available Hyaluronan is a linear sugar polymer synthesized by three isoforms of hyaluronan synthases (HAS1, 2, and 3 that forms a hydrated scaffold around cells and is an essential component of the extracellular matrix. The morphological changes of cells induced by active hyaluronan synthesis are well recognized but not studied in detail with high resolution before. We have previously found that overexpression of HAS3 induces growth of long plasma membrane protrusions that act as platforms for hyaluronan synthesis. The study of these thin and fragile protrusions is challenging, and they are difficult to preserve by fixation unless they are adherent to the substrate. Thus their structure and regulation are still partly unclear despite careful imaging with different microscopic methods in several cell types. In this study, correlative light and electron microscopy (CLEM was utilized to correlate the GFP-HAS3 signal and the surface ultrastructure of cells in order to study in detail the morphological changes induced by HAS3 overexpression. Surprisingly, this method revealed that GFP-HAS3 not only localizes to ruffles but in fact induces dorsal ruffle formation. Dorsal ruffles regulate diverse cellular functions, such as motility, regulation of glucose metabolism, spreading, adhesion, and matrix degradation, the same functions driven by active hyaluronan synthesis.

  4. Correlative Light and Electron Microscopy Reveals the HAS3-Induced Dorsal Plasma Membrane Ruffles.

    Science.gov (United States)

    Rilla, Kirsi; Koistinen, Arto

    2015-01-01

    Hyaluronan is a linear sugar polymer synthesized by three isoforms of hyaluronan synthases (HAS1, 2, and 3) that forms a hydrated scaffold around cells and is an essential component of the extracellular matrix. The morphological changes of cells induced by active hyaluronan synthesis are well recognized but not studied in detail with high resolution before. We have previously found that overexpression of HAS3 induces growth of long plasma membrane protrusions that act as platforms for hyaluronan synthesis. The study of these thin and fragile protrusions is challenging, and they are difficult to preserve by fixation unless they are adherent to the substrate. Thus their structure and regulation are still partly unclear despite careful imaging with different microscopic methods in several cell types. In this study, correlative light and electron microscopy (CLEM) was utilized to correlate the GFP-HAS3 signal and the surface ultrastructure of cells in order to study in detail the morphological changes induced by HAS3 overexpression. Surprisingly, this method revealed that GFP-HAS3 not only localizes to ruffles but in fact induces dorsal ruffle formation. Dorsal ruffles regulate diverse cellular functions, such as motility, regulation of glucose metabolism, spreading, adhesion, and matrix degradation, the same functions driven by active hyaluronan synthesis. PMID:26448759

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. Application of Bacteriorhodopsin Films in an Adaptive-Focusing Schlieren System

    Science.gov (United States)

    Downie, John D.

    1995-01-01

    The photochromic property of bacteriorhodopsin films is exploited in the application of a focusing schlieren optical system for the visualization of optical phase information. By encoding an image on the film with light of one wavelength and reading out with a different wavelength, the readout beam can effectively see the photographic negative of the original image. The potential advantage of this system over previous focusing schlieren systems is that the updatable nature of the bacteriorhodopsin film allows system adaptation. I discuss two image encoding and readout techniques for the bacteriorhodopsin and use film transmission characteristics to choose the more appropriate method. I demonstrate the system principle with experimental results using argon-ion and He-Cd lasers as the two light sources of different wavelengths, and I discuss current limitations to implementation with a white-light source.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. Alternative translocation of protons and halide ions by bacteriorhodopsin

    International Nuclear Information System (INIS)

    Bacteriorhodopsin (bR568) in purple membrane near pH 2 shifts its absorption maximum from 568 to 605 nm forming the blue protein bRacid605, which no longer transports protons and which shows no transient deprotonation of the Schiff base upon illumination. Continued acid titration with HCl or HBr but not H2SO4 restores the purple chromophore to yield bRHCl564 or bRHBr568. These acid purple forms also regain transmembrane charge transport, but no transient Schiff base deprotonation is observed. In contrast to bR568, no rate decrease of the bRacidpurple transport kinetics is detected in 2H2O; however, the transport rate decreases by a factor of ∼ 2 in bRHBr568 compared with bRHCl564. The data indicate that in the acid purple form bR transports the halide anions instead of protons. The authors present a testable model for the transport mechanism, which should also be applicable to halorhodopsin

  3. 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

  4. Nonlinear Coherent Optical Image Processing Using Logarithmic Transmittance of Bacteriorhodopsin Films

    Science.gov (United States)

    Downie, John D.

    1995-01-01

    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 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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...

  11. Comparative Genomic Hybridizations of Entamoeba Strains Reveal Unique Genetic Fingerprints That Correlate with Virulence

    OpenAIRE

    Shah, Preetam H.; MacFarlane, Ryan C.; Bhattacharya, Dhruva; Matese, John C.; Demeter, Janos; Stroup, Suzanne E.; Singh, Upinder

    2005-01-01

    Variable phenotypes have been identified for Entamoeba species. Entamoeba histolytica is invasive and causes colitis and liver abscesses but only in ∼10% of infected individuals; 90% remain asymptomatically colonized. Entamoeba dispar, a closely related species, is avirulent. To determine the extent of genetic diversity among Entamoeba isolates and potential genotype-phenotype correlations, we have developed an E. histolytica genomic DNA microarray and used it to genotype strains of E. histol...

  12. 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.

  13. 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

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

    International Nuclear Information System (INIS)

    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

  15. 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.

  16. White Light Schlieren Optics Using Bacteriorhodopsin as an Adaptive Image Grid

    Science.gov (United States)

    Peale, Robert; Ruffin, Boh; Donahue, Jeff; Barrett, Carolyn

    1996-01-01

    A Schlieren apparatus using a bacteriorhodopsin film as an adaptive image grid with white light illumination is demonstrated for the first time. The time dependent spectral properties of the film are characterized. Potential applications include a single-ended Schlieren system for leak detection.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Trapping the M sub 1 and M sub 2 substrates of bacteriorhodopsin for electron diffraction studies

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, G.A.

    1992-05-01

    Visible and Fourier transform infrared (FTIR) absorption spectroscopies are used to observe protein conformational changes occuring during the bacteriorhodopsin photocycle. Spectroscopic measurements which define the conditions under which bacteriorhodopsin can be isolated and trapped in two distinct substates of the m intermediate of the photocycle, M{sub 1}, and M{sub 2}, are described. A protocol that can be used for high-resolution electron diffraction studies is presented that will trap glucose-embedded purple membrane in the M{sub 1}and M{sub 2} substates at greater than 90% concentration. It was discovered that glucose alone does not provide a fully hydrated environment for bacteriorhodopsin. Equilibration of glucose-embedded samples at high humidity can result in a physical state that is demonstrably closer to the native, fully hydrated state. An extension of the C-T Model of bacteriorhodopsin functionality (Fodor et al., 1988; Mathies et al., 1991) is proposed based on FTIR results and guided by published spectra from resonance Raman and FTIR work. 105 refs.

  3. 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

  4. 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.

  5. Statistical anomalies in 2011-2012 Russian elections revealed by 2D correlation analysis

    CERN Document Server

    Kobak, Dmitry; Pshenichnikov, Maxim S

    2012-01-01

    Here we perform a statistical analysis of the official data from recent Russian parliamentary and presidential elections (held on December 4th, 2011 and March 4th, 2012, respectively). A number of anomalies are identified that persistently skew the results in favour of the pro-government party, United Russia (UR), and its leader Vladimir Putin. The main irregularities are: (i) remarkably high correlation between turnout and voting results; (ii) a large number of polling stations where the UR/Putin results are given by a round number of percent; (iii) constituencies showing improbably low or (iv) anomalously high dispersion of results across polling stations; (v) substantial difference between results at paper-based and electronic polling stations. These anomalies, albeit less prominent in the presidential elections, hardly conform to the assumptions of fair and free voting. The approaches proposed here can be readily extended to quantify fingerprints of electoral fraud in any other problematic elections.

  6. 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

  7. 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.

  8. 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...

  9. 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.

  10. 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.

  11. Time-resolved laser studies on the proton pump mechanism of bacteriorhodopsin

    Energy Technology Data Exchange (ETDEWEB)

    El-Sayed, M.A.

    1991-01-01

    The research work carried out in 1991 can be classified as follows: (1) Work on the nature of the binding site of Eu{sup 3+} in which a fluorescence technique was used to determine the binding equilibrium constant from the concentration of the free Eu{sup 3+} in equilibrium with the bound ions. (2) The mechanism of the slow deprotonation process of bacteriorhodopsin during its photocycle from the observed temperature and pH dependence of its kinetics. (3) Using the circular dichroism spectrum of bR and its perturbed forms to examine the nature of the primary process as well as the origin of the non-exponential kinetic behavior of its photocycle. (4) Studies of bacteriorhodopsin mutants to identify the important amino acids that are part of the reaction coordinate of the deprotonation process as well as to assign the species that are important in giving rise to UV transient absorption whose origin was controversial.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. Long-distance amplitude correlations in the high γ band reveal segregation and integration within the reading network.

    Science.gov (United States)

    Vidal, Juan R; Freyermuth, Samson; Jerbi, Karim; Hamamé, Carlos M; Ossandon, Tomas; Bertrand, Olivier; Minotti, Lorella; Kahane, Philippe; Berthoz, Alain; Lachaux, Jean-Philippe

    2012-05-01

    Reading sentences involves a distributed network of brain regions acting in concert surrounding the left sylvian fissure. The mechanisms of neural communication underlying the extraction and integration of verbal information across subcomponents of this reading network are still largely unknown. We recorded intracranial EEG activity in 12 epileptic human patients performing natural sentence reading and analyzed long-range corticocortical interactions between local neural activations. During a simple task contrasting semantic, phonological, and purely visual processes, we found process-specific neural activity elicited at the single-trial level, characterized by energy increases in a broad gamma band (40-150 Hz). Correlation analysis between task-induced gamma-band activations revealed a selective fragmentation of the network into specialized subnetworks supporting sentence-level semantic analysis and phonological processing. We extend the implications of our results beyond reading, to propose that gamma-band amplitude correlations might constitute a fundamental mechanism for large-scale neural integration during high-level cognition. PMID:22573665

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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...

  6. 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...

  7. General model for lipid-mediated two-dimensional array formation of membrane proteins: Application to bacteriorhodopsin

    DEFF Research Database (Denmark)

    Sabra, Mads Christian; Uitdehaag, J.C.M.; Watts, A

    1998-01-01

    Based on experimental evidence for 2D array formation of bacteriorhodopsin, we propose a general model for lipid-mediated 2D array formation of membrane proteins in lipid bilayers. The model includes two different lipid Species; "annular" lipids and "neutral" lipids, and one protein species. The ...

  8. 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.

  9. Trapping the M{sub 1} and M{sub 2} substrates of bacteriorhodopsin for electron diffraction studies

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, G.A.

    1992-05-01

    Visible and Fourier transform infrared (FTIR) absorption spectroscopies are used to observe protein conformational changes occuring during the bacteriorhodopsin photocycle. Spectroscopic measurements which define the conditions under which bacteriorhodopsin can be isolated and trapped in two distinct substates of the m intermediate of the photocycle, M{sub 1}, and M{sub 2}, are described. A protocol that can be used for high-resolution electron diffraction studies is presented that will trap glucose-embedded purple membrane in the M{sub 1}and M{sub 2} substates at greater than 90% concentration. It was discovered that glucose alone does not provide a fully hydrated environment for bacteriorhodopsin. Equilibration of glucose-embedded samples at high humidity can result in a physical state that is demonstrably closer to the native, fully hydrated state. An extension of the C-T Model of bacteriorhodopsin functionality (Fodor et al., 1988; Mathies et al., 1991) is proposed based on FTIR results and guided by published spectra from resonance Raman and FTIR work. 105 refs.

  10. 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

  11. 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.

  12. 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.

  13. Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

    Directory of Open Access Journals (Sweden)

    Deng Xuemei

    2007-11-01

    Full Text Available Abstract Background Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation. Results We have developed a method called Base Skew Double Triangle (BSDT for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture, except for some microchromosomes. No other organisms studied (18 species show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens. Conclusion Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic

  14. 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...

  15. The Neural Correlates of Implicit and Explicit Sequence Learning: Interacting Networks Revealed by the Process Dissociation Procedure

    Science.gov (United States)

    Laureys, Steven; Degueldre, Christian; Del Fiore, Guy; Aerts, Joel; Luxen, Andre; Van Der Linden, Martial; Cleeremans, Axel; Maquet, Pierre; Destrebecqz, Arnaud; Peigneux, Philippe

    2005-01-01

    In two H[subscript 2] [superscript 15]O PET scan experiments, we investigated the cerebral correlates of explicit and implicit knowledge in a serial reaction time (SRT) task. To do so, we used a novel application of the Process Dissociation Procedure, a behavioral paradigm that makes it possible to separately assess conscious and unconscious…

  16. Spectral Signatures of the Pentagonal Water Cluster in Bacteriorhodopsin

    International Nuclear Information System (INIS)

    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

  17. 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.

  18. 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...

  19. "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.

  20. 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...

  1. 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.

  2. 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...

  3. 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

  4. The effect of charged lipids on bacteriorhodopsin membrane reconstitution and its photochemical activities

    International Nuclear Information System (INIS)

    Bacteriorhodopsin (BR) was reconstituted into artificial lipid membrane containing various charged lipid compositions. The proton pumping activity of BR under flash and continuous illumination, proton permeability across membrane, as well as the decay kinetics of the photocycle intermediate M412 were studied. The results showed that lipid charges would significantly affect the orientation of BR inserted into lipid membranes. In liposomes containing anionic lipids, BRs were more likely to take natural orientation as in living cells. In neutral or positively charged liposomes, most BRs were reversely assembled, assuming an inside out orientation. Moreover, the lipids charges also affect BR's M intermediate kinetics, especially the slow component in M intermediate decay. The half-life M412s increased significantly in BRs in liposomes containing cationic lipids, while decreased in those in anionic liposomes

  5. Steady-State Characterization of Bacteriorhodopsin-D85N Photocycle

    Science.gov (United States)

    Timucin, Dogan A.; Downie, John D.; Norvig, Peter (Technical Monitor)

    1999-01-01

    An operational characterization of the photocycle of the genetic mutant D85N of bacteriorhodopsin, BR-D85N, is presented. Steady-state bleach spectra and pump-probe absorbance data are obtained with thick hydrated films containing BR-D85N embedded in a gelatin host. Simple two- and three-state models are used to analyze the photocycle dynamics and extract relevant information such as pure-state absorption spectra, photochemical-transition quantum efficiencies, and thermal lifetimes of dominant states appearing in the photocycle, the knowledge of which should aid in the analysis of optical recording and retrieval of data in films incorporating this photochromic material. The remarkable characteristics of this material and their implications from the viewpoint of optical data storage and processing are discussed.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Systems Issues Pertaining to Holographic Optical Data Storage in Thick Bacteriorhodopsin Films

    Science.gov (United States)

    Downie, John D.; Timucin, Dogan A.; Gary, Charles K.; Oezcan, Meric; Smithey, Daniel T.; Crew, Marshall; Lau, Sonie (Technical Monitor)

    1998-01-01

    The optical data storage capacity and raw bit-error-rate achievable with thick photochromic bacteriorhodopsin (BR) films are investigated for sequential recording and read- out of angularly- and shift-multiplexed digital holograms inside a thick blue-membrane D85N BR film. We address the determination of an exposure schedule that produces equal diffraction efficiencies among each of the multiplexed holograms. This exposure schedule is determined by numerical simulations of the holographic recording process within the BR material, and maximizes the total grating strength. We also experimentally measure the shift selectivity and compare the results to theoretical predictions. Finally, we evaluate the bit-error-rate of a single hologram, and of multiple holograms stored within the film.

  13. 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.

  14. 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

  15. Critical correlations in an ultra-cold Bose gas revealed by means of a temporal Talbot–Lau interferometer

    International Nuclear Information System (INIS)

    The transition from a thermal cloud to a Bose–Einstein condensate (BEC) in an interacting ultra-cold Bose gas is a prototype in a universality class of diverse phase transitions. For a trapped ultra-cold Bose gas, we were able to study the critical regime both above and below the critical temperature with a Talbot–Lau interferometer, observing a peak in the correlation length. From this peak, we managed to determine the universal critical exponents for this phase transition as well as the finite-size and interaction corrections to the critical temperature. The results are all in quantitative agreement with theory. This work demonstrates the potential application of the Talbot–Lau interferometer to a wide range of critical phase transitions in ultra-cold atomic gases. (letter)

  16. Combination of DTI and fMRI reveals the white matter changes correlating with the decline of default-mode network activity in Alzheimer's disease

    Science.gov (United States)

    Wu, Xianjun; Di, Qian; Li, Yao; Zhao, Xiaojie

    2009-02-01

    Recently, evidences from fMRI studies have shown that there was decreased activity among the default-mode network in Alzheimer's disease (AD), and DTI researches also demonstrated that demyelinations exist in white matter of AD patients. Therefore, combining these two MRI methods may help to reveal the relationship between white matter damages and alterations of the resting state functional connectivity network. In the present study, we tried to address this issue by means of correlation analysis between DTI and resting state fMRI images. The default-mode networks of AD and normal control groups were compared to find the areas with significantly declined activity firstly. Then, the white matter regions whose fractional anisotropy (FA) value correlated with this decline were located through multiple regressions between the FA values and the BOLD response of the default networks. Among these correlating white matter regions, those whose FA values also declined were found by a group comparison between AD patients and healthy elderly control subjects. Our results showed that the areas with decreased activity among default-mode network included left posterior cingulated cortex (PCC), left medial temporal gyrus et al. And the damaged white matter areas correlated with the default-mode network alterations were located around left sub-gyral temporal lobe. These changes may relate to the decreased connectivity between PCC and medial temporal lobe (MTL), and thus correlate with the deficiency of default-mode network activity.

  17. 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

  18. 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

  19. Quantitative Correlation between Infectivity and Gp120 Density on HIV-1 Virions Revealed by Optical Trapping Virometry.

    Science.gov (United States)

    DeSantis, Michael C; Kim, Jin H; Song, Hanna; Klasse, Per Johan; Cheng, Wei

    2016-06-17

    The envelope glycoprotein (Env) gp120/gp41 is required for HIV-1 infection of host cells. Although in general it has been perceived that more Env gives rise to higher infectivity, the precise quantitative dependence of HIV-1 virion infectivity on Env density has remained unknown. Here we have developed a method to examine this dependence. This method involves 1) production of a set of single-cycle HIV-1 virions with varied density of Env on their surface, 2) site-specific labeling of Env-specific antibody Fab with a fluorophore at high efficiency, and 3) optical trapping virometry to measure the number of gp120 molecules on individual HIV-1 virions. The resulting gp120 density per virion is then correlated with the infectivity of the virions measured in cell culture. In the presence of DEAE-dextran, the polycation known to enhance HIV-1 infectivity in cell culture, virion infectivity follows gp120 density as a sigmoidal dependence and reaches an apparent plateau. This quantitative dependence can be described by a Hill equation, with a Hill coefficient of 2.4 ± 0.6. In contrast, in the absence of DEAE-dextran, virion infectivity increases monotonically with gp120 density and no saturation is observed under the experimental conditions. These results provide the first quantitative evidence that Env trimers cooperate on the virion surface to mediate productive infection by HIV-1. Moreover, as a result of the low number of Env trimers on individual virions, the number of additional Env trimers per virion that is required for the optimal infectivity will depend on the inclusion of facilitating agents during infection. PMID:27129237

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

    International Nuclear Information System (INIS)

    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. 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. 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. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. Surface modification by using of immobilized electrostatic self-assembly of bacteriorhodopsin as protein memory

    Directory of Open Access Journals (Sweden)

    Ashkan Zare Karizak

    2014-11-01

    Full Text Available Bacteriorhodopsin (BR is the light harvesting and photoactive proton pump found in the membrane of a salt marsh bacteria. This protein has significant potential to use in optical computing and memory devices due to unique intrinsic physical properties of photo and bioelectric. All these features make BR one of the most promising protein candidates in protein memories. Protein memory is a kind of optical memory with a large storage capacity and high speed processing features. BR protein was used with the polymer film in order to create better stability. In order to investigate immobilization of electrostatic self-assembly of BR on glass and polycarbonate as protein memories was used. Polycarbonate is a layer of compact disc (CD structure which considered dye immobilized on its surface and have reading and writing abilities of information via 0,1 bites. In this study, surfaces of polycarbonate modified by the mixture of 5% sulfuric acid and 20% acetic acid; furthermore, by using of PEI as cationic resin the surface of polycarbonate was charged and BR immobilized on it electrostatically. The modified surfaces were characterized by AFM technique. Also, light activity for reading data is retained. This is an appropriate method for optimal stability and activity assay of the protein and also is suitable for preparation of protein memories.

  6. 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

  7. 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.

  8. 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.

  9. 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.

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

    International Nuclear Information System (INIS)

    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. (author)

  11. 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.

  12. 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

    2013-01-01

    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. PMID:23271605

  13. 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

  14. 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.

  15. 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.

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

    International Nuclear Information System (INIS)

    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.

  17. Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long-Term Outcomes.

    Science.gov (United States)

    Modena, B D; Kurian, S M; Gaber, L W; Waalen, J; Su, A I; Gelbart, T; Mondala, T S; Head, S R; Papp, S; Heilman, R; Friedewald, J J; Flechner, S M; Marsh, C L; Sung, R S; Shidban, H; Chan, L; Abecassis, M M; Salomon, D R

    2016-07-01

    Interstitial fibrosis and tubular atrophy (IFTA) is found in approximately 25% of 1-year biopsies posttransplant. It is known that IFTA correlates with decreased graft survival when histological evidence of inflammation is present. Identifying the mechanistic etiology of IFTA is important to understanding why long-term graft survival has not changed as expected despite improved immunosuppression and dramatically reduced rates of clinical acute rejection (AR) (Services UDoHaH. http://www.ustransplant.org/annual_reports/current/509a_ki.htm). Gene expression profiles of 234 graft biopsy samples were obtained with matching clinical and outcome data. Eighty-one IFTA biopsies were divided into subphenotypes by degree of histological inflammation: IFTA with AR, IFTA with inflammation, and IFTA without inflammation. Samples with AR (n = 54) and normally functioning transplants (TX; n = 99) were used in comparisons. A novel analysis using gene coexpression networks revealed that all IFTA phenotypes were strongly enriched for dysregulated gene pathways and these were shared with the biopsy profiles of AR, including IFTA samples without histological evidence of inflammation. Thus, by molecular profiling we demonstrate that most IFTA samples have ongoing immune-mediated injury or chronic rejection that is more sensitively detected by gene expression profiling. These molecular biopsy profiles correlated with future graft loss in IFTA samples without inflammation. PMID:26990570

  18. A Combination of Cross Correlation and Trend Analyses Reveals that Kawasaki Disease is a Pollen-Induced Delayed-Type Hyper-Sensitivity Disease

    Directory of Open Access Journals (Sweden)

    Akira Awaya

    2014-03-01

    Full Text Available Based on ecological analyses we proposed in 2003 the relation of Kawasaki Disease (KD onset causing acute febrile systemic vasculitis, and pollen exposure. This study was aimed at investigating the correlation between pollen release and the change in the numbers of KD patients from 1991 to 2002 in Kanagawa, Japan. Short-term changes in the number of KD patients and medium- to long-term trends were analyzed separately. Short-term changes in the number of KD patients showed a significant positive cross correlation (CC with 9- to 10-month delay following pollen releases, and a smaller but significant CC with 3- to 4-month delay. Further, a temporal relationship revealed by positive CC distribution showed that pollen release preceded KD development, suggesting that pollen release leads to KD development. A trend in patient numbers was fitted by an exponential curve with the time constant of 0.005494. We hypothesized that the trend was caused by the cumulative effects of pollen exposure for elapsed months on patients who may develop KD. By comparing the time constants of fitted exponential curve for each pollen accumulation period with 0.005494, the exposure period was estimated to be 21.4 months, which explains why approximately 50% of patients developed KD within 24 months from birth.

  19. 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.

  20. 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.

  1. Coherent control of the isomerization of retinal in bacteriorhodopsin in the high intensity regime

    International Nuclear Information System (INIS)

    Coherent control protocols provide a direct experimental determination of the relative importance of quantum interference or phase relationships of coupled states along a selected pathway. These effects are most readily observed in the high intensity regime where the field amplitude is sufficient to overcome decoherence effects. The coherent response of retinal photoisomerization in bacteriorhodopsin to the phase of the photoexcitation pulses was examined at fluences of 1015- 2.5 x 1016 photons per square centimeter, comparable to or higher than the saturation excitation level of the S0-S1 retinal electronic transition. At moderate excitation levels of ∼6 x 1015 photons/cm2 (2), chirping the excitation pulses increases the all-trans to 13-cis isomerization yield by up to 16% relative to transform limited pulses. The reported results extend previous weak-field studies [Prokhorenko et al., Science 313, 1257 (2006)] and further illustrate that quantum coherence effects persist along the reaction coordinate in strong fields even for systems as complex as biological molecules. However, for higher excitation levels of ∼200 GW/cm2, there is a dramatic change in photophysics that leads to multiphoton generated photoproducts unrelated to the target isomerization reaction channel and drastically changes the observed isomerization kinetics that appears, in particular, as a red shift of the transient spectra. These results explain the apparent contradictions of the work by Florean et al.[Proc. Natl. Acad. Sci. U.S.A. 106, 10896 (2009)] in the high intensity regime. We are able to show that the difference in observations and interpretation is due to artifacts associated with additional multiphoton-induced photoproducts. At the proper monitoring wavelengths, coherent control in the high intensity regime is clearly observable. The present work highlights the importance of conducting coherent control experiments in the low intensity regime to access information on quantum

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin

    Science.gov (United States)

    Urano, Ryo; Okamoto, Yuko

    2015-12-01

    We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank's data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.

  7. Comparative Proteomic Analysis of saccharopolyspora spinosa SP06081 and PR2 strains reveals the differentially expressed proteins correlated with the increase of spinosad yield

    Science.gov (United States)

    2011-01-01

    Background Saccharopolyspora spinosa produces the environment-friendly biopesticide spinosad, a mixture of two polyketide-derived macrolide active ingredients called spinosyns A and D. Therefore considerable interest is in the improvement of spinosad production because of its low yield in wild-type S. spinosa. Recently, a spinosad-hyperproducing PR2 strain with stable heredity was obtained from protoplast regeneration of the wild-type S. spinosa SP06081 strain. A comparative proteomic analysis was performed on the two strains during the first rapid growth phase (RG1) in seed medium (SM) by using label-free quantitative proteomics to investigate the underlying mechanism leading to the enhancement of spinosad yield. Results In total, 224 proteins from the SP06081 strain and 204 proteins from the PR2 strain were unambiguously identified by liquid chromatography-tandem mass spectrometry analysis, sharing 140 proteins. A total of 12 proteins directly related to spinosad biosynthesis were identified from the two strains in RG1. Comparative analysis of the shared proteins revealed that approximately 31% of them changed their abundance significantly and fell in all of the functional groups, such as tricarboxylic acid cycles, glycolysis, biosynthetic processes, catabolic processes, transcription, translation, oxidation and reduction. Several key enzymes involved in the synthesis of primary metabolic intermediates used as precursors for spinosad production, energy supply, polyketide chain assembly, deoxysugar methylation, and antioxidative stress were differentially expressed in the same pattern of facilitating spinosad production by the PR2 strain. Real-time reverse transcriptase polymerase chain reaction analysis revealed that four of five selected genes showed a positive correlation between changes at the translational and transcriptional expression level, which further confirmed the proteomic analysis. Conclusions The present study is the first comprehensive and

  8. Proton uptake mechanism of bacteriorhodopsin as determined by time-resolved stroboscopic-FTIR-spectroscopy.

    Science.gov (United States)

    Souvignier, G; Gerwert, K

    1992-11-01

    Bacteriorhodopsin's proton uptake reaction mechanism in the M to BR reaction pathway was investigated by time-resolved FTIR spectroscopy under physiological conditions (293 K, pH 6.5, 1 M KCl). The time resolution of a conventional fast-scan FTIR spectrometer was improved from 10 ms to 100 mus, using the stroboscopic FTIR technique. Simultaneously, absorbance changes at 11 wavelengths in the visible between 410 and 680 nm were recorded. Global fit analysis with sums of exponentials of both the infrared and visible absorbance changes yields four apparent rate constants, k(7) = 0.3 ms, k(4) = 2.3 ms, k(3) = 6.9 ms, k(6) = 30 ms, for the M to BR reaction pathway. Although the rise of the N and O intermediates is dominated by the same apparent rate constant (k(4)), protein reactions can be attributed to either the N or the O intermediate by comparison of data sets taken at 273 and 293 K. Conceptionally, the Schiff base has to be oriented in its deprotonated state from the proton donor (asp 85) to the proton acceptor (asp 96) in the M(1) to M(2) transition. However, experimentally two different M intermediates are not resolved, and M(2) and N are merged. From the results the following conclusions are drawn: (a) the main structural change of the protein backbone, indicated by amide I, amide II difference bands, takes place in the M to N (conceptionally M(2)) transition. This reaction is proposed to be involved in the "reset switch" of the pump, (b) In the M to N (conceptionally M(2)) transition, most likely, asp-85's carbonyl frequency shifts from 1,762 to 1,753 cm(-1) and persists in O. Protonation of asp-85 explains the red-shift of the absorbance maximum in O. (c) The catalytic proton uptake binding site asp-96 is deprotonated in the M to N transition and is reprotonated in O. PMID:19431858

  9. 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

  10. 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.)

  11. Towards structural investigations on isotope labelled native bacteriorhodopsin in detergent micelles by solution-state NMR spectroscopy

    International Nuclear Information System (INIS)

    1H NMR signals of the retinal moiety in detergent-solubilized bacteriorhodopsin are assigned, enabling the interpretation of NOEs within the chromophore. To achieve this, a number of differently labelled samples were prepared to test the applicability of the various assignment and distance measurement strategies. In measurements with and without light,1H and 13C chemical shifts of the retinal in the native protein were partially assigned for both the dark- and the light-adapted states. Additionally, samples with residue-specific1H amino acids and/or retinal in an otherwise deuterated protein were prepared to measure the distances between either two kinds of amino acids or between individual amino acids and the retinal moiety. With the observation of NOE within the bound retinal and between retinal and its neighbouring aminoacids, an important step towards the elucidation of distance constraints in the binding pocket of the proton pump is made

  12. Time-resolved laser studies on the proton pump mechanism of bacteriorhodopsin. Progress report, January 31,1991--February 1, 1992

    Energy Technology Data Exchange (ETDEWEB)

    El-Sayed, M.A.

    1991-12-31

    The research work carried out in 1991 can be classified as follows: (1) Work on the nature of the binding site of Eu{sup 3+} in which a fluorescence technique was used to determine the binding equilibrium constant from the concentration of the free Eu{sup 3+} in equilibrium with the bound ions. (2) The mechanism of the slow deprotonation process of bacteriorhodopsin during its photocycle from the observed temperature and pH dependence of its kinetics. (3) Using the circular dichroism spectrum of bR and its perturbed forms to examine the nature of the primary process as well as the origin of the non-exponential kinetic behavior of its photocycle. (4) Studies of bacteriorhodopsin mutants to identify the important amino acids that are part of the reaction coordinate of the deprotonation process as well as to assign the species that are important in giving rise to UV transient absorption whose origin was controversial.

  13. Protein changes associated with reprotonation of the Schiff base in the photocycle of Asp96-->Asn bacteriorhodopsin. The MN intermediate with unprotonated Schiff base but N-like protein structure

    Science.gov (United States)

    Sasaki, J.; Shichida, Y.; Lanyi, J. K.; Maeda, A.

    1992-01-01

    The difference Fourier transform infrared spectrum for the N intermediate in the photoreaction of the light-adapted form of bacteriorhodopsin can be recorded at pH 10 at 274 K (Pfefferle, J.-M., Maeda, A., Sasaki, J., and Yoshizawa, T. (1991) Biochemistry 30, 6548-6556). Under these conditions, Asp96-->Asn bacteriorhodopsin gives a photoproduct which shows changes in protein structure similar to those observed in N of wild-type bacteriorhodopsin. However, decreased intensity of the chromophore bands and the single absorbance maximum at about 400 nm indicate that the Schiff base is unprotonated, as in the M intermediate. This photoproduct was named MN. At pH 7, where the supply of proton is not as restricted as at pH 10, Asp96-->Asn bacteriorhodopsin yields N with a protonated Schiff base. The Asn96 residue, which cannot deprotonate as Asp96 in wild-type bacteriorhodopsin, is perturbed upon formation of both MN at pH 10 and N at pH 7. We suggest that the reprotonation of the Schiff base is preceded by a large change in the protein structure including perturbation of the residue at position 96.

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

    Science.gov (United States)

    Lee, Yonghoon; Ham, Kyung-Sik; Han, Song-Hee; Yoo, Jonghyun; Jeong, Sungho

    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.

  15. 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

  16. 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.

  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. Genetic–geographic correlation revealed across a broad European ecotypic sample of perennial ryegrass (Lolium perenne) using array-based SNP genotyping

    OpenAIRE

    Blackmore, T.; Thomas, I.; McMahon, R.; Powell, W.; Hegarty, M

    2015-01-01

    Key message Publically available SNP array increases the marker density for genotyping of forage crop, Lolium perenne . Applied to 90 European ecotypes composed of 716 individuals identifies a significant genetic–geographic correlation. Abstract Grassland ecosystems are ubiquitous across temperate and tropical regions, totalling 37 % of the terrestrial land cover of the planet, and thus represent a global resource for understanding local adaptations to environment. However, genomic resources ...

  19. A Combination of Cross Correlation and Trend Analyses Reveals that Kawasaki Disease is a Pollen-Induced Delayed-Type Hyper-Sensitivity Disease

    OpenAIRE

    Akira Awaya; Chiaki Nishimura

    2014-01-01

    Based on ecological analyses we proposed in 2003 the relation of Kawasaki Disease (KD) onset causing acute febrile systemic vasculitis, and pollen exposure. This study was aimed at investigating the correlation between pollen release and the change in the numbers of KD patients from 1991 to 2002 in Kanagawa, Japan. Short-term changes in the number of KD patients and medium- to long-term trends were analyzed separately. Short-term changes in the number of KD patients showed a significant pos...

  20. 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.

  1. 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.

  2. 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.

  3. Variable expression levels of keratin and vimentin reveal differential EMT status of circulating tumor cells and correlation with clinical characteristics and outcome of patients with metastatic breast cancer

    International Nuclear Information System (INIS)

    CTCs expressing variable levels of epithelial and mesenchymal markers in breast cancer have previously been reported. However, no information exists for keratin expression levels of CTCs in association with disease status, whereas assays for the characterization of transitional EMT phenotypes of CTCs in breast cancer are rather lacking. We investigated the correlation between keratin expression of CTCs and patients’ outcome and characterized the EMT status of CTCs via the establishment of a numerical “ratio” value of keratin and vimentin expression levels on a single cell basis. Keratin expression was evaluated in 1262 CTCs from 61 CTC-positive patients with metastatic breast cancer, using analysis of images obtained through the CellSearch System. For the determination of vimentin/keratin (vim/K) ratios, expression levels of keratin and vimentin were measured in cytospin preparations of luminal (MCF-7 and T47D) and basal (MDA.MB231 and Hs578T) breast cancer cell lines and 110 CTCs from 5 CTC-positive patients using triple immunofluorescence laser scanning microscopy and image analysis. MCF-7 and T47D displayed lower vim/K ratios compared to MDA.MB231 and Hs578T cells, while MCF-7 cells that had experimentally undergone EMT were characterized by varying intermediate vim/K ratios. CTCs were consisted of an heterogeneous population presenting variable vim/K values with 46% of them being in the range of luminal breast cancer cell lines. Keratin expression levels of CTCs detected by the CellSearch System correlated with triple negative (p = 0.039) and ER-negative (p = 0.025) breast cancer, and overall survival (p = 0.038). Keratin expression levels of CTCs correlate with tumor characteristics and clinical outcome. Moreover, CTCs display significant heterogeneity in terms of the degree of EMT phenotype that probably reflects differential invasive potential. The assessment of the vim/K ratios as a surrogate marker for the EMT status of CTCs merits further

  4. Super-resolution 2-photon microscopy reveals that the morphology of each dendritic spine correlates with diffusive but not synaptic properties

    Directory of Open Access Journals (Sweden)

    Bernardo Sabatini

    2014-05-01

    Full Text Available The structure of dendritic spines suggests a specialized function in compartmentalizing synaptic signals near active synapses. Indeed, theoretical and experimental analyses indicate that the diffusive resistance of the spine neck is sufficient to effectively compartmentalize some signaling molecules in a spine for the duration of their activated lifetime. Here we describe the application of 2-photon microscopy combined with stimulated emission depletion (STED-2P to the biophysical study of the relationship between synaptic signals and spine morphology, demonstrating the utility of combining STED-2P with modern optical and electrophysiological techniques. Morphological determinants of fluorescence recovery time were identified and evaluated within the context of a simple compartmental model describing diffusive transfer between spine and dendrite. Correlations between the neck geometry and the amplitude of synapse potentials and calcium transients evoked by 2-photon glutamate uncaging were also investigated.

  5. 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.

  6. 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.

  7. Structural Transition of Bacteriorhodopsin Is Preceded by Deprotonation of Schiff Base: Microsecond Time-Resolved X-Ray Diffraction Study of Purple Membrane

    OpenAIRE

    Oka, Toshihiko; Inoue, Katsuaki; Kataoka, Mikio; Yagi, Naoto

    2004-01-01

    The structural changes in the photoreaction cycle of bacteriorhodopsin, a light-driven proton pump, was investigated at a resolution of 7 Å by a time-resolved x-ray diffraction experiment utilizing synchrotron x rays from an undulator of SPring-8. The x-ray diffraction measurement system, used in coupling with a pulsed YAG laser, enabled us to record a diffraction pattern from purple membrane film at a time-resolution of 6 μs over the time domain of 5 μs to 500 ms. In the time domain, the fun...

  8. 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

  9. 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.

  10. Oxygen ordering in the high-T$_c$ superconductor HgBa$_2$CaCu$_2$O$_{6+\\delta}$ as revealed by perturbed angular correlation

    CERN Document Server

    Mendonca, Tania Melo; Haas, Heinz; Odier, Philippe; Tavares, Pedro; Silva, Manuel Ribeiro; Lopes, Armandina; Pereira, Andre; Goncalves, Joao Nuno; Amaral, Joao; Darie, Celine; Araujo, Joao Pedro

    2011-01-01

    Lattice sites and collective ordering of oxygen atoms in HgBa$_2$CaCu$_2$O$_{6+\\delta}$ were studied using the perturbed angular correlation (PAC) technique at ISOLDE/CERN. The electric field gradients (EFG) at $^{199m}$Hg nuclei have been measured as functions of oxygen doping on the Hg planes, above and below T$_c$. In comparison with the results obtained for oxygen and fluorine doping in Hg-1201, the analysis shows a different oxygen ordering exhibited by Hg-1212. Moreover, for all studied cases, the experimental results show that at a local scale there is non-uniform oxygen distribution. A series of ab initio EFG calculations allowed to infer that at low concentrations, regions without oxygen coexist with regions where O$_{2\\delta}$ dumbbell molecules are located at the center of the Hg mesh. On the other side, at high concentrations, O$_{2\\delta}$ dumbbell molecules coexist with single O$_\\delta$ atoms occupying the center of the Hg mesh. The present results suggest that oxygen sits on the Hg planes in t...

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. Photochromic Bacteriorhodopsin Mutant with High Holographic Efficiency and Enhanced Stability via a Putative Self-Repair Mechanism

    Science.gov (United States)

    2015-01-01

    The Q photoproduct of bacteriorhodopsin (BR) is the basis of several biophotonic technologies that employ BR as the photoactive element. Several blue BR (bBR) mutants, generated by using directed evolution, were investigated with respect to the photochemical formation of the Q state. We report here a new bBR mutant, D85E/D96Q, which is capable of efficiently converting the entire sample to and from the Q photoproduct. At pH 8.5, where Q formation is optimal, the Q photoproduct requires 65 kJ mol-1 of amber light irradiation (590 nm) for formation and 5 kJ mol-1 of blue light (450 nm) for reversion, respectively. The melting temperature of the resting state and Q photoproduct, measured via differential scanning calorimetry, is observed at 100 °C and 89 °C at pH 8.5 or 91 °C and 82 °C at pH 9.5, respectively. We hypothesize that the protein stability of D85E/D96Q compared to other blue mutants is associated with a rapid equilibrium between the blue form E85(H) and the purple form E85(−) of the protein, the latter providing enhanced structural stability. Additionally, the protein is shown to be stable and functional when suspended in an acrylamide matrix at alkaline pH. Real-time photoconversion to and from the Q state is also demonstrated with the immobilized protein. Finally, the holographic efficiency of an ideal thin film using the Q state of D85E/D96Q is calculated to be 16.7%, which is significantly better than that provided by native BR (6–8%) and presents the highest efficiency of any BR mutant to date. PMID:24498928

  17. Nonlinear Optical Properties of Bacteriorhodopsin and Retinal Chromophores and Their Applications for Optical Information Storage and Processing.

    Science.gov (United States)

    Chen, Zhongping

    Retinal, a conjugated polyene, plays a crucial role in biology. Both the visual pigments and the energy transducing protein, bacteriorhodopsin (BR) have a form of retinal as their chromophores. Because visual excitation and energy transduction in these systems is initiated by the promotion of retinal to an excited electronic state, information about the excited-state structure of retinal and the effect of chromophore/protein interactions on this structure are essential to understanding the functions of these systems. In this thesis, surface second harmonic (SH) generation is used to measure the light-induced dipole moment changes of a series of retinal derivatives that were designed and synthesized to model specific components of chromophore/protein interactions. In addition, we report an in situ probe of the dipole moment change of the retinal chromophore bound in BR by SH generation from oriented purple membranes. The dipole moment changes of various forms of BR, including light-adapted, dark-adapted, blue, and acid purple membrane, were measured and compared. These results, combined with the results from model compounds, elucidate the effects of the chromophore/protein interactions on light-induced charge redistribution and give insight on the fundamental nature of light excitation and energy storage in SR and rhodopsin. Furthermore, the dependence of the molecular hyperpolarizability of the conjugated molecules on donor/acceptor strength, protonation, conjugate length, planarity, and nonconjugate charges is investigated. Our study shows for the first time that nonconjugated charges have a very large effect on the nonlinear optical properties of conjugated molecules. BR has interesting photochromic characteristics, very large optical nonlinearities, and a unique optoelectrical property where the polarity of the photovoltage depends on both its photochromic state and the excitation wavelength. These unique characteristics coupled with its high stability make BR

  18. A pKa calculation of residues in a proton pump, bacteriorhodopsin, from structures determined by electron crystallography.

    Science.gov (United States)

    Mitsuoka, Kaoru

    2014-11-01

    Bacteriorhodopsin (bR) is a light-driven proton pump, which is a membrane protein found in halophilic archeae like Halobacterium salinarum and in eubacteria [1]. When the covalently bound retinal chromophore absorbs the light energy, it changes the conformation from all-trans to 13-cis. This configuration change initiates ion translocation across the cell membrane and a proton moves from inside to outside of the cell. The bR molecules are forming two-dimensional crystals on the membranes of halophilic archeae, and therefore the atomic model of bR was first determined by electron crystallography. The determined structure can be used to determine the pKa values, through which the charge states of ionizable residues in bR determine their pH-dependent properties. The pH-dependent properties are crucial for proton translocation from ionizable residues or to ionizable residues. Detection of the intermediate states of the reaction cycle (photocycle) produced spectroscopic information, which can predict the ionization state of the ionozable residues. In the transition from the L intermediate to the M intermediate, it is known that a proton moves from the Shiff base on the retinal chromophore to Asp85, while a proton is released to the extracellar side from proton-releasing groups including Glu194 and Glu204. Experimentally the pKa value of the proton release is determined to be about 9.7, while the pKa value of Asp85 was measured to change from 2.6 to 7.5 by the proton release from the proton-releasing groups [2]. Here we used the PROPKA program [3] to calculate the pKa values of Asp85 and the proton-releasing groups from the structures at pH 5.5 and at pH 10.0 determined by electron crystallography. The calculation showed that the pKa value of Asp85 changes from 5.3 to 6.1, which qualitatively show the similar changes with the measured difference. The largest change between the structures is the shift of Arg82 by the proton release from the proton-releasing groups

  19. 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

  20. 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...

  1. 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...

  2. 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.

  3. Correlations of Cosmic Tidal Fields

    OpenAIRE

    Catelan, Paolo; Porciani, Cristiano

    2000-01-01

    We study correlations amongst tidal fields originated by the large-scale distribution of matter in the Universe. The two-point tidal correlation is described as a rank-4 tensor, whose elements can be written in terms of four fundamental scalar functions ranging, with respect the spatial separation, from purely transversal to purely longitudinal correlations. Tidal fields, both on galaxy and cluster scales, reveal to be correlated over distances larger than the mass-density correlation lenght,...

  4. FTIR Studies of Internal Water Molecules of Bacteriorhodopsin: Structural Analysis of Halide-bound D85S and D212N Mutants in the Schiff Base Region

    Science.gov (United States)

    Shibata, Mikihiro; Kandori, Hideki

    2007-12-01

    Bacteriorhodopsin (BR), a membrane protein found in Halobacterium salinarum, functions as a light-driven proton pump. The Schiff base region has a quadropolar structure with positive charges located at the protonated Schiff base and Arg82, and counterbalancing negative charges located at Asp85 and Asp212 (Figure 1A). It is known that BR lacks a proton-pumping activity if Asp85 or Asp212 is neutralized by mutation. On the other hand, binding of C1- brings different effects for pumping functions in mutants at D85 and D212 position. While C1--bound D85T and D85S pump C1-, photovoltage measurements suggested that C1--bound D212N pumps protons at low pH. In this study, we measured low-temperature FTIR spectra of D85S and D212N containing various halides to compare the halide binding site of both proteins. In the case of D85S, the N-D stretching vibrations of the Schiff base were halide-dependent. This result suggests that the halide is a hydrogen-bond acceptor of the Schiff base, being consistent with the X-ray crystal structure. On the other hand, no halide dependence was observed for vibrational bands of the retinal skeleton and the Schiff base in the D212N mutant. This result suggests that the halide does not form a hydrogen bond with the Schiff base directly, unlike the mutation at D85 position. Halide-dependent water bands in the Schiff base region also differ between D85S and D212N. From these results, halide binding site of both proteins and role of two negative charges in BR will be discussed.

  5. 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.

  6. Isolation of a new Pseudomonas halophila strain possess bacteriorhodopsin-like protein by a novel method for screening of photoactive protein producing bacteria.

    Science.gov (United States)

    Fanaei, Maryam; Emtiazi, Giti

    2014-02-01

    Bacteriorhodopsin (bR) is a transmembrane protein deposited in the purple membrane of Halobacterium salinarum which absorbs energy from photons to create a photo-induced proton gradient across the membrane. A bR molecule can be considered as a natural solar device transforming light into other types of energy and therefore is of interest for a wide range of applications including two and three-dimensional memory storage, optical data processing, artificial cells, holographic media, the artificial retina and photo sensor devices. H. salinarum is a slow-growing, halophilic Archaea present in red salt waters. The present study introduces a novel bR-like pigment from a new strain of Pseudomonas halophila (with registered accession number KC959570 in the NCBI databank) which has a very significant degree of light-dependent activity. This is the first report on the presence of functional bR-like protein in the Pseudomonas family. The isolate is a fast-growing, halophilic bacterium and is comparable with other photoactive protein producer microorganisms. Also, in the present study a novel isolation method for screen light-stimulating protein producing microorganisms is introduced. For this purpose 2,3,5-triphenyltetrazolium chloride (TTC) was employed for the first time as an artificial hydrogen acceptor in the proton-transfer processes. The TTC test is an easy and susceptible method for estimating hydrogen production during the proton transport process. This is the first report of the use of TTC for photo activity measurement and selection of bacteria containing light dependent proteins. PMID:24002576

  7. 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...

  8. 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.

  9. 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...

  10. 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.)

  11. 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

    International Nuclear Information System (INIS)

    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.)

  12. Quantitative three-dimensional analysis of poly (lactic-co-glycolic acid) microsphere using hard X-ray nano-tomography revealed correlation between structural parameters and drug burst release.

    Science.gov (United States)

    Huang, Xiaozhou; Li, Na; Wang, Dajiang; Luo, Yuyan; Wu, Ziyu; Guo, Zhefei; Jin, Qixing; Liu, Zhuying; Huang, Yafei; Zhang, Yongming; Wu, Chuanbin

    2015-08-10

    The objective of this study was to investigate the use of transmission hard X-ray nano-computed-tomography (nano-CT) for characterization of the pore structure and drug distribution in poly (lactic-co-glycolic acid) (PLGA) microspheres encapsulating bovine serum albumin and to study the correlation between drug distribution and burst release. The PLGA microspheres were fabricated using a double-emulsion method. The results of pore structure analysis accessed with nano-CT were compared with those acquired by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Surface pore interconnectivity and surface protein interconnectivity were obtained using combined nano-CT and pixel analysis. The correlation between surface protein interconnectivity with the initial burst release across various tested formulations was also analyzed. The size, shape, and distribution of the pores and protein could be clearly observed in the whole microsphere using nano-CT, whereas only the sectional information was observed using SEM or CLSM. Interconnected pores and surface connected pores could be clearly distinguished in nano-CT, which enables the quantitative analysis of surface pore interconnectivity and surface protein interconnectivity. The surface protein interconnectivity in different formulations correlated well with the burst release at 5-10h. Nano-CT provided a nondestructive, high-resolution, and three-dimensional analysis method to characterize the porous microsphere. PMID:25951620

  13. 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

  14. 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.

  15. Integrative Analysis of mRNA, microRNA, and Protein Correlates of Relative Cerebral Blood Volume Values in GBM Reveals the Role for Modulators of Angiogenesis and Tumor Proliferation

    Science.gov (United States)

    Rao, Arvind; Manyam, Ganiraju; Rao, Ganesh; Jain, Rajan

    2016-01-01

    Dynamic susceptibility contrast-enhanced magnetic resonance imaging is routinely used to provide hemodynamic assessment of brain tumors as a diagnostic as well as a prognostic tool. Recently, it was shown that the relative cerebral blood volume (rCBV), obtained from the contrast-enhancing as well as -nonenhancing portion of glioblastoma (GBM), is strongly associated with overall survival. In this study, we aim to characterize the genomic correlates (microRNA, messenger RNA, and protein) of this vascular parameter. This study aims to provide a comprehensive radiogenomic and radioproteomic characterization of the hemodynamic phenotype of GBM using publicly available imaging and genomic data from the Cancer Genome Atlas GBM cohort. Based on this analysis, we identified pathways associated with angiogenesis and tumor proliferation underlying this hemodynamic parameter in GBM. PMID:27053917

  16. 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.

  17. Score Correlation

    Czech Academy of Sciences Publication Activity Database

    Fabián, Zdeněk

    2010-01-01

    Roč. 20, č. 6 (2010), s. 793-798. ISSN 1210-0552 R&D Projects: GA ČR GA205/09/1079 Institutional research plan: CEZ:AV0Z10300504 Keywords : score function * correlation * rank correlation coefficient * heavy tails Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.511, year: 2010

  18. 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.

  19. 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.

  20. 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

    International Nuclear Information System (INIS)

    The aim of this study was to find clinically relevant MIBG-avid metastatic patterns in patients with newly diagnosed stage 4 neuroblastoma. Diagnostic 123I-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 diffuse'' pattern found mainly in patients with MYCNsc neuroblastoma. (orig.)

  1. 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.

  2. 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

  3. 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.

  4. Correlation measurement of squeezed light

    DEFF Research Database (Denmark)

    Krivitsky, Leonid; Andersen, Ulrik Lund; Dong, R.; Huck, Alexander; Wittmann, C.; Leuchs, G.

    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...

  5. 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

  6. 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。

  7. 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.

  8. Variable angle correlation spectroscopy

    International Nuclear Information System (INIS)

    In this dissertation, a novel nuclear magnetic resonance (NMR) technique, variable angle correlation spectroscopy (VACSY) is described and demonstrated with 13C 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

  9. 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.

  10. 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.

  11. 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

  12. 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...

  13. 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.

  14. Two and Three Particle Flavor Dependent Correlations

    International Nuclear Information System (INIS)

    In recent work, the PHENIX collaboration has applied a novel technique to the analysis of azimuthal correlations which extinguishes the harmonic part of the underlying event revealing the true jet shape. The extension of this method to three particle correlations allows a much more detailed study of jet topologies. Correlation functions and extracted jet landscapes are studied for wide range of pT and centrality selections and particle flavors in Au+Au collisions at √(sNN)=200 GeV. They reveal substantial modifications of jet properties resulting from the coupling of jets to the strongly interacting matter produced in RHIC collisions

  15. Proverbs Reveal Culture Diversity

    OpenAIRE

    Hou, Rong

    2013-01-01

    Through the analysis of property of culture and proverb, it can be known that proverb can help one to understand a culture. The way proverb reveals culture diversity can be connected with the patterns of value dimension, which conveys the information of a culture’s deep meaning. From the perspective of uncertainty-avoidance, it can be seen that although Ireland and America both are low-uncertainty-avoidance cultures, they mainly have different life attitudes, because that Americans put more e...

  16. 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 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...

  17. 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

  18. Geometric correlations and multifractals

    International Nuclear Information System (INIS)

    There are many situations where the usual statistical methods are not adequate to characterize correlations in the system. To characterize such situations we introduce mutual correlation dimensions which describe geometric correlations in the system. These dimensions allow us to distinguish between variables which are perfectly correlated with or without a phase lag, variables which are uncorrelated and variables which are partially correlated. We demonstrate the utility of our formalism by considering two examples from dynamical systems. The first example is about the loss of memory in chaotic signals and describes auto-correlations while the second example is about synchronization of chaotic signals and describes cross-correlations. (author). 19 refs, 6 figs

  19. Community Detection for Correlation Matrices

    Science.gov (United States)

    MacMahon, Mel; Garlaschelli, Diego

    2015-04-01

    A challenging problem in the study of complex systems is that of resolving, without prior information, the emergent, mesoscopic organization determined by groups of units whose dynamical activity is more strongly correlated internally than with the rest of the system. The existing techniques to filter correlations are not explicitly oriented towards identifying such modules and can suffer from an unavoidable information loss. A promising alternative is that of employing community detection techniques developed in network theory. Unfortunately, this approach has focused predominantly on replacing network data with correlation matrices, a procedure that we show to be intrinsically biased because of its inconsistency with the null hypotheses underlying the existing algorithms. Here, we introduce, via a consistent redefinition of null models based on random matrix theory, the appropriate correlation-based counterparts of the most popular community detection techniques. Our methods can filter out both unit-specific noise and system-wide dependencies, and the resulting communities are internally correlated and mutually anticorrelated. We also implement multiresolution and multifrequency approaches revealing hierarchically nested subcommunities with "hard" cores and "soft" peripheries. We apply our techniques to several financial time series and identify mesoscopic groups of stocks which are irreducible to a standard, sectorial taxonomy; detect "soft stocks" that alternate between communities; and discuss implications for portfolio optimization and risk management.

  20. 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.

  1. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    This work presents a method for designing facial interfaces for sociable android robots with respect to the fundamental rules of human affect expression. Extending the work of Paul Ekman towards a robotic direction, we follow the judgment-based approach for evaluating facial expressions to test 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...... findings are based on the results derived from a number of judgments, and suggest that before programming the facial expressions of a Geminoid, the Original should pass through the proposed procedure. According to our recommendations, the facial expressions of an android should be tested by judges, even in...

  2. 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

  3. 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

  4. 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 ...

  5. Canonical Correlation Forests

    OpenAIRE

    Rainforth, Tom; Wood, Frank

    2015-01-01

    We introduce canonical correlation forests (CCFs), a new decision tree ensemble method for classification. Individual canonical correlation trees are binary decision trees with hyperplane splits based on canonical correlation components. Unlike axis-aligned alternatives, the decision surfaces of CCFs are not restricted to the coordinate system of the input features and therefore more naturally represent data with correlation between the features. Additionally we introduce a novel alternative ...

  6. Quantum correlation games

    OpenAIRE

    Iqbal, Azhar; Weigert, S.

    2004-01-01

    A new approach to play games quantum mechanically is proposed. We consider two players who perform measurements in an EPR-type setting. The payoff relations are defined as functions of *correlations*, i.e. without reference to classical or quantum mechanics. Classical bi-matrix games are reproduced if the input states are classical and perfectly anti-correlated, that is, for a classical correlation game. However, for a quantum correlation game, with an entangled singlet state as input, qualit...

  7. What Is Strong Correlation?

    Science.gov (United States)

    Kozak, Marcin

    2009-01-01

    Interpretation of correlation is often based on rules of thumb in which some boundary values are given to help decide whether correlation is non-important, weak, strong or very strong. This article shows that such rules of thumb may do more harm than good, and instead of supporting interpretation of correlation--which is their aim--they teach a…

  8. Constrained Canonical Correlation.

    Science.gov (United States)

    DeSarbo, Wayne S.; And Others

    1982-01-01

    A variety of problems associated with the interpretation of traditional canonical correlation are discussed. A response surface approach is developed which allows for investigation of changes in the coefficients while maintaining an optimum canonical correlation value. Also, a discrete or constrained canonical correlation method is presented. (JKS)

  9. 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.

  10. Integral and Multidimensional Linear Distinguishers with Correlation Zero

    DEFF Research Database (Denmark)

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

    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...

  11. Multicolour correlative imaging using phosphor probes

    OpenAIRE

    Morrison, IEG; Samilian, A; Coppo, P.; Ireland, TG; Fern, GR; Silver, J; Withnall, R; O’Toole, PJ

    2015-01-01

    Correlative light and electron microscopy exploits the advantages of optical methods, such as multicolour probes and their use in hydrated live biological samples, to locate functional units, which are then correlated with structural details that can be revealed by the superior resolution of electron microscopes. One difficulty is locating the area imaged by the electron beam in the much larger optical field of view. Multifunctional probes that can be imaged in both modalities and thus regist...

  12. 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...

  13. 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.

  14. Complementarity and Correlations

    Science.gov (United States)

    Maccone, Lorenzo; Bruß, Dagmar; Macchiavello, Chiara

    2015-04-01

    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 first result holds also for other measures (e.g., the Pearson correlation coefficient or the sum of conditional probabilities).

  15. Complementarity and correlations.

    Science.gov (United States)

    Maccone, Lorenzo; Bruß, Dagmar; Macchiavello, Chiara

    2015-04-01

    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 first result holds also for other measures (e.g., the Pearson correlation coefficient or the sum of conditional probabilities). PMID:25884117

  16. 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...

  17. Particle number correlations in nuclear disassembly

    International Nuclear Information System (INIS)

    An investigation of data and model calculations pertaining to the disassembly of an excited nucleus reveals that the probability of occurrence of various partitions is, in the cases considered, well approximated by expressions of the multinomial form. This finding implies that static (number) correlations (apart from those implied by the constraint of fixed total mass or charge) are rather weak and leads to the conclusion that dynamical correlations need to be measured in order to investigate details of the disassembly mechanism. The sensitivity of correlations to conserved quantitites may however be useful for the investigation of certain aspects of the reaction mechanism, in particular for the distinction between central and peripheral collisions. (orig.)

  18. 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.

  19. Protecting quantum entanglement and correlation by local filtering operations

    Science.gov (United States)

    Huang, Chunyu; Ma, Wenchao; Ye, Liu

    2016-05-01

    In this work, the protection of different quantum entanglement and correlation is explored by local filtering operations. The results show that the filtering operations can indeed be useful for combating amplitude-damping decoherence and recovering the quantum entanglement and correlation. In this scheme, although the final states satisfy the quantum entanglement and correlation, the corresponding initial noisy states does not satisfy them, which means that the filtering operations can reveal the hidden genuine quantum entanglement and correlation of these initial noisy states.

  20. 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

  1. RHIC Data Correlation Methodology

    International Nuclear Information System (INIS)

    A requirement for RHIC data plotting software and physics analysis is the correlation of data from all accelerator data gathering systems. Data correlation provides the capability for a user to request a plot of multiple data channels vs. time, and to make meaningful time-correlated data comparisons. The task of data correlation for RHIC requires careful consideration because data acquisition triggers are generated from various asynchronous sources including events from the RHIC Event Link, events from the two Beam Sync Links, and other unrelated clocks. In order to correlate data from asynchronous acquisition systems a common time reference is required. The RHIC data correlation methodology will allow all RHIC data to be converted to a common wall clock time, while still preserving native acquisition trigger information. A data correlation task force team, composed of the authors of this paper, has been formed to develop data correlation design details and provide guidelines for software developers. The overall data correlation methodology will be presented in this paper

  2. 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.

  3. Intercluster Correlation in Seismicity

    CERN Document Server

    Helmstetter, A; Helmstetter, Agnes; Sornette, Didier

    2003-01-01

    Mega et al.(cond-mat/0212529) proposed to use the "diffusion entropy" (DE) method to demonstrate that the distribution of time intervals between a large earthquake (the mainshock of a given seismic sequence) and the next one does not obey Poisson statistics. We have performed synthetic tests which show that the DE is unable to detect correlations between clusters, thus negating the claimed possibility of detecting an intercluster correlation. We also show that the LR model, proposed by Mega et al. to reproduce inter-cluster correlation, is insufficient to account for the correlation observed in the data.

  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. 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…

  7. Correlation and clustering

    OpenAIRE

    Labini, Francesco Sylos; Gabrielli, Andrea

    2001-01-01

    In this lecture we clarify the basic difference between the correlation properties for systems characterized by small or large fluctuations. The concepts of correlation length, homogeneity scale, scale invariance and criticality are discussed as well. We relate these concepts to the interpretation of galaxy clsutering.

  8. Most Correlated Arms Identification

    OpenAIRE

    Liu, Che-Yu; Bubeck, Sébastien

    2014-01-01

    We study the problem of finding the most mutually correlated arms among many arms. We show that adaptive arms sampling strategies can have significant advantages over the non-adaptive uniform sampling strategy. Our proposed algorithms rely on a novel correlation estimator. The use of this accurate estimator allows us to get improved results for a wide range of problem instances.

  9. Quantum Correlation Games

    CERN Document Server

    Iqbal, A; Iqbal, Azhar; Weigert, Stefan

    2003-01-01

    A new approach to play games quantum mechanically is proposed. We consider two players who perform measurements in an EPR-type setting. The payoff relations are defined as functions of *correlations*, i.e. without reference to classical or quantum mechanics. Classical bi-matrix games are reproduced if the input states are classical and perfectly anti-correlated, that is, for a classical correlation game. However, for a quantum correlation game, with quantum mechanical singlet states as input, qualitatively different solutions are obtained. For example, the Prisoners' Dilemma acquires a Nash equilibrium if the players both apply a mixed strategy. It appears to be conceptually impossible to reproduce the properties of quantum correlation games within the frame work of classical games.

  10. Quantum correlation games

    Energy Technology Data Exchange (ETDEWEB)

    Iqbal, Azhar; Weigert, Stefan [HuMP-Hull Mathematical Physics, Department of Mathematics, University of Hull (United Kingdom)

    2004-06-04

    A new approach to play games quantum mechanically is proposed. We consider two players who perform measurements in an EPR-type setting. The payoff relations are defined as functions of correlations, i.e. without reference to classical or quantum mechanics. Classical bi-matrix games are reproduced if the input states are classical and perfectly anti-correlated, that is, for a classical correlation game. However, for a quantum correlation game, with an entangled singlet state as input, qualitatively different solutions are obtained. For example, the Prisoners' Dilemma acquires a Nash equilibrium if both players apply a mixed strategy. It appears to be conceptually impossible to reproduce the properties of quantum correlation games within the framework of classical games.

  11. 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...

  12. Correlation plenoptic imaging

    CERN Document Server

    D'Angelo, Milena; Pepe, Francesco V; Vaccarelli, Ornella; Scarcelli, Giuliano

    2016-01-01

    Plenoptic imaging is a promising optical modality that simultaneously captures the location and the propagation direction of light in order to enable tridimensional imaging in a single shot. However, in classical imaging systems, the maximum spatial and angular resolutions are fundamentally linked; thereby, the maximum achievable depth of field is inversely proportional to the spatial resolution. We propose to take advantage of the second-order correlation properties of light to overcome this fundamental limitation. In this paper, we demonstrate that the momentum/position correlation of chaotic light leads to the enhanced refocusing power of correlation plenoptic imaging with respect to standard plenoptic imaging.

  13. 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

  14. 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.

  15. Revealed Cores: Characterizations and Structure

    OpenAIRE

    Stefano Vannucci

    2010-01-01

    Characterizations of the choice functions that select the cores or the externally stable cores induced by an underlying revealed dominance digraph are provided. Relying on such characterizations, the basic order-theoretic structure of the corresponding sets of revealed cores is also analyzed

  16. Bose-Einstein correlations

    International Nuclear Information System (INIS)

    Two quite different but interconnected topics are covered: the Bose-Einstein effect in two-jet events at LEP, i.e. events with a single string structure, and a new test on hydrodynamical models. In this test the interferometrical correlator plays a key role and can be used to bring information on the matter evolution in time and space. A preliminary DELPHI analysis has however shown that the extraction of the two-particle correlation function is contaminated by large systematic uncertainties. Three different analysis, all using standard methods, give inconsistent results. Furthermore the two-particle correlation itself is shown to be due not only to Bose-Einstein correlations but also to the decay of heavy quark resonances, so the determination of the Bose-Einstein effect depends on the modelling of these other sources. This modelling is at the moment not accurate enough. More work is needed to clarify the situation. (author) 25 refs.; 16 figs.; 1 tab

  17. Pair Correlation Function Integrals

    DEFF Research Database (Denmark)

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

    2011-01-01

    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...

  18. Strongly Correlated Materials

    OpenAIRE

    Morosan, Emilia; Natelson, Douglas; Nevidomskyy, Andriy H.; Si, Qimiao

    2013-01-01

    Strongly correlated materials are profoundly affected by the repulsive electron-electron interaction. This stands in contrast to many commonly used materials such as silicon and aluminum, whose properties are comparatively unaffected by the Coulomb repulsion. Correlated materials often have remarkable properties and transitions between distinct, competing phases with dramatically different electronic and magnetic orders. These rich phenomena are fascinating from the basic science perspective ...

  19. Emerging Correlation Optics

    DEFF Research Database (Denmark)

    Angelsky, Oleg V.; Gbur, Gregory J.; Polyanskii, Peter; Hanson, Steen G.; Volyar, Alexander; Zimnyakov, Dmitry A.; Mokhun, Igor

    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....

  20. Correlation and Regression

    OpenAIRE

    O'Brien, Donal; Sharkey Scott, Pamela

    2012-01-01

    A correlation is a measure of the linear relationship between two variables. It is used when aresearcher wishes to describe the strength and direction of the relationship between twonormally continuous variables. The statistic obtained is Pearson’s product-momentcorrelation (r), and SPSS also provides the statistical significance of r. In addition, if theresearcher needs to explore the relationship between two variables while statisticallycontrolling for a third variable, partial correlation ...

  1. 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.

  2. 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.

  3. 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)

  4. 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

  5. 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.)

  6. Censored correlated cytokine concentrations

    DEFF Research Database (Denmark)

    Andersen, Andreas; Benn, Christine Stabell; Jørgensen, Mathias J;

    2013-01-01

    Interest in cytokines as markers for the function of the immune system is increasing. Methods quantifying cytokine concentrations are often subject to detection limits, which lead to non-detectable observations and censored distributions. When distributions are skewed, geometric mean ratios (GMRs......) can be used to describe the relative concentration between two cytokines, and the GMR ratio (GMRR) can be used to compare two groups. The problem is how to estimate GMRRs from censored distributions.We evaluated methods, including simple deletion and substitution, in simulated and real data. One...... method applies Tobit directly to the censored difference between the two cytokine log-concentrations (Diff). However, censoring is correlated to the outcome and is therefore not independent. The correlation increases as the correlation between the two log-concentrations decreases. We propose a Tobit...

  7. 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.

  8. Bias in Estimation and Hypothesis Testing of Correlation

    OpenAIRE

    Zimmerman D. W.; Zumbo B. D.; Williams R. H.

    2003-01-01

    This study examined bias in the sample correlation coefficient, r, and its correction by unbiased estimators. Computer simulations revealed that the expected value of correlation coefficients in samples from a normal population is slightly less than the population correlation, ρ, and that the bias is almost eliminated by an estimator suggested by R.A. Fisher and is more completely eliminated by a related estimator recommended by Olkin and Pratt. Transfor...

  9. 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....

  10. Correlation for aerosol sedimentation

    International Nuclear Information System (INIS)

    The fission product source term from a postulated light water reactor (LWR) accident has several components. One of these components is the suspended aerosols present in the atmosphere during containment degradation and failure. Sedimentation, inertial impaction, and Stefan-Nusselt flows are the dominant natural removal mechanisms in the containment atmosphere for the majority of the postulated LWR severe accidents. The sedimentation correlation described was developed for conditions applicable to the primary coolant system and containment under severe accident conditions. The correlation exists as a result of a unique nondimensional mass concentration versus nondimensional particle volume

  11. 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.

  12. Confinement from Correlation Functions

    CERN Document Server

    Fister, Leonard

    2013-01-01

    We compute the Polyakov loop potential in Yang--Mills theory from the fully dressed primitively divergent correlation functions only. This is done in a variety of functional approaches ranging from functional renormalisation group equations over Dyson--Schwinger equations to two-particle irreducible functionals. We present a confinement criterion that links the infrared behaviour of propagators and vertices to the Polyakov loop expectation value. The present work extends the works of [1-3] to general functional methods and sharpens the confinement criterion presented there. The computations are based on the thermal correlation functions in the Landau gauge calculated in [4-6].

  13. 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.

  14. Clustering of correlated networks

    OpenAIRE

    Dorogovtsev, S. N.

    2003-01-01

    We obtain the clustering coefficient, the degree-dependent local clustering, and the mean clustering of networks with arbitrary correlations between the degrees of the nearest-neighbor vertices. The resulting formulas allow one to determine the nature of the clustering of a network.

  15. Multivariate Intraclass Correlation.

    Science.gov (United States)

    Wiley, David E.; Hawkes, Thomas H.

    This paper is an explication of a statistical model which will permit an interpretable intraclass correlation coefficient that is negative, and a generalized extension of that model to cover a multivariate problem. The methodological problem has its practical roots in an attempt to find a statistic which could indicate the degree of similarity or…

  16. Modeling correlated human dynamics

    CERN Document Server

    Wang, Peng; Zhou, Tao; Wang, Bing-Hong

    2010-01-01

    Current models of human activity are fundamentally stochastic such as the priority-queue model and the cascading nonhomogeneous poisson model, partly because of the lack of short-term correlation in some human activities. In this paper, we study the activity pattern of individual blog-posting and find significant short-term correlation as well as the heavy-tailed nature. Interestingly, when the time lag K is less than 10 the correlation coefficient decays as a power law and when K is more than 10 it decrease exponentially. Moreover, we also find that the exponents of the interevent time distribution depend on the Activity of the users. We think there is another kind of human activity which is driven by personal interest/preference and is characterized by the correlation and this dependent relationship. A simple model based on the personal preference was supposed by us. Different from the previous studies which only focused on the exponent, our model reproduced all these three key features: the heavy-tails, th...

  17. Maximum abundant isotopes correlation

    International Nuclear Information System (INIS)

    The neutron excess of the most abundant isotopes of the element shows an overall linear dependence upon the neutron number for nuclei between neutron closed shells. This maximum abundant isotopes correlation supports the arguments for a common history of the elements during nucleosynthesis. (Auth.)

  18. 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)

  19. 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.

  20. 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...

  1. 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).

  2. Generalized reflood heat transfer correlation

    International Nuclear Information System (INIS)

    A reflood heat transfer correlation has been developed from the FLECHT reflood data for different axial power shapes and arbitrary variable flooding rate conditions. This correlation consists of a separate quench correlation and a heat transfer coefficient correlation. The reflood correlation predicts both the quench front, location and the heat transfer coefficient above the quench front.. The reflood heat transfer correlation prediction is in good agreement with both the cosine and the skewed axial power shape FLECHT reflooding data. (author)

  3. 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

  4. 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.

  5. 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.

  6. 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)

  7. Wind and Yaw correlation

    DEFF Research Database (Denmark)

    Kock, Carsten Weber; Vesth, Allan

    The report describes measurements carried out on a given wind turbine. A comparison between wind speed on the metmast and Nacelle Windspeed are made and the results are presented on graphs and in a table. The data used for the comparison are identical with the data used for the Risø-I-3246(EN) po......) power curve report. The measurements are carried out in accordance to Ref. [1] and the wind and yaw correlation is analyzed in accordance to Ref. [2]....

  8. Correlation functions of BCFT

    OpenAIRE

    Setare, M.R.(Department of Science, University of Kurdistan, Campus of Bijar, Bijar, Iran); Kamali, V.

    2011-01-01

    Boundary conformal field theory (BCFT) is the study of conformal field theory (CFT) on manifolds with a boundary. We can use conformal symmetry to constrain correlation functions of conformal invariant fields. We compute two-point and three-point functions of conformal invariant fields which live in semi-infinite space. For a situation with a boundary condition in surface $z=\\bar{z}$ ($t=0$), the results agree with gravity dual results. We also explore representations of conformal group in tw...

  9. Multiple correlation function approach

    OpenAIRE

    Grebenkov, Denis S.

    2016-01-01

    The multiple correlation function approach is briefly presented and applied to investigate spin-echo signal attenuation due to restricted diffusion in simple geometries (slab, cylinder, and sphere) in the presence of surface relaxation. Exact and explicit representations for the zeroth and second moments of the total phase accumulated by diffusing spins are derived by using the Laplace transform summation technique. Within the Gaussian phrase approximation, these two moments determine the ...

  10. 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.

  11. Biological Correlates of Empathy

    OpenAIRE

    E. Timucin Oral; Kursat Altınbas; Sinan Guloksuz; Serap Ozcetinkaya

    2010-01-01

    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...

  12. Biological Correlates of Empathy

    OpenAIRE

    Altınbaş, Kürşat; Gülöksüz, Sinan; Özçetinkaya, Serap; Oral, E.Timuçin

    2010-01-01

    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 psychot...

  13. Implied Basket Correlation Dynamics

    OpenAIRE

    Härdle, Wolfgang Karl; Silyakova, Elena

    2012-01-01

    Equity basket correlation is an important risk factor. It characterizes the strength of linear dependence between assets and thus measures the degree of portfolio diversification. It can be estimated both under the physical measure from return series, and under the risk neutral measure from option prices. The difference between the two estimates motivates a so called "dispersion strategy". We study the performance of this strategy on the German market over the recent 2 years and propose sever...

  14. 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

  15. Energy calibration via correlation

    Science.gov (United States)

    Maier, Daniel; Limousin, Olivier

    2016-03-01

    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 241Am 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 less than ~ 0.1 keV. Energy calibration via correlation can be applied to any kind of calibration spectra and shows a robust behavior at low counting statistics. It enables a fast and accurate calibration that can be used to monitor the spectroscopic properties of a detector system in near realtime.

  16. PREFACE: Strongly correlated electron systems Strongly correlated electron systems

    Science.gov (United States)

    Saxena, Siddharth S.; Littlewood, P. B.

    2012-07-01

    make use of 'small' electrons packed to the highest possible density. These are by definition 'strongly correlated'. For example: good photovoltaics must be efficient optical absorbers, which means that photons will generate tightly bound electron-hole pairs (excitons) that must then be ionised at a heterointerface and transported to contacts; efficient solid state refrigeration depends on substantial entropy changes in a unit cell, with large local electrical or magnetic moments; efficient lighting is in a real sense the inverse of photovoltaics; the limit of an efficient battery is a supercapacitor employing mixed valent ions; fuel cells and solar to fuel conversion require us to understand electrochemistry on the scale of a single atom; and we already know that the only prospect for effective high temperature superconductivity involves strongly correlated materials. Even novel IT technologies are now seen to have value not just for novel function but also for efficiency. While strongly correlated electron systems continue to excite researchers and the public alike due to the fundamental science issues involved, it seems increasingly likely that support for the science will be leveraged by its impact on energy and sustainability. Strongly correlated electron systems contents Strongly correlated electron systemsSiddharth S Saxena and P B Littlewood Magnetism, f-electron localization and superconductivity in 122-type heavy-fermion metalsF Steglich, J Arndt, O Stockert, S Friedemann, M Brando, C Klingner, C Krellner, C Geibel, S Wirth, S Kirchner and Q Si High energy pseudogap and its evolution with doping in Fe-based superconductors as revealed by optical spectroscopyN L Wang, W Z Hu, Z G Chen, R H Yuan, G Li, G F Chen and T Xiang Structural investigations on YbRh2Si2: from the atomic to the macroscopic length scaleS Wirth, S Ernst, R Cardoso-Gil, H Borrmann, S Seiro, C Krellner, C Geibel, S Kirchner, U Burkhardt, Y Grin and F Steglich Confinement of chiral magnetic

  17. Wavelet Correlation Coefficient of 'strongly correlated' financial time series

    OpenAIRE

    Ashok Razdan

    2003-01-01

    In this paper we use wavelet concepts to show that correlation coefficient between two financial data's is not constant but varies with scale from high correlation value to strongly anti-correlation value This studies is important because correlation coefficient is used to quantify degree of independence between two variables. In econophysics correlation coefficient forms important input to evolve hierarchial tree and minimum spanning tree of financial data.

  18. 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.

  19. 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...

  20. 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…

  1. 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

  2. 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. ....... Given advances in evolutionary psychology and neuroscience, I propose one way to model those evolutionary pressures that will hopefully prove useful in expanding normative economics.......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...

  3. Lipid sorting revealed by SANS

    International Nuclear Information System (INIS)

    We have investigated the lipid sorting in a binary small unilamellar vesicle (SUV) composed of cone-shaped (1,2-dihexanoyl-sn-glycero-3-phosphocholine: DHPC) and cylinder-shaped (1,2-dipalmitoyl-sn-glycero-3-phosphocholine: DPPC) lipids. In order to reveal the lipid sorting we adopted a contrast matching technique of small angle neutron scattering (SANS), which extracts the distribution of deuterated lipids in the bilayer quantitatively. The SANS profile of deuterated SUVs at the contrast matching condition showed a characteristic scattering profile, indicating an asymmetric distribution of cone-shaped lipids in the bilayer. The fitting of the observed SANS profile revealed that most DHPC molecules are localized in the outer leaflet, which supports that the shape of the lipid is strongly coupled with the membrane curvature. We compared the obtained asymmetric distribution of the cone-shaped lipids in the bilayer with the theoretical prediction based on the curvature energy model. (author)

  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)

    Secrecy and the act of concealing and revealing knowledge effectually segregate the initiated and the uninitiated. The act of sharing or hiding knowledge plays a central role in all human relations private or public, political or religious. This volume explores the concept of secrecy and its impl...... the concept of secrecy and its potential for illuminating the agendas behind identity constructions, political propaganda, literary works, religous practices and shared history....

  6. 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.

  7. Symmetric Gini Covariance and Correlation

    OpenAIRE

    Sang, Yongli; Dang, Xin; Sang, Hailin

    2016-01-01

    Standard Gini covariance and Gini correlation play important roles in measuring the dependence of random variables with heavy tails. However, the asymmetry brings a substantial difficulty in interpretation. In this paper, we propose a symmetric Gini-type covariance and a symmetric Gini correlation ($\\rho_g$) based on the joint rank function. The proposed correlation $\\rho_g$ is more robust than the Pearson correlation but less robust than the Kendall's $\\tau$ correlation. We establish the rel...

  8. 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

  9. 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

  10. Unbalanced Homodyne Correlation Measurements

    Science.gov (United States)

    Kühn, B.; Vogel, W.

    2016-04-01

    A method is introduced that allows one to measure normal-ordered moments of the displaced photon-number operator up to higher orders, without the need of photon-number resolving detectors. It is based on unbalanced homodyne correlation measurements, with the local oscillator being replaced by a displaced dephased laser. The measured moments yield a simple approximation of quasiprobabilities, representing the full quantum state. Quantum properties of light are efficiently certified through normal-ordered observables directly accessible by our method, which is illustrated for a weakly squeezed vacuum and a single-photon-added thermal state.

  11. 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.

  12. 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...

  13. 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

  14. Correlative Light and Electron Microscopy Reveals the HAS3-Induced Dorsal Plasma Membrane Ruffles

    OpenAIRE

    Kirsi Rilla; Arto Koistinen

    2015-01-01

    Hyaluronan is a linear sugar polymer synthesized by three isoforms of hyaluronan synthases (HAS1, 2, and 3) that forms a hydrated scaffold around cells and is an essential component of the extracellular matrix. The morphological changes of cells induced by active hyaluronan synthesis are well recognized but not studied in detail with high resolution before. We have previously found that overexpression of HAS3 induces growth of long plasma membrane protrusions that act as platforms for hyaluro...

  15. Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.

    Science.gov (United States)

    Ye, Zhenqing; Chen, Zhong; Lan, Xun; Hara, Stephen; Sunkel, Benjamin; Huang, Tim H-M; Elnitski, Laura; Wang, Qianben; Jin, Victor X

    2014-03-01

    Alternative splicing (AS), in higher eukaryotes, is one of the mechanisms of post-transcriptional regulation that generate multiple transcripts from the same gene. One particular mode of AS is the skipping event where an exon may be alternatively excluded or constitutively included in the resulting mature mRNA. Both transcript isoforms from this skipping event site, i.e. in which the exon is either included (inclusion isoform) or excluded (skipping isoform), are typically present in one cell, and maintain a subtle balance that is vital to cellular function and dynamics. However, how the prevailing conditions dictate which isoform is expressed and what biological factors might influence the regulation of this process remain areas requiring further exploration. In this study, we have developed a novel computational method, graph-based exon-skipping scanner (GESS), for de novo detection of skipping event sites from raw RNA-seq reads without prior knowledge of gene annotations, as well as for determining the dominant isoform generated from such sites. We have applied our method to publicly available RNA-seq data in GM12878 and K562 cells from the ENCODE consortium and experimentally validated several skipping site predictions by RT-PCR. Furthermore, we integrated other sequencing-based genomic data to investigate the impact of splicing activities, transcription factors (TFs) and epigenetic histone modifications on splicing outcomes. Our computational analysis found that splice sites within the skipping-isoform-dominated group (SIDG) tended to exhibit weaker MaxEntScan-calculated splice site strength around middle, 'skipping', exons compared to those in the inclusion-isoform-dominated group (IIDG). We further showed the positional preference pattern of splicing factors, characterized by enrichment in the intronic splice sites immediately bordering middle exons. Finally, our analysis suggested that different epigenetic factors may introduce a variable obstacle in the process of exon-intron boundary establishment leading to skipping events. PMID:24369421

  16. Developing Neocortex Organization and Connectivity in Cats Revealed by Direct Correlation of Diffusion Tractography and Histology

    OpenAIRE

    Takahashi, Emi; Dai, Guangping; Glenn D. Rosen; Wang, Ruopeng; Ohki, Kenichi; Rebecca D. Folkerth; Galaburda, Albert M.; Wedeen, Van J.; P. Ellen Grant

    2010-01-01

    The immature cortex (cortical plate [CP]) and underlying subplate (SP), a transient cell layer just below the CP, play critical roles in the formation of intracerebral connections. The purpose of this study was to examine the diffusion characteristics of the developing cortex and subcortical structures and compare to histology. We obtained high-resolution diffusion spectrum images of postnatal day (P) 0 (newborn), P35 (pediatric), and P100 (adult) cat brains, performed tractography analysis, ...

  17. 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.)

  18. Endophenotyping reveals differential phenotype-genotype correlations between myopia-associated polymorphisms and eye biometric parameters

    OpenAIRE

    Chen, Jian Huan; Chen, Haoyu; Huang, Shulan; Lin, Jianwei; Zheng, Yuqian; Xie, Mingliang; Lin, Wenjie; Pang, Chi Pui; ZHANG, MINGZHI

    2012-01-01

    Purpose To investigate the association with ocular biometric parameters in myopia-associated single nucleotide polymorphisms (SNPs) of the gap junction protein delta 2 (GJD2), insulin-like growth factor-1 (IGF1) and hepatocyte growth factor (HGF) genes in two geographically different Chinese cohorts. Methods In 814 unrelated Han Chinese individuals aged above 50 years including 362 inland residents and 432 island dwellers, comprehensive ophthalmic examinations were performed. Three SNPs, incl...

  19. 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.)

  20. 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...

  1. Real-time correlates of phonological quantity reveal unity of tonal and non-tonal languages.

    Directory of Open Access Journals (Sweden)

    Juhani Järvikivi

    Full Text Available Discrete phonological phenomena form our conscious experience of language: continuous changes in pitch appear as distinct tones to the speakers of tone languages, whereas the speakers of quantity languages experience duration categorically. The categorical nature of our linguistic experience is directly reflected in the traditionally clear-cut linguistic classification of languages into tonal or non-tonal. However, some evidence suggests that duration and pitch are fundamentally interconnected and co-vary in signaling word meaning in non-tonal languages as well. We show that pitch information affects real-time language processing in a (non-tonal quantity language. The results suggest that there is no unidirectional causal link from a genetically-based perceptual sensitivity towards pitch information to the appearance of a tone language. They further suggest that the contrastive categories tone and quantity may be based on simultaneously co-varying properties of the speech signal and the processing system, even though the conscious experience of the speakers may highlight only one discrete variable at a time.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Paths correlation matrix.

    Science.gov (United States)

    Qian, Weixian; Zhou, Xiaojun; Lu, Yingcheng; Xu, Jiang

    2015-09-15

    Both the Jones and Mueller matrices encounter difficulties when physically modeling mixed materials or rough surfaces due to the complexity of light-matter interactions. To address these issues, we derived a matrix called the paths correlation matrix (PCM), which is a probabilistic mixture of Jones matrices of every light propagation path. Because PCM is related to actual light propagation paths, it is well suited for physical modeling. Experiments were performed, and the reflection PCM of a mixture of polypropylene and graphite was measured. The PCM of the mixed sample was accurately decomposed into pure polypropylene's single reflection, pure graphite's single reflection, and depolarization caused by multiple reflections, which is consistent with the theoretical derivation. Reflection parameters of rough surface can be calculated from PCM decomposition, and the results fit well with the theoretical calculations provided by the Fresnel equations. These theoretical and experimental analyses verify that PCM is an efficient way to physically model light-matter interactions. PMID:26371930

  7. 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.

  8. 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.

  9. 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.

  10. Understanding Correlations: Two Computer Exercises.

    Science.gov (United States)

    Goldstein, Miriam D.; Strube, Michael J.

    1995-01-01

    Describes two QuickBASIC programs that provide students direct experience with interpreting correlation scatter-plots. Maintains that the programs can be used in classroom exercises to highlight factors that influence the size of a Pearson correlation coefficient. (CFR)

  11. Magnitude correlations in global seismicity

    International Nuclear Information System (INIS)

    By employing natural time analysis, we analyze the worldwide seismicity and study the existence of correlations between earthquake magnitudes. We find that global seismicity exhibits nontrivial magnitude correlations for earthquake magnitudes greater than Mw6.5.

  12. 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.

  13. The 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. Important insights were obtained from tracer experiments, but the full complexity of plutonium chemistry was not revealed until macroscopic amounts (milligrams) became available. Because processes for separation from fission products were aqueous solution based, 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, it was found that 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 will be reported

  14. Archimedes: Accelerator Reveals Ancient Text

    International Nuclear Information System (INIS)

    Archimedes (287-212 BC), who is famous for shouting 'Eureka' (I found it) is considered one of the most brilliant thinkers of all times. The 10th-century parchment document known as the 'Archimedes Palimpsest' is the unique source for two of the great Greek's treatises. Some of the writings, hidden under gold forgeries, have recently been revealed at the Stanford Synchrotron Radiation Laboratory at SLAC. An intense x-ray beam produced in a particle accelerator causes the iron in original ink, which has been partly erased and covered, to send out a fluorescence glow. A detector records the signal and a digital image showing the ancient writings is produced. Please join us in this fascinating journey of a 1,000-year-old parchment from its origin in the Mediterranean city of Constantinople to a particle accelerator in Menlo Park.

  15. 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...

  16. 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 ...

  17. 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...

  18. 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)

  19. 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.

  20. Towards jet tomography: γ-hadron correlations

    International Nuclear Information System (INIS)

    Hard pQCD processes taking place in ultrarelativistic heavy-ion collisions are a well-calibrated probe. It is believed that the interaction with the surrounding medium of outgoing partons from a hard vertex is capable of revealing details of the medium. We demonstrate that correlation measurements of hard photon-hadron back-to-back coincidences are a tool suitable for extracting such tomographic information. Introducing the concept of averaged energy loss probability distributions, we first argue that almost no information about details of the medium evolution is reflected in the nuclear suppression factor RAA. Thus, a wide variety of jet quenching scenarios and geometries are compatible with the measured data. This problem can be overcome by a γ-hadron correlation measurement. We show that averaged probability distributions for quarks are accessible experimentally, and we sketch an analysis procedure capable of distinguishing different energy loss scenarios leading to the same nuclear suppression factor

  1. 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

  2. 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

  3. CORRELATION AND PATH COEFFICIENT ANALYSIS IN GROUNDNUT (ARACHIS HYPOGAEA L.)

    OpenAIRE

    C. Pavan Kumar; R Rekha; O. Venkateswarulu; R P Vasanthi

    2014-01-01

    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 percentag...

  4. Nonlinear correlations of daily temperature records over land

    OpenAIRE

    Bartos, I.; I. M. Jánosi

    2006-01-01

    We present a near global statistics on the correlation properties of daily temperature records. Data from terrestrial meteorological stations in the Global Daily Climatology Network are analyzed by means of detrended fluctuation analysis. Long-range temporal correlations extending up to several years are detected for each station. In order to reveal nonlinearity, we evaluated the magnitude of daily temperature changes (volatility) by the same method. The results clearly indi...

  5. 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

  6. 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.

  7. 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.

  8. 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...

  9. Modeling Complex System Correlation Using Detrended Cross-Correlation Coefficient

    OpenAIRE

    2014-01-01

    The understanding of complex systems has become an area of active research for physicists because such systems exhibit interesting dynamical properties such as scale invariance, volatility correlation, heavy tails, and fractality. We here focus on traffic dynamic as an example of a complex system. By applying the detrended cross-correlation coefficient method to traffic time series, we find that the traffic fluctuation time series may exhibit cross-correlation characteristic. Further, we show...

  10. Correlation Structures of Correlated Binomial Models and Implied Default Distribution

    OpenAIRE

    Mori, S.; K. Kitsukawa; M. Hisakado

    2006-01-01

    We show how to analyze and interpret the correlation structures, the conditional expectation values and correlation coefficients of exchangeable Bernoulli random variables. We study implied default distributions for the iTraxx-CJ tranches and some popular probabilistic models, including the Gaussian copula model, Beta binomial distribution model and long-range Ising model. We interpret the differences in their profiles in terms of the correlation structures. The implied default distribution h...

  11. Reveal for Salmonella test system.

    Science.gov (United States)

    Bird, C B; Miller, R L; Miller, B M

    1999-01-01

    The Reveal for Salmonella (RSS) test system is a presumptive qualitative test that detects the presence of Salmonella organisms in foods within 21 h total testing time, allowing the user to release negative products 24 h earlier than when using other rapid test kits. Foods are enriched with a proprietary resuscitation medium called Revive and then selectively enriched with either Selenite Cystine or Rappaport-Vassiliadis selective media. The enriched culture is used to inoculate the RSS detection device, which initiates a lateral flow through a reagent zone containing anti-Salmonella antibodies conjugated to colloidal gold particles that capture antigens present in the culture. The antigen-antibody complex migrates farther and is captured by an additional anti-Salmonella antibody, causing the colloidal gold to precipitate and form a visual line, indicating a positive result. A procedural control line also will form regardless of the presence of Salmonella organisms to indicate the test is working properly. Existing AOAC Official Methods for Salmonella organisms require a 48 h enrichment before testing. Hence, a food product has to be held before release, adding extra cost to the company and the consumer. The RSS test system was evaluated by quantitative spiking studies. Although AOAC encourages inclusion of naturally contaminated foods, almost all microbiological AOAC validation studies have been performed with artificially contaminated foods for absolute control over the study. The RSS test system is designed to test many food types for Salmonella organisms and has a limit of detection of 5-10 colony-forming units (cfu)/25 g with a false-negative rate of < 1% and a false-positive rate of < 5.0%. It showed an 81% overall agreement with the traditional procedure of the U.S. Department of Agriculture's Food Safety Inspection Service. PMID:10367381

  12. 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.

  13. INTERPRETING THE DISTANCE CORRELATION RESULTS FOR THE COMBO-17 SURVEY

    International Nuclear Information System (INIS)

    The accurate classification of galaxies in large-sample astrophysical databases of galaxy clusters depends sensitively on the ability to distinguish between morphological types, especially at higher redshifts. This capability can be enhanced through a new statistical measure of association and correlation, called the distance correlation coefficient, which has more statistical power to detect associations than does the classical Pearson measure of linear relationships between two variables. The distance correlation measure offers a more precise alternative to the classical measure since it is capable of detecting nonlinear relationships that may appear in astrophysical applications. We showed recently that the comparison between the distance and Pearson correlation coefficients can be used effectively to isolate potential outliers in various galaxy data sets, and this comparison has the ability to confirm the level of accuracy associated with the data. In this work, we elucidate the advantages of distance correlation when applied to large databases. We illustrate how the distance correlation measure can be used effectively as a tool to confirm nonlinear relationships between various variables in the COMBO-17 database, including the lengths of the major and minor axes, and the alternative redshift distribution. For these outlier pairs, the distance correlation coefficient is routinely higher than the Pearson coefficient since it is easier to detect nonlinear relationships with distance correlation. The V-shaped scatter plots of Pearson versus distance correlation coefficients also reveal the patterns with increasing redshift and the contributions of different galaxy types within each redshift range

  14. 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...

  15. 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...

  16. Constrained correlation dynamics of QCD

    International Nuclear Information System (INIS)

    The complete version of constrained correlation dynamics of SU(N) gauge theories in temporal gauge and canonical form has been formulated in three steps. (1) With the aid of generating-functional technique and in the framework of correlation dynamics, a closed set of equations of motion for correlation Green's functions have been established. (2) Gauge constraint conditions are analysed by means of Dirac theory. The algebraic representations of Gauss law and Ward identities are given. In accordance with the truncation approximations of correlation dynamics, the conserved Gauss law and Ward identities due to residual gauge invariance are shifted to initial value problems. (3) The equations of motion for multi-time correlation Green's functions have been transformed into those for equal-time correlation Green's functions. In two-body truncation approximation, a tractable set of equations of motion, Gauss law, and Ward identities are given explicitly

  17. 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

  18. 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...

  19. Intermittency analysis of correlated data

    International Nuclear Information System (INIS)

    We describe the method of the analysis of the dependence of the factorial moments on the bin size in which the correlations between the moments computed for different bin sizes are taken into account. For large multiplicity nucleus-nucleus data inclusion of the correlations does not change the values of the slope parameter, but gives errors significantly reduced as compared to the case of fits with no correlations. (author)

  20. 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...

  1. Programming services with correlation sets

    DEFF Research Database (Denmark)

    Montesi, Fabrizio; Carbone, Marco

    2011-01-01

    Correlation sets define a powerful mechanism for routing incoming communications to the correct running session within a server, by inspecting the content of the received messages. We present a language for programming services based on correlation sets taking into account key aspects of service...... properties of programs with respect to correlation sets. We provide an implementation as an extension of the JOLIE language and apply it to a nontrivial real-world example of a fully-functional distributed user authentication system....

  2. Interpretation of correlation analysis results

    OpenAIRE

    Kılıç, Selim

    2012-01-01

    Correlation analysis is used to quantify the degree of linear association between two variables. Correlation coefficient is showed as “r” and it may have values between (-) 1 and (+)1. The symbols (-) or (+) in front of “r coefficient” show the direction of correlation. The direction of association does not affect the strength of association. A “ r coefficient” which is equal or greater than 0.70 is accepted as a good association. Correlation coeefficient only remarks the strength of associat...

  3. Correlation functions for a strongly correlated boson system

    CERN Document Server

    Bogolyubov, N N; Kitanine, N A

    1997-01-01

    The correlation functions for a strongly correlated exactly solvable one-dimensional boson system on a finite chain as well as in the thermodynamic limit are calculated explicitly. This system which we call the phase model is the strong coupling limit of the integrable q-boson hopping model. The results are presented as determinants.

  4. 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.

  5. Charge order, superconducting correlations, and positive muons

    Energy Technology Data Exchange (ETDEWEB)

    Sonier, J.E., E-mail: jsonier@sfu.ca

    2015-02-15

    The recent discoveries of short-range charge-density wave order in the normal state of several hole-doped cuprate superconductors constitute a significant addition to the known intrinsic properties of these materials. Besides likely being associated with the normal-state pseudogap, the charge-density wave order presumably influences the build-up of known superconducting correlations as the temperature is lowered toward the superconducting state. As a pure magnetic probe, muon spin rotation (μ SR) is not directly sensitive to charge order, but may sense its presence via the effect it has on the magnetic dipolar coupling of the muon with the host nuclei at zero or low magnetic field. At higher field where μ SR is completely blind to the effects of charge order, experiments have revealed a universal inhomogeneous normal-state response extending to temperatures well above T{sub c}. The measured inhomogeneous line broadening has been attributed to regions of superconducting correlations that exhibit varying degrees of fluctuation diamagnetism. Here, the compatibility of these results with other measurements showing charge order correlations or superconducting fluctuations above T{sub c} is discussed. - Highlights: • Superconducting fluctuations in high-T cuprates probed by positive muons are discussed. • Superconducting fluctuations are detected at higher temperatures than by other methods. • The muon experiments indicate that the superconducting fluctuations are inhomogeneous. • The compatibility with short-range charge order in the normal state is considered.

  6. 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.

  7. Quantum correlations are not contained in the initial state

    OpenAIRE

    Cabello, Adan

    1999-01-01

    Two proofs are presented which show that quantum mechanics is incompatible with the following assumption: all possible correlations between subsystems of an individual isolated composite quantum system are contained in the initial quantum state of the whole system, although just a subset of them is revealed by the actual experiment.

  8. Electron correlation in the continuum

    International Nuclear Information System (INIS)

    We consider a class of problems, notably double ionization, which require accurate descriptions of correlation in both the initial and final states. Methods are presented for representing correlated wavefunctions on a basis spline lattice, and for calculating bound-continuum transition probabilities. 13 refs

  9. Correlation functions of Coulomb pair

    International Nuclear Information System (INIS)

    The correlation functions of two electrostatically interacting particles have been obtained for the first time, by using the direct algebraic method for finding the cross-correlation functions. The efficiency of this method has been demonstrated by finding almost all unknown elements of the decomposition matrices in the second-order approximation

  10. Heteronuclear Long-Range Correlation

    DEFF Research Database (Denmark)

    Sørensen, Ole W.

    The lecture will cover heteronuclear long-range correlation techniques like HMBC, H2BC, and HAT HMBC with the emphasis on determining the number of covalent bonds between two spins being correlated. H2BC and HMBC spectra are quite complementary as a peak can be strong in one of the two spectra and...

  11. Correlators of the phase model

    CERN Document Server

    Bogolyubov, N N; Kitanine, N A

    1996-01-01

    We introduce the phase model on a lattice and solve it using the algebraic Bethe ansatz. Time-dependent temperature correlation functions of phase operators and the "darkness formation probability" are calculated in the thermodynamical limit. These results can be used to construct integrable equations for the correlation functions and to calculate there asymptotics.

  12. Correlation Weights in Multiple Regression

    Science.gov (United States)

    Waller, Niels G.; Jones, Jeff A.

    2010-01-01

    A general theory on the use of correlation weights in linear prediction has yet to be proposed. In this paper we take initial steps in developing such a theory by describing the conditions under which correlation weights perform well in population regression models. Using OLS weights as a comparison, we define cases in which the two weighting…

  13. Regularized Generalized Canonical Correlation Analysis

    Science.gov (United States)

    Tenenhaus, Arthur; Tenenhaus, Michel

    2011-01-01

    Regularized generalized canonical correlation analysis (RGCCA) is a generalization of regularized canonical correlation analysis to three or more sets of variables. It constitutes a general framework for many multi-block data analysis methods. It combines the power of multi-block data analysis methods (maximization of well identified criteria) and…

  14. 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.

  15. 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.

  16. Short range correlations in nuclei

    International Nuclear Information System (INIS)

    Studying nucleon-nucleon (NN) correlated pairs will teach us a great deal about the high momentum part of the nuclear wave function,the short range part of the NN interaction, and the nature of cold dense nuclear matter. These correlations are similar in all nuclei, differing only in magnitude. High momentum nucleons, p > pfermi, all have a correlated partner with approximately equal and opposite momentum. At pair relative momenta of 300 rel < 500 MeV/c, these correlated pairs are dominated by tensor correlations. This is shown by the dominance of pn over pp pairs at pair total momentum and by the parity of pn to pp pairs at large pair total momentum. (author)

  17. 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...

  18. Correlation Functions and Power Spectra

    DEFF Research Database (Denmark)

    Larsen, Jan

    2006-01-01

    possible to define correlation functions and associated spectra for aperiodic, periodic and random signals although the interpretation is different. Moreover, we will discuss correlation functions when mixing these basic signal types. In addition, the note include several examples for the purpose of......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 and...... spectra for discrete-time and continuous-time (analog) signals are pretty similar. Consequently, we confine the discussion mainly to real discrete-time signals. The Appendix contains detailed definitions and properties of correlation functions and spectra for analog as well as discrete-time signals. It is...

  19. Regional brain activity correlates of nicotine dependence.

    Science.gov (United States)

    Rose, Jed E; Behm, Frederique M; Salley, Alfred N; Bates, James E; Coleman, R Edward; Hawk, Thomas C; Turkington, Timothy G

    2007-12-01

    Fifteen smokers participated in a study investigating brain correlates of nicotine dependence. Dependence was reduced by having subjects switch to denicotinized cigarettes for 2 weeks while wearing nicotine skin patches. Positron emission tomography (PET) scans assessed regional cerebral metabolic rate for glucose (rCMRglc) after overnight nicotine abstinence on three occasions: (1) at baseline; (2) after 2 weeks of exposure to denicotinized cigarettes+nicotine patches; and (3) 2 weeks after returning to smoking the usual brands of cigarettes. Craving for cigarettes and scores on the Fagerström Test of Nicotine Dependence (FTND) questionnaire decreased at the second session relative to the first and last sessions. Regional brain metabolic activity (normalized to whole brain values) at session 2 also showed a significant decrease in the right hemisphere anterior cingulate cortex. Exploratory post hoc analyses showed that the change in craving across sessions was negatively correlated with the change in rCMRglc in several structures within the brain reward system, including the ventral striatum, orbitofrontal cortex and pons. The between-session difference in thalamus activity (right hemisphere) was positively correlated with the difference in FTND scores. Correlational analyses also revealed that reported smoking for calming effects was associated with a decrease (at session 2) in thalamus activity (bilaterally) and with an increase in amygdala activity (left hemisphere). Reported smoking to enhance pleasurable relaxation was associated with an increase in metabolic activity of the dorsal striatum (caudate, putamen) at session 2. These findings suggest that reversible changes in regional brain metabolic activity occur in conjunction with alterations in nicotine dependence. The results also highlight the likely role of thalamic gating processes as well as striatal reward and corticolimbic regulatory pathways in the maintenance of cigarette addiction. PMID:17356570

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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 fo...... found a "universal" scaling relationship, where the f-electron bandwidth reduction due to correlation effects is shown to depend only upon the local density approximation (LDA) bandwidth and is otherwise independent of crystal structure and lattice constant....

  6. Quantum Correlations in Quantum Cloning

    CERN Document Server

    Chakrabarty, Indranil

    2010-01-01

    We utilize quantum discord to charecterize the correlation present in Buzek-Hillery quantum copying machine \\cite{bh} (not necessarily universal quantum cloning machine). In other words we quantify the correlation present beetween the original and the replicated copy of the quantum state obtained at the outport port, Interestingly, we find some domain of the machine parameter, for which the quantum disord is non negative even in the mere absence of entanglement. These non zero values of the quantum discord is a strong signature for the presence of non classical correlations. This is one step forward evidence in the support of the fact that quantum discord and entanglement are not synonymous.

  7. Correlation among oxygen vacancies in bismuth titanate ferroelectric ceramics

    International Nuclear Information System (INIS)

    Pure Bi4Ti3O12 ceramics were prepared using the conventional solid-state reaction method and their dielectric properties were investigated. A dielectric loss peak with the relaxation-type characteristic was observed at about 370 K at 100 Hz frequency. This peak was confirmed to be associated with the migration of oxygen vacancies inside ceramics. The Cole-Cole fitting to this peak reveals a strong correlation among oxygen vacancies and this strong correlation is considered to commonly exist among oxygen vacancies in ferroelectrics. Therefore, the migration of oxygen vacancies in ferroelectric materials would demonstrate a collective behavior instead of an individual one due to this strong correlation. Furthermore, this correlation is in proportion to the concentration and in inverse proportion to the activation energy of oxygen vacancies. These results could be helpful to the understanding of the fatigue mechanisms in ferroelectric materials

  8. 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.

  9. 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

  10. Organizational Design Correlates of Entrepreneurship

    DEFF Research Database (Denmark)

    Foss, Nicolai Juul; Lyngsie, Jacob; Zahra, Shaker A.

    2015-01-01

    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...

  11. Largescale QSO - Galaxy Correlations Revisited

    Science.gov (United States)

    Bartelmann, M.; Schneider, P.

    1993-04-01

    Fugmann (1990) claimed indications for correlations between Lick galaxies and high-redshift, radio-loud background sources. We re- analyze these correlations using an improved statistical method based on Spearman's rank-order test, which we have introduced recently (Bartelmann & Schneider 1993). To our surprise, we are not able to reproduce Fugmann's results, but we detect a significant correlation between moderate-redshift sources from the 1-Jansky catalog and Lick galaxies, which increases when we apply an optical flux limit to the source sample. We interpret these empirical results in terms of an amplification bias caused by gravitational light deflection by dark matter; in particular, we argue that the observed large-scale QSO-galaxy correlations can provide a proof for the association of luminous matter (galaxies) with dark matter.

  12. 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...

  13. Conformity, Equity and Correlated Equilibrium

    OpenAIRE

    Edward Cartwright; Myrna Wooders

    2008-01-01

    We explore the potential for correlated equilibrium to capture conformity to norms and the coordination of behavior within social groups. Given a partition of players into social groups we propose three properties one may expect of a correlated equilibrium: within-group anonymity, group independence and stereotyped beliefs. Within-group anonymity requires that players within the same social group have equal opportunities and equal payoffs. Group independence requires that there be no correlat...

  14. 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 ...

  15. Spatiotemporal correlations of aftershock sequences

    OpenAIRE

    Peixoto, Tiago P.; Doblhoff-Dier, Katharina; 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 H...

  16. Correlation Functions and Power Spectra

    OpenAIRE

    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 and spectra for discrete-time and continuous-time (analog) signals are pretty similar. Consequently, we confine the discussion mainly to real discrete-time signals. The Appendix contains detailed defin...

  17. Resistant Multiple Sparse Canonical Correlation

    OpenAIRE

    Coleman, Jacob; Replogle, Joseph; Chandler, Gabriel; Hardin, Johanna

    2014-01-01

    Canonical Correlation Analysis (CCA) is a multivariate technique that takes two datasets and forms the most highly correlated possible pairs of linear combinations between them. Each subsequent pair of linear combinations is orthogonal to the preceding pair, meaning that new information is gleaned from each pair. By looking at the magnitude of coefficient values, we can find out which variables can be grouped together, thus better understanding multiple interactions that are otherwise difficu...

  18. 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...

  19. 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

  20. Classical, quantum and superquantum correlations

    CERN Document Server

    Ghirardi, GianCarlo

    2012-01-01

    A deeper understanding of the origin of quantum correlations is expected to shred light on the physical principles underlying quantum mechanics. In this work, we reconsider the possibility of devising "crypto-nonlocal theories", using a terminology firstly introduced by Leggett. We generalize and simplify the investigations on this subject which can be found in the literature. At their deeper level, such theories allow nonlocal correlations which can overcome the quantum limit.

  1. Classical, Quantum and Superquantum Correlations

    Science.gov (United States)

    Ghirardi, Giancarlo; Romano, Raffaele

    2013-01-01

    A deeper understanding of the origin of quantum correlations is expected to allow a better comprehension of the physical principles underlying quantum mechanics. In this work, we reconsider the possibility of devising "crypto-nonlocal theories", using a terminology firstly introduced by Leggett. We generalize and simplify the investigations on this subject which can be found in the literature. At their deeper level, such theories allow nonlocal correlations which can overcome the quantum limit.

  2. 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 ...

  3. 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...

  4. The 'revealed preferences' theory: Assumptions and conjectures

    International Nuclear Information System (INIS)

    Being kind of intuitive psychology the 'Revealed-Preferences'- theory based approaches towards determining the acceptable risks are a useful method for the generation of hypotheses. In view of the fact that reliability engineering develops faster than methods for the determination of reliability aims the Revealed-Preferences approach is a necessary preliminary help. Some of the assumptions on which the 'Revealed-Preferences' theory is based will be identified and analysed and afterwards compared with experimentally obtained results. (orig./DG)

  5. Marine bacterial, archaeal and protistan association networks reveal ecological linkages.

    Science.gov (United States)

    Steele, Joshua A; Countway, Peter D; Xia, Li; Vigil, Patrick D; Beman, J Michael; Kim, Diane Y; Chow, Cheryl-Emiliane T; Sachdeva, Rohan; Jones, Adriane C; Schwalbach, Michael S; Rose, Julie M; Hewson, Ian; Patel, Anand; Sun, Fengzhu; Caron, David A; Fuhrman, Jed A

    2011-09-01

    Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes. PMID:21430787

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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; Dyre, J. C.

    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 by...

  12. 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.; Dyre, J.C.

    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 by...

  13. 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.

  14. Correlated alteration effects in CM carbonaceous chondrites

    Science.gov (United States)

    Browning, Lauren B.; McSween, Harry Y., Jr.; Zolensky, Michael E.

    1996-07-01

    Three parameters are proposed to determine the relative extent of alteration in CM chondrites. The mineralogic alteration index monitors the relative progress of coupled substitutions in the progressive alteration of cronstedtite to Mg-serpentine and increases with increasing alteration. To calculate values of this index, an algorithm has been developed to estimate the average matrix phyllosilicate composition in individual CM chondrites. The second parameter is the volume percent of isolated matrix silicates, which decreases with progressive alteration due to mineral hydration. Finally, the volume percent of chondrule alteration monitors the extent of chondrule phyllosilicate production and increases as alteration proceeds. These parameters define the first CM alteration scale that relies on multiple indicators of progressive alteration. The following relative order of increasing alteration is established by this model: Murchison ≤ Bells Cochabamba and Boriskino experienced is less precisely constrained, although both fall near the middle of this sequence. A comparison between the mineralogic alteration index and literature values for the whole-rock chemistry of CM chondrites reveals several correlations. A positive, nearly linear correlation between bulk H content and progressive CM alteration suggests an approximately constant production rate of new phyllosilicates relative to the mineralogical transition from cronstedtite to Mg-serpentine. The abundance of trapped planetary 36Ar decreases systematically in progressively altered CM chondrites, suggesting the wholesale destruction of primary noble gas carrier phase (s) by aqueous reactions. Because low temperature fluid-rock reactions are generally associated with large isotopic mass fractionation factors, we also compared our model predictions with δ18O values for bulk CM samples. Although some of these data are poorly resolved, the order of increasing δ18O values approximates the order of increasing

  15. 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...

  16. 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.

  17. 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.

  18. Positivity in the presence of initial system-environment correlation

    CERN Document Server

    Modi, Kavan; Aspuru-Guzik, Alán

    2012-01-01

    Dynamical maps can be nonpositive due to the constraints imposed by the initial system-environment correlation. We find the conditions for positivity and complete positivity of such dynamical maps by using the assignment map. Any initial system-environment correlations make the assignment map nonpositive, while the positivity of the dynamical depends on the interplay between the assignment map and the system-environment coupling. We show how this interplay can reveal and/or hide the nonpositivity of the assignment map. We discuss how this is related to many Markovian models.

  19. Library correlation nuclide identification algorithm

    International Nuclear Information System (INIS)

    A novel nuclide identification algorithm, Library Correlation Nuclide Identification (LibCorNID), is proposed. In addition to the spectrum, LibCorNID requires the standard energy, peak shape and peak efficiency calibrations. Input parameters include tolerances for some expected variations in the calibrations, a minimum relative nuclide peak area threshold, and a correlation threshold. Initially, the measured peak spectrum is obtained as the residual after baseline estimation via peak erosion, removing the continuum. Library nuclides are filtered by examining the possible nuclide peak areas in terms of the measured peak spectrum and applying the specified relative area threshold. Remaining candidates are used to create a set of theoretical peak spectra based on the calibrations and library entries. These candidate spectra are then simultaneously fit to the measured peak spectrum while also optimizing the calibrations within the bounds of the specified tolerances. Each candidate with optimized area still exceeding the area threshold undergoes a correlation test. The normalized Pearson's correlation value is calculated as a comparison of the optimized nuclide peak spectrum to the measured peak spectrum with the other optimized peak spectra subtracted. Those candidates with correlation values that exceed the specified threshold are identified and their optimized activities are output. An evaluation of LibCorNID was conducted to verify identification performance in terms of detection probability and false alarm rate. LibCorNID has been shown to perform well compared to standard peak-based analyses

  20. 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…

  1. 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.

  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. 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...

  4. 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.

  5. 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)

  6. 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

  7. 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.

  8. Flooding correlations in narrow channel

    International Nuclear Information System (INIS)

    Heat transfer in narrow gap is considered as important phenomena in severe accidents in nuclear power plants. Also in heat removal of electric chip. Critical heat flux(CHF) in narrow gap limits the maximum heat transfer rate in narrow channel. In case of closed bottom channel, flooding limited CHF occurrence is observed. Flooding correlations will be helpful to predict the CHF in closed bottom channel. In present study, flooding data for narrow channel geometry were collected and the work to recognize the effect of the span, w and gap size, s were performed. And new flooding correlations were suggested for high-aspect-ratio geometry. Also, flooding correlation was applied to flooding limited CHF data

  9. Correlations in charged bosons systems

    International Nuclear Information System (INIS)

    The two and three-dimensional charge Bose gas have been studied. In the bidimensional case two different types of interaction were considered: l/r and l n(r). The method of self-consistent-field was applied to these systems, which takes into account the short range correlations between the bosons through a local-field correction. By using self-consistent numerical calculations, the structure factor S(k→) was determined. The pair-correlation function, the ground-state energy, the pressure of the gas and the spectrum of elementary excitations were obtained from S (k→). The screening density induced by a fixed charged impurity was calculated. In the high-density limit our calculations reproduce the results given by Bogoliubov's perturbation theory. In the intermediate-density region, corresponding to the strongly coupled systems, the results are in very good agreement with calculations based on HNC approximation as well as Monte Carlo method. The results are compared in several situations with RPA results showing that the self-consistent method is much more accurate. The two-dimensional systems showed to be more correlated than the three-dimensional systems showed to be more correlated than the three-dimensional one; the gas with interaction l/r is also more correlated than the logarithmic one at high densities, but it begins to be less correlated than this one in the low-density region. The thermodynamic functions of the two and three-dimensional systems at finite temperatures near absolute zero are calculated based upon the gas excitation spectra at zero temperature. (author)

  10. 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...

  11. Spatial quantum correlations induced by random multiple scattering of quadrature squeezed light

    DEFF Research Database (Denmark)

    Lodahl, Peter

    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....

  12. 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)

  13. 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.

  14. Converting Coherence to Quantum Correlations

    Science.gov (United States)

    Ma, Jiajun; Yadin, Benjamin; Girolami, Davide; Vedral, Vlatko; Gu, Mile

    2016-04-01

    Recent results in quantum information theory characterize quantum coherence in the context of resource theories. Here, we study the relation between quantum coherence and quantum discord, a kind of quantum correlation which appears even in nonentangled states. We prove that the creation of quantum discord with multipartite incoherent operations is bounded by the amount of quantum coherence consumed in its subsystems during the process. We show how the interplay between quantum coherence consumption and creation of quantum discord works in the preparation of multipartite quantum correlated states and in the model of deterministic quantum computation with one qubit.

  15. Correlation Integral Decomposition for Classification

    Czech Academy of Sciences Publication Activity Database

    Jiřina, Marcel; Jiřina jr., M.

    Vol. Part II. Berlin : Springer, 2008 - (Kůrková, V.; Neruda, R.; Koutník, J.), s. 62-71 ISBN 978-3-540-87558-1. - (Lecture Notes in Computer Science. 5164). [ICANN 2008. International Conference on Artificial Neural Networks /18./. Prague (CZ), 03.09.2008-06.09.2008] R&D Projects: GA MŠk(CZ) 1M0567 Institutional research plan: CEZ:AV0Z10300504 Keywords : correlation integral decomposition * correlation dimension * distribution mapping exponent * probability density estimation * classification Subject RIV: BA - General Mathematics

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

    regions, and an unusually diverse range of feeding habits at the larval stage (e.g., saprophagy, phytophagy, carnivory, endoparasitism, haematophagy). We here review muscid classification and biology and present a molecular phylogeny based on four mitochondrial genes (12S, 16S, COI, CYTB) and three...

  1. Correlations in a band insulator

    Czech Academy of Sciences Publication Activity Database

    Sentef, M.; Kuneš, Jan; Werner, P.; Kampf, A. P.

    2009-01-01

    Roč. 80, č. 15 (2009), 155116/1-155116/7. ISSN 1098-0121 Institutional research plan: CEZ:AV0Z10100521 Keywords : electronic correlations * dynamical mean-field theory * band insulator Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.475, year: 2009

  2. 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 ...

  3. Neural correlates of viewing paintings

    DEFF Research Database (Denmark)

    Vartanian, Oshin; Skov, Martin

    2014-01-01

    meta-analysis of fifteen experiments using the activation likelihood estimation (ALE) method was conducted. As predicted, viewing paintings was correlated with activation in a distributed system including the occipital lobes, temporal lobe structures in the ventral stream involved in object (fusiform...

  4. Resistant multiple sparse canonical correlation.

    Science.gov (United States)

    Coleman, Jacob; Replogle, Joseph; Chandler, Gabriel; Hardin, Johanna

    2016-04-01

    Canonical correlation analysis (CCA) is a multivariate technique that takes two datasets and forms the most highly correlated possible pairs of linear combinations between them. Each subsequent pair of linear combinations is orthogonal to the preceding pair, meaning that new information is gleaned from each pair. By looking at the magnitude of coefficient values, we can find out which variables can be grouped together, thus better understanding multiple interactions that are otherwise difficult to compute or grasp intuitively. CCA appears to have quite powerful applications to high-throughput data, as we can use it to discover, for example, relationships between gene expression and gene copy number variation. One of the biggest problems of CCA is that the number of variables (often upwards of 10,000) makes biological interpretation of linear combinations nearly impossible. To limit variable output, we have employed a method known as sparse canonical correlation analysis (SCCA), while adding estimation which is resistant to extreme observations or other types of deviant data. In this paper, we have demonstrated the success of resistant estimation in variable selection using SCCA. Additionally, we have used SCCA to find multiple canonical pairs for extended knowledge about the datasets at hand. Again, using resistant estimators provided more accurate estimates than standard estimators in the multiple canonical correlation setting. R code is available and documented at https://github.com/hardin47/rmscca. PMID:26963062

  5. Correlation Dimension Estimation for Classification

    Czech Academy of Sciences Publication Activity Database

    Jiřina, Marcel; Jiřina jr., M.

    2006-01-01

    Roč. 1, č. 3 (2006), s. 547-557. ISSN 1895-8648 R&D Projects: GA MŠk(CZ) 1M0567 Institutional research plan: CEZ:AV0Z10300504 Keywords : correlation dimension * probability density estimation * classification * UCI MLR Subject RIV: BA - General Mathematics

  6. 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)

  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. Tetrachoric Correlation: A Permutation Alternative

    Science.gov (United States)

    Long, Michael A.; Berry, Kenneth J.; Mielke, Paul W., Jr.

    2009-01-01

    An exact permutation test is provided for the tetrachoric correlation coefficient. Comparisons with the conventional test employing Student's t distribution demonstrate the necessity of using the permutation approach for small sample sizes and/or disproportionate marginal frequency totals. (Contains 4 tables.)

  9. Correlation-assisted quantum communication

    International Nuclear Information System (INIS)

    Quantum dense coding is considered to be one of the most remarkable demonstrations of the existence of quantum entanglement. In this paper, we analyze the role of correlations (both classical and quantum) in quantum communication protocols. We study how the capacity of a single-qubit quantum channel depends on correlations between Alice and Bob. In particular, we consider a scenario when Alice and Bob share a pair of qubits in a state such that Alice's qubit is in the state described by the density operator ρ=(1/2)1+n-vector·σ-vector. We evaluate a capacity of the noiseless channel for two cases: (1) when Bob performs measurement just on the particle received from Alice, and (2) in the case when he utilizes correlations that have been established prior to the communication. We present a simple classical scenario which might serve as a prototype of quantum dense coding. We generalize our results also for qudits. In addition, we address some aspects of the issue of security in correlation-assisted communication protocols

  10. 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

  11. 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.

  12. Correlation Dimension-Based Classifier

    Czech Academy of Sciences Publication Activity Database

    Jiřina, Marcel; Jiřina jr., M.

    2014-01-01

    Roč. 44, č. 12 (2014), s. 2253-2263. ISSN 2168-2267 R&D Projects: GA MŠk(CZ) LG12020 Institutional support: RVO:67985807 Keywords : classifier * multidimensional data * correlation dimension * scaling exponent * polynomial expansion Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 3.469, year: 2014

  13. 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

  14. 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.

  15. 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 ...

  16. 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...

  17. 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...

  18. 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 ...

  19. 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...

  20. 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.