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Sample records for absolutely localized molecular

  1. Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals

    SciTech Connect

    Khaliullin, Rustam Z.; Head-Gordon, Martin; Bell, Alexis T.

    2008-05-14

    A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.

  2. Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals.

    PubMed

    Khaliullin, Rustam Z; Bell, Alexis T; Head-Gordon, Martin

    2008-05-14

    A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.

  3. Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals

    NASA Astrophysics Data System (ADS)

    Khaliullin, Rustam Z.; Bell, Alexis T.; Head-Gordon, Martin

    2008-05-01

    A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.

  4. Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.

    PubMed

    Khaliullin, Rustam Z; Cobar, Erika A; Lochan, Rohini C; Bell, Alexis T; Head-Gordon, Martin

    2007-09-13

    An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.

  5. An energy decomposition analysis for second-order Møller-Plesset perturbation theory based on absolutely localized molecular orbitals.

    PubMed

    Thirman, Jonathan; Head-Gordon, Martin

    2015-08-28

    An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller-Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond.

  6. An energy decomposition analysis for second-order Møller–Plesset perturbation theory based on absolutely localized molecular orbitals

    SciTech Connect

    Thirman, Jonathan Head-Gordon, Martin

    2015-08-28

    An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller–Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond.

  7. An energy decomposition analysis for second-order Møller-Plesset perturbation theory based on absolutely localized molecular orbitals

    NASA Astrophysics Data System (ADS)

    Thirman, Jonathan; Head-Gordon, Martin

    2015-08-01

    An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller-Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond.

  8. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C{sub s}-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  9. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level.

    PubMed

    Azar, R Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C(s)-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  10. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level

    NASA Astrophysics Data System (ADS)

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-01

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the Cs-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  11. Examination of the hydrogen-bonding networks in small water clusters (n = 2-5, 13, 17) using absolutely localized molecular orbital energy decomposition analysis.

    PubMed

    Cobar, Erika A; Horn, Paul R; Bergman, Robert G; Head-Gordon, Martin

    2012-11-28

    Using the ωB97X-D and B3LYP density functionals, the absolutely localized molecular orbital energy decomposition method (ALMO-EDA) is applied to the water dimer through pentamer, 13-mer and 17-mer clusters. Two-body, three-body, and total interaction energies are decomposed into their component energy terms: frozen density interaction energy, polarization energy, and charge transfer energy. Charge transfer, polarization, and frozen orbital interaction energies are all found to be significant contributors to the two-body and total interaction energies; the three-body interaction energies are dominated by polarization. Each component energy term for the two-body interactions is highly dependent on the associated hydrogen bond distance. The favorability of the three-body terms associated with the 13- and 17-mer structures depends on the hydrogen-donor or hydrogen-acceptor roles played by each of the three component waters. Only small errors arise from neglect of three-body interactions without two adjacent water molecules, or beyond three-body interactions. Interesting linear correlations are identified between the contributions of charge-transfer and polarization terms to the two and three-body interactions, which permits elimination of explicit calculation of charge transfer to a good approximation.

  12. Absolute determination of local tropospheric OH concentrations

    NASA Technical Reports Server (NTRS)

    Armerding, Wolfgang; Comes, Franz-Josef

    1994-01-01

    Long path absorption (LPA) according to Lambert Beer's law is a method to determine absolute concentrations of trace gases such as tropospheric OH. We have developed a LPA instrument which is based on a rapid tuning of the light source which is a frequency doubled dye laser. The laser is tuned across two or three OH absorption features around 308 nm with a scanning speed of 0.07 cm(exp -1)/microsecond and a repetition rate of 1.3 kHz. This high scanning speed greatly reduces the fluctuation of the light intensity caused by the atmosphere. To obtain the required high sensitivity the laser output power is additionally made constant and stabilized by an electro-optical modulator. The present sensitivity is of the order of a few times 10(exp 5) OH per cm(exp 3) for an acquisition time of a minute and an absorption path length of only 1200 meters so that a folding of the optical path in a multireflection cell was possible leading to a lateral dimension of the cell of a few meters. This allows local measurements to be made. Tropospheric measurements have been carried out in 1991 resulting in the determination of OH diurnal variation at specific days in late summer. Comparison with model calculations have been made. Interferences are mainly due to SO2 absorption. The problem of OH self generation in the multireflection cell is of minor extent. This could be shown by using different experimental methods. The minimum-maximum signal to noise ratio is about 8 x 10(exp -4) for a single scan. Due to the small size of the absorption cell the realization of an open air laboratory is possible in which by use of an additional UV light source or by additional fluxes of trace gases the chemistry can be changed under controlled conditions allowing kinetic studies of tropospheric photochemistry to be made in open air.

  13. A direct way to observe absolute molecular handedness

    NASA Astrophysics Data System (ADS)

    Vager, Zeev

    2014-07-01

    We claim that the polarization of electrons tunneling through the molecular electric dipole direction uniquely determines the handedness of chiral centers. Unique labeling of chiral stereo-centers must include their handedness. The conventional method is formally known as the R, S nomenclature or the Ingold-Prelog priority (CIP) rules. It requires knowledge of the spatial absolute configuration of that center. Traditionally, experimental methods of extracting handedness go through the absolute configuration and only then would the CIP convention be applied. Here we show that a direct experimental method of determination of the natural molecular handedness by the polarization of tunneling electrons is almost always compatible with the CIP convention. By the sole use of symmetry arguments we show that the chiral molecular symmetry eliminates the need of fine structure splitting. As a consequence, the polarization of electrons tunneling through the molecular electric dipole direction uniquely determines their handedness.

  14. Absolute configuration determination using enantiomeric pairs of molecularly imprinted polymers.

    PubMed

    Meador, Danielle S; Spivak, David A

    2014-03-07

    A new method for determination of absolute configuration (AC) is demonstrated using an enantiomeric pair of molecularly imprinted polymers, referred to as "DuoMIPs". The ratio of HPLC capacity factors (k') for the analyte on each of the DuoMIPs is defined as the γ factor and can be used to determine AC when above 1.2. A mnemonic based on the complementary binding geometry of the DuoMIPs was used to aid in understanding and prediction of AC.

  15. Absolute and relative pitch: Global versus local processing of chords.

    PubMed

    Ziv, Naomi; Radin, Shulamit

    2014-01-01

    Absolute pitch (AP) is the ability to identify or produce notes without any reference note. An ongoing debate exists regarding the benefits or disadvantages of AP in processing music. One of the main issues in this context is whether the categorical perception of pitch in AP possessors may interfere in processing tasks requiring relative pitch (RP). Previous studies, focusing mainly on melodic and interval perception, have obtained inconsistent results. The aim of the present study was to examine the effect of AP and RP separately, using isolated chords. Seventy-three musicians were categorized into four groups of high and low AP and RP, and were tested on two tasks: identifying chord types (Task 1), and identifying a single note within a chord (Task 2). A main effect of RP on Task 1 and an interaction between AP and RP in reaction times were found. On Task 2 main effects of AP and RP, and an interaction were found, with highest performance in participants with both high AP and RP. Results suggest that AP and RP should be regarded as two different abilities, and that AP may slow down reaction times for tasks requiring global processing.

  16. Absolute and relative pitch: Global versus local processing of chords

    PubMed Central

    Ziv, Naomi; Radin, Shulamit

    2014-01-01

    Absolute pitch (AP) is the ability to identify or produce notes without any reference note. An ongoing debate exists regarding the benefits or disadvantages of AP in processing music. One of the main issues in this context is whether the categorical perception of pitch in AP possessors may interfere in processing tasks requiring relative pitch (RP). Previous studies, focusing mainly on melodic and interval perception, have obtained inconsistent results. The aim of the present study was to examine the effect of AP and RP separately, using isolated chords. Seventy-three musicians were categorized into four groups of high and low AP and RP, and were tested on two tasks: identifying chord types (Task 1), and identifying a single note within a chord (Task 2). A main effect of RP on Task 1 and an interaction between AP and RP in reaction times were found. On Task 2 main effects of AP and RP, and an interaction were found, with highest performance in participants with both high AP and RP. Results suggest that AP and RP should be regarded as two different abilities, and that AP may slow down reaction times for tasks requiring global processing. PMID:24855499

  17. First Absolutely Calibrated Localized Measurements of Ion Velocity in the MST in Locked and Rotating Plasmas

    NASA Astrophysics Data System (ADS)

    Baltzer, M.; Craig, D.; den Hartog, D. J.; Nornberg, M. D.; Munaretto, S.

    2015-11-01

    An Ion Doppler Spectrometer (IDS) is used on MST for high time-resolution passive and active measurements of impurity ion emission. Absolutely calibrated measurements of flow are difficult because the spectrometer records data within 0.3 nm of the C+5 line of interest, and commercial calibration lamps do not produce lines in this narrow range . A novel optical system was designed to absolutely calibrate the IDS. The device uses an UV LED to produce a broad emission curve in the desired region. A Fabry-Perot etalon filters this light, cutting transmittance peaks into the pattern of the LED emission. An optical train of fused silica lenses focuses the light into the IDS with f/4. A holographic diffuser blurs the light cone to increase homogeneity. Using this light source, the absolute Doppler shift of ion emissions can be measured in MST plasmas. In combination with charge exchange recombination spectroscopy, localized ion velocities can now be measured. Previously, a time-averaged measurement along the chord bisecting the poloidal plane was used to calibrate the IDS; the quality of these central chord calibrations can be characterized with our absolute calibration. Calibration errors may also be quantified and minimized by optimizing the curve-fitting process. Preliminary measurements of toroidal velocity in locked and rotating plasmas will be shown. This work has been supported by the US DOE.

  18. Dynamical Localization in Molecular Systems.

    NASA Astrophysics Data System (ADS)

    Wang, Xidi

    In the first four chapters of this thesis we concentrate on the Davydov model which describes the vibrational energy quanta of Amide I bonds (C=O bonds on the alpha -helix) coupled to the acoustic phonon modes of the alpha-helix backbone in the form of a Frohlich Hamiltonian. Following a brief introduction in chapter one, in chapter two we formulate the dynamics of vibrational quanta at finite temperature by using coherent state products. The fluctuation-dissipation relation is derived. At zero temperature, in the continuum limit, we recover the original results of Davydov. We also achieve good agreement with numerical simulations. In chapter three, the net contraction of the lattice is calculated exactly at any temperature, and its relation to the so -call "topological stability" of the Davydov soliton is discussed. In the second section of the chapter three we calculate the overtone spectra of crystalline acetanilide (according to some opinions ACN provides experimental evidence for the existence of Davydov solitons). Good agreement with experimental data has been obtained. In chapter four we study the self-trapped vibrational excitations by the Quantum Monte Carlo technique. For a single excitation, the temperature dependence of different physical observables is calculated. The quasi-particle which resembles the Davydov soliton has been found to be fairly narrow using the most commonly used data for the alpha -helix; at temperatures above a few Kelvin, the quasi-particle reaches its smallest limit (extends over three sites), which implies diffusive motion of the small polaron-like quasi-particle at high temperatures. For the multi-excitation case, bound pairs and clusters of excitations are found at low temperatures; they gradually dissociate when the temperature of the system is increased as calculated from the density-density correlation function. In the last chapter of this thesis, we study a more general model of dynamical local modes in molecular systems

  19. Absolute and comparative subcutaneous bioavailability of ardeparin sodium, a low molecular weight heparin.

    PubMed

    Troy, S; Fruncillo, R; Ozawa, T; Mammen, E; Holloway, S; Chiang, S

    1997-08-01

    Ardeparin sodium (Normiflo, Wyeth-Ayerst) is a low molecular weight heparin undergoing clinical evaluation as an antithrombotic agent. The objective of this study was to evaluate the absolute and comparative bioavailability of ardeparin following subcutaneous administration of three different formulations [two formulations of ardeparin at 10,000 anti-factor Xa (aXa) U/ml, but with different preservatives, and a 20,000 aXa U/ml formulation]. The study was conducted using a randomized 4-period crossover design (three subcutaneous treatments and one intravenous treatment) in 24 healthy subjects, and the pharmacokinetics of ardeparin were characterized by plasma anti-factor IIa (aIIa) and anti-factor Xa (aXa) activities. The mean absolute bioavailability of ardeparin based on aIIa activity ranged from 62% to 64% and the mean absolute bioavailability based on aXa activity ranged from 88% to 97%. Based on bioequivalence testing criteria, the three ardeparin formulations were bioequivalent.

  20. The Question of Absolute Space and Time Directions in Relation to Molecular Chirality, Parity Violation, and Biomolecular Homochirality

    SciTech Connect

    Quack, Martin

    2001-03-21

    The questions of the absolute directions of space and time or the “observability” of absolute time direction as well as absolute handedness-left or right- are related to the fundamental symmetries of physics C, P, T as well as their combinations, in particular CPT, and their violations, such as parity violation. At the same time there is a relation to certain still open questions in chemistry concerning the fundamental physical- chemical principles of molecular chirality and in biochemistry concerning the selection of homochirality in evolution. In the lecture we shall introduce the concepts and then report new theoretical results from our work on parity violation in chiral molecules, showing order of magnitude increases with respect to previously accepted values. We discus as well our current experimental efforts. We shall briefly mention the construction of an absolute molecular clock.

  1. The Question of Absolute Space and Time Directions in Relation to Molecular Chirality, Parity Violation, and Biomolecular Homochirality

    SciTech Connect

    Quack, Martin

    2001-03-21

    The questions of the absolute directions of space and time or the 'observability' of absolute time direction as well as absolute handedness - left or right - are related to the fundamental symmetries of physics C, P, T as well as their combinations, in particular CPT, and their violations, such as parity violation. At the same time there is a relation to certain still open questions in chemistry concerning the fundamental physical-chemical principles of molecular chirality and in biochemistry concerning the selection of homochirality in evolution. In the lecture we shall introduce the concepts and then report new theoretical results from our work on parity violation in chiral molecules, showing order of magnitude increases with respect to previously accepted values. We discuss as well our current experimental efforts. We shall briefly mention the construction of an absolute molecular clock.

  2. Dynamic localization and negative absolute conductance in terahertz driven semiconductor superlattices

    SciTech Connect

    Keay, B.J.; Allen, S.J.; Campman, K.L.

    1995-12-31

    We report the first observation of Negative Absolute Conductance (NAC), dynamic localization and multiphoton stimulated emission assisted tunneling in terahertz driven semiconductor superlattices. Theories predicting NAC in semiconductor superlattices subjected to AC electric fields have existed for twenty years, but have never been verified experimentally. Most theories are based upon semiclassical arguments and are only valid for superlattices in the miniband or coherent tunneling regime. We are not aware of models predicting NAC in superlattices in the sequential tunneling regime, although there has been recent theoretical work on double-barrier structures. Perhaps the most remarkable result is found in the power dependence of the current-voltage (I-V) characteristics near zero DC bias. As the laser power is increased the current decreases towards zero and then becomes negative. This result implies that the electrons are absorbing energy from the laser field, producing a net current in the direction opposite to the applied voltage. NAC around zero DC bias is a particularly surprising observation considering photon-assisted tunneling is not expected to be observable between the ground states of neighboring quantum wells in a semiconductor superlattice. Contrary to this believe our results are most readily attributable to photon absorption and multiphoton emission between ground states of neighboring wells. The I-V characteristics measured in the presence of terahertz radiation at low DC bias also contain steps and plateaus analogous to photon-assisted steps observed in superconducting junctions. As many as three steps have been clearly resolved corresponding to stimulated emission into the terahertz field by a three-photon process.

  3. Dating Phylogenies with Hybrid Local Molecular Clocks

    PubMed Central

    Aris-Brosou, Stéphane

    2007-01-01

    Background Because rates of evolution and species divergence times cannot be estimated directly from molecular data, all current dating methods require that specific assumptions be made before inferring any divergence time. These assumptions typically bear either on rates of molecular evolution (molecular clock hypothesis, local clocks models) or on both rates and times (penalized likelihood, Bayesian methods). However, most of these assumptions can affect estimated dates, oftentimes because they underestimate large amounts of rate change. Principal Findings A significant modification to a recently proposed ad hoc rate-smoothing algorithm is described, in which local molecular clocks are automatically placed on a phylogeny. This modification makes use of hybrid approaches that borrow from recent theoretical developments in microarray data analysis. An ad hoc integration of phylogenetic uncertainty under these local clock models is also described. The performance and accuracy of the new methods are evaluated by reanalyzing three published data sets. Conclusions It is shown that the new maximum likelihood hybrid methods can perform better than penalized likelihood and almost as well as uncorrelated Bayesian models. However, the new methods still tend to underestimate the actual amount of rate change. This work demonstrates the difficulty of estimating divergence times using local molecular clocks. PMID:17849008

  4. Atom-chip based quantum gravimetry for the precise determination of absolute local gravity

    NASA Astrophysics Data System (ADS)

    Abend, S.

    2015-12-01

    We present a novel technique for the precise measurement of absolute local gravity based on cold atom interferometry. Atom interferometry utilizes the interference of matter waves interrogated by laser light to read out inertial forces. Today's generation of these devices typically operate with test mass samples, that consists of ensembles of laser cooled atoms. Their performance is limited by the velocity spread and finite-size of the test masses that impose systematic uncertainties at the level of a few μGal. Rather than laser cooled atoms we employ quantum degenerate ensembles, so called Bose-Einstein condensates, as ultra-sensitive probes for gravity. These sources offer unique properties in temperature as well as in ensemble size that will allow to overcome the current limitations with the next generation of sensors. Furthermore, atom-chip technologies offer the possibility to generate Bose-Einstein condensates in a fast and reliable way. We show a lab-based prototype that uses the atom-chip itself to retro-reflect the interrogation laser and thus serving as inertial reference inside the vacuum. With this setup it is possible to demonstrate all necessary steps to measure gravity, including the preparation of the source, spanning an interferometer as well as the detection of the output signal, within an area of 1 cm3 right below the atom-chip and to analyze relevant systematic effects. In the framework of the center of excellence geoQ a next generation device is under construction at the Institut für Quantenoptik, that will allow for in-field measurements. This device will feature a state-of-the-art atom-chip source with a high-flux of ultra-cold atoms at a repetition rate of 1-2 Hz. In cooperation with the Müller group at the Institut für Erdmessung the sensor will be characterized in the laboratory first, to be ultimately employed in campaigns to measure the Fennoscandian uplift at the level of 1 μGal. The presented work is part of the center of

  5. Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids

    PubMed Central

    White, Ronald P.; Meirovitch, Hagai

    2006-01-01

    The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy, S, and free energy, F, by analyzing Boltzmann samples obtained by Monte Carlo (MC) or molecular dynamics (MD) techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by gradually placing the molecules in their positions at i using transition probabilities (TPs). With our recent version of HS, called HSMC-EV, each TP is calculated from MC simulations, where the simulated particles are excluded from the volume reconstructed in previous steps. In this paper we remove the excluded volume (EV) restriction, replacing it by a “free volume” (FV) approach. For liquid argon, HSMC-FV leads to an improvement in efficiency over HSMC-EV by a factor of 2–3. Importantly, the FV treatment greatly simplifies the HS implementation for liquids, allowing a much more natural application of the method for MD simulations. Given the success and popularity of MD, the present development of the HSMD method for liquids is an important advancement for HS methodology. Results for the HSMD-FV approach presented here agree well with our HSMC and thermodynamic integration results. The efficiency of HSMD-FV is equivalent to HSMC-EV. The potential use of HSMC(MD)-FV in protein systems with explicit water is discussed. PMID:16774320

  6. Design, validation, and absolute sensitivity of a novel test for the molecular detection of avian pneumovirus.

    PubMed

    Cecchinato, Mattia; Catelli, Elena; Savage, Carol E; Jones, Richard C; Naylor, Clive J

    2004-11-01

    This study describes attempts to increase and measure sensitivity of molecular tests to detect avian pneumovirus (APV). Polymerase chain reaction (PCR) diagnostic tests were designed for the detection of nucleic acid from an A-type APV genome. The objective was selection of PCR oligonucleotide combinations, which would provide the greatest test sensitivity and thereby enable optimal detection when used for later testing of field materials. Relative and absolute test sensitivities could be determined because of laboratory access to known quantities of purified full-length DNA copies of APV genome derived from the same A-type virus. Four new nested PCR tests were designed in the fusion (F) protein (2 tests), small hydrophobic (SH) protein (1 test), and nucleocapsid (N) protein (1 test) genes and compared with an established test in the attachment (G) protein gene. Known amounts of full-length APV genome were serially diluted 10-fold, and these dilutions were used as templates for the different tests. Sensitivities were found to differ between the tests, the most sensitive being the established G test, which proved able to detect 6,000 copies of the G gene. The G test contained predominantly pyrimidine residues at its 3' termini, and because of this, oligonucleotides for the most sensitive F test were modified to incorporate the same residue types at their 3' termini. This was found to increase sensitivity, so that after full 3' pyrimidine substitutions, the F test became able to detect 600 copies of the F gene.

  7. Electron localization following attosecond molecular photoionization.

    PubMed

    Sansone, G; Kelkensberg, F; Pérez-Torres, J F; Morales, F; Kling, M F; Siu, W; Ghafur, O; Johnsson, P; Swoboda, M; Benedetti, E; Ferrari, F; Lépine, F; Sanz-Vicario, J L; Zherebtsov, S; Znakovskaya, I; L'huillier, A; Ivanov, M Yu; Nisoli, M; Martín, F; Vrakking, M J J

    2010-06-10

    For the past several decades, we have been able to directly probe the motion of atoms that is associated with chemical transformations and which occurs on the femtosecond (10(-15)-s) timescale. However, studying the inner workings of atoms and molecules on the electronic timescale has become possible only with the recent development of isolated attosecond (10(-18)-s) laser pulses. Such pulses have been used to investigate atomic photoexcitation and photoionization and electron dynamics in solids, and in molecules could help explore the prompt charge redistribution and localization that accompany photoexcitation processes. In recent work, the dissociative ionization of H(2) and D(2) was monitored on femtosecond timescales and controlled using few-cycle near-infrared laser pulses. Here we report a molecular attosecond pump-probe experiment based on that work: H(2) and D(2) are dissociatively ionized by a sequence comprising an isolated attosecond ultraviolet pulse and an intense few-cycle infrared pulse, and a localization of the electronic charge distribution within the molecule is measured that depends-with attosecond time resolution-on the delay between the pump and probe pulses. The localization occurs by means of two mechanisms, where the infrared laser influences the photoionization or the dissociation of the molecular ion. In the first case, charge localization arises from quantum mechanical interference involving autoionizing states and the laser-altered wavefunction of the departing electron. In the second case, charge localization arises owing to laser-driven population transfer between different electronic states of the molecular ion. These results establish attosecond pump-probe strategies as a powerful tool for investigating the complex molecular dynamics that result from the coupling between electronic and nuclear motions beyond the usual Born-Oppenheimer approximation.

  8. Unitary Optimization of Localized Molecular Orbitals.

    PubMed

    Lehtola, Susi; Jónsson, Hannes

    2013-12-10

    A unified formalism and its implementation is presented for Foster-Boys, fourth moment, Pipek-Mezey, and Edmiston-Ruedenberg type localization schemes of molecular orbitals through unitary optimization of the localizing transform matrix using a recently proposed algorithm [ Abrudan ; et al. Signal Processing 2009 , 89 , 1704 ]. A conjugate gradient algorithm is used with an efficient line search method. The option of using complex valued orbitals is included. Applications to fullerenes from C20 to C100, as well as benzene and arachic acid are presented, showing the capability of the method, which has been implemented in ERKALE, an open source program for electronic structure calculations of atoms and molecules.

  9. Host-Guest Assembly of a Molecular Reporter with Chiral Cyanohydrins for Assignment of Absolute Stereochemistry.

    PubMed

    Gholami, Hadi; Anyika, Mercy; Zhang, Jun; Vasileiou, Chrysoula; Borhan, Babak

    2016-06-27

    The absolute stereochemistry of cyanohydrins, derived from ketones and aldehydes, is obtained routinely, in a microscale and derivatization-free manner, upon their complexation with Zn-MAPOL, a zincated porphyrin host with a binding pocket comprised of a biphenol core. The host-guest complex leads to observable exciton-coupled circular dichroism (ECCD), the sign of which is easily correlated to the absolute stereochemistry of the bound cyanohydrin. A working model, based on the ECCD signal of cyanohydrins with known configuration, is proposed.

  10. Local control theory applied to molecular photoassociation.

    PubMed

    Marquetand, Philipp; Engel, Volker

    2007-08-28

    Local control theory (LCT) is employed to achieve molecular photoassociation with shaped laser pulses. Within LCT, the control fields are constructed from the response of the system to the perturbation which makes them accessible to a straightforward interpretation. This is shown regarding the ground-state collision of H+F and H+I atoms. Different objectives are defined, which aim at the formation of vibrational cold or hot associated molecules, respectively. Results are presented for s-wave scattering, where the rotational degree of freedom is ignored and also for full scale calculations including rotations, in order to describe more realistic conditions.

  11. Absolute entropy and free energy of fluids using the hypothetical scanning method. I. Calculation of transition probabilities from local grand canonical partition functions

    NASA Astrophysics Data System (ADS)

    Szarecka, Agnieszka; White, Ronald P.; Meirovitch, Hagai

    2003-12-01

    The hypothetical scanning (HS) method provides the absolute entropy and free energy from a Boltzmann sample generated by Monte Carlo, molecular dynamics or any other exact simulation procedure. Thus far HS has been applied successfully to magnetic and polymer chain models; in this paper and the following one it is extended to fluid systems by treating a Lennard-Jones model of argon. With HS a probability Pi approximating the Boltzmann probability of system configuration i is calculated with a stepwise reconstruction procedure, based on adding atoms gradually layer-by-layer to an initially empty volume, where they are replaced in their positions at i. At each step a transition probability (TP) is obtained from local grand canonical partition functions calculated over a limited space of the still unvisited (future) volume, the larger this space the better the approximation. Pi is the product of the step TPs, where ln Pi is an upper bound of the absolute entropy, which leads to upper and lower bounds for the free energy. We demonstrate that very good results for the entropy and the free energy can be obtained for a wide range of densities of the argon system by calculating TPs that are based on only a very limited future volume.

  12. Easy Absolute Values? Absolutely

    ERIC Educational Resources Information Center

    Taylor, Sharon E.; Mittag, Kathleen Cage

    2015-01-01

    The authors teach a problem-solving course for preservice middle-grades education majors that includes concepts dealing with absolute-value computations, equations, and inequalities. Many of these students like mathematics and plan to teach it, so they are adept at symbolic manipulations. Getting them to think differently about a concept that they…

  13. Absolute vacuum ultraviolet photoabsorption cross section studies of atomic and molecular species: Techniques and observational data

    NASA Technical Reports Server (NTRS)

    Judge, D. L.; Wu, C. Y. R.

    1990-01-01

    Absorption of a high energy photon (greater than 6 eV) by an isolated molecule results in the formation of highly excited quasi-discrete or continuum states which evolve through a wide range of direct and indirect photochemical processes. These are: photoionization and autoionization, photodissociation and predissociation, and fluorescence. The ultimate goal is to understand the dynamics of the excitation and decay processes and to quantitatively measure the absolute partial cross sections for all processes which occur in photoabsorption. Typical experimental techniques and the status of observational results of particular interest to solar system observations are presented.

  14. Learning molecular energies using localized graph kernels

    NASA Astrophysics Data System (ADS)

    Ferré, Grégoire; Haut, Terry; Barros, Kipton

    2017-03-01

    Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

  15. Local microstructural organization in carbogenic molecular sieves

    SciTech Connect

    Kane, M.S.; Foley, H.C.

    1996-12-31

    The microstructure of nanoporous, carbogenic molecular sieves (CMS) was studied using high resolution electron microscopy and neutron diffraction. The narrow range of pore sizes observed in these complex materials suggests that although these materials are globally amorphous, the local microstructural features are more organized. This work, focused on poly(furfuryl alcohol)-derived CMS, is aimed at characterizing the evolution of this microstructure. Microscopy results show that materials synthesized at low temperature have some degree of organization but that the microstructure is featureless and symmetric at longer length scales. This symmetry is broken at higher synthesis temperatures as thermodynamic driving forces lead to further organization of the carbon atoms into more ordered structures but the length scales remain short. Micrographs of high temperature CMS show a high degree of curvature and features reminiscent of fullerene. The connectivity of the carbon atoms in the CMS has been probed using powder neutron diffraction. This data suggests that the atoms in the CMS form ordered structures on the length scale of 15{angstrom} which are distinctly different from the structure of graphite. These observed changes in the microstructure directly impact the adsorptive and molecular sieving characteristics of the CMS as illustrated by the marked differences between the diffusivities of oxygen and nitrogen. This property is crucial for the very demanding separation of nitrogen from oxygen in air.

  16. Saddle point localization of molecular wavefunctions

    NASA Astrophysics Data System (ADS)

    Mellau, Georg Ch.; Kyuberis, Alexandra A.; Polyansky, Oleg L.; Zobov, Nikolai; Field, Robert W.

    2016-09-01

    The quantum mechanical description of isomerization is based on bound eigenstates of the molecular potential energy surface. For the near-minimum regions there is a textbook-based relationship between the potential and eigenenergies. Here we show how the saddle point region that connects the two minima is encoded in the eigenstates of the model quartic potential and in the energy levels of the [H, C, N] potential energy surface. We model the spacing of the eigenenergies with the energy dependent classical oscillation frequency decreasing to zero at the saddle point. The eigenstates with the smallest spacing are localized at the saddle point. The analysis of the HCN ↔ HNC isomerization states shows that the eigenstates with small energy spacing relative to the effective (v1, v3, ℓ) bending potentials are highly localized in the bending coordinate at the transition state. These spectroscopically detectable states represent a chemical marker of the transition state in the eigenenergy spectrum. The method developed here provides a basis for modeling characteristic patterns in the eigenenergy spectrum of bound states.

  17. Saddle point localization of molecular wavefunctions

    PubMed Central

    Mellau, Georg Ch.; Kyuberis, Alexandra A.; Polyansky, Oleg L.; Zobov, Nikolai; Field, Robert W.

    2016-01-01

    The quantum mechanical description of isomerization is based on bound eigenstates of the molecular potential energy surface. For the near-minimum regions there is a textbook-based relationship between the potential and eigenenergies. Here we show how the saddle point region that connects the two minima is encoded in the eigenstates of the model quartic potential and in the energy levels of the [H, C, N] potential energy surface. We model the spacing of the eigenenergies with the energy dependent classical oscillation frequency decreasing to zero at the saddle point. The eigenstates with the smallest spacing are localized at the saddle point. The analysis of the HCN ↔ HNC isomerization states shows that the eigenstates with small energy spacing relative to the effective (v1, v3, ℓ) bending potentials are highly localized in the bending coordinate at the transition state. These spectroscopically detectable states represent a chemical marker of the transition state in the eigenenergy spectrum. The method developed here provides a basis for modeling characteristic patterns in the eigenenergy spectrum of bound states. PMID:27629262

  18. Saddle point localization of molecular wavefunctions.

    PubMed

    Mellau, Georg Ch; Kyuberis, Alexandra A; Polyansky, Oleg L; Zobov, Nikolai; Field, Robert W

    2016-09-15

    The quantum mechanical description of isomerization is based on bound eigenstates of the molecular potential energy surface. For the near-minimum regions there is a textbook-based relationship between the potential and eigenenergies. Here we show how the saddle point region that connects the two minima is encoded in the eigenstates of the model quartic potential and in the energy levels of the [H, C, N] potential energy surface. We model the spacing of the eigenenergies with the energy dependent classical oscillation frequency decreasing to zero at the saddle point. The eigenstates with the smallest spacing are localized at the saddle point. The analysis of the HCN ↔ HNC isomerization states shows that the eigenstates with small energy spacing relative to the effective (v1, v3, ℓ) bending potentials are highly localized in the bending coordinate at the transition state. These spectroscopically detectable states represent a chemical marker of the transition state in the eigenenergy spectrum. The method developed here provides a basis for modeling characteristic patterns in the eigenenergy spectrum of bound states.

  19. Faraday screens associated with local molecular clouds

    NASA Astrophysics Data System (ADS)

    Wolleben, M.; Reich, W.

    2004-11-01

    Polarization observations at λ 21 cm and λ 18 cm towards the local Taurus molecular cloud complex were made with the Effelsberg 100-m telescope. Highly structured, frequency-dependent polarized emission features were detected. We discuss polarization minima with excessive rotation m easures located at the boundaries of molecular clouds. These minima get less pronounced at the higher frequencies. The multi-frequency polarization data have been successfully modeled by considering magneto-ionic Faraday screens at the surface of the molecular clouds. Faraday rotated background emiss ion adds to foreground emission towards these screens in a different way than in its surroundings. The physical size of the Faraday screens is of the order of 2 pc for 140 pc distance to the Taurus clouds. Intrinsic rotation measures between about -18 rad m-2 to -30 rad m-2 are required to model the observations. Depolarization of the background emission is quite small (compatible with zero), indicating a regular magnetic field structure with little turbulence within the Faraday screens. With observational {constraints} for the thermal electron density from Hα observations of less than 0.8 cm-3 we conclude that the regular magnetic field strength along the line of sight exceeds 20 μ G, to account for the observed rotation measure. We discuss some possibilities for the origin of such strong and well ordered magnetic fields. The modeling also predicts a large-scale, regularly polarized emission in the foreground of the Taurus clouds which is of the order of 0.18 K at λ 21 cm. This in turn constrains the observed synchrotron emission in total intensity within 140 pc of the Taurus clouds. A lower limit of about 0.24 K, or about 1.7 K/kpc, is required for a perfectly ordered magnetic field with intrinsic (˜ 75%) percentage polarization. Since this is rather unlikely to be the case, the fraction of foreground synchrotron emission is even larger. This amount of synchrotron emission is

  20. Simultaneous determination of protein aggregation, degradation, and absolute molecular weight by size exclusion chromatography-multiangle laser light scattering.

    PubMed

    Ye, Hongping

    2006-09-01

    The feasibility of size exclusion chromotography (SEC)-multiangle laser-light scattering as a technique to investigate aggregation and degradation of glycosylated and nonglycosylated proteins, and antibodies under various conditions such as addition of detergent, changes in pH, and variation of protein concentration and heat stress temperature was examined. Separation of proteins and their aggregates was performed using SEC-high-performance liquid chromatography. Detection of analytes was carried out with on-line UV, refractive index, and multiangle laser light-scattering detectors. Quantification and molecular weight determination were performed using commercial software. Aggregation and degradation were examined under various conditions and quantitative results are presented for bovine serum albumin, choriogonadotropin, glyceraldehyde-3-phosphate dehydrogenase, Herceptin, and ReoPro. This method can simultaneously determine both the quantities and the molecular weights of macromolecules from a single injection. The determination of molecular weight is absolute which avoids misleading results caused by molecular shape or interactions with the column matrix. This technique is valuable not only for assessing the extent of aggregation but also for effectively monitoring molecule degradation as evidenced by molecular weight reduction and change in monomer amount.

  1. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.

    PubMed

    Shivakumar, Devleena; Williams, Joshua; Wu, Yujie; Damm, Wolfgang; Shelley, John; Sherman, Woody

    2010-05-11

    The accurate prediction of protein-ligand binding free energies is a primary objective in computer-aided drug design. The solvation free energy of a small molecule provides a surrogate to the desolvation of the ligand in the thermodynamic process of protein-ligand binding. Here, we use explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules. We also compare the performance of absolute solvation free energies obtained using the OPLS_2005 force field with two other commonly used small molecule force fields-general AMBER force field (GAFF) with AM1-BCC charges and CHARMm-MSI with CHelpG charges. Using the OPLS_2005 force field, we obtain high correlation with experimental solvation free energies (R(2) = 0.94) and low average unsigned errors for a majority of the functional groups compared to AM1-BCC/GAFF or CHelpG/CHARMm-MSI. However, OPLS_2005 has errors of over 1.3 kcal/mol for certain classes of polar compounds. We show that predictions on these compound classes can be improved by using a semiempirical charge assignment method with an implicit bond charge correction.

  2. Saddle Point Localization of Molecular Wavefunctions

    NASA Astrophysics Data System (ADS)

    Mellau, Georg Ch.; Kyuberis, Aleksandra; Polyansky, Oleg; Zobov, Nikolay Fedorovich; Field, Robert W.

    2016-06-01

    The quantum mechanical description of isomerization is based on bound eigenstates of the molecular potential energy surface. For the near-minimum regions there is a textbook-based relationship between the potential and eigenenergies. Here we show how the saddle point region that connects the two minima is encoded in the energy levels and wave functions of the potential energy surface.

  3. Quantitative vapor-phase IR intensities and DFT computations to predict absolute IR spectra based on molecular structure: I. Alkanes

    NASA Astrophysics Data System (ADS)

    Williams, Stephen D.; Johnson, Timothy J.; Sharpe, Steven W.; Yavelak, Veronica; Oates, R. P.; Brauer, Carolyn S.

    2013-11-01

    Recently recorded quantitative IR spectra of a variety of gas-phase alkanes are shown to have integrated intensities in both the C3H stretching and C3H bending regions that depend linearly on the molecular size, i.e. the number of C3H bonds. This result is well predicted from CH4 to C15H32 by density functional theory (DFT) computations of IR spectra using Becke's three parameter functional (B3LYP/6-31+G(d,p)). Using the experimental data, a simple model predicting the absolute IR band intensities of alkanes based only on structural formula is proposed: For the C3H stretching band envelope centered near 2930 cm-1 this is given by (km/mol) CH_str=(34±1)×CH-(41±23) where CH is number of C3H bonds in the alkane. The linearity is explained in terms of coordinated motion of methylene groups rather than the summed intensities of autonomous -CH2-units. The effect of alkyl chain length on the intensity of a C3H bending mode is explored and interpreted in terms of conformer distribution. The relative intensity contribution of a methyl mode compared to the total C3H stretch intensity is shown to be linear in the number of methyl groups in the alkane, and can be used to predict quantitative spectra a priori based on structure alone.

  4. Quantitative Vapor-phase IR Intensities and DFT Computations to Predict Absolute IR Spectra based on Molecular Structure: I. Alkanes

    SciTech Connect

    Williams, Stephen D.; Johnson, Timothy J.; Sharpe, Steven W.; Yavelak, Veronica; Oats, R. P.; Brauer, Carolyn S.

    2013-11-13

    Recently recorded quantitative IR spectra of a variety of gas-phase alkanes are shown to have integrated intensities in both the C-H stretching and C-H bending regions that depend linearly on the molecular size, i.e. the number of C-H bonds. This result is well predicted from CH4 to C15H32 by DFT computations of IR spectra at the B3LYP/6-31+G(d,p) level of DFT theory. A simple model predicting the absolute IR band intensities of alkanes based only on structural formula is proposed: For the C-H stretching band near 2930 cm-1 this is given by (in km/mol): CH¬_str = (34±3)*CH – (41±60) where CH is number of C-H bonds in the alkane. The linearity is explained in terms of coordinated motion of methylene groups rather than the summed intensities of autonomous -CH2- units. The effect of alkyl chain length on the intensity of a C-H bending mode is explored and interpreted in terms of conformer distribution. The relative intensity contribution of a methyl mode compared to the total C-H stretch intensity is shown to be linear in the number of terminal methyl groups in the alkane, and can be used to predict quantitative spectra a priori based on structure alone.

  5. Controlling local currents in molecular junctions

    NASA Astrophysics Data System (ADS)

    Yadalam, Hari Kumar; Harbola, Upendra

    2016-09-01

    The effects of nonequilibrium constraints and dephasing on the circulating currents in molecular junctions are analyzed. Circulating currents are manifestations of quantum effects and can be induced either by externally applied bias or an external magnetic field through the molecular system. In a symmetric Aharonov-Bohm ring, bond currents have two contributions, bias driven and magnetic field driven. We analyze the competition between these two contributions and show that, as a consequence, current through one of the branches can be completely suppressed. We then study the effect of asymmetry (as a result of chemical substitution) on the current pathways inside the molecule and study asymmetry-induced circulating currents (without magnetic field) by tuning the coupling strength of the substituent (at finite bias).

  6. 1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies.

    PubMed

    Garrido, Nuno M; Queimada, António J; Jorge, Miguel; Macedo, Eugénia A; Economou, Ioannis G

    2009-09-08

    The 1-octanol/water partition coefficient is an important thermodynamic variable usually employed to understand and quantify the partitioning of solutes between aqueous and organic phases. It finds widespread use in many empirical correlations to evaluate the environmental fate of pollutants as well as in the design of pharmaceuticals. The experimental evaluation of 1-octanol/water partition coefficients is an expensive and time-consuming procedure, and thus, theoretical estimation methods are needed, particularly when a physical sample of the solute may not yet be available, such as in pharmaceutical screening. 1-Octanol/water partition coefficients can be obtained from Gibbs free energies of solvation of the solute in both the aqueous and the octanol phases. The accurate evaluation of free energy differences remains today a challenging problem in computational chemistry. In order to study the absolute solvation Gibbs free energies in 1-octanol, a solvent that can mimic many properties of important biological systems, free energy calculations for n-alkanes in the range C1-C8 were performed using molecular simulation techniques, following the thermodynamic integration approach. In the first part of this paper, we test different force fields by evaluating their performance in reproducing pure 1-octanol properties. It is concluded that all-atom force fields can provide good accuracy but at the cost of a higher computational time compared to that of the united-atom force fields. Recent versions of united-atom force fields, such as Gromos and TraPPE, provide satisfactory results and are, thus, useful alternatives to the more expensive all-atom models. In the second part of the paper, the Gibbs free energy of solvation in 1-octanol is calculated for several n-alkanes using three force fields to describe the solutes, namely Gromos, TraPPE, and OPLS-AA. Generally, the results obtained are in excellent agreement with the available experimental data and are of similar

  7. Localization of energy on the molecular scale

    SciTech Connect

    Lindenberg, K.; Brown, D.W.

    1997-12-31

    We discuss the spontaneous localization of vibrational energy in translationally invariant anharmonic chains at finite temperatures. In addition to the familiar energy-driven coherent mechanisms, which are rapidly degraded by thermal fluctuations, we identify the entropy-driven phenomenon we call {open_quotes}stochastic localization{close_quotes}, within which we include a number of characteristics of soft anharmonic oscillators in thermal equilibrium. Principal among these are a tendency for soft oscillators to spend more time at higher energies than comparable harmonic oscillators, and for high-energy fluctuations in soft oscillators to persist for longer times than lower-energy fluctuations, leading to a tendency for energy fluctuations to be organized into {open_quotes}bursts{close_quotes} separated by intervals of relative quiet. We illustrate the effects of stochastic localization on a bistable impurity embedded in a chain of soft oscillators by comparing it to an impurity embedded in a harmonic chain. Effects on transition rates at a given system energy can be quite dramatic.

  8. Structural determination of molecular stereochemistry using VCD spectroscopy and a conformational code: absolute configuration and solution conformation of a chiral liquid pesticide, (R)-(+)-malathion.

    PubMed

    Izumi, Hiroshi; Ogata, Atsushi; Nafie, Laurence A; Dukor, Rina K

    2009-01-01

    The absolute configuration and solution conformation of (R)-(+)-malathion were determined by using vibrational circular dichroism spectroscopy and a fragment-conformational search with a recently published conformational code. The determination of molecular stereochemistry was carried out without a conformational search using molecular mechanics calculations. Density functional theory calculations of the fragments of (R)-malathion, ethyl propionate, (R)-ethyl 2-(methylthio)propanoate, (R)-diethyl 2-(methylthio)succinate, and O,O,S-trimethyl phosphorodithioate were carried out, and the principal conformational features of the fragments were profiled. This fragment-conformational search reduces the time needed for the selection of the predominant conformations for (R)-malathion and significantly improves the accuracy of the determination of absolute configuration.

  9. Absolute infrared vibrational band intensities of molecular ions determined by direct laser absorption spectroscopy in fast ion beams

    SciTech Connect

    Keim, E.R.; Polak, M.L.; Owrutsky, J.C.; Coe, J.V.; Saykally, R.J. )

    1990-09-01

    The technique of direct laser absorption spectroscopy in fast ion beams has been employed for the determination of absolute integrated band intensities ({ital S}{sup 0}{sub {ital v}}) for the {nu}{sub 3} fundamental bands of H{sub 3}O{sup +} and NH{sup +}{sub 4}. In addition, the absolute band intensities for the {nu}{sub 1} fundamental bands of HN{sup +}{sub 2} and HCO{sup +} have been remeasured. The values obtained in units of cm{sup {minus}2} atm{sup {minus}1} at STP are 1880(290) and 580(90) for the {nu}{sub 1} fundamentals of HN{sup +}{sub 2} and HCO{sup +}, respectively; and 4000(800) and 1220(190) for the {nu}{sub 3} fundamentals of H{sub 3}O{sup +} and NH{sup +}{sub 4}, respectively. Comparisons with {ital ab} {ital initio} results are presented.

  10. Absolute Zero

    NASA Astrophysics Data System (ADS)

    Donnelly, Russell J.; Sheibley, D.; Belloni, M.; Stamper-Kurn, D.; Vinen, W. F.

    2006-12-01

    Absolute Zero is a two hour PBS special attempting to bring to the general public some of the advances made in 400 years of thermodynamics. It is based on the book “Absolute Zero and the Conquest of Cold” by Tom Shachtman. Absolute Zero will call long-overdue attention to the remarkable strides that have been made in low-temperature physics, a field that has produced 27 Nobel Prizes. It will explore the ongoing interplay between science and technology through historical examples including refrigerators, ice machines, frozen foods, liquid oxygen and nitrogen as well as much colder fluids such as liquid hydrogen and liquid helium. A website has been established to promote the series: www.absolutezerocampaign.org. It contains information on the series, aimed primarily at students at the middle school level. There is a wealth of material here and we hope interested teachers will draw their student’s attention to this website and its substantial contents, which have been carefully vetted for accuracy.

  11. Absolute localization of ground robots by matching LiDAR and image data in dense forested environments

    NASA Astrophysics Data System (ADS)

    Hussein, Marwan; Renner, Matthew; Iagnemma, Karl

    2014-06-01

    A method for the autonomous geolocation of ground vehicles in forest environments is discussed. The method provides an estimate of the global horizontal position of a vehicle strictly based on finding a geometric match between a map of observed tree stems, scanned in 3D by Light Detection and Ranging (LiDAR) sensors onboard the vehicle, to another stem map generated from the structure of tree crowns analyzed from high resolution aerial orthoimagery of the forest canopy. Extraction of stems from 3D data is achieved by using Support Vector Machine (SVM) classifiers and height above ground filters that separate ground points from vertical stem features. Identification of stems from overhead imagery is achieved by finding the centroids of tree crowns extracted using a watershed segmentation algorithm. Matching of the two maps is achieved by using a robust Iterative Closest Point (ICP) algorithm that determines the rotation and translation vectors to align the datasets. The alignment is used to calculate the absolute horizontal location of the vehicle. The method has been tested with real-world data and has been able to estimate vehicle geoposition with an average error of less than 2 m. It is noted that the algorithm's accuracy performance is currently limited by the accuracy and resolution of aerial orthoimagery used. The method can be used in real-time as a complement to the Global Positioning System (GPS) in areas where signal coverage is inadequate due to attenuation by the forest canopy, or due to intentional denied access. The method has two key properties that are significant: i) It does not require a priori knowledge of the area surrounding the robot. ii) Uses the geometry of detected tree stems as the only input to determine horizontal geoposition.

  12. Absolute Summ

    NASA Astrophysics Data System (ADS)

    Phillips, Alfred, Jr.

    Summ means the entirety of the multiverse. It seems clear, from the inflation theories of A. Guth and others, that the creation of many universes is plausible. We argue that Absolute cosmological ideas, not unlike those of I. Newton, may be consistent with dynamic multiverse creations. As suggested in W. Heisenberg's uncertainty principle, and with the Anthropic Principle defended by S. Hawking, et al., human consciousness, buttressed by findings of neuroscience, may have to be considered in our models. Predictability, as A. Einstein realized with Invariants and General Relativity, may be required for new ideas to be part of physics. We present here a two postulate model geared to an Absolute Summ. The seedbed of this work is part of Akhnaton's philosophy (see S. Freud, Moses and Monotheism). Most important, however, is that the structure of human consciousness, manifest in Kenya's Rift Valley 200,000 years ago as Homo sapiens, who were the culmination of the six million year co-creation process of Hominins and Nature in Africa, allows us to do the physics that we do. .

  13. Absolute Photometry

    NASA Astrophysics Data System (ADS)

    Hartig, George

    1990-12-01

    The absolute sensitivity of the FOS will be determined in SV by observing 2 stars at 3 epochs, first in 3 apertures (1.0", 0.5", and 0.3" circular) and then in 1 aperture (1.0" circular). In cycle 1, one star, BD+28D4211 will be observed in the 1.0" aperture to establish the stability of the sensitivity and flat field characteristics and improve the accuracy obtained in SV. This star will also be observed through the paired apertures since these are not calibrated in SV. The stars will be observed in most detector/grating combinations. The data will be averaged to form the inverse sensitivity functions required by RSDP.

  14. Extragalactic chemistry of molecular gas: lessons from the local universe.

    PubMed

    García-Burillo, S; Fuente, A; Martín-Pintado, J; Usero, A; Graciá-Carpio, J; Planesas, P

    2006-01-01

    Observational constraints provided by high resolution and high sensitivity observations of external galaxies made in the millimetre and sub-millimetre range have started to put on a firm footing the study of the extragalactic chemistry of molecular gas. In particular, the availability of multi-species and multi-line surveys of nearby galaxies is central to the interpretation of existent and forthcoming millimetre observations of the high redshift universe. Probing the physical and chemical status of molecular gas in starbursts and active galaxies (AGN) requires the use of specific tracers of the relevant energetic phenomena that are known to be at play in these galaxies: large-scale shocks, strong UV fields, cosmic rays and X-rays. We present below the first results of an ongoing survey, allying the IRAM 30 m telescope with the Plateau de Bure interferometer (PdBI), devoted to the study of the chemistry of molecular gas in a sample of starbursts and AGN of the local universe. These observations highlight the existence of a strong chemical differentiation in the molecular disks of starbursts and AGN.

  15. Characterising the Dense Molecular Gas in Exceptional Local Galaxies

    NASA Astrophysics Data System (ADS)

    Tunnard, Richard C. A.

    2016-08-01

    The interferometric facilities now coming online (the Atacama Large Millimetre Array (ALMA) and the NOrthern Extended Millimeter Array (NOEMA)) and those planned for the coming decade (the Next Generation Very Large Array (ngVLA) and the Square Kilometre Array (SKA)) in the radio to sub-millimetre regimes are opening a window to the molecular gas in high-redshift galaxies. However, our understanding of similar galaxies in the local universe is still far from complete and the data analysis techniques and tools needed to interpret the observations in consistent and comparable ways are yet to be developed. I first describe the Monte Carlo Markov Chain (MCMC) script developed to empower a public radiative transfer code. I characterise both the public code and MCMC script, including an exploration of the effect of observing molecular lines at high redshift where the Cosmic Microwave Background (CMB) can provide a significant background, as well as the effect this can have on well-known local correlations. I present two studies of ultraluminous infrared galaxies (ULIRGs) in the local universe making use of literature and collaborator data. In the first of these, NGC6240, I use the wealth of available data and the geometry of the source to develop a multi-phase, multi-species model, finding evidence for a complex medium of hot diffuse and cold dense gas in pressure equilibrium. Next, I study the prototypical ULIRG Arp 220; an extraordinary galaxy rendered especially interesting by the controversy over the power source of the western of the two merger nuclei and its immense luminosity and dust obscuration. Using traditional grid based methods I explore the molecular gas conditions within the nuclei and find evidence for chemical differentiation between the two nuclei, potentially related to the obscured power source. Finally, I investigate the potential evolution of proto-clusters over cosmic time with sub-millimetre observations of 14 radio galaxies, unexpectedly finding

  16. Molecular gas in supernova local environments unveiled by EDGE

    NASA Astrophysics Data System (ADS)

    Galbany, L.; Mora, L.; González-Gaitán, S.; Bolatto, A.; Dannerbauer, H.; López-Sánchez, Á. R.; Maeda, K.; Pérez, S.; Pérez-Torres, M. A.; Sánchez, S. F.; Wong, T.; Badenes, C.; Blitz, L.; Marino, R. A.; Utomo, D.; Van de Ven, G.

    2017-03-01

    CO observations allow estimation of the gas content of molecular clouds, which trace the reservoir of cold gas fuelling star formation, as well as determination of extinction via H2 column density, N(H2). Here, we study millimetric and optical properties at 26 supernovae (SNe) locations of different types in a sample of 23 nearby galaxies, by combining molecular 12C16O (J = 1 → 0) resolved maps from the Extragalactic Database for Galaxy Evolution (EDGE) survey and optical Integral Field Spectroscopy (IFS) from the Calar Alto Legacy Integral Field Area (CALIFA) survey. We found an even clearer separation between type II and type Ibc SNe in terms of molecular gas than is found in the optical using Hα emission as a proxy for the current star formation (SF) rate, which reinforces the fact that SNe Ibc are more associated with SF environments. While AV at SN locations is similar for SNe II and SNe Ibc and higher than for SNe Ia, N(H2) is significantly higher for SNe Ibc than for SNe II and Ia. When compared with alternative extinction estimations made directly from SN photometry and spectroscopy, we find that our SNe Ibc also have redder colour excess, but showed standard Na i D absorption pseudo-equivalent widths (˜1 Å). In some cases, we find no extinction when IT is estimated from the environment but high amounts of extinction when measured from SN observations, which suggests that circumstellar material or dust sublimation may be playing a role. This work serves as a benchmark for future studies combining last-generation millimetre and optical IFS instruments to reveal the local environmental properties of extragalactic SNe.

  17. Indole Localization in an Explicit Bilayer Revealed via Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Norman, Kristen

    2005-11-01

    It is well known that the amino-acid tryptophan is particularly stable in the interfacial region of biological membranes, and this preference is a property of the tryptophan side-chain. Analogues of this side-chain, such as indole, strongly localize in the interfacial region, especially near the glycerol moiety of the lipids in the bilayer. Using molecular dynamics calculations, we determine the potential of mean force (PMF) for indoles in the bilayer. We compare the calculated PMF for indole with that of benzene to show that exclusion from the center of the lipid bilayer does not occur in all aromatics, but is strong in indoles. We find three minima in the PMF. Indole is most stabilized near the glycerol moiety. A weaker binding location is found near the choline groups of the lipid molecules. An even weaker binding side is found near the center of the lipid hydrocarbon core. Comparisions between uncharged, weakly charged, and highly charged indoles demonstrate that the exclusion is caused by the charge distribution on the indole rather than the ``lipo-phobic'' effect. High temperature simulations are used to determine the relative contribution of enthalpy and entropy to indole localization. The orientation of indole is found to be largely charge independent and is a strong function of depth within the bilayer. We find good agreement between simulated SCD order parameters for indole and experimentally determined order parameters.

  18. Molecular Outflows in Local ULIRGs: Energetics from Multitransition OH Analysis

    NASA Astrophysics Data System (ADS)

    González-Alfonso, E.; Fischer, J.; Spoon, H. W. W.; Stewart, K. P.; Ashby, M. L. N.; Veilleux, S.; Smith, H. A.; Sturm, E.; Farrah, D.; Falstad, N.; Meléndez, M.; Graciá-Carpio, J.; Janssen, A. W.; Lebouteiller, V.

    2017-02-01

    We report on the energetics of molecular outflows in 14 local ultraluminous infrared galaxies (ULIRGs) that show unambiguous outflow signatures (P Cygni profiles or high-velocity absorption wings) in the far-infrared lines of OH measured with the Herschel/PACS spectrometer. All sample galaxies are gas-rich mergers at various stages of the merging process. Detection of both ground-state (at 119 and 79 μm) and one or more radiatively excited (at 65 and 84 μm) lines allows us to model the nuclear gas (≲300 pc) and the more extended components using spherically symmetric radiative transfer models. Reliable models and the corresponding energetics are found in 12 of the 14 sources. The highest molecular outflow velocities are found in buried sources, in which slower but massive expansion of the nuclear gas is also observed. With the exception of a few outliers, the outflows have momentum fluxes of (2–5) × L IR/c and mechanical luminosities of (0.1–0.3)% of L IR. The moderate momentum boosts in these sources (≲3) suggest that the outflows are mostly momentum driven by the combined effects of active galactic nuclei (AGNs) and nuclear starbursts, as a result of radiation pressure, winds, and supernova remnants. In some sources (∼20%), however, powerful (1010.5–11 L ⊙) AGN feedback and (partially) energy-conserving phases are required, with momentum boosts in the range of 3–20. These outflows appear to be stochastic, strong AGN feedback events that occur throughout the merging process. In a few sources, the outflow activity in the innermost regions has subsided in the past ∼1 Myr. While OH traces the molecular outflows at subkiloparsec scales, comparison of the masses traced by OH with those previously inferred from tracers of more extended outflowing gas suggests that most mass is loaded (with loading factors of \\dot{M}/{SFR}=1{--}10) from the central galactic cores (a few × 100 pc), qualitatively consistent with an ongoing inside-out quenching of

  19. Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details.

    PubMed

    Massarczyk, M; Rudack, T; Schlitter, J; Kuhne, J; Kötting, C; Gerwert, K

    2017-02-08

    Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call local mode analysis (LMA) for calculating IR spectra and assigning spectral IR-bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory. Through LMA the decoding of IR spectra no longer requires several simulations or optimizations. The novel approach correlates the motions of atoms of a single simulation with the corresponding IR bands and provides direct access to the structural information encoded in IR spectra. Either the contributions of a particular atom or atom group to the complete IR spectrum of the molecule are visualized, or an IR-band is selected to visualize the corresponding structural motions. Thus, LMA decodes the detailed information contained in IR spectra and provides an intuitive approach for structural biologists and biochemists. The unique feature of LMA is the bidirectional analysis connecting structural details to spectral features and vice versa spectral features to molecular motions.

  20. Molecular Designs for Controlling the Local Environments around Metal Ions

    PubMed Central

    Cook, Sarah A.; Borovik, A.S.

    2015-01-01

    CONSPECTUS The functions of metal complexes are directly linked to the local environment in which they are housed; modifications to the local environment (or secondary coordination sphere) are known to produce changes in key properties of the metal centers that can affect reactivity. Non-covalent interactions are the most common and influential forces that regulate the properties of secondary coordination spheres, which leads to complexities in structure that are often difficult to achieve in synthetic systems. Using key architectural features from the active sites of metalloproteins as inspiration, we have developed molecular systems that enforce intramolecular hydrogen bonds (H-bonds) around a metal center via incorporation of H-bond donors and acceptors into rigid ligand scaffolds. We have utilized these molecular species to probe mechanistic aspects of biological dioxygen activation and water oxidation. This Account describes the stabilization and characterization of unusual M–oxo and heterobimetallic complexes. These types of species have been implicated in a range of oxidative processes in biology but are often difficult to study because of their inherent reactivity. Our H-bonding ligand systems allowed us to prepare an FeIII–oxo species directly from the activation of O2 that was subsequently oxidized to form a monomeric FeIV–oxo species with an S = 2 spin state, similar to those species proposed as key intermediates in non-heme monooxygenases. We also demonstrated that a single MnIII–oxo center that was prepared from water could be converted to a high spin MnV–oxo species via stepwise oxidation—a process that mimics the oxidative charging of the oxygen-evolving complex (OEC) of photosystem II. Current mechanisms for photosynthetic O–O bond formation invoke a MnIV–oxyl species rather than the isoelectronic MnV–oxo system as the key oxidant based on computational studies. However, there is no experimental information to support the existence

  1. Molecular designs for controlling the local environments around metal ions.

    PubMed

    Cook, Sarah A; Borovik, A S

    2015-08-18

    The functions of metal complexes are directly linked to the local environment in which they are housed; modifications to the local environment (or secondary coordination sphere) are known to produce changes in key properties of the metal centers that can affect reactivity. Noncovalent interactions are the most common and influential forces that regulate the properties of secondary coordination spheres, which leads to complexities in structure that are often difficult to achieve in synthetic systems. Using key architectural features from the active sites of metalloproteins as inspiration, we have developed molecular systems that enforce intramolecular hydrogen bonds (H-bonds) around a metal center via incorporation of H-bond donors and acceptors into rigid ligand scaffolds. We have utilized these molecular species to probe mechanistic aspects of biological dioxygen activation and water oxidation. This Account describes the stabilization and characterization of unusual M-oxo and heterobimetallic complexes. These types of species have been implicated in a range of oxidative processes in biology but are often difficult to study because of their inherent reactivity. Our H-bonding ligand systems allowed us to prepare an Fe(III)-oxo species directly from the activation of O2 that was subsequently oxidized to form a monomeric Fe(IV)-oxo species with an S = 2 spin state, similar to those species proposed as key intermediates in non-heme monooxygenases. We also demonstrated that a single Mn(III)-oxo center that was prepared from water could be converted to a high-spin Mn(V)-oxo species via stepwise oxidation, a process that mimics the oxidative charging of the oxygen-evolving complex (OEC) of photosystem II. Current mechanisms for photosynthetic O-O bond formation invoke a Mn(IV)-oxyl species rather than the isoelectronic Mn(V)-oxo system as the key oxidant based on computational studies. However, there is no experimental information to support the existence of a Mn

  2. Teaching Absolute Value Meaningfully

    ERIC Educational Resources Information Center

    Wade, Angela

    2012-01-01

    What is the meaning of absolute value? And why do teachers teach students how to solve absolute value equations? Absolute value is a concept introduced in first-year algebra and then reinforced in later courses. Various authors have suggested instructional methods for teaching absolute value to high school students (Wei 2005; Stallings-Roberts…

  3. Locality and topology in the molecular Aharonov-Bohm effect.

    PubMed

    Sjöqvist, Erik

    2002-11-18

    It is shown that the molecular Aharonov-Bohm effect is neither nonlocal nor topological in the sense of the standard magnetic Aharonov-Bohm effect. It is further argued that there is a close relationship between the molecular Aharonov-Bohm effect and the Aharonov-Casher effect for an electrically neutral spin -1 / 2 particle encircling a line of charge.

  4. Assessment of delocalized and localized molecular orbitals through electron momentum spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Yuan; Cheung, Ling-Fung; Ning, Chuan-Gang

    2014-06-01

    Recently, there was a hot controversy about the concept of localized orbitals, which was triggered by Grushow's work titled “Is it time to retire the hybrid atomic orbital?” [J. Chem. Educ. 88, 860 (2011)]. To clarify the issue, we assess the delocalized and localized molecular orbitals from an experimental view using electron momentum spectroscopy. The delocalized and localized molecular orbitals based on various theoretical models for CH4, NH3, and H2O are compared with the experimental momentum distributions. Our results show that the delocalized molecular orbitals rather than the localized ones can give a direct interpretation of the experimental (e, 2e) results.

  5. Localized excitations in hydrogen-bonded molecular crystals

    NASA Astrophysics Data System (ADS)

    Alexander, D. M.; Krumhansl, J. A.

    1986-05-01

    Localized excitations analogous to the small Holstein polaron, to localized modes in alkali halides, and to localized excitonic states, are postulated for a set of internal vibrational modes in crystalline acetanilide. The theoretical framework in which one can describe the characteristics of the ir and Raman spectroscopy peaks associated with these localized states is adequately provided by the Davydov model (formally equivalent to the Holstein polaron model). The possible low-lying excitations arising from this model are determined using a variational approach. Hence, the contribution to the spectral function due to each type of excitation can be calculated. The internal modes of chief concern here are the amide-I (CO stretch) and the N-H stretch modes for which we demonstrate consistency of the theoretical model with the available ir data. Past theoretical approaches will be discussed and reasons why one should prefer one description over another will be examined.

  6. Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

    SciTech Connect

    Bresme, F.; Armstrong, J.

    2014-01-07

    We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation.

  7. Local indices for similarity analysis (LISA)-a 3D-QSAR formalism based on local molecular similarity.

    PubMed

    Verma, Jitender; Malde, Alpeshkumar; Khedkar, Santosh; Iyer, Radhakrishnan; Coutinho, Evans

    2009-12-01

    A simple quantitative structure activity relationship (QSAR) approach termed local indices for similarity analysis (LISA) has been developed. In this technique, the global molecular similarity is broken up as local similarity at each grid point surrounding the molecules and is used as a QSAR descriptor. In this way, a view of the molecular sites permitting favorable and rational changes to enhance activity is obtained. The local similarity index, calculated on the basis of Petke's formula, segregates the regions into "equivalent", "favored similar", and "disfavored similar" (alternatively "favored dissimilar") potentials with respect to a reference molecule in the data set. The method has been tested on three large and diverse data sets-thrombin, glycogen phosphorylase b, and thermolysin inhibitors. The QSAR models derived using genetic algorithm incorporated partial least square analysis statistics are found to be comparable to the ones obtained by the standard three-dimensional (3D)-QSAR methods, such as comparative molecular field analysis and comparative molecular similarity indices analysis. The graphical interpretation of the LISA models is straightforward, and the outcome of the models corroborates well with literature data. The LISA models give insight into the binding mechanisms of the ligand with the enzyme and allow fine-tuning of the molecules at the local level to improve their activity.

  8. Absolutely classical spin states

    NASA Astrophysics Data System (ADS)

    Bohnet-Waldraff, F.; Giraud, O.; Braun, D.

    2017-01-01

    We introduce the concept of "absolutely classical" spin states, in analogy to absolutely separable states of bipartite quantum systems. Absolutely classical states are states that remain classical (i.e., a convex sum of projectors on coherent states of a spin j ) under any unitary transformation applied to them. We investigate the maximal size of the ball of absolutely classical states centered on the maximally mixed state and derive a lower bound for its radius as a function of the total spin quantum number. We also obtain a numerical estimate of this maximal radius and compare it to the case of absolutely separable states.

  9. Analyzing the molecular mechanism of lipoprotein localization in Brucella

    PubMed Central

    Goolab, Shivani; Roth, Robyn L.; van Heerden, Henriette; Crampton, Michael C.

    2015-01-01

    Bacterial lipoproteins possess diverse structure and functionality, ranging from bacterial physiology to pathogenic processes. As such many lipoproteins, originating from Brucella are exploited as potential vaccines to countermeasure brucellosis infection in the host. These membrane proteins are translocated from the cytoplasm to the cell membrane where they are anchored peripherally by a multifaceted targeting mechanism. Although much research has focused on the identification and classification of Brucella lipoproteins and their potential use as vaccine candidates for the treatment of Brucellosis, the underlying route for the translocation of these lipoproteins to the outer surface of the Brucella (and other pathogens) outer membrane (OM) remains mostly unknown. This is partly due to the complexity of the organism and evasive tactics used to escape the host immune system, the variation in biological structure and activity of lipoproteins, combined with the complex nature of the translocation machinery. The biosynthetic pathway of Brucella lipoproteins involves a distinct secretion system aiding translocation from the cytoplasm, where they are modified by lipidation, sorted by the lipoprotein localization machinery pathway and thereafter equipped for export to the OM. Surface localized lipoproteins in Brucella may employ a lipoprotein flippase or the β-barrel assembly complex for translocation. This review provides an overview of the characterized Brucella OM proteins that form part of the OM, including a handful of other characterized bacterial lipoproteins and their mechanisms of translocation. Lipoprotein localization pathways in gram negative bacteria will be used as a model to identify gaps in Brucella lipoprotein localization and infer a potential pathway. Of particular interest are the dual topology lipoproteins identified in Escherichia coli and Haemophilus influenza. The localization and topology of these lipoproteins from other gram negative bacteria

  10. Absolute multilateration between spheres

    NASA Astrophysics Data System (ADS)

    Muelaner, Jody; Wadsworth, William; Azini, Maria; Mullineux, Glen; Hughes, Ben; Reichold, Armin

    2017-04-01

    Environmental effects typically limit the accuracy of large scale coordinate measurements in applications such as aircraft production and particle accelerator alignment. This paper presents an initial design for a novel measurement technique with analysis and simulation showing that that it could overcome the environmental limitations to provide a step change in large scale coordinate measurement accuracy. Referred to as absolute multilateration between spheres (AMS), it involves using absolute distance interferometry to directly measure the distances between pairs of plain steel spheres. A large portion of each sphere remains accessible as a reference datum, while the laser path can be shielded from environmental disturbances. As a single scale bar this can provide accurate scale information to be used for instrument verification or network measurement scaling. Since spheres can be simultaneously measured from multiple directions, it also allows highly accurate multilateration-based coordinate measurements to act as a large scale datum structure for localized measurements, or to be integrated within assembly tooling, coordinate measurement machines or robotic machinery. Analysis and simulation show that AMS can be self-aligned to achieve a theoretical combined standard uncertainty for the independent uncertainties of an individual 1 m scale bar of approximately 0.49 µm. It is also shown that combined with a 1 µm m‑1 standard uncertainty in the central reference system this could result in coordinate standard uncertainty magnitudes of 42 µm over a slender 1 m by 20 m network. This would be a sufficient step change in accuracy to enable next generation aerospace structures with natural laminar flow and part-to-part interchangeability.

  11. Global and local properties used as analyses tools for molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Bachlechner, Martina E.; Anderson, Jonas T.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Schiffbauer, Jarrod E.; Burky, Melissa R.; Ducatman, Samuel C.; Guffey, Eric J.; Serrano Ramos2, Fernando

    2006-03-01

    Molecular dynamics simulations have been used to study mechanical failure in realistic interface materials. Averaging over the individual atoms' contributions yields local and global information including displacements, bond angles, strains, stress tensor components, and pair distribution functions. A combined analysis of global and local properties facilitates detailed insight in the mechanisms of failure, which will eventually guide on how to prevent failure of interfaces.

  12. Adjusting Local Molecular Environment for Giant Ambient Thermal Contraction.

    PubMed

    Shen, Xingyuan; Connolly, Timothy; Huang, Yuhui; Colvin, Michael; Wang, Changchun; Lu, Jennifer

    2016-12-01

    A low-energy triggered switch that can generate mechanoresponse has great technological potential. A submolecular moiety, S-dibenzocyclooctadiene (DBCOD) that is composed of a flexible eight-membered ring connecting to a phenyl ring at each end, undergoes a conformational change from twist-boat to chair under a low-energy stimulus such as near infrared irradiation, resulting in thermal contraction of DBCOD-based polymer. Experimental evidence corroborated by theoretical calculations indicates that introducing molecular asymmetry can reduce crystallinity significantly and consequently facilitate the kinetics of the conformational change. It has been demonstrated that the negative thermal expansion (NTE) coefficient of a DBCOD-based polymer system can be adjusted in a range from -1140 to -2350 ppm K(-1) . -2350 ppm K(-1) is ≈10 times better than the value reported by the second best NTE system.

  13. Absolute nuclear material assay

    DOEpatents

    Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

    2012-05-15

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  14. Absolute nuclear material assay

    DOEpatents

    Prasad, Manoj K.; Snyderman, Neal J.; Rowland, Mark S.

    2010-07-13

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  15. Experimental observation of Anderson localization in laser-kicked molecular rotors

    NASA Astrophysics Data System (ADS)

    Bitter, Martin; Milner, Valery

    2016-05-01

    For the first time, the phenomenon of Anderson localization is observed and studied in a system of true quantum kicked rotors. Nitrogen molecules in a supersonic molecular jet are cooled down to 27 K and are rotationally excited by a periodic train of 24 high-intensity femtosecond pulses. Exponential distribution of the molecular angular momentum - the most unambiguous signature of Anderson localization - is measured directly by means of coherent Raman scattering. We demonstrate the suppressed growth of the molecular rotational energy with the number of laser kicks and study the dependence of the localization length on the kick strength. Both timing and amplitude noise in the pulse train is shown to destroy the localization and revive the diffusive growth of angular momentum.

  16. Absolute instability of the Gaussian wake profile

    NASA Technical Reports Server (NTRS)

    Hultgren, Lennart S.; Aggarwal, Arun K.

    1987-01-01

    Linear parallel-flow stability theory has been used to investigate the effect of viscosity on the local absolute instability of a family of wake profiles with a Gaussian velocity distribution. The type of local instability, i.e., convective or absolute, is determined by the location of a branch-point singularity with zero group velocity of the complex dispersion relation for the instability waves. The effects of viscosity were found to be weak for values of the wake Reynolds number, based on the center-line velocity defect and the wake half-width, larger than about 400. Absolute instability occurs only for sufficiently large values of the center-line wake defect. The critical value of this parameter increases with decreasing wake Reynolds number, thereby indicating a shrinking region of absolute instability with decreasing wake Reynolds number. If backflow is not allowed, absolute instability does not occur for wake Reynolds numbers smaller than about 38.

  17. Influence of local anesthetics on molecular organization in phosphatidylethanolamine membranes

    SciTech Connect

    Kelusky, E.C.; Smith, I.C.

    1984-09-01

    The influence of the local anesthetics tetracaine (TTC) and procaine (PRC) on bilayers of specifically deuterated phosphatidylethanolamines (PE) has been studied by /sup 2/H and /sup 31/P NMR. Dimyristoylphosphatidylethanolamines (DMPE), deuterated at positions 2, 4, and 14 of the sn-2 chain, position 2 of the sn-1 chain, and in the ethanolamine headgroup, were mixed 1:1 with a semisynthetic egg PE and the effect of measured quantities of TTC and PRC on the /sup 2/H quadrupole splittings, spin-lattice relaxation times, and /sup 31/P chemical shift anisotropy were observed. Experiments were performed at pH 5.5, when the anesthetics are primarily charged, and at pH 9.5, when they are uncharged. Tetracaine was observed to disorder the hydrocarbon region of the bilayer and to induce a conformational change in the PE headgroup. Conversely, procaine had little or no effect on the hydrocarbon region and induced only a small change in the headgroup. These conformational changes and disordering effects, when adjusted for anesthetic partitioning, are essentially independent of the charge on the anesthetic. However, at pH 5.5 and low TTC/PE molar ratios (less than 0.1), the /sup 2/H NMR spectra showed two lipid environments--one corresponding to free PE and the other to PE in contact with TTC. Continued addition of TTC resulted in the eventual disappearance of the free PE signal and the corresponding growth of the signal from PE in contact with TTC. At pH 9.5, when TTC is uncharged, only one signal is observed. In mixtures of PE and phosphatidylserine, a conformational change in the headgroup was noted which was similar to that seen in the pure PE; however, there was no evidence for slow lateral diffusion of the anesthetics.

  18. Ionic photofragmentation and photoionization of dimethyl ether in the VUV and soft X-ray regions (8.5 80 eV) absolute oscillator strengths for molecular and dissociative photoionization

    NASA Astrophysics Data System (ADS)

    Feng, Renfei; Cooper, Glyn; Brion, C. E.

    2001-08-01

    The branching ratios for molecular and dissociative photoionization of dimethyl ether (CH 3OCH 3, DME) have been measured in the VUV and soft X-ray regions using dipole (e,e+ion) coincidence spectroscopy (˜1 eV FWHM) at equivalent photon energies from the first ionization threshold up to 80 eV. The absolute partial oscillator strengths (cross-sections) for molecular and dissociative photoionization have been determined from recently published absolute photoabsorption oscillator strength data [R. Feng, G. Cooper, C.E. Brion, Chem. Phys. 260 (2000) 391] together with the photoionization branching ratios and the (multi-dissociative-corrected) photoionization efficiency obtained from time-of-flight mass spectra reported in the present work. No stable multiply charged molecular ion(s) from DME have been found in the present work. However, the fact that the photoionization efficiency has been measured as greater than unity above ˜30 eV indicates the existence of multi-dissociative products from Coulomb explosion of multiply charged ions. Appearance potentials of all ion products from DME are also reported. The presently reported results are compared with the previously published data where possible.

  19. New molecular descriptors based on local properties at the molecular surface and a boiling-point model derived from them.

    PubMed

    Ehresmann, Bernd; de Groot, Marcel J; Alex, Alexander; Clark, Timothy

    2004-01-01

    New molecular descriptors based on statistical descriptions of the local ionization potential, local electron affinity, and the local polarizability at the surface of the molecule are proposed. The significance of these descriptors has been tested by calculating them for the Maybridge database in addition to our set of 26 descriptors reported previously. The new descriptors show little correlation with those already in use. Furthermore, the principal components of the extended set of descriptors for the Maybridge data show that especially the descriptors based on the local electron affinity extend the variance in our set of descriptors, which we have previously shown to be relevant to physical properties. The first nine principal components are shown to be most significant. As an example of the usefulness of the new descriptors, we have set up a QSPR model for boiling points using both the old and new descriptors.

  20. Evaluation of the absolute photoluminescence quantum yields of molecularly doped organic composite films and the electroluminescence efficiencies of molecular light-emitting devices containing oligoheterocycles as efficient emission centers

    NASA Astrophysics Data System (ADS)

    Kushto, Gary P.; Hill, Ian G.; Mitschke, Ullrich; Baeuerle, Peter; Kafafi, Zakya H.

    2001-02-01

    The absolute photoluminescence quantum yields ((Phi) PL) of three end-capped oligothiophene derivatives dispersed in N,N'-((alpha) -naphthyl)-N,N'-diphenyl-1,1'-biphenyl ((alpha) -NPD) have been evaluated and the most efficient of the emitters was used as a dopant in molecular organic LEDs. Composite films of 2,5-bis [5-(4,5,6,7- tetrahydrobenzo[b]thien-2-yl) thien-2-yl]-furan (EC5FUR); 2,5-bis [5-(4,5,6,7- tetrahydrobenzo[b]thien-2-yl) thien-2-yl]-oxazole (EC5OXZ) and 2,5-bis [5-(4,5,6,7- tetrahydrobenzo[b]thien-2-yl)thien-2-yl]-1,3,4- oxadiazole (EC5OXD) doped into (alpha) -NPD were found to have (Phi) PL values of 78, 62 and 28%, respectively. MOLED devices were fabricated using an EC5FUR/(alpha) -NPD composite as the emitting layer and the external quantum efficiencies ((eta) EL) of these devices were evaluated. The results of the device characterization show that the inclusion of EC5FUR in the NPD hole transport layer increases the device (eta) EL to 1.45% at a current density of 10 mA/cm2. In addition, the concentration dependence of the (eta) EL on the EC5FUR dopant in certain device structures when considered in conjunction with the current results of ultraviolet photoemission spectroscopic experiments suggests that this dopant species may be acting as both a hole and electron trap in the (alpha) -NPD host.

  1. Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies.

    PubMed

    Bulat, Felipe A; Toro-Labbé, Alejandro; Brinck, Tore; Murray, Jane S; Politzer, Peter

    2010-11-01

    We describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules.

  2. Localization of open-shell molecular orbitals via least change from fragments to molecule

    NASA Astrophysics Data System (ADS)

    Li, Hongyang; Liu, Wenjian; Suo, Bingbing

    2017-03-01

    Both top-down and bottom-up localization schemes are proposed for constructing localized molecular orbitals (LMOs) of open-shell systems, via least change from fragments to molecule. The success of both schemes stems from (1) the primitive fragment LMOs that are local not only in space but also in energy and (2) the "conquer step" that allows arbitrary assignment of the unpaired electrons to fragments. Moreover, integral occupations are retained, so as to facilitate subsequent treatment of electron correlation and excitation.

  3. Photo-electron momentum distribution and electron localization studies from laser-induced atomic and molecular dissociations

    NASA Astrophysics Data System (ADS)

    Ray, Dipanwita

    The broad objective of ultrafast strong-field studies is to be able to measure and control atomic and molecular dynamics on a femtosecond timescale. This thesis work has two major themes: (1) Study of high-energy photoelectron distributions from atomic targets. (2) Electron localization control in atomic and molecular reactions using shaped laser pulses. The first section focuses on the study of photoelectron diffraction patterns of simple atomic targets to understand the target structure. We measure the full vector momentum spectra of high energy photoelectrons from atomic targets (Xe, Ar and Kr) generated by intense laser pulses. The target dependence of the angular distribution of the highest energy photoelectrons as predicted by Quantitative Rescattering Theory (QRS) is explored. More recent developments show target structure information can be retrieved from photoelectrons over a range of energies, from 4Up up to 10Up, independent of the peak intensity at which the photoelectron spectra have been measured. Controlling the fragmentation pathways by manipulating the pulse shape is another major theme of ultrafast science today. In the second section we study the asymmetry of electron (and ion) emission from atoms (and molecules) by interaction with asymmetric pulses formed by the superposition of two colors (800 & 400 nm). Xe electron momentum spectra obtained as a function of the two-color phase exhibit a pronounced asymmetry. Using QRS theory we can analyze this asymmetric yield of the high energy photoelectrons to determine accurately the laser peak intensity and the absolute phase of the two-color electric field. This can be used as a standard pulse calibration method for all two-color studies. Experiments showing strong left-right asymmetry in D+ ion yield from D2 molecules using two-color pulses is also investigated. The asymmetry effect is found to be very ion-energy dependent.

  4. Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals.

    PubMed

    Cui, Ganglong; Fang, Weihai; Yang, Weitao

    2010-01-14

    Time-dependent density functional theory (TDDFT) has broad application in the study of electronic response, excitation and transport. To extend such application to large and complex systems, we develop a reformulation of TDDFT equations in terms of non-orthogonal localized molecular orbitals (NOLMOs). NOLMO is the most localized representation of electronic degrees of freedom and has been used in ground state calculations. In atomic orbital (AO) representation, the sparsity of NOLMO is transferred to the coefficient matrix of molecular orbitals (MOs). Its novel use in TDDFT here leads to a very simple form of time propagation equations which can be solved with linear-scaling effort. We have tested the method for several long-chain saturated and conjugated molecular systems within the self-consistent charge density-functional tight-binding method (SCC-DFTB) and demonstrated its accuracy. This opens up pathways for TDDFT applications to large bio- and nano-systems.

  5. Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy.

    PubMed

    Gao, Xian; Wei, Zhipeng; Zhao, Fenghuan; Yang, Yahui; Chen, Rui; Fang, Xuan; Tang, Jilong; Fang, Dan; Wang, Dengkui; Li, Ruixue; Ge, Xiaotian; Ma, Xiaohui; Wang, Xiaohua

    2016-07-06

    We report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration.

  6. Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy

    PubMed Central

    Gao, Xian; Wei, Zhipeng; Zhao, Fenghuan; Yang, Yahui; Chen, Rui; Fang, Xuan; Tang, Jilong; Fang, Dan; Wang, Dengkui; Li, Ruixue; Ge, Xiaotian; Ma, Xiaohui; Wang, Xiaohua

    2016-01-01

    We report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration. PMID:27381641

  7. Experimental Observation of Dynamical Localization in Laser-Kicked Molecular Rotors

    NASA Astrophysics Data System (ADS)

    Bitter, M.; Milner, V.

    2016-09-01

    The periodically kicked rotor is a paradigm system for studying quantum effects on classically chaotic dynamics. The wave function of the quantum rotor localizes in angular momentum space, similarly to Anderson localization of the electronic wave function in disordered solids. Here, we observe dynamical localization in a system of true quantum rotors by subjecting nitrogen molecules to periodic sequences of femtosecond pulses. Exponential distribution of the molecular angular momentum—the hallmark of dynamical localization—is measured directly by means of coherent Raman scattering. We demonstrate the suppressed rotational energy growth with the number of laser kicks and study the dependence of the localization length on the kick strength. Because of its quantum coherent nature, both timing and amplitude noise are shown to destroy the localization and revive the diffusive growth of energy.

  8. Absolute molecular weight determination of hypromellose acetate succinate by size exclusion chromatography: use of a multi angle laser light scattering detector and a mixed solvent.

    PubMed

    Chen, Raymond; Ilasi, Nicholas; Sekulic, Sonja S

    2011-12-05

    Molecular weight distribution is an important quality attribute for hypromellose acetate succinate (HPMCAS), a pharmaceutical excipient used in spray-dried dispersions. Our previous study showed that neither relative nor universal calibration method of size exclusion chromatography (SEC) works for HPMCAS polymers. We here report our effort to develop a SEC method using a mass sensitive multi angle laser light scattering detector (MALLS) to determine molecular weight distributions of HPMCAS polymers. A solvent screen study reveals that a mixed solvent (60:40%, v/v 50mM NaH(2)PO(4) with 0.1M NaNO(3) buffer: acetonitrile, pH* 8.0) is the best for HPMCAS-LF and MF sub-classes. Use of a mixed solvent creates a challenging condition for the method that uses refractive index detector. Therefore, we thoroughly evaluated the method performance and robustness. The mean weight average molecular weight of a polyethylene oxide standard has a 95% confidence interval of (28,443-28,793) g/mol vs. 28,700g/mol from the Certificate of Analysis. The relative standard deviations of average molecular weights for all polymers are 3-6%. These results and the Design of Experiments study demonstrate that the method is accurate and robust.

  9. Absolute and relative blindsight.

    PubMed

    Balsdon, Tarryn; Azzopardi, Paul

    2015-03-01

    The concept of relative blindsight, referring to a difference in conscious awareness between conditions otherwise matched for performance, was introduced by Lau and Passingham (2006) as a way of identifying the neural correlates of consciousness (NCC) in fMRI experiments. By analogy, absolute blindsight refers to a difference between performance and awareness regardless of whether it is possible to match performance across conditions. Here, we address the question of whether relative and absolute blindsight in normal observers can be accounted for by response bias. In our replication of Lau and Passingham's experiment, the relative blindsight effect was abolished when performance was assessed by means of a bias-free 2AFC task or when the criterion for awareness was varied. Furthermore, there was no evidence of either relative or absolute blindsight when both performance and awareness were assessed with bias-free measures derived from confidence ratings using signal detection theory. This suggests that both relative and absolute blindsight in normal observers amount to no more than variations in response bias in the assessment of performance and awareness. Consideration of the properties of psychometric functions reveals a number of ways in which relative and absolute blindsight could arise trivially and elucidates a basis for the distinction between Type 1 and Type 2 blindsight.

  10. Absolute neutrino mass scale

    NASA Astrophysics Data System (ADS)

    Capelli, Silvia; Di Bari, Pasquale

    2013-04-01

    Neutrino oscillation experiments firmly established non-vanishing neutrino masses, a result that can be regarded as a strong motivation to extend the Standard Model. In spite of being the lightest massive particles, neutrinos likely represent an important bridge to new physics at very high energies and offer new opportunities to address some of the current cosmological puzzles, such as the matter-antimatter asymmetry of the Universe and Dark Matter. In this context, the determination of the absolute neutrino mass scale is a key issue within modern High Energy Physics. The talks in this parallel session well describe the current exciting experimental activity aiming to determining the absolute neutrino mass scale and offer an overview of a few models beyond the Standard Model that have been proposed in order to explain the neutrino masses giving a prediction for the absolute neutrino mass scale and solving the cosmological puzzles.

  11. Molecular Gas and Star Formation in Local Early-type Galaxies

    NASA Astrophysics Data System (ADS)

    Bureau, M.; Davis, T. A.; Alatalo, K.; Crocker, A. F.; Blitz, L.; Young, L. M.; Combes, F.; Bois, M.; Bournaud, F.; Cappellari, M.; Davies, R. L.; de Zeeuw, P. T.; Duc, P.-A.; Emsellem, E.; Khochfar, S.; Krajnović, D.; Kuntschner, H.; Lablanche, P.-Y.; McDermid, R. M.; Morganti, R.; Naab, T.; Oosterloo, T.; Sarzi, M.; Scott, N.; Serra, P.; Weijmans, A.

    2011-12-01

    The molecular gas content of local early-type galaxies is constrained and discussed in relation to their evolution. First, as part of the ATLAS3D survey, we present the first complete, large (260 objects), volume-limited single-dish survey of CO in normal local early-type galaxies. We find a surprisingly high detection rate of 22%, independent of luminosity and at best weakly dependent on environment. Second, the extent of the molecular gas is constrained with CO synthesis imaging, and a variety of morphologies is revealed. The kinematics of the molecular gas and stars are often misaligned, implying an external gas origin in over a third of the systems, although this behaviour is drastically diffferent between field and cluster environments. Third, many objects appear to be in the process of forming regular kpc-size decoupled disks, and a star formation sequence can be sketched by piecing together multi-wavelength information on the molecular gas, current star formation, and young stars. Last, early-type galaxies do not seem to systematically obey all our usual prejudices regarding star formation, following the standard Schmidt-Kennicutt law but not the far infrared-radio correlation. This may suggest a greater diversity in star formation processes than observed in disk galaxies. Using multiple molecular tracers, we are thus starting to probe the physical conditions of the cold gas in early-types.

  12. The absolute path command

    SciTech Connect

    Moody, A.

    2012-05-11

    The ap command traveres all symlinks in a given file, directory, or executable name to identify the final absolute path. It can print just the final path, each intermediate link along with the symlink chan, and the permissions and ownership of each directory component in the final path. It has functionality similar to "which", except that it shows the final path instead of the first path. It is also similar to "pwd", but it can provide the absolute path to a relative directory from the current working directory.

  13. Shifting molecular localization by plasmonic coupling in a single-molecule mirage

    NASA Astrophysics Data System (ADS)

    Raab, Mario; Vietz, Carolin; Stefani, Fernando Daniel; Acuna, Guillermo Pedro; Tinnefeld, Philip

    2017-01-01

    Over the last decade, two fields have dominated the attention of sub-diffraction photonics research: plasmonics and fluorescence nanoscopy. Nanoscopy based on single-molecule localization offers a practical way to explore plasmonic interactions with nanometre resolution. However, this seemingly straightforward technique may retrieve false positional information. Here, we make use of the DNA origami technique to both control a nanometric separation between emitters and a gold nanoparticle, and as a platform for super-resolution imaging based on single-molecule localization. This enables a quantitative comparison between the position retrieved from single-molecule localization, the true position of the emitter and full-field simulations. We demonstrate that plasmonic coupling leads to shifted molecular localizations of up to 30 nm: a single-molecule mirage.

  14. Shifting molecular localization by plasmonic coupling in a single-molecule mirage.

    PubMed

    Raab, Mario; Vietz, Carolin; Stefani, Fernando Daniel; Acuna, Guillermo Pedro; Tinnefeld, Philip

    2017-01-11

    Over the last decade, two fields have dominated the attention of sub-diffraction photonics research: plasmonics and fluorescence nanoscopy. Nanoscopy based on single-molecule localization offers a practical way to explore plasmonic interactions with nanometre resolution. However, this seemingly straightforward technique may retrieve false positional information. Here, we make use of the DNA origami technique to both control a nanometric separation between emitters and a gold nanoparticle, and as a platform for super-resolution imaging based on single-molecule localization. This enables a quantitative comparison between the position retrieved from single-molecule localization, the true position of the emitter and full-field simulations. We demonstrate that plasmonic coupling leads to shifted molecular localizations of up to 30 nm: a single-molecule mirage.

  15. Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

    2004-03-01

    Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the “Wannier gauge.” An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches.

  16. Absolute quantitation of protein posttranslational modification isoform.

    PubMed

    Yang, Zhu; Li, Ning

    2015-01-01

    Mass spectrometry has been widely applied in characterization and quantification of proteins from complex biological samples. Because the numbers of absolute amounts of proteins are needed in construction of mathematical models for molecular systems of various biological phenotypes and phenomena, a number of quantitative proteomic methods have been adopted to measure absolute quantities of proteins using mass spectrometry. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) coupled with internal peptide standards, i.e., the stable isotope-coded peptide dilution series, which was originated from the field of analytical chemistry, becomes a widely applied method in absolute quantitative proteomics research. This approach provides more and more absolute protein quantitation results of high confidence. As quantitative study of posttranslational modification (PTM) that modulates the biological activity of proteins is crucial for biological science and each isoform may contribute a unique biological function, degradation, and/or subcellular location, the absolute quantitation of protein PTM isoforms has become more relevant to its biological significance. In order to obtain the absolute cellular amount of a PTM isoform of a protein accurately, impacts of protein fractionation, protein enrichment, and proteolytic digestion yield should be taken into consideration and those effects before differentially stable isotope-coded PTM peptide standards are spiked into sample peptides have to be corrected. Assisted with stable isotope-labeled peptide standards, the absolute quantitation of isoforms of posttranslationally modified protein (AQUIP) method takes all these factors into account and determines the absolute amount of a protein PTM isoform from the absolute amount of the protein of interest and the PTM occupancy at the site of the protein. The absolute amount of the protein of interest is inferred by quantifying both the absolute amounts of a few PTM

  17. Muscle activation described with a differential equation model for large ensembles of locally coupled molecular motors.

    PubMed

    Walcott, Sam

    2014-10-01

    Molecular motors, by turning chemical energy into mechanical work, are responsible for active cellular processes. Often groups of these motors work together to perform their biological role. Motors in an ensemble are coupled and exhibit complex emergent behavior. Although large motor ensembles can be modeled with partial differential equations (PDEs) by assuming that molecules function independently of their neighbors, this assumption is violated when motors are coupled locally. It is therefore unclear how to describe the ensemble behavior of the locally coupled motors responsible for biological processes such as calcium-dependent skeletal muscle activation. Here we develop a theory to describe locally coupled motor ensembles and apply the theory to skeletal muscle activation. The central idea is that a muscle filament can be divided into two phases: an active and an inactive phase. Dynamic changes in the relative size of these phases are described by a set of linear ordinary differential equations (ODEs). As the dynamics of the active phase are described by PDEs, muscle activation is governed by a set of coupled ODEs and PDEs, building on previous PDE models. With comparison to Monte Carlo simulations, we demonstrate that the theory captures the behavior of locally coupled ensembles. The theory also plausibly describes and predicts muscle experiments from molecular to whole muscle scales, suggesting that a micro- to macroscale muscle model is within reach.

  18. Resonant Coupling between Molecular Vibrations and Localized Surface Plasmon Resonance of Faceted Metal Oxide Nanocrystals.

    PubMed

    Agrawal, Ankit; Singh, Ajay; Yazdi, Sadegh; Singh, Amita; Ong, Gary K; Bustillo, Karen; Johns, Robert W; Ringe, Emilie; Milliron, Delia J

    2017-04-12

    Doped metal oxides are plasmonic materials that boast both synthetic and postsynthetic spectral tunability. They have already enabled promising smart window and optoelectronic technologies and have been proposed for use in surface enhanced infrared absorption spectroscopy (SEIRA) and sensing applications. Herein, we report the first step toward realization of the former utilizing cubic F and Sn codoped In2O3 nanocrystals (NCs) to couple to the C-H vibration of surface-bound oleate ligands. Electron energy loss spectroscopy is used to map the strong near-field enhancement around these NCs that enables localized surface plasmon resonance (LSPR) coupling between adjacent nanocrystals and LSPR-molecular vibration coupling. Fourier transform infrared spectroscopy measurements and finite element simulations are applied to observe and explain the nature of the coupling phenomena, specifically addressing coupling in mesoscale assembled films. The Fano line shape signatures of LSPR-coupled molecular vibrations are rationalized with two-port temporal coupled mode theory. With this combined theoretical and experimental approach, we describe the influence of coupling strength and relative detuning between the molecular vibration and LSPR on the enhancement factor and further explain the basis of the observed Fano line shape by deconvoluting the combined response of the LSPR and molecular vibration in transmission, absorption and reflection. This study therefore illustrates various factors involved in determining the LSPR-LSPR and LSPR-molecular vibration coupling for metal oxide materials and provides a fundamental basis for the design of sensing or SEIRA substrates.

  19. Influence of antioxidant structure on local molecular mobility in amorphous sucrose.

    PubMed

    Liang, Jun; Corradini, Maria G; Ludescher, Richard D

    2014-01-13

    The effect of the antioxidants gallic acid and methyl, propyl, and octyl gallate on the molecular mobility and hydrogen bond network in amorphous sucrose was studied. Solid amorphous sucrose films with and without the addition of antioxidants at a mole ratio of 1:5 (antioxidant/sucrose) were cast from solution onto quartz slides. Local molecular mobility from 0 to 70°C was measured using tryptophan amino acid as a luminescent probe dispersed in the films. Phosphorescence from the tryptophan probe provides spectroscopic characteristics-emission spectrum and lifetime-that are sensitive to changes in molecular mobility induced by the addition of antioxidants. Local molecular mobility detected by tryptophan increased in the following order: sucrosesucrose-gallic acid>sucrose-propyl gallate>sucrose>sucrose-octyl gallate) that was nearly the reverse of that seen in matrix mobility. Analysis of the differential effects of the antioxidants suggests that the presence of the hydroxyl benzoyl head group increased matrix molecular mobility and hydrogen bond strength while the saturated carbon chain decreased mobility and bond strength. The influence of the carboxyl group on matrix properties was comparable to that of the formyloxy group. These results indicate that the addition of specific functional ingredients such as antioxidants may significantly affect the physical properties and consequently functional properties of amorphous edible films in ways that might condition their use. The observed changes are closely related to the chemical structure of the added species.

  20. Deformation Localization in Molecular Layers Constrained between Self-Assembled Au Nanoparticles.

    PubMed

    Copie, G; Biaye, M; Diesinger, H; Melin, T; Krzeminski, C; Cleri, F

    2017-03-14

    The localized deformation of molecular monolayers constrained between the spherical surfaces of Au nanoparticles is studied by means of molecular dynamics simulations. Alkyl or polyethylene glycol long-chain molecules were homogeneously distributed over the curved Au surface, pushed against each other by repeated cycles of force relaxation and constant-volume equilibration at temperatures increasing from 50 to 300 K before being slowly quenched to near-zero temperature. Plots of minimum configurational energy can be obtained as a function of the nanoparticle distance, according to different directions of approach; therefore, such simulations describe a range of deformations, from perfectly uniaxial compression to a combination of compression and shear. Despite the relative rigidity of molecular backbones, the deformation is always found to be localized at the interface between the opposing molecular monolayers. We find that shorter ligands can be more densely packed on the surface but do no interdigitate upon compression; they respond to the applied force by bending and twisting, thus changing their conformation while remaining disjointed. On the contrary, longer ligands attain lower surface densities and can interprenetrate when the nanoparticles are compressed against each other; such molecules remain rather straight and benefit from the increased overlap to maximize the adhesion by dispersion forces. The apparent Young's and shear moduli of a dense nanostructure, composed of a triangular arrangement of identical MUDA-decorated Au nanoparticles, are found to be smaller than estimates indirectly deduced by atomic-force experiments but quite close to previous computer simulations of molecular monolayers on flat surfaces and of bulk nanoparticle assemblies.

  1. Identification and subcellular localization of molecular complexes of Gq/11α protein in HEK293 cells.

    PubMed

    Drastichova, Zdenka; Novotny, Jiri

    2012-08-01

    Heterotrimeric G-proteins localized in the plasma membrane convey the signals from G-protein-coupled receptors (GPCRs) to different effectors. At least some types of G-protein α subunits have been shown to be partly released from plasma membranes and to move into the cytosol after receptor activation by the agonists. However, the mechanism underlying subcellular redistribution of trimeric G-proteins is not well understood and no definitive conclusions have been reached regarding the translocation of Gα subunits between membranes and cytosol. Here we used subcellular fractionation and clear-native polyacrylamide gel electrophoresis to identify molecular complexes of G(q/11)α protein and to determine their localization in isolated fractions and stability in naïve and thyrotropin-releasing hormone (TRH)-treated HEK293 cells expressing high levels of TRH receptor and G(11)α protein. We identified two high-molecular-weight complexes of 300 and 140 kDa in size comprising the G(q/11) protein, which were found to be membrane-bound. Both of these complexes dissociated after prolonged treatment with TRH. Still other G(q/11)α protein complexes of lower molecular weight were determined in the cytosol. These 70 kDa protein complexes were barely detectable under control conditions but their levels markedly increased after prolonged (4-16 h) hormone treatment. These results support the notion that a portion of G(q/11)α can undergo translocation from the membrane fraction into soluble fraction after a long-term activation of TRH receptor. At the same time, these findings indicate that the redistribution of G(q/11)α is brought about by the dissociation of high-molecular-weight complexes and concomitant formation of low-molecular-weight complexes containing the G(q/11)α protein.

  2. Cytoprotective Mitochondrial Chaperone TRAP-1 As a Novel Molecular Target in Localized and Metastatic Prostate Cancer

    PubMed Central

    Leav, Irwin; Plescia, Janet; Goel, Hira Lal; Li, Jing; Jiang, Zhong; Cohen, Ronald J.; Languino, Lucia R.; Altieri, Dario C.

    2010-01-01

    Molecular chaperones of the heat shock protein-90 (Hsp90) family promote cell survival, but the molecular requirements of this pathway in tumor progression are not understood. Here, we show that a mitochondria-localized Hsp90 chaperone, tumor necrosis factor receptor-associated protein-1 (TRAP-1), is abundantly and ubiquitously expressed in human high-grade prostatic intraepithelial neoplasia, Gleason grades 3 through 5 prostatic adenocarcinomas, and metastatic prostate cancer, but largely undetectable in normal prostate or benign prostatic hyperplasia in vivo. Prostate lesions formed in genetic models of the disease, including the transgenic adenocarcinoma of the mouse prostate and mice carrying prostate-specific deletion of the phosphatase tensin homolog tumor suppressor (Ptenpc−/−), also exhibit high levels of TRAP-1. Expression of TRAP-1 in nontransformed prostatic epithelial BPH-1 cells inhibited cell death, whereas silencing of TRAP-1 in androgen-independent PC3 or DU145 prostate cancer cells by small interfering RNA enhanced apoptosis. Targeting TRAP-1 with a novel class of mitochondria-directed Hsp90 inhibitors, ie, Gamitrinibs, caused rapid and complete killing of androgen-dependent or -independent prostate cancer, but not BPH-1 cells, whereas reintroduction of TRAP-1 in BPH-1 cells conferred sensitivity to Gamitrinib-induced cell death. These data identify TRAP-1 as a novel mitochondrial survival factor differentially expressed in localized and metastatic prostate cancer compared with normal prostate. Targeting this pathway with Gamitrinibs could be explored as novel molecular therapy in patients with advanced prostate cancer. PMID:19948822

  3. Molecular modeling of phosphorylation sites in proteins using a database of local structure segments.

    PubMed

    Plewczynski, Dariusz; Jaroszewski, Lukasz; Godzik, Adam; Kloczkowski, Andrzej; Rychlewski, Leszek

    2005-11-01

    A new bioinformatics tool for molecular modeling of the local structure around phosphorylation sites in proteins has been developed. Our method is based on a library of short sequence and structure motifs. The basic structural elements to be predicted are local structure segments (LSSs). This enables us to avoid the problem of non-exact local description of structures, caused by either diversity in the structural context, or uncertainties in prediction methods. We have developed a library of LSSs and a profile--profile-matching algorithm that predicts local structures of proteins from their sequence information. Our fragment library prediction method is publicly available on a server (FRAGlib), at http://ffas.ljcrf.edu/Servers/frag.html . The algorithm has been applied successfully to the characterization of local structure around phosphorylation sites in proteins. Our computational predictions of sequence and structure preferences around phosphorylated residues have been confirmed by phosphorylation experiments for PKA and PKC kinases. The quality of predictions has been evaluated with several independent statistical tests. We have observed a significant improvement in the accuracy of predictions by incorporating structural information into the description of the neighborhood of the phosphorylated site. Our results strongly suggest that sequence information ought to be supplemented with additional structural context information (predicted with our segment similarity method) for more successful predictions of phosphorylation sites in proteins.

  4. Screening the Molecular Framework Underlying Local Dendritic mRNA Translation

    PubMed Central

    Namjoshi, Sanjeev V.; Raab-Graham, Kimberly F.

    2017-01-01

    In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches. PMID:28286470

  5. Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate.

    PubMed

    Chen, Liao Y

    2015-04-14

    Computing the free energy of binding a ligand to a protein is a difficult task of essential importance for which purpose various theoretical/computational approaches have been pursued. In this paper, we develop a hybrid steered molecular dynamics (hSMD) method capable of resolving one ligand–protein complex within a few wall-clock days with high enough accuracy to compare with the experimental data. This hSMD approach is based on the relationship between the binding affinity and the potential of mean force (PMF) in the established literature. It involves simultaneously steering n (n = 1, 2, 3, ...) centers of mass of n selected segments of the ligand using n springs of infinite stiffness. Steering the ligand from a single initial state chosen from the bound state ensemble to the corresponding dissociated state, disallowing any fluctuations of the pulling centers along the way, one can determine a 3n-dimensional PMF curve connecting the two states by sampling a small number of forward and reverse pulling paths. This PMF constitutes a large but not the sole contribution to the binding free energy. Two other contributors are (1) the partial partition function containing the equilibrium fluctuations of the ligand at the binding site and the deviation of the initial state from the PMF minimum and (2) the partial partition function containing rotation and fluctuations of the ligand around one of the pulling centers that is fixed at a position far from the protein. We implement this hSMD approach for two ligand–protein complexes whose structures were determined and whose binding affinities were measured experimentally: caprylic acid binding to bovine β-lactoglobulin and glutathione binding to Schistosoma japonicum glutathione S-transferase tyrosine 7 to phenylalanine mutant. Our computed binding affinities agree with the experimental data within a factor of 1.5. The total time of computation for these two all-atom model systems (consisting of 96K and 114K atoms

  6. Exploring the local elastic properties of bilayer membranes using molecular dynamics simulations.

    PubMed

    Pieffet, Gilles; Botero, Alonso; Peters, Günther H; Forero-Shelton, Manu; Leidy, Chad

    2014-11-13

    Membrane mechanical elastic properties regulate a variety of cellular processes involving local membrane deformation, such as ion channel function and vesicle fusion. In this work, we used molecular dynamics simulations to estimate the local elastic properties of a membrane. For this, we calculated the energy needed to extract a DOPE lipid molecule, modified with a linker chain, from a POPC bilayer membrane using the umbrella sampling technique. Although the extraction energy entails several contributions related not only to elastic deformation but also to solvation, careful analysis of the potential of mean force (PMF) allowed us to dissect the elastic contribution. With this information, we calculated an effective linear spring constant of 44 ± 4 kJ·nm(-2)·mol(-1) for the DOPC membrane, in agreement with experimental estimates. The membrane deformation profile was determined independently during the stretching process in molecular detail, allowing us to fit this profile to a previously proposed continuum elastic model. Through this approach, we calculated an effective membrane spring constant of 42 kJ·nm(-2)·mol(-1), which is in good agreement with the PMF calculation. Furthermore, the solvation energy we derived from the data is shown to match the solvation energy estimated from critical micelle formation constants. This methodology can be used to determine how changes in lipid composition or the presence of membrane modifiers can affect the elastic properties of a membrane at a local level.

  7. Edge localized mode characteristics during edge localized mode mitigation by supersonic molecular beam injection in Korea Superconducting Tokamak Advanced Research

    SciTech Connect

    Lee, H. Y.; Hong, J. H.; Jang, J. H.; Park, J. S.; Choe, Wonho; Hahn, S. H.; Bak, J. G.; Lee, J. H.; Ko, W. H.; Lee, K. D.; Lee, S. H.; Lee, H. H.; Juhn, J.-W.; Kim, H. S.; Yoon, S. W.; Han, H.; Ghim, Y.-C.

    2015-12-15

    It has been reported that supersonic molecular beam injection (SMBI) is an effective means of edge localized mode (ELM) mitigation. This paper newly reports the changes in the ELM, plasma profiles, and fluctuation characteristics during ELM mitigation by SMBI in Korea Superconducting Tokamak Advanced Research. During the mitigated ELM phase, the ELM frequency increased by a factor of 2–3 and the ELM size, which was estimated from the D{sub α} amplitude, the fractional changes in the plasma-stored energy and the line-averaged electron density, and divertor heat flux during an ELM burst, decreased by a factor of 0.34–0.43. Reductions in the electron and ion temperatures rather than in the electron density were observed during the mitigated ELM phase. In the natural ELM phase, frequency chirping of the plasma fluctuations was observed before the ELM bursts; however, the ELM bursts occurred without changes in the plasma fluctuation frequency in the mitigated ELM phase.

  8. Weak links between fast mobility and local structure in molecular and atomic liquids

    SciTech Connect

    Bernini, S.; Puosi, F.; Leporini, D.

    2015-03-28

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  9. The effects of flow-inhomogeneities on molecular cloud formation: Local versus global collapse

    SciTech Connect

    Carroll-Nellenback, Jonathan J.; Frank, Adam; Heitsch, Fabian

    2014-07-20

    Observational evidence from local star-forming regions mandates that star formation occurs shortly after, or even during, molecular cloud formation. Models of molecular cloud formation in large-scale converging flows have identified the physical mechanisms driving the necessary rapid fragmentation. They also point to global gravitational collapse driving supersonic turbulence in molecular clouds. Previous cloud formation models have focused on turbulence generation, gravitational collapse, magnetic fields, and feedback. Here, we explore the effect of structure in the flow on the resulting clouds and the ensuing gravitational collapse. We compare two extreme cases, one with a collision between two smooth streams, and one with streams containing small clumps. We find that structured converging flows lead to a delay of local gravitational collapse ({sup c}ore formation{sup )}. Hence, the cloud has more time to accumulate mass, eventually leading to a strong global collapse, and thus to a high core formation rate. Uniform converging flows fragment hydrodynamically early on, leading to the rapid onset of local gravitational collapse and an overall low core formation rate. This is also mirrored in the core mass distribution: the uniform initial conditions lead to more low-mass cores than the clumpy initial conditions. Kinetic (E{sub k} ) and gravitational energy (E{sub g} ) budgets suggest that collapse is only prevented for E{sub k} >> E{sub g} , which occurs for large scales in the smooth flow, and for small scales for the clumpy flow. Whenever E{sub k} ≈ E{sub g} , we observe gravitational collapse on those scales. Signatures of chemical abundance variations evolve differently for the gas phase and for the stellar population. For smooth flows, the forming cloud is well mixed, while its stellar population retains more information about the initial metallicities. For clumpy flows, the gas phase is less well mixed, while the stellar population has lost most of the

  10. Electronic Absolute Cartesian Autocollimator

    NASA Technical Reports Server (NTRS)

    Leviton, Douglas B.

    2006-01-01

    An electronic absolute Cartesian autocollimator performs the same basic optical function as does a conventional all-optical or a conventional electronic autocollimator but differs in the nature of its optical target and the manner in which the position of the image of the target is measured. The term absolute in the name of this apparatus reflects the nature of the position measurement, which, unlike in a conventional electronic autocollimator, is based absolutely on the position of the image rather than on an assumed proportionality between the position and the levels of processed analog electronic signals. The term Cartesian in the name of this apparatus reflects the nature of its optical target. Figure 1 depicts the electronic functional blocks of an electronic absolute Cartesian autocollimator along with its basic optical layout, which is the same as that of a conventional autocollimator. Referring first to the optical layout and functions only, this or any autocollimator is used to measure the compound angular deviation of a flat datum mirror with respect to the optical axis of the autocollimator itself. The optical components include an illuminated target, a beam splitter, an objective or collimating lens, and a viewer or detector (described in more detail below) at a viewing plane. The target and the viewing planes are focal planes of the lens. Target light reflected by the datum mirror is imaged on the viewing plane at unit magnification by the collimating lens. If the normal to the datum mirror is parallel to the optical axis of the autocollimator, then the target image is centered on the viewing plane. Any angular deviation of the normal from the optical axis manifests itself as a lateral displacement of the target image from the center. The magnitude of the displacement is proportional to the focal length and to the magnitude (assumed to be small) of the angular deviation. The direction of the displacement is perpendicular to the axis about which the

  11. Absolute airborne gravimetry

    NASA Astrophysics Data System (ADS)

    Baumann, Henri

    This work consists of a feasibility study of a first stage prototype airborne absolute gravimeter system. In contrast to relative systems, which are using spring gravimeters, the measurements acquired by absolute systems are uncorrelated and the instrument is not suffering from problems like instrumental drift, frequency response of the spring and possible variation of the calibration factor. The major problem we had to resolve were to reduce the influence of the non-gravitational accelerations included in the measurements. We studied two different approaches to resolve it: direct mechanical filtering, and post-processing digital compensation. The first part of the work describes in detail the different mechanical passive filters of vibrations, which were studied and tested in the laboratory and later in a small truck in movement. For these tests as well as for the airborne measurements an absolute gravimeter FG5-L from Micro-G Ltd was used together with an Inertial navigation system Litton-200, a vertical accelerometer EpiSensor, and GPS receivers for positioning. These tests showed that only the use of an optical table gives acceptable results. However, it is unable to compensate for the effects of the accelerations of the drag free chamber. The second part describes the strategy of the data processing. It is based on modeling the perturbing accelerations by means of GPS, EpiSensor and INS data. In the third part the airborne experiment is described in detail, from the mounting in the aircraft and data processing to the different problems encountered during the evaluation of the quality and accuracy of the results. In the part of data processing the different steps conducted from the raw apparent gravity data and the trajectories to the estimation of the true gravity are explained. A comparison between the estimated airborne data and those obtained by ground upward continuation at flight altitude allows to state that airborne absolute gravimetry is feasible and

  12. Non-linear non-local molecular electrodynamics with nano-optical fields.

    PubMed

    Chernyak, Vladimir Y; Saurabh, Prasoon; Mukamel, Shaul

    2015-10-28

    The interaction of optical fields sculpted on the nano-scale with matter may not be described by the dipole approximation since the fields may vary appreciably across the molecular length scale. Rather than incrementally adding higher multipoles, it is advantageous and more physically transparent to describe the optical process using non-local response functions that intrinsically include all multipoles. We present a semi-classical approach for calculating non-local response functions based on the minimal coupling Hamiltonian. The first, second, and third order response functions are expressed in terms of correlation functions of the charge and the current densities. This approach is based on the gauge invariant current rather than the polarization, and on the vector potential rather than the electric and magnetic fields.

  13. Molecular dynamics simulations on local structure and diffusion in liquid Ti x Al 1- x alloys

    NASA Astrophysics Data System (ADS)

    Xia, J. H.; Liu, C. S.; Cheng, Z. F.; Shi, D. P.

    2011-10-01

    The microscopic structure and dynamics of liquid Ti xAl 1- x alloys together with pure liquid Ti and Al metals were investigated by means of molecular dynamics simulations. This work gives the structural properties, including pair-correlation function, bond-angle distribution function, HA and Voronoi indices, and their composition dependence. The dynamical properties have also been studied. The calculated pair-correlation function, bond-angle distribution function, and HA and Voronoi indices suggest that the stoichiometric composition Ti 0.75Al 0.25 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum diffusion coefficient at this composition. These results indicate that the mobility of atoms strongly depends on their atomic local structure.

  14. Absolute-structure reports.

    PubMed

    Flack, Howard D

    2013-08-01

    All the 139 noncentrosymmetric crystal structures published in Acta Crystallographica Section C between January 2011 and November 2012 inclusive have been used as the basis of a detailed study of the reporting of absolute structure. These structure determinations cover a wide range of space groups, chemical composition and resonant-scattering contribution. Defining A and D as the average and difference of the intensities of Friedel opposites, their level of fit has been examined using 2AD and selected-D plots. It was found, regardless of the expected resonant-scattering contribution to Friedel opposites, that the Friedel-difference intensities are often dominated by random uncertainty and systematic error. An analysis of data collection strategy is provided. It is found that crystal-structure determinations resulting in a Flack parameter close to 0.5 may not necessarily be from crystals twinned by inversion. Friedifstat is shown to be a robust estimator of the resonant-scattering contribution to Friedel opposites, very little affected by the particular space group of a structure nor by the occupation of special positions. There is considerable confusion in the text of papers presenting achiral noncentrosymmetric crystal structures. Recommendations are provided for the optimal way of treating noncentrosymmetric crystal structures for which the experimenter has no interest in determining the absolute structure.

  15. The Dense Molecular Gas and Nuclear Activity in the Local ULIRG IRAS 13120-5453

    NASA Astrophysics Data System (ADS)

    Privon, George C.; Aalto, Susanne; Falstad, Niklas; Muller, Sebastien; González-Alfonso, Eduardo; Sliwa, Kazimierz; Treister, Ezequiel; Costagliola, Francesco; Armus, Lee; Evans, Aaron S.; Garcia-Burillo, Santiago; Izumi, Takuma; Sakamoto, Kazushi; van der Werf, Paul

    2017-01-01

    Ultraluminous infrared galaxies (ULIRGs) are the most luminous and concentrated star-forming galaxies in the local Universe. With a galaxy's worth of gas in the central kiloparsec and star formation rates in excess of 100 solar masses per year, these systems can have infrared surface densities that approach predictions for radiation pressure-limited starbursts. We will present a case study of a local ULIRG, IRAS 13120-5453, using ALMA observations of dense gas tracers HCN and HCO+, and the 330 GHz continuum emission. We find the HCN/HCO+ ratio to be elevated above typical values for star-forming galaxies and suggest the enhancement can be explained by increased HCN abundance driven by mechanical heating from supernovae in the starburst. The 330 GHz continuum size is resolved, with a size of ~500 pc. Using this as a measure of the starburst size, we show the IR luminosity surface density is below that for a radiation pressure-limited starburst. We also find tentative evidence for non-virial motions of HCN, suggesting dense molecular gas may be entrained the molecular wind (previously detected in OH).

  16. Local Elastic Constants for Epoxy-Nanotube Composites from Molecular Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Gates, T. S.

    2007-01-01

    A method from molecular dynamics simulation is developed for determining local elastic constants of an epoxy/nanotube composite. The local values of C11, C33, K12, and K13 elastic constants are calculated for an epoxy/nanotube composite as a function of radial distance from the nanotube. While the results possess a significant amount of statistical uncertainty resulting from both the numerical analysis and the molecular fluctuations during the simulation, the following observations can be made. If the size of the region around the nanotube is increased from shells of 1 to 6 in thickness, then the scatter in the data reduces enough to observe trends. All the elastic constants determined are at a minimum 20 from the center of the nanotube. The C11, C33, and K12 follow similar trends as a function of radial distance from the nanotube. The K13 decreases greater distances from the nanotube and becomes negative which may be a symptom of the statistical averaging.

  17. Comparative study of local structure of two cyanobiphenyl liquid crystals by molecular dynamics method

    SciTech Connect

    Gerts, Egor D. Komolkin, Andrei V.; Burmistrov, Vladimir A.; Alexandriysky, Victor V.; Dvinskikh, Sergey V.

    2014-08-21

    Fully-atomistic molecular dynamics simulations were carried out on two similar cyanobiphenyl nematogens, HO-6OCB and 7OCB, in order to study effects of hydrogen bonds on local structure of liquid crystals. Comparable length of these two molecules provides more evident results on the effects of hydrogen bonding. The analysis of radial and cylindrical distribution functions clearly shows the differences in local structure of two mesogens. The simulations showed that anti-parallel alignment is preferable for the HO-6OCB. Hydrogen bonds between OH-groups are observed for 51% of HO-6OCB molecules, while hydrogen bonding between CN- and OH-groups occurs only for 16% of molecules. The lifetimes of H-bonds differ due to different mobility of molecular fragments (50 ps for N⋅⋅⋅H–O and 41 ps for O⋅⋅⋅H–O). Although the standard Optimized Potentials for Liquid Simulations - All-Atom force field cannot reproduce some experimental parameters quantitatively (order parameters are overestimated, diffusion coefficients are not reproduced well), the comparison of relative simulated results for the pair of mesogens is nevertheless consistent with the same relative experimental parameters. Thus, the comparative study of simulated and experimental results for the pair of similar liquid crystals still can be assumed plausible.

  18. A localized momentum constraint for non-equilibrium molecular dynamics simulations.

    PubMed

    Smith, E R; Heyes, D M; Dini, D; Zaki, T A

    2015-02-21

    A method which controls momentum evolution in a sub-region within a molecular dynamics simulation is derived from Gauss's principle of least constraint. The technique for localization is founded on the equations by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] expressed in a weak form according to the control volume (CV) procedure derived by Smith et al. [Phys. Rev. E. 85, 056705 (2012)]. A term for the advection of molecules appears in the derived constraint and is shown to be essential in order to exactly control the time evolution of momentum in the subvolume. The numerical procedure converges the total momentum in the CV to the target value to within machine precision in an iterative manner. The localized momentum constraint can prescribe essentially arbitrary flow fields in non-equilibrium molecular dynamics simulations. The methodology also forms a rigorous mathematical framework for introducing coupling constraints at the boundary between continuum and discrete systems. This functionality is demonstrated with a boundary-driven flow test case.

  19. Molecular organization, localization and orientation of antifungal antibiotic amphotericin B in a single lipid bilayer

    PubMed Central

    Grudzinski, Wojciech; Sagan, Joanna; Welc, Renata; Luchowski, Rafal; Gruszecki, Wieslaw I.

    2016-01-01

    Amphotericin B is a popular antifungal antibiotic, a gold standard in treatment of systemic mycotic infections, due to its high effectiveness. On the other hand, applicability of the drug is limited by its considerable toxicity to patients. Biomembranes are a primary target of physiological activity of amphotericin B and both the pharmacologically desired and toxic side effects of the drug relay on its molecular organization in the lipid phase. In the present work, molecular organization, localization and orientation of amphotericin B, in a single lipid bilayer system, was analysed simultaneously, thanks to application of a confocal fluorescence lifetime imaging microscopy of giant unilamellar vesicles. The results show that the presence of sterols, in the lipid phase, promotes formation of supramolecular structures of amphotericin B and their penetration into the membrane hydrophobic core. The fact that such an effect is substantially less pronounced in the case of cholesterol than ergosterol, the sterol of fungal membranes, provides molecular insight into the selectivity of the drug. PMID:27620838

  20. Molecular adsorbates as probes of the local properties of doped graphene

    PubMed Central

    Pham, Van Dong; Joucken, Frédéric; Repain, Vincent; Chacon, Cyril; Bellec, Amandine; Girard, Yann; Rousset, Sylvie; Sporken, Robert; Santos, Maria Cristina dos; Lagoute, Jérôme

    2016-01-01

    Graphene-based sensors are among the most promising of graphene’s applications. The ability to signal the presence of molecular species adsorbed on this atomically thin substrate has been explored from electric measurements to light scattering. Here we show that the adsorbed molecules can be used to sense graphene properties. The interaction of porphyrin molecules with nitrogen-doped graphene has been investigated using scanning tunneling microscopy and ab initio calculations. Molecular manipulation was used to reveal the surface below the adsorbed molecules allowing to achieve an atomic-scale measure of the interaction of molecules with doped graphene. The adsorbate’s frontier electronic states are downshifted in energy as the molecule approaches the doping site, with largest effect when the molecule sits over the nitrogen dopant. Theoretical calculations showed that, due to graphene’s high polarizability, the adsorption of porphyrin induces a charge rearrangement on the substrate similar to the image charges on a metal. This charge polarization is enhanced around nitrogen site, leading to an increased interaction of molecules with their image charges on graphene. Consequently, the molecular states are stabilized and shift to lower energies. These findings reveal the local variation of polarizability induced by nitrogen dopant opening new routes towards the electronic tuning of graphene. PMID:27097555

  1. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    PubMed

    Genoni, Alessandro

    2013-07-09

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  2. Absolute Equilibrium Entropy

    NASA Technical Reports Server (NTRS)

    Shebalin, John V.

    1997-01-01

    The entropy associated with absolute equilibrium ensemble theories of ideal, homogeneous, fluid and magneto-fluid turbulence is discussed and the three-dimensional fluid case is examined in detail. A sigma-function is defined, whose minimum value with respect to global parameters is the entropy. A comparison is made between the use of global functions sigma and phase functions H (associated with the development of various H-theorems of ideal turbulence). It is shown that the two approaches are complimentary though conceptually different: H-theorems show that an isolated system tends to equilibrium while sigma-functions allow the demonstration that entropy never decreases when two previously isolated systems are combined. This provides a more complete picture of entropy in the statistical mechanics of ideal fluids.

  3. Differential submitochondrial localization of PINK1 as a molecular switch for mediating distinct mitochondrial signaling pathways.

    PubMed

    Fallaize, Dana; Chin, Lih-Shen; Li, Lian

    2015-12-01

    Mutations in mitochondrial kinase PINK1 cause Parkinson disease (PD), but the submitochondrial site(s) of PINK1 action remains unclear. Here, we report that three-dimensional structured illumination microscopy (3D-SIM) enables super-resolution imaging of protein submitochondrial localization. Dual-color 3D-SIM imaging analysis revealed that PINK1 resides in the cristae membrane and intracristae space but not on the outer mitochondrial membrane (OMM) of healthy mitochondria. Under normal physiological conditions, PINK1 colocalizes with its substrate TRAP1 in the cristae membrane and intracristae space. In response to mitochondrial depolarization, PINK1, but not TRAP1, translocates to the OMM. The PINK1 translocation to the OMM of depolarized mitochondria is independent of new protein synthesis and requires combined action of PINK1 transmembrane domain and C-terminal region. We found that mitochondrial depolarization-induced PINK1 OMM translocation is required for recruitment of parkin to the OMM of damaged mitochondria. Our findings suggest that differential submitochondrial localization of PINK1 serves as a molecular switch for mediating two distinct mitochondrial signaling pathways in maintenance of mitochondrial homeostasis. Furthermore, our study provides evidence for the involvement of deregulated PINK1 submitochondrial localization in PD pathogenesis.

  4. Radiative interactions in molecular gases under local and nonlocal thermodynamic equilibrium conditions

    NASA Technical Reports Server (NTRS)

    Tiwari, S. N.; Jha, M. K.

    1993-01-01

    Basic formulations, analyses, and numerical procedures are presented to investigate radiative heat interactions in diatomic and polyatomic gases under local and nonlocal thermodynamic equilibrium conditions. Essential governing equations are presented for both gray and nongray gases. Information is provided on absorption models, relaxation times, and transfer equations. Radiative flux equations are developed which are applicable under local and nonlocal thermodynamic equilibrium conditions. The problem is solved for fully developed laminar incompressible flows between two parallel plates under the boundary condition of a uniform surface heat flux. For specific applications, three diatomic and three polyatomic gases are considered. The results are obtained numerically by employing the method of variation of parameters. The results are compared under local and nonlocal thermodynamic equilibrium conditions at different temperature and pressure conditions. Both gray and nongray studies are conducted extensively for all molecular gases considered. The particular gases selected for this investigation are CO, NO, OH, CO2, H2O, and CH4. The temperature and pressure range considered are 300-2000 K and 0.1-10 atmosphere, respectively. In general, results demonstrate that the gray gas approximation overestimates the effect of radiative interaction for all conditions. The conditions of NLTE, however, result in underestimation of radiative interactions. The method developed for this study can be extended to solve complex problems of radiative heat transfer involving nonequilibrium phenomena.

  5. Localized Programmable Gas Phase Electrodeposition Yielding Functional Nanostructured Materials and Molecular Arrays

    NASA Astrophysics Data System (ADS)

    Lin, En-Chiang

    when compared with traditional vapor deposition methods. In the second application, we demonstrate the fabrication of 3D nanostructured electrodes for photovoltaic application. The second application adjusts the material flux in selected domains to identify nanostructures and device metrics in a combinatorial way. Section (B) applies the process to the localized collection of airborne molecules. The goal was to determine if the process can be scaled to particles with molecular dimensions. This turned out to be the case. As an application we demonstrate enhanced collection efficiencies of molecular species in gas sensor applications. The research recognizes that various nanostructured sensor designs currently aim to achieve or claim single molecular detection by a reduction of the active sensor size. However, a reduction of the sensor size has the negative effect of reducing the capture probability considering the diffusion based analyte transport commonly used. Specifically, we applied the discovered localized programmable electrodynamic precipitation concept to collect, spot, and detect airborne species in an active-matrix array-like fashion. The method is tested using surface enhanced Raman spectroscopy (SERS). The process can produce hybrid molecular arrays on a single chip over a broad range of molecular weights including small molecules or large macromolecules. From a gas sensor system point of view it was possible to improved collection efficiencies and sensitivity over previously method.

  6. Local Platinum Environments in a Solid Analogue of the Molecular Periana Catalyst

    DOE PAGES

    Soorholtz, Mario; Jones, Louis C.; Samuelis, Dominik; ...

    2016-02-16

    Combining advantages of homogeneous and heterogeneous catalysis by incorporating active species on a solid support is often an effective strategy for improving overall catalyst performance, although the influences of the support are generally challenging to establish, especially at a molecular level. In this paper, we report the local compositions, and structures of platinum species incorporated into covalent triazine framework (Pt-CTF) materials, a solid analogue of the molecular Periana catalyst, Pt(bpym)Cl2, both of which are active for the selective oxidation of methane in the presence of concentrated sulfuric acid. By using a combination of solid-state 195Pt nuclear magnetic resonance (NMR) spectroscopy,more » aberration-corrected scanning transmission electron microscopy (AC-STEM), X-ray photoelectron spectroscopy (XPS), and X-ray absorption spectroscopy (XAS), important similarities and differences are observed between the Pt-CTF and Periana catalysts, which are likely related to their respective macroscopic reaction properties. In particular, wide-line solid-state 195Pt NMR spectra enable direct measurement, identification, and quantification of distinct platinum species in as-synthesized and used Pt-CTF catalysts. The results indicate that locally ordered and disordered Pt sites are present in as-synthesized Pt-CTF, with the former being similar to one of the two crystallographically distinct Pt sites in crystalline Pt(bpym)Cl2. A distribution of relatively disordered Pt moieties is also present in the used catalyst, among which are the principal active sites. Similarly XAS shows good agreement between the measured data of Pt-CTF and a theoretical model based on Pt(bpym)Cl2. Analyses of the absorption spectra of Pt-CTF used for methane oxidation suggests ligand exchange, as predicted for the molecular catalyst. XPS analyses of Pt(bpym)Cl2, Pt-CTF, as well as the unmodified ligands, further corroborate platinum coordination by pyridinic N atoms

  7. Local Platinum Environments in a Solid Analogue of the Molecular Periana Catalyst

    SciTech Connect

    Soorholtz, Mario; Jones, Louis C.; Samuelis, Dominik; Weidenthaler, Claudia; White, Robin J.; Titirici, Maria-Magdalena; Cullen, David A.; Zimmermann, Tobias; Antonietti, Markus; Maier, Joachim; Palkovits, Regina; Chmelka, Bradley F.; Schüth, Ferdi

    2016-02-16

    Combining advantages of homogeneous and heterogeneous catalysis by incorporating active species on a solid support is often an effective strategy for improving overall catalyst performance, although the influences of the support are generally challenging to establish, especially at a molecular level. In this paper, we report the local compositions, and structures of platinum species incorporated into covalent triazine framework (Pt-CTF) materials, a solid analogue of the molecular Periana catalyst, Pt(bpym)Cl2, both of which are active for the selective oxidation of methane in the presence of concentrated sulfuric acid. By using a combination of solid-state 195Pt nuclear magnetic resonance (NMR) spectroscopy, aberration-corrected scanning transmission electron microscopy (AC-STEM), X-ray photoelectron spectroscopy (XPS), and X-ray absorption spectroscopy (XAS), important similarities and differences are observed between the Pt-CTF and Periana catalysts, which are likely related to their respective macroscopic reaction properties. In particular, wide-line solid-state 195Pt NMR spectra enable direct measurement, identification, and quantification of distinct platinum species in as-synthesized and used Pt-CTF catalysts. The results indicate that locally ordered and disordered Pt sites are present in as-synthesized Pt-CTF, with the former being similar to one of the two crystallographically distinct Pt sites in crystalline Pt(bpym)Cl2. A distribution of relatively disordered Pt moieties is also present in the used catalyst, among which are the principal active sites. Similarly XAS shows good agreement between the measured data of Pt-CTF and a theoretical model based on Pt(bpym)Cl2. Analyses of the absorption spectra of Pt-CTF used for methane oxidation suggests ligand exchange, as predicted for the molecular catalyst. XPS analyses of Pt(bpym)Cl2, Pt-CTF, as well as the unmodified ligands, further

  8. Total and local (atom and atom type) molecular quadratic indices: significance interpretation, comparison to other molecular descriptors, and QSPR/QSAR applications.

    PubMed

    Ponce, Yovani Marrero

    2004-12-15

    This paper describes the significance interpretation, comparison to other molecular descriptors, and QSPR/QSAR applications of a new set of molecular descriptors: atom, atom type, and total molecular quadratic indices. The features of the kth total and local quadratic indices are illustrated by examples of various types of molecular structures, including chain lengthening, branching, heteroatoms content, and multiple bonds. The linear independence of the local (atom type) quadratic indices to others 0D, 1D, 2D, and 3D molecular descriptors is demonstrated by using principal component analysis for 42 heterogeneous molecules. It is concluded that the local quadratic indices are independent indices containing important structural information to be used in QSPR/QSAR and drug design studies. In this sense, molecular quadratic indices were used to the description and prediction of the boiling point of 28 alkyl alcohols and to the modeling of the partition coefficient (logP), specific rate constant (logk), and antibacterial activity of 2-furylethylene derivatives. These models were statistically significant and showed very good stability to data variation in leave-one-out (LOO) cross-validation experiment. The comparison with the other approaches also revealed good behaviors of our method in this QSAR study.

  9. Correlative microscopy methods that maximize specimen fidelity and data completeness, and improve molecular localization capabilities.

    PubMed

    Smith, Elizabeth A; Cinquin, Bertrand P; McDermott, Gerry; Le Gros, Mark A; Parkinson, Dilworth Y; Kim, Hong Tae; Larabell, Carolyn A

    2013-10-01

    Correlative microscopy techniques interrogate biological systems more thoroughly than is possible using a single modality. This is particularly true if disparate data types can be acquired from the same specimen. Recently, there has been significant progress towards combining the structural information obtained from soft X-ray tomography (SXT) with molecular localization data. Here we will compare methods for determining the position of molecules in a cell viewed by SXT, including direct visualization using electron dense labels, and by indirect methods, such as fluorescence microscopy and high numerical aperture cryo-light microscopy. We will also discuss available options for preserving the in vivo structure and organization of the specimen during multi-modal data collection, and how some simple specimen mounting concepts can ensure maximal data completeness in correlative imaging experiments.

  10. Locally advanced and metastatic basal cell carcinoma: molecular pathways, treatment options and new targeted therapies.

    PubMed

    Ruiz Salas, Veronica; Alegre, Marta; Garcés, Joan Ramón; Puig, Lluis

    2014-06-01

    The hedgehog (Hh) signaling pathway has been identified as important to normal embryonic development in living organisms and it is implicated in processes including cell proliferation, differentiation and tissue patterning. Aberrant Hh pathway has been involved in the pathogenesis and chemotherapy resistance of different solid and hematologic malignancies. Basal cell carcinoma (BCC) and medulloblastoma are two well-recognized cancers with mutations in components of the Hh pathway. Vismodegib has recently approved as the first inhibitor of one of the components of the Hh pathway (smoothened). This review attempts to provide current data on the molecular pathways involved in the development of BCC and the therapeutic options available for the treatment of locally advanced and metastatic BCC, and the new targeted therapies in development.

  11. Combination of cross-sectional and molecular imaging studies in the localization of gastroenteropancreatic neuroendocrine tumors.

    PubMed

    Toumpanakis, Christos; Kim, Michelle K; Rinke, Anja; Bergestuen, Deidi S; Thirlwell, Christina; Khan, Mohid S; Salazar, Ramon; Oberg, Kjell

    2014-01-01

    Molecular imaging modalities exploit aspects of neuroendocrine tumors (NET) pathophysiology for both diagnostic imaging and therapeutic purposes. The characteristic metabolic pathways of NET determine which tracers are useful for their visualization. In this review, we summarize the diagnostic value of all available molecular imaging studies, present data about their use in daily practice in NET centers globally, and finally make recommendations about the appropriate use of those modalities in specific clinical scenarios. Somatostatin receptor scintigraphy (SRS) continues to have a central role in the diagnostic workup of patients with NET, as it is also widely available. However, and despite the lack of prospective randomized studies, many NET experts predict that Gallium-68 ((68)Ga)-DOTA positron emission tomography (PET) techniques may replace SRS in the future, not only because of their technical advantages, but also because they are superior in patients with small-volume disease, in patients with skeletal metastases, and in those with occult primary tumors. Carbon-11 ((11)C)-5-hydroxy-L-tryptophan (5-HTP) PET and (18)F-dihydroxyphenylalanine ((18)F-DOPA) PET are new molecular imaging techniques of limited availability, and based on retrospective data, their sensitivities seem to be inferior to that of (68)Ga-DOTA PET. Glucagon-like-peptide-1 (GLP-1) receptor imaging seems promising for localization of the primary in benign insulinomas, but is currently available only in a few centers. Fluorine-18 ((18)F)-fluorodeoxyglucose ((18)F-FDG) PET was initially thought to be of limited value in NET, due to their usually slow-growing nature. However, according to subsequent data, (18)F-FDG PET is particularly helpful for visualizing the more aggressive NET, such as poorly differentiated neuroendocrine carcinomas, and well-differentiated tumors with Ki67 values >10%. According to limited data, (18)F-FDG-avid tumor lesions, even in slow-growing NET, may indicate a more

  12. ``Molecular spectrometers'' in the condensed phase: local THz-FIR response from femtosecond fluorescence

    NASA Astrophysics Data System (ADS)

    Ernsting, Nikolaus

    2011-03-01

    We examine dye molecules whose color depends on the polarity of the environment. Following fast optical excitation, their fluorescence band typically red-shifts by 0.5 eV on femtosecond to nanosecond time scales. This ``dynamic Stokes shift'' reflects the joint molecular and environmental reorganisation of the system. Solvation dynamics has been studied for decades in the hope that the dynamics of the environment itself can be extracted. We contribute with two research lines: (1) development of rigid polar solvation probes whose vibrational response is removed from that of water, for example, and (2) fluorescence techniques which measure the dynamic Stokes shifts more precisely. Two results will be shown. The frequency-dependent permittivity ɛ (ω) of water surrounding N-Methyl-6-Quinolone is extracted up to about 100 cm-1 from the time-resolved fluorescence shift R(t). The key consists in an analytical connection ɛ (ω) --> R(t) which is needed for data fitting. Measurements with the cryoprotectant disaccharide trehalose in water serve to establish the method. Its unique feature is locality, i . e . the possibility to measure ɛ (ω) around a supramolecular structure with a covalently connected or embedded probe. THz vibrational activity of a biopolymer is thus measured locally, on the effective length scale for polar solvation, with an embedded molecular probe. For this purpose 2-hydroxy-7-nitro-fluorene was linked into a 13mer duplex opposite an abasic site. The NMR solution structure shows that the fluorene moiety occupies a well-defined position in place of a base-pair. The dynamic Stokes shifts for solution in H2 O and D2 O are quantified. Their difference is much larger than expected for free water, suggesting that only bound water is observed. A weak 26 cm-1 spectral oscillation of the emission band is observed which is not present when the probe is free in solution, and is therefore caused by the supramolecular structure (DNA and hydration water).

  13. The Search for Molecular Outflows in Local Volume AGNs with Herschel-PACS

    NASA Astrophysics Data System (ADS)

    Stone, M.; Veilleux, S.; Meléndez, M.; Sturm, E.; Graciá-Carpio, J.; González-Alfonso, E.

    2016-08-01

    We present the results from a systematic search for galactic-scale, molecular (OH 119 μm) outflows in a sample of 52 Local Volume (d\\lt 50 Mpc) Burst Alert Telescope detected active galactic nuclei (BAT AGNs) with Herschel-PACS. We combine the results from our analysis of the BAT AGNs with the published Herschel/PACS data of 43 nearby (z\\lt 0.3) galaxy mergers, mostly ultra-luminous infrared galaxies (ULIRGs) and QSOs. The objects in our sample of BAT AGNs have, on average, ˜ 10{--}100 times lower AGN luminosities, star formation rates, and stellar masses than those of the ULIRG and QSO samples. OH 119 μm is detected in 42 of our BAT AGN targets. Evidence for molecular outflows (i.e., OH absorption profiles with median velocities more blueshifted than -50 km s-1 and/or blueshifted wings with 84% velocities less than -300 km s-1) is seen in only four BAT AGNs (NGC 7479 is the most convincing case). Evidence for molecular inflows (i.e., OH absorption profiles with median velocities more redshifted than 50 km s-1) is seen in seven objects, although an inverted P-Cygni profile is detected unambiguously in only one object (Circinus). Our data show that both the starburst and AGN contribute to driving OH outflows, but the fastest OH winds require AGNs with quasar-like luminosities. We also confirm that the total absorption strength of OH 119 μm is a good proxy for dust optical depth as it correlates strongly with the 9.7 μm silicate absorption feature, a measure of obscuration originating in both the nuclear torus and host galaxy disk. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  14. Molecular characterization and physical localization of highly repetitive DNA sequences from Brazilian Alstroemeria species.

    PubMed

    Kuipers, A G J; Kamstra, S A; de Jeu, M J; Visser, R G F

    2002-01-01

    Highly repetitive DNA sequences were isolated from genomic DNA libraries of Alstroemeria psittacina and A. inodora. Among the repetitive sequences that were isolated, tandem repeats as well as dispersed repeats could be discerned. The tandem repeats belonged to a family of interlinked Sau3A subfragments with sizes varying from 68-127 bp, and constituted a larger HinfI repeat of approximately 400 bp. Southern hybridization showed a similar molecular organization of the tandem repeats in each of the Brazilian Alstroemeria species tested. None of the repeats hybridized with DNA from Chilean Alstroemeria species, which indicates that they are specific for the Brazilian species. In-situ localization studies revealed the tandem repeats to be localized in clusters on the chromosomes of A. inodora and A. psittacina: distal hybridization sites were found on chromosome arms 2PS, 6PL, 7PS, 7PL and 8PL, interstitial sites on chromosome arms 2PL, 3PL, 4PL and 5PL. The applicability of the tandem repeats for cytogenetic analysis of interspecific hybrids and their role in heterochromatin organization are discussed.

  15. A rational reduction of CI expansions: combining localized molecular orbitals and selected charge excitations.

    PubMed

    Krah, Tim; Ben Amor, Nadia; Maynau, Daniel; Berger, J A; Robert, Vincent

    2014-07-01

    Based on localized molecular orbitals, the proposed method reduces large configuration interaction (CI) spaces while maintaining agreement with reference values. Our strategy concentrates the numerical effort on physically pertinent CI-contributions and is to be considered as a tool to tackle large systems including numerous open-shells. To show the efficiency of our method we consider two 4-electron parent systems. First, we illustrate our approach by describing the van der Waals interactions in the (H2)2 system. By systematically including local correlation, dispersion and charge transfer mechanisms, we show that 90% of the reference full CI dissociation energy of the H2 dimer is reproduced using only 3% of the full CI space. Second, the conformational cis/trans rotation barrier of the butadiene molecule is remarkably reproduced (97% of the reference value) with less than 1% of the reference space. This work paves the way to numerical strategies which afford the electronic structure determination of large open-shell systems avoiding the exponential limitation. At the same time, a physical analysis of the contents of the wave function is offered.

  16. Estimating Absolute Site Effects

    SciTech Connect

    Malagnini, L; Mayeda, K M; Akinci, A; Bragato, P L

    2004-07-15

    The authors use previously determined direct-wave attenuation functions as well as stable, coda-derived source excitation spectra to isolate the absolute S-wave site effect for the horizontal and vertical components of weak ground motion. They used selected stations in the seismic network of the eastern Alps, and find the following: (1) all ''hard rock'' sites exhibited deamplification phenomena due to absorption at frequencies ranging between 0.5 and 12 Hz (the available bandwidth), on both the horizontal and vertical components; (2) ''hard rock'' site transfer functions showed large variability at high-frequency; (3) vertical-motion site transfer functions show strong frequency-dependence, and (4) H/V spectral ratios do not reproduce the characteristics of the true horizontal site transfer functions; (5) traditional, relative site terms obtained by using reference ''rock sites'' can be misleading in inferring the behaviors of true site transfer functions, since most rock sites have non-flat responses due to shallow heterogeneities resulting from varying degrees of weathering. They also use their stable source spectra to estimate total radiated seismic energy and compare against previous results. they find that the earthquakes in this region exhibit non-constant dynamic stress drop scaling which gives further support for a fundamental difference in rupture dynamics between small and large earthquakes. To correct the vertical and horizontal S-wave spectra for attenuation, they used detailed regional attenuation functions derived by Malagnini et al. (2002) who determined frequency-dependent geometrical spreading and Q for the region. These corrections account for the gross path effects (i.e., all distance-dependent effects), although the source and site effects are still present in the distance-corrected spectra. The main goal of this study is to isolate the absolute site effect (as a function of frequency) by removing the source spectrum (moment-rate spectrum) from

  17. Development of Prediction Models for the Reactivity of Organic Compounds with Ozone in Aqueous Solution by Quantum Chemical Calculations: The Role of Delocalized and Localized Molecular Orbitals.

    PubMed

    Lee, Minju; Zimmermann-Steffens, Saskia G; Arey, J Samuel; Fenner, Kathrin; von Gunten, Urs

    2015-08-18

    Second-order rate constants (kO3) for the reaction of ozone with micropollutants are essential parameters for the assessment of micropollutant elimination efficiency during ozonation in water and wastewater treatment. Prediction models for kO3 were developed for aromatic compounds, olefins, and amines by quantum chemical molecular orbital calculations employing ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods. The kO3 values for aromatic compounds correlated well with the energy of a delocalized molecular orbital first appearing on an aromatic ring (i.e., the highest occupied molecular orbital (HOMO) or HOMO-n (n ≥ 0) when the HOMO is not located on the aromatic ring); the number of compounds tested (N) was 112, and the correlation coefficient (R(2)) values were 0.82-1.00. The kO3 values for olefins and amines correlated well with the energy of a localized molecular orbital (i.e., the natural bond orbital (NBO)) energy of the carbon-carbon π bond of olefins (N = 45, R(2) values of 0.82-0.85) and the NBO energy of the nitrogen lone-pair electrons of amines (N = 59, R(2) values of 0.81-0.83), respectively. Considering the performance of the kO3 prediction model and the computational costs, the HF/6-31G method is recommended for all aromatic groups and olefins investigated herein, whereas the HF/MIDI!, HF/6-31G*, or HF/6-311++G** methods are recommended for amines. Based on their mean absolute errors, the above models could predict kO3 within a factor of 4, on average, relative to the experimentally determined values. Overall, good correlations were also observed (R(2) values of 0.77-0.96) between kO3 predictions by quantum molecular orbital descriptors in this study and by the Hammett (σ) and Taft (σ*) constants from previously developed quantitative structure-activity relationship (QSAR) models. Hence, the quantum molecular orbital descriptors are an alternative to σ and σ*-values in QSAR applications and can also be utilized to

  18. Pattern of Local Recurrence and Distant Metastasis in Breast Cancer By Molecular Subtype

    PubMed Central

    Wu, Xingrao; Baig, Ayesha; Kasymjanova, Goulnar; Kafi, Kamran; Holcroft, Christina; Mekouar, Hind; Carbonneau, Annie; Bahoric, Boris; Sultanem, Khalil

    2016-01-01

    Background and Purpose: No longer considered a single disease entity, breast cancer is being classified into several distinct molecular subtypes based on gene expression profiling. These subtypes appear to carry prognostic implications and have the potential to be incorporated into treatment decisions. In this study, we evaluated patterns of local recurrence (LR), distant metastasis (DM), and association of survival with molecular subtype in breast cancer patients in the post–adjuvant radiotherapy setting. Material and Methods: The medical records of 1,088 consecutive, non-metastatic breast cancer patients treated at a single institution between 2004 and 2012 were reviewed. Estrogen/progesterone receptors (ER/PR) and human epidermal growth factor receptor-2 (HER2) enrichment were evaluated by immunohistochemistry. Patients were categorized into one of four subtypes: luminal-A (LA; ER/PR+, HER2-, Grade 1-2), luminal-B (LB; ER/PR+, HER2-, Grade > 2), HER2 over-expression (HER2; ER/PR-, HER2+), and triple negative (TN; ER/PR-, HER2-).  Results: The median follow-up time was 6.9 years. During the follow-up, 16% (174/1,088) of patients failed initial treatment and developed either LR (48) or DM (126). The prevalence of LR was the highest in TN (12%) and the lowest in LA (2%). Breast or chest wall relapse was the most frequent site (≈80%) of recurrence in LA, LB, and HER2 subtypes, whereas the regional lymph nodes and chest wall were the common sites of relapse in the TN group (50.0%). DM rates were 6.4% in LA, 12.1% in LB, 19.2% in HER2, and 27.4% in TN subgroups. Five-year survival rates were 84%, 83%, 84%, and 77% in the LA, LB, HER2 and TN subgroups, respectively. There was a statistically significant association between survival and molecular subtypes in an univariate analysis. In the adjusted multivariate analysis, the following variables were independent prognostic factors for survival: T stage, N stage, and molecular subtype. Conclusions: Of the four

  19. Molecular and atomic gas in the Local Group galaxy M 33

    NASA Astrophysics Data System (ADS)

    Gratier, P.; Braine, J.; Rodriguez-Fernandez, N. J.; Schuster, K. F.; Kramer, C.; Xilouris, E. M.; Tabatabaei, F. S.; Henkel, C.; Corbelli, E.; Israel, F.; van der Werf, P. P.; Calzetti, D.; Garcia-Burillo, S.; Sievers, A.; Combes, F.; Wiklind, T.; Brouillet, N.; Herpin, F.; Bontemps, S.; Aalto, S.; Koribalski, B.; van der Tak, F.; Wiedner, M. C.; Röllig, M.; Mookerjea, B.

    2010-11-01

    We present high-resolution large-scale observations of the molecular and atomic gas in the Local Group galaxy M 33. The observations were carried out using the HEterodyne Receiver Array (HERA) at the 30 m IRAM telescope in the CO(2-1) line, achieving a resolution of 12” × 2.6 km s-1, enabling individual giant molecular clouds (GMCs) to be resolved. The observed region is 650 square arcminutes mainly along the major axis and out to a radius of 8.5 kpc, and covers entirely the 2' × 40' radial strip observed with the HIFI and PACS Spectrometers as part of the HERM33ES Herschel key program. The achieved sensitivity in main-beam temperature is 20-50 mK at 2.6 km s-1 velocity resolution. The CO(2-1) luminosity of the observed region is 1.7±0.1 × 107 K km s-1 pc2 and is estimated to be 2.8±0.3 × 107 K km s-1 pc2 for the entire galaxy, corresponding to H2 masses of 1.9 × 108 Msun and 3.3 × 108 Msun respectively (including He), calculated with N(H2)/ICO(1-0) twice the Galactic value due to the half-solar metallicity of M 33. The H i 21 cm VLA archive observations were reduced, and the mosaic was imaged and cleaned using the multi-scale task in the CASA software package, yielding a series of datacubes with resolutions ranging from 5” to 25”. The H i mass within a radius of 8.5 kpc is estimated to be 1.4 × 109 Msun. The azimuthally averaged CO surface brightness decreases exponentially with a scale length of 1.9±0.1 kpc whereas the atomic gas surface density is constant at ΣH I = 6±2 Msun pc-2 deprojected to face-on. For an N(H2)/ICO(1-0) conversion factor twice that of the Milky Way, the central kiloparsec H2 surface density is ΣH2 = 8.5±0.2 Msun pc-2. The star formation rate per unit molecular gas (SF efficiency, the rate of transformation of molecular gas into stars), as traced by the ratio of CO to Hα and FIR brightness, is constant with radius. The SFE, with a N(H2)/ICO(1-0) factor twice galactic, appears 2-4 times greater than for large spiral

  20. Local and systemic vasodilatory effects of low molecular weight S-nitrosothiols.

    PubMed

    Liu, Taiming; Schroeder, Hobe J; Wilson, Sean M; Terry, Michael H; Romero, Monica; Longo, Lawrence D; Power, Gordon G; Blood, Arlin B

    2016-02-01

    S-nitrosothiols (SNOs) such as S-nitroso-L-cysteine (L-cysNO) are endogenous compounds with potent vasodilatory activity. During circulation in the blood, the NO moiety can be exchanged among various thiol-containing compounds by S-transnitrosylation, resulting in SNOs with differing capacities to enter the cell (membrane permeability). To determine whether the vasodilating potency of SNOs is dependent upon membrane permeability, membrane-permeable L-cysNO and impermeable S-nitroso-D-cysteine (D-cysNO) and S-nitroso-glutathione (GSNO) were infused into one femoral artery of anesthetized adult sheep while measuring bilateral femoral and systemic vascular conductances. L-cysNO induced vasodilation in the infused hind limb, whereas D-cysNO and GSNO did not. L-cysNO also increased intracellular NO in isolated arterial smooth muscle cells, whereas GSNO did not. The infused SNOs remained predominantly in a low molecular weight form during first-passage through the hind limb vasculature, but were converted into high molecular weight SNOs upon systemic recirculation. At systemic concentrations of ~0.6 μmol/L, all three SNOs reduced mean arterial blood pressure by ~50%, with pronounced vasodilation in the mesenteric bed. Pharmacokinetics of L-cysNO and GSNO were measured in vitro and in vivo and correlated with their hemodynamic effects, membrane permeability, and S-transnitrosylation. These results suggest local vasodilation by SNOs in the hind limb requires membrane permeation, whereas systemic vasodilation does not. The systemic hemodynamic effects of SNOs occur after equilibration of the NO moiety amongst the plasma thiols via S-transnitrosylation.

  1. Mechanistic Insights into Molecular Targeting and Combined Modality Therapy for Aggressive, Localized Prostate Cancer

    PubMed Central

    Dal Pra, Alan; Locke, Jennifer A.; Borst, Gerben; Supiot, Stephane; Bristow, Robert G.

    2016-01-01

    Radiation therapy (RT) is one of the mainstay treatments for prostate cancer (PCa). The potentially curative approaches can provide satisfactory results for many patients with non-metastatic PCa; however, a considerable number of individuals may present disease recurrence and die from the disease. Exploiting the rich molecular biology of PCa will provide insights into how the most resistant tumor cells can be eradicated to improve treatment outcomes. Important for this biology-driven individualized treatment is a robust selection procedure. The development of predictive biomarkers for RT efficacy is therefore of utmost importance for a clinically exploitable strategy to achieve tumor-specific radiosensitization. This review highlights the current status and possible opportunities in the modulation of four key processes to enhance radiation response in PCa by targeting the: (1) androgen signaling pathway; (2) hypoxic tumor cells and regions; (3) DNA damage response (DDR) pathway; and (4) abnormal extra-/intracell signaling pathways. In addition, we discuss how and which patients should be selected for biomarker-based clinical trials exploiting and validating these targeted treatment strategies with precision RT to improve cure rates in non-indolent, localized PCa. PMID:26909338

  2. Balancing local order and long-ranged interactions in the molecular theory of liquid water.

    PubMed

    Shah, J K; Asthagiri, D; Pratt, L R; Paulaitis, M E

    2007-10-14

    A molecular theory of liquid water is identified and studied on the basis of computer simulation of the TIP3P model of liquid water. This theory would be exact for models of liquid water in which the intermolecular interactions vanish outside a finite spatial range, and therefore provides a precise analysis tool for investigating the effects of longer-ranged intermolecular interactions. We show how local order can be introduced through quasichemical theory. Long-ranged interactions are characterized generally by a conditional distribution of binding energies, and this formulation is interpreted as a regularization of the primitive statistical thermodynamic problem. These binding-energy distributions for liquid water are observed to be unimodal. The Gaussian approximation proposed is remarkably successful in predicting the Gibbs free energy and the molar entropy of liquid water, as judged by comparison with numerically exact results. The remaining discrepancies are subtle quantitative problems that do have significant consequences for the thermodynamic properties that distinguish water from many other liquids. The basic subtlety of liquid water is found then in the competition of several effects which must be quantitatively balanced for realistic results.

  3. Topology, localization, and quantum information in atomic, molecular and optical systems

    NASA Astrophysics Data System (ADS)

    Yao, Norman Ying

    The scientific interface between atomic, molecular and optical (AMO) physics, condensed matter, and quantum information science has recently led to the development of new insights and tools that bridge the gap between macroscopic quantum behavior and detailed microscopic intuition. While the dialogue between these fields has sharpened our understanding of quantum theory, it has also raised a bevy of new questions regarding the out-of-equilibrium dynamics and control of many-body systems. This thesis is motivated by experimental advances that make it possible to produce and probe isolated, strongly interacting ensembles of disordered particles, as found in systems ranging from trapped ions and Rydberg atoms to ultracold polar molecules and spin defects in the solid state. The presence of strong interactions in these systems underlies their potential for exploring correlated many-body physics and this thesis presents recent results on realizing fractionalization and localization. From a complementary perspective, the controlled manipulation of individual quanta can also enable the bottom-up construction of quantum devices. To this end, this thesis also describes blueprints for a room-temperature quantum computer, quantum credit cards and nanoscale quantum thermometry.

  4. Molecular imaging of brain localization of liposomes in mice using MALDI mass spectrometry

    PubMed Central

    Fülöp, Annabelle; Sammour, Denis A.; Erich, Katrin; von Gerichten, Johanna; van Hoogevest, Peter; Sandhoff, Roger; Hopf, Carsten

    2016-01-01

    Phospholipids have excellent biocompatibility and are therefore often used as main components of liposomal drug carriers. In traditional bioanalytics, the in-vivo distribution of liposomal drug carriers is assessed using radiolabeled liposomal constituents. This study presents matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) as an alternative, label-free method for ex-vivo molecular imaging of liposomal drug carriers in mouse tissue. To this end, indocyanine green as cargo and two liposomal markers, 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine conjugated with monodisperse polyethylene glycol (PEG36-DSPE) were incorporated into liposomal carriers and administered to mice. We used MALDI MSI of the two lipid markers in both positive and negative ion mode for visualization of liposome integrity and distribution in mouse organs. Additional MSI of hemoglobin in the same tissue slice and pixel-by-pixel computational analysis of co-occurrence of lipid markers and hemoglobin served as indicator of liposome localization either in parenchyma or in blood vessels. Our proof-of-concept study suggests that liposomal components and indocyanine green distributed into all investigated organs. PMID:27650487

  5. Probing absolute spin polarization at the nanoscale.

    PubMed

    Eltschka, Matthias; Jäck, Berthold; Assig, Maximilian; Kondrashov, Oleg V; Skvortsov, Mikhail A; Etzkorn, Markus; Ast, Christian R; Kern, Klaus

    2014-12-10

    Probing absolute values of spin polarization at the nanoscale offers insight into the fundamental mechanisms of spin-dependent transport. Employing the Zeeman splitting in superconducting tips (Meservey-Tedrow-Fulde effect), we introduce a novel spin-polarized scanning tunneling microscopy that combines the probing capability of the absolute values of spin polarization with precise control at the atomic scale. We utilize our novel approach to measure the locally resolved spin polarization of magnetic Co nanoislands on Cu(111). We find that the spin polarization is enhanced by 65% when increasing the width of the tunnel barrier by only 2.3 Å due to the different decay of the electron orbitals into vacuum.

  6. Cryogenic, Absolute, High Pressure Sensor

    NASA Technical Reports Server (NTRS)

    Chapman, John J. (Inventor); Shams. Qamar A. (Inventor); Powers, William T. (Inventor)

    2001-01-01

    A pressure sensor is provided for cryogenic, high pressure applications. A highly doped silicon piezoresistive pressure sensor is bonded to a silicon substrate in an absolute pressure sensing configuration. The absolute pressure sensor is bonded to an aluminum nitride substrate. Aluminum nitride has appropriate coefficient of thermal expansion for use with highly doped silicon at cryogenic temperatures. A group of sensors, either two sensors on two substrates or four sensors on a single substrate are packaged in a pressure vessel.

  7. Influence of molecular order on the local work function of nanographene architectures: a Kelvin-probe force microscopy study.

    PubMed

    Palermo, Vincenzo; Palma, Matteo; Tomović, Zeljko; Watson, Mark D; Friedlein, Rainer; Müllen, Klaus; Samorì, Paolo

    2005-11-11

    We report a Kelvin-probe force microscopy (KPFM) investigation on the structural and electronic properties of different submicron-scale supramolecular architectures of a synthetic nanographene, including extended layers, percolated networks and broken patterns grown from solutions at surfaces. This study made it possible to determine the local work function (WF) of the different pi-conjugated nanostructures adsorbed on mica with a resolution below 10 nm and 0.05 eV. It revealed that the WF strongly depends on the local molecular order at the surface, in particular on the delocalization of electrons in the pi-states, on the molecular orientation at surfaces, on the molecular packing density, on the presence of defects in the film and on the different conformations of the aliphatic peripheral chains that might cover the conjugated core. These results were confirmed by comparing the KPFM-estimated local WF of layers supported on mica, where the molecules are preferentially packed edge-on on the substrate, with the ultraviolet photoelectron spectroscopy microscopically measured WF of layers adsorbed on graphite, where the molecules should tend to assemble face-on at the surface. It appears that local WF studies are of paramount importance for understanding the electronic properties of active organic nanostructures, being therefore fundamental for the building of high-performance organic electronic devices, including field-effect transistors, light-emitting diodes and solar cells.

  8. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

    PubMed

    Li, Hongzhi; Fajer, Mikolai; Yang, Wei

    2007-01-14

    A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.

  9. Negative absolute temperature for mobile particles

    NASA Astrophysics Data System (ADS)

    Braun, Simon; Ronzheimer, Philipp; Schreiber, Michael; Hodgman, Sean; Bloch, Immanuel; Schneider, Ulrich

    2013-05-01

    Absolute temperature is usually bound to be strictly positive. However, negative absolute temperature states, where the occupation probability of states increases with their energy, are possible in systems with an upper energy bound. So far, such states have only been demonstrated in localized spin systems with finite, discrete spectra. We realized a negative absolute temperature state for motional degrees of freedom with ultracold bosonic 39K atoms in an optical lattice, by implementing the attractive Bose-Hubbard Hamiltonian. This new state strikingly revealed itself by a quasimomentum distribution that is peaked at maximum kinetic energy. The measured kinetic energy distribution and the extracted negative temperature indicate that the ensemble is close to degeneracy, with coherence over several lattice sites. The state is as stable as a corresponding positive temperature state: The negative temperature stabilizes the system against mean-field collapse driven by negative pressure. Negative temperatures open up new parameter regimes for cold atoms, enabling fundamentally new many-body states. Additionally, they give rise to several counterintuitive effects such as heat engines with above unity efficiency.

  10. Measurement of absolute gravity acceleration in Firenze

    NASA Astrophysics Data System (ADS)

    de Angelis, M.; Greco, F.; Pistorio, A.; Poli, N.; Prevedelli, M.; Saccorotti, G.; Sorrentino, F.; Tino, G. M.

    2011-01-01

    This paper reports the results from the accurate measurement of the acceleration of gravity g taken at two separate premises in the Polo Scientifico of the University of Firenze (Italy). In these laboratories, two separate experiments aiming at measuring the Newtonian constant and testing the Newtonian law at short distances are in progress. Both experiments require an independent knowledge on the local value of g. The only available datum, pertaining to the italian zero-order gravity network, was taken more than 20 years ago at a distance of more than 60 km from the study site. Gravity measurements were conducted using an FG5 absolute gravimeter, and accompanied by seismic recordings for evaluating the noise condition at the site. The absolute accelerations of gravity at the two laboratories are (980 492 160.6 ± 4.0) μGal and (980 492 048.3 ± 3.0) μGal for the European Laboratory for Non-Linear Spectroscopy (LENS) and Dipartimento di Fisica e Astronomia, respectively. Other than for the two referenced experiments, the data here presented will serve as a benchmark for any future study requiring an accurate knowledge of the absolute value of the acceleration of gravity in the study region.

  11. Why to compare absolute numbers of mitochondria.

    PubMed

    Schmitt, Sabine; Schulz, Sabine; Schropp, Eva-Maria; Eberhagen, Carola; Simmons, Alisha; Beisker, Wolfgang; Aichler, Michaela; Zischka, Hans

    2014-11-01

    Prompted by pronounced structural differences between rat liver and rat hepatocellular carcinoma mitochondria, we suspected these mitochondrial populations to differ massively in their molecular composition. Aiming to reveal these mitochondrial differences, we came across the issue on how to normalize such comparisons and decided to focus on the absolute number of mitochondria. To this end, fluorescently stained mitochondria were quantified by flow cytometry. For rat liver mitochondria, this approach resulted in mitochondrial protein contents comparable to earlier reports using alternative methods. We determined similar protein contents for rat liver, heart and kidney mitochondria. In contrast, however, lower protein contents were determined for rat brain mitochondria and for mitochondria from the rat hepatocellular carcinoma cell line McA 7777. This result challenges mitochondrial comparisons that rely on equal protein amounts as a typical normalization method. Exemplarily, we therefore compared the activity and susceptibility toward inhibition of complex II of rat liver and hepatocellular carcinoma mitochondria and obtained significant discrepancies by either normalizing to protein amount or to absolute mitochondrial number. Importantly, the latter normalization, in contrast to the former, demonstrated a lower complex II activity and higher susceptibility toward inhibition in hepatocellular carcinoma mitochondria compared to liver mitochondria. These findings demonstrate that solely normalizing to protein amount may obscure essential molecular differences between mitochondrial populations.

  12. Database applicaton for absolute spectrophotometry

    NASA Astrophysics Data System (ADS)

    Bochkov, Valery V.; Shumko, Sergiy

    2002-12-01

    32-bit database application with multidocument interface for Windows has been developed to calculate absolute energy distributions of observed spectra. The original database contains wavelength calibrated observed spectra which had been already passed through apparatus reductions such as flatfielding, background and apparatus noise subtracting. Absolute energy distributions of observed spectra are defined in unique scale by means of registering them simultaneously with artificial intensity standard. Observations of sequence of spectrophotometric standards are used to define absolute energy of the artificial standard. Observations of spectrophotometric standards are used to define optical extinction in selected moments. FFT algorithm implemented in the application allows performing convolution (deconvolution) spectra with user-defined PSF. The object-oriented interface has been created using facilities of C++ libraries. Client/server model with Windows Socket functionality based on TCP/IP protocol is used to develop the application. It supports Dynamic Data Exchange conversation in server mode and uses Microsoft Exchange communication facilities.

  13. Absolute classification with unsupervised clustering

    NASA Technical Reports Server (NTRS)

    Jeon, Byeungwoo; Landgrebe, D. A.

    1992-01-01

    An absolute classification algorithm is proposed in which the class definition through training samples or otherwise is required only for a particular class of interest. The absolute classification is considered as a problem of unsupervised clustering when one cluster is known initially. The definitions and statistics of the other classes are automatically developed through the weighted unsupervised clustering procedure, which is developed to keep the cluster corresponding to the class of interest from losing its identity as the class of interest. Once all the classes are developed, a conventional relative classifier such as the maximum-likelihood classifier is used in the classification.

  14. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    SciTech Connect

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-12-31

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

  15. Laser-induced perturbation into molecular dynamics localized in neuronal cell

    NASA Astrophysics Data System (ADS)

    Hosokawa, Chie; Takeda, Naoko; Kudoh, Suguru N.; Taguchi, Takahisa

    2015-03-01

    Molecular dynamics at synaptic terminals in neuronal cells is essential for synaptic plasticity and subsequent modulation of cellular functions in a neuronal network. For realizing artificial control of living neuronal network, we demonstrate laser-induced perturbation into molecular dynamics in the neuronal cells. The optical trapping of cellular molecules such as synaptic vesicles or neural cell adhesion molecules labeled with quantum dots was evaluated by fluorescence imaging and fluorescence correlation spectroscopy. The trapping and assembling dynamics was revealed that the molecular motion was constrained at the focal spot of a focused laser beam due to optical trapping force. Our method has a potential to manipulate synaptic transmission at single synapse level.

  16. Molecular level detection and localization of mechanical damage in collagen enabled by collagen hybridizing peptides

    NASA Astrophysics Data System (ADS)

    Zitnay, Jared L.; Li, Yang; Qin, Zhao; San, Boi Hoa; Depalle, Baptiste; Reese, Shawn P.; Buehler, Markus J.; Yu, S. Michael; Weiss, Jeffrey A.

    2017-03-01

    Mechanical injury to connective tissue causes changes in collagen structure and material behaviour, but the role and mechanisms of molecular damage have not been established. In the case of mechanical subfailure damage, no apparent macroscale damage can be detected, yet this damage initiates and potentiates in pathological processes. Here, we utilize collagen hybridizing peptide (CHP), which binds unfolded collagen by triple helix formation, to detect molecular level subfailure damage to collagen in mechanically stretched rat tail tendon fascicle. Our results directly reveal that collagen triple helix unfolding occurs during tensile loading of collagenous tissues and thus is an important damage mechanism. Steered molecular dynamics simulations suggest that a likely mechanism for triple helix unfolding is intermolecular shearing of collagen α-chains. Our results elucidate a probable molecular failure mechanism associated with subfailure injuries, and demonstrate the potential of CHP targeting for diagnosis, treatment and monitoring of tissue disease and injury.

  17. Molecular level detection and localization of mechanical damage in collagen enabled by collagen hybridizing peptides

    PubMed Central

    Zitnay, Jared L.; Li, Yang; Qin, Zhao; San, Boi Hoa; Depalle, Baptiste; Reese, Shawn P.; Buehler, Markus J.; Yu, S. Michael; Weiss, Jeffrey A.

    2017-01-01

    Mechanical injury to connective tissue causes changes in collagen structure and material behaviour, but the role and mechanisms of molecular damage have not been established. In the case of mechanical subfailure damage, no apparent macroscale damage can be detected, yet this damage initiates and potentiates in pathological processes. Here, we utilize collagen hybridizing peptide (CHP), which binds unfolded collagen by triple helix formation, to detect molecular level subfailure damage to collagen in mechanically stretched rat tail tendon fascicle. Our results directly reveal that collagen triple helix unfolding occurs during tensile loading of collagenous tissues and thus is an important damage mechanism. Steered molecular dynamics simulations suggest that a likely mechanism for triple helix unfolding is intermolecular shearing of collagen α-chains. Our results elucidate a probable molecular failure mechanism associated with subfailure injuries, and demonstrate the potential of CHP targeting for diagnosis, treatment and monitoring of tissue disease and injury. PMID:28327610

  18. Absolute transition probabilities of phosphorus.

    NASA Technical Reports Server (NTRS)

    Miller, M. H.; Roig, R. A.; Bengtson, R. D.

    1971-01-01

    Use of a gas-driven shock tube to measure the absolute strengths of 21 P I lines and 126 P II lines (from 3300 to 6900 A). Accuracy for prominent, isolated neutral and ionic lines is estimated to be 28 to 40% and 18 to 30%, respectively. The data and the corresponding theoretical predictions are examined for conformity with the sum rules.-

  19. Relativistic Absolutism in Moral Education.

    ERIC Educational Resources Information Center

    Vogt, W. Paul

    1982-01-01

    Discusses Emile Durkheim's "Moral Education: A Study in the Theory and Application of the Sociology of Education," which holds that morally healthy societies may vary in culture and organization but must possess absolute rules of moral behavior. Compares this moral theory with current theory and practice of American educators. (MJL)

  20. Absolute Standards for Climate Measurements

    NASA Astrophysics Data System (ADS)

    Leckey, J.

    2016-10-01

    In a world of changing climate, political uncertainty, and ever-changing budgets, the benefit of measurements traceable to SI standards increases by the day. To truly resolve climate change trends on a decadal time scale, on-orbit measurements need to be referenced to something that is both absolute and unchanging. One such mission is the Climate Absolute Radiance and Refractivity Observatory (CLARREO) that will measure a variety of climate variables with an unprecedented accuracy to definitively quantify climate change. In the CLARREO mission, we will utilize phase change cells in which a material is melted to calibrate the temperature of a blackbody that can then be observed by a spectrometer. A material's melting point is an unchanging physical constant that, through a series of transfers, can ultimately calibrate a spectrometer on an absolute scale. CLARREO consists of two primary instruments: an infrared (IR) spectrometer and a reflected solar (RS) spectrometer. The mission will contain orbiting radiometers with sufficient accuracy to calibrate other space-based instrumentation and thus transferring the absolute traceability. The status of various mission options will be presented.

  1. Control of quantum localization and classical diffusion in laser-kicked molecular rotors

    NASA Astrophysics Data System (ADS)

    Bitter, M.; Milner, V.

    2017-01-01

    We experimentally study a system of quantum kicked rotors—an ensemble of diatomic molecules exposed to a periodic sequence of ultrashort laser pulses. In the regime where the underlying classical dynamics is chaotic, we investigate the quantum phenomenon of dynamical localization by means of state-resolved coherent Raman spectroscopy. We examine the dependence of the exponentially localized angular momentum distribution and of the total rotational energy on the time period between the pulses and their amplitude. The former parameter is shown to provide control over the localization center, whereas the latter one controls the localization length. Similar control of the center and width of a nonlocalized rotational distribution is demonstrated in the limit of classical diffusion, established by adding noise to the periodic pulse sequence.

  2. Absolute calibration of optical flats

    DOEpatents

    Sommargren, Gary E.

    2005-04-05

    The invention uses the phase shifting diffraction interferometer (PSDI) to provide a true point-by-point measurement of absolute flatness over the surface of optical flats. Beams exiting the fiber optics in a PSDI have perfect spherical wavefronts. The measurement beam is reflected from the optical flat and passed through an auxiliary optic to then be combined with the reference beam on a CCD. The combined beams include phase errors due to both the optic under test and the auxiliary optic. Standard phase extraction algorithms are used to calculate this combined phase error. The optical flat is then removed from the system and the measurement fiber is moved to recombine the two beams. The newly combined beams include only the phase errors due to the auxiliary optic. When the second phase measurement is subtracted from the first phase measurement, the absolute phase error of the optical flat is obtained.

  3. The Absolute Spectrum Polarimeter (ASP)

    NASA Technical Reports Server (NTRS)

    Kogut, A. J.

    2010-01-01

    The Absolute Spectrum Polarimeter (ASP) is an Explorer-class mission to map the absolute intensity and linear polarization of the cosmic microwave background and diffuse astrophysical foregrounds over the full sky from 30 GHz to 5 THz. The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r much greater than 1O(raised to the power of { -3}) and Compton distortion y < 10 (raised to the power of{-6}). We describe the ASP instrument and mission architecture needed to detect the signature of an inflationary epoch in the early universe using only 4 semiconductor bolometers.

  4. Physics of negative absolute temperatures

    NASA Astrophysics Data System (ADS)

    Abraham, Eitan; Penrose, Oliver

    2017-01-01

    Negative absolute temperatures were introduced into experimental physics by Purcell and Pound, who successfully applied this concept to nuclear spins; nevertheless, the concept has proved controversial: a recent article aroused considerable interest by its claim, based on a classical entropy formula (the "volume entropy") due to Gibbs, that negative temperatures violated basic principles of statistical thermodynamics. Here we give a thermodynamic analysis that confirms the negative-temperature interpretation of the Purcell-Pound experiments. We also examine the principal arguments that have been advanced against the negative temperature concept; we find that these arguments are not logically compelling, and moreover that the underlying "volume" entropy formula leads to predictions inconsistent with existing experimental results on nuclear spins. We conclude that, despite the counterarguments, negative absolute temperatures make good theoretical sense and did occur in the experiments designed to produce them.

  5. Optomechanics for absolute rotation detection

    NASA Astrophysics Data System (ADS)

    Davuluri, Sankar

    2016-07-01

    In this article, we present an application of optomechanical cavity for the absolute rotation detection. The optomechanical cavity is arranged in a Michelson interferometer in such a way that the classical centrifugal force due to rotation changes the length of the optomechanical cavity. The change in the cavity length induces a shift in the frequency of the cavity mode. The phase shift corresponding to the frequency shift in the cavity mode is measured at the interferometer output to estimate the angular velocity of absolute rotation. We derived an analytic expression to estimate the minimum detectable rotation rate in our scheme for a given optomechanical cavity. Temperature dependence of the rotation detection sensitivity is studied.

  6. Localized spatially nonlinear matter waves in atomic-molecular Bose-Einstein condensates with space-modulated nonlinearity

    PubMed Central

    Yao, Yu-Qin; Li, Ji; Han, Wei; Wang, Deng-Shan; Liu, Wu-Ming

    2016-01-01

    The intrinsic nonlinearity is the most remarkable characteristic of the Bose-Einstein condensates (BECs) systems. Many studies have been done on atomic BECs with time- and space- modulated nonlinearities, while there is few work considering the atomic-molecular BECs with space-modulated nonlinearities. Here, we obtain two kinds of Jacobi elliptic solutions and a family of rational solutions of the atomic-molecular BECs with trapping potential and space-modulated nonlinearity and consider the effect of three-body interaction on the localized matter wave solutions. The topological properties of the localized nonlinear matter wave for no coupling are analysed: the parity of nonlinear matter wave functions depends only on the principal quantum number n, and the numbers of the density packets for each quantum state depend on both the principal quantum number n and the secondary quantum number l. When the coupling is not zero, the localized nonlinear matter waves given by the rational function, their topological properties are independent of the principal quantum number n, only depend on the secondary quantum number l. The Raman detuning and the chemical potential can change the number and the shape of the density packets. The stability of the Jacobi elliptic solutions depends on the principal quantum number n, while the stability of the rational solutions depends on the chemical potential and Raman detuning. PMID:27403634

  7. A Molecular Dynamics Study on the Local Structure of Liquid-Vapor Interface of Water and L-J Fluid

    NASA Astrophysics Data System (ADS)

    Kikugawa, Gota; Takagi, Shu; Matsumoto, Yoichiro; Ohara, Taku

    Microscopic structures of a liquid-vapor interface are investigated by molecular dynamics simulations. In the previous studies, we proposed the local and instantaneous definition of the interface at the molecular level, which can capture the thermal fluctuation of the interface. By using this definition, the layering structure of water molecules at the interface was found, in other words, the structurization phenomena of water at the molecular level were clearly seen as usually found at the liquid-solid interface. In this study, we investigated the liquid-vapor interface of Lenard-Jones fluid. The effect of well depth of L-J potential parameter on the structure was also studied. Although the structurization was found at the L-J fluid as well as water, characteristic of this structure was clearly different from that of water. We consider that the difference is ascribed to the intrinsic structure of liquid and associative trend of molecules. We also discussed the anisotropic characteristics of the molecular diffusion at the interface. The anisotropy of the translational diffusion at the interface of water is stronger than that of the L-J fluid.

  8. Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

    DOE PAGES

    Giera, Brian; Lawrence Livermore National Lab.; Henson, Neil; ...

    2015-02-27

    We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drivemore » strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.« less

  9. Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

    SciTech Connect

    Giera, Brian; Henson, Neil; Kober, Edward M.; Shell, M. Scott; Squires, Todd M.

    2015-02-27

    We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drive strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.

  10. Molecular dipole static polarisabilities and hyperpolarisabilities of conjugated oligomer chains calculated with the local π-electron coupled cluster theory

    NASA Astrophysics Data System (ADS)

    Ivanov, Vladimir V.; Zakharov, Anton B.; Adamowicz, Ludwik

    2013-12-01

    A new semi-empirical π-electron local coupled cluster theory has been developed to calculate static dipole polarisabilities and hyperpolarisabilities of extended π-conjugated systems. The key idea of the approach is the use of the ethylene molecular orbitals as the orbital basis set for π-conjugated compounds (the method is termed the Covalent Unbonded Molecules of Ethylene method, cue). Test calculations of some small model organic conjugated compounds demonstrate high accuracy of the version of the cue local coupled cluster theory developed in this work in comparison with the π-electron full configuration interaction (FCI) method. Calculations of different conjugated carbon-based oligomer chains (polyenes, polyynes, polyacenes, polybenzocyclobutadiene, etc.) demonstrate fast convergence (per π-electron) of the polarisability and hyperpolarisability values in the calculations when more classes of orbital excitations are included in the coupled cluster single and double (CCSD) excitation operator. The results show qualitatively correct dependence on the system size.

  11. EVIDENCE FOR 1000 km s{sup -1} MOLECULAR OUTFLOWS IN THE LOCAL ULIRG POPULATION

    SciTech Connect

    Chung, Aeree; Yun, Min S.; Naraynan, Gopal; Heyer, Mark; Erickson, Neal R.

    2011-05-01

    The feedback from galactic outflows is thought to play an important role in shaping the gas content, star formation history, and ultimately the stellar mass function of galaxies. Here we present evidence for massive molecular outflows associated with ultra-luminous infrared galaxies (ULIRGs) in the co-added Redshift Search Receiver {sup 12}CO (1-0) spectrum. Our stacked spectrum of 27 ULIRGs at z = 0.043-0.11 ({nu}{sub rest} = 110-120 GHz) shows broad wings around the CO line with {Delta}V(FWZI) {approx} 2000 km s{sup -1}. Its integrated line flux accounts for up to 25% {+-} 5% of the total CO line luminosity. When interpreted as a massive molecular outflow wind, the associated mechanical energy can be explained by a concentrated starburst with star formation rate (SFR) {>=}100 M{sub sun} yr{sup -1}, which agrees well with their SFR derived from the FIR luminosity. Using the high signal-to-noise stacked composite spectrum, we also probe {sup 13}CO and {sup 12}CN emission in the sample and discuss how the chemical abundance of molecular gas may vary depending on the physical conditions of the nuclear region.

  12. Strong impact of lattice vibrations on electronic and magnetic properties of paramagnetic Fe revealed by disordered local moments molecular dynamics

    NASA Astrophysics Data System (ADS)

    Alling, B.; Körmann, F.; Grabowski, B.; Glensk, A.; Abrikosov, I. A.; Neugebauer, J.

    2016-06-01

    We study the impact of lattice vibrations on magnetic and electronic properties of paramagnetic bcc and fcc iron at finite temperature, employing the disordered local moments molecular dynamics (DLM-MD) method. Vibrations strongly affect the distribution of local magnetic moments at finite temperature, which in turn correlates with the local atomic volumes. Without the explicit consideration of atomic vibrations, the mean local magnetic moment and mean field derived magnetic entropy of paramagnetic bcc Fe are larger compared to paramagnetic fcc Fe, which would indicate that the magnetic contribution stabilizes the bcc phase at high temperatures. In the present study we show that this assumption is not valid when the coupling between vibrations and magnetism is taken into account. At the γ -δ transition temperature (1662 K), the lattice distortions cause very similar magnetic moments of both bcc and fcc structures and hence magnetic entropy contributions. This finding can be traced back to the electronic densities of states, which also become increasingly similar between bcc and fcc Fe with increasing temperature. Given the sensitive interplay of the different physical excitation mechanisms, our results illustrate the need for an explicit consideration of vibrational disorder and its impact on electronic and magnetic properties to understand paramagnetic Fe. Furthermore, they suggest that at the γ -δ transition temperature electronic and magnetic contributions to the Gibbs free energy are extremely similar in bcc and fcc Fe.

  13. Temperature dependence of the partially localized state in a 2D molecular nanoporous network

    NASA Astrophysics Data System (ADS)

    Piquero-Zulaica, Ignacio; Nowakowska, Sylwia; Ortega, J. Enrique; Stöhr, Meike; Gade, Lutz H.; Jung, Thomas A.; Lobo-Checa, Jorge

    2017-01-01

    Two-dimensional organic and metal-organic nanoporous networks can scatter surface electrons, leading to their partial localization. Such quantum states are related to intrinsic surface states of the substrate material. We further corroborate this relation by studying the thermally induced energy shifts of the electronic band stemming from coupled quantum states hosted in a metal-organic array formed by a perylene derivative on Cu(111). We observe by angle-resolved photoemission spectroscopy (ARPES), that both, the Shockley and the partially localized states, shift by the same amount to higher binding energies upon decreasing the sample temperature, providing evidence of their common origin. Our experimental approach and results further support the use of surface states for modelling these systems, which are expected to provide new insight into the physics concerning partially confined electronic states: scattering processes, potential barrier strengths, excited state lifetimes or the influence of guest molecules.

  14. Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

    PubMed Central

    2008-01-01

    Background Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources. Results We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus. Conclusion Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution. PMID:18302790

  15. Absolute calibration of optical tweezers

    SciTech Connect

    Viana, N.B.; Mazolli, A.; Maia Neto, P.A.; Nussenzveig, H.M.; Rocha, M.S.; Mesquita, O.N.

    2006-03-27

    As a step toward absolute calibration of optical tweezers, a first-principles theory of trapping forces with no adjustable parameters, corrected for spherical aberration, is experimentally tested. Employing two very different setups, we find generally very good agreement for the transverse trap stiffness as a function of microsphere radius for a broad range of radii, including the values employed in practice, and at different sample chamber depths. The domain of validity of the WKB ('geometrical optics') approximation to the theory is verified. Theoretical predictions for the trapping threshold, peak position, depth variation, multiple equilibria, and 'jump' effects are also confirmed.

  16. Molecular mechanism by which acyclic retinoid induces nuclear localization of transglutaminase 2 in human hepatocellular carcinoma cells

    PubMed Central

    Shrestha, R; Tatsukawa, H; Shrestha, R; Ishibashi, N; Matsuura, T; Kagechika, H; Kose, S; Hitomi, K; Imamoto, N; Kojima, S

    2015-01-01

    Nuclear accumulation of transglutaminase 2 (TG2) is an important step in TG2-dependent cell death. However, the underlying molecular mechanisms for nuclear translocation of TG2 are still poorly understood. In this study, we demonstrated that acyclic retinoid (ACR) induced nuclear accumulation of TG2 in JHH-7 cells, a hepatocellular carcinoma (HCC) leading to their apoptosis. We further demonstrated molecular mechanism in nuclear-cytoplasmic trafficking of TG2 and an effect of ACR on it. We identified a novel 14-amino acid nuclear localization signal (NLS) 466AEKEETGMAMRIRV479 in the ‘C' domain and a leucine-rich nuclear export signal (NES) 657LHMGLHKL664 in the ‘D' domain that allowed TG2 to shuttle between the nuclear and cytosolic milieu. Increased nuclear import of GAPDH myc-HIS fused with the identified NLS was observed, confirming its nuclear import ability. Leptomycin B, an inhibitor of exportin-1 as well as point mutation of all leucine residues to glutamine residues in the NES of TG2 demolished its nuclear export. TG2 formed a trimeric complex with importin-α and importin-β independently from transamidase activity which strongly suggested the involvement of a NLS-based translocation of TG2 to the nucleus. ACR accelerated the formation of the trimeric complex and that may be at least in part responsible for enhanced nuclear localization of TG2 in HCC cells treated with ACR. PMID:26633708

  17. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin.

    PubMed Central

    Caves, L. S.; Evanseck, J. D.; Karplus, M.

    1998-01-01

    Multiple molecular dynamics (MD) simulations of crambin with different initial atomic velocities are used to sample conformations in the vicinity of the native structure. Individual trajectories of length up to 5 ns sample only a fraction of the conformational distribution generated by ten independent 120 ps trajectories at 300 K. The backbone atom conformational space distribution is analyzed using principal components analysis (PCA). Four different major conformational regions are found. In general, a trajectory samples only one region and few transitions between the regions are observed. Consequently, the averages of structural and dynamic properties over the ten trajectories differ significantly from those obtained from individual trajectories. The nature of the conformational sampling has important consequences for the utilization of MD simulations for a wide range of problems, such as comparisons with X-ray or NMR data. The overall average structure is significantly closer to the X-ray structure than any of the individual trajectory average structures. The high frequency (less than 10 ps) atomic fluctuations from the ten trajectories tend to be similar, but the lower frequency (100 ps) motions are different. To improve conformational sampling in molecular dynamics simulations of proteins, as in nucleic acids, multiple trajectories with different initial conditions should be used rather than a single long trajectory. PMID:9541397

  18. Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

    NASA Astrophysics Data System (ADS)

    Rino, José Pedro; Borges, Denilson; Mota, Rita C.; Silva, Maurício A. P.

    2008-05-01

    Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.

  19. Profiling of low molecular weight proteins in plasma from locally irradiated individuals

    PubMed Central

    Nylund, Reetta; Lemola, Elina; Hartwig, Sonja; Lehr, Stefan; Acheva, Anna; Jahns, Jutta; Hildebrandt, Guido; Lindholm, Carita

    2014-01-01

    In studies reported in the 1960s and since, blood plasma from radiation-exposed individuals has been shown to induce chromosome damage when transferred into lymphocyte cultures of non-irradiated persons. This effect has been described to occur via clastogenic factors, whose nature is still mostly unknown. We have previously examined clastogenic factors from irradiated individuals by looking at plasma-induced DNA damage in reporter cells. Plasma was tested from ca. 30 locally exposed clinical patients receiving fractionated radiation treatment, as well as from three radiological accident victims exposed in 1994, albeit sampled 14 years post-accident. In the current work, proteome changes in the plasma from all subjects were examined with 2D gel electrophoresis-based proteomics techniques, in order to evaluate the level of protein expression with respect to the findings of a clastogenic factor effect. No differences were observed in protein expression due to local radiation exposure (pre- vs post-exposure). In contrast, plasma from the radiation accident victims showed alterations in the expression of 18 protein spots (in comparison with plasma from the control group). Among these, proteins such as haptoglobin, serotransferrin/transferrin, fibrinogen and ubiquitin-60S ribosomal protein L40 were observed, none of them likely to be clastogenic factors. In conclusion, the proteomics techniques applied were unable to identify changes in the proteome of the locally irradiated patients, whereas such differences were observed for the accident victims. However, association with the clastogenic effect or any specific clastogenic factor remains unresolved and thus further studies with more sensitive techniques are warranted. PMID:24570173

  20. Profiling of low molecular weight proteins in plasma from locally irradiated individuals.

    PubMed

    Nylund, Reetta; Lemola, Elina; Hartwig, Sonja; Lehr, Stefan; Acheva, Anna; Jahns, Jutta; Hildebrandt, Guido; Lindholm, Carita

    2014-07-01

    In studies reported in the 1960s and since, blood plasma from radiation-exposed individuals has been shown to induce chromosome damage when transferred into lymphocyte cultures of non-irradiated persons. This effect has been described to occur via clastogenic factors, whose nature is still mostly unknown. We have previously examined clastogenic factors from irradiated individuals by looking at plasma-induced DNA damage in reporter cells. Plasma was tested from ca. 30 locally exposed clinical patients receiving fractionated radiation treatment, as well as from three radiological accident victims exposed in 1994, albeit sampled 14 years post-accident. In the current work, proteome changes in the plasma from all subjects were examined with 2D gel electrophoresis-based proteomics techniques, in order to evaluate the level of protein expression with respect to the findings of a clastogenic factor effect. No differences were observed in protein expression due to local radiation exposure (pre- vs post-exposure). In contrast, plasma from the radiation accident victims showed alterations in the expression of 18 protein spots (in comparison with plasma from the control group). Among these, proteins such as haptoglobin, serotransferrin/transferrin, fibrinogen and ubiquitin-60S ribosomal protein L40 were observed, none of them likely to be clastogenic factors. In conclusion, the proteomics techniques applied were unable to identify changes in the proteome of the locally irradiated patients, whereas such differences were observed for the accident victims. However, association with the clastogenic effect or any specific clastogenic factor remains unresolved and thus further studies with more sensitive techniques are warranted.

  1. Reaction-diffusion-advection approach to spatially localized treadmilling aggregates of molecular motors

    NASA Astrophysics Data System (ADS)

    Yochelis, Arik; Bar-On, Tomer; Gov, Nir S.

    2016-04-01

    Unconventional myosins belong to a class of molecular motors that walk processively inside cellular protrusions towards the tips, on top of actin filament. Surprisingly, in addition, they also form retrograde moving self-organized aggregates. The qualitative properties of these aggregates are recapitulated by a mass conserving reaction-diffusion-advection model and admit two distinct families of modes: traveling waves and pulse trains. Unlike the traveling waves that are generated by a linear instability, pulses are nonlinear structures that propagate on top of linearly stable uniform backgrounds. Asymptotic analysis of isolated pulses via a simplified reaction-diffusion-advection variant on large periodic domains, allows to draw qualitative trends for pulse properties, such as the amplitude, width, and propagation speed. The results agree well with numerical integrations and are related to available empirical observations.

  2. A new clinical and molecular form of Unverricht-Lundborg disease localized by homozygosity mapping.

    PubMed

    Berkovic, Samuel F; Mazarib, Aziz; Walid, Simri; Neufeld, Miriam Y; Manelis, Judith; Nevo, Yoram; Korczyn, Amos D; Yin, Jinggang; Xiong, Lan; Pandolfo, Massimo; Mulley, John C; Wallace, Robyn H

    2005-03-01

    Progressive myoclonus epilepsy (PME) has a number of causes, of which Unverricht-Lundborg disease (ULD) is the most common. ULD has previously been mapped to a locus on chromosome 21 (EPM1). Subsequently, mutations in the cystatin B gene have been found in most cases. In the present work we identified an inbred Arab family with a clinical pattern compatible with ULD, but mutations in the cystatin B gene were absent. We sought to characterize the clinical and molecular features of the disorder. The family was studied by multiple field trips to their town to clarify details of the complex consanguineous relationships and to personally examine the family. DNA was collected for subsequent molecular analyses from 21 individuals. A genome-wide screen was performed using 811 microsatellite markers. Homozygosity mapping was used to identify loci of interest. There were eight affected individuals. Clinical onset was at 7.3 +/- 1.5 years with myoclonic or tonic-clonic seizures. All had myoclonus that progressed in severity over time and seven had tonic-clonic seizures. Ataxia, in addition to myoclonus, occurred in all. Detailed cognitive assessment was not possible, but there was no significant progressive dementia. There was intrafamily variation in severity; three required wheelchairs in adult life; the others could walk unaided. MRI, muscle and skin biopsies on one individual were unremarkable. We mapped the family to a 15-megabase region at the pericentromeric region of chromosome 12 with a maximum lod score of 6.32. Although the phenotype of individual subjects was typical of ULD, the mean age of onset (7.3 years versus 11 years for ULD) was younger. The locus on chromosome 12 does not contain genes for any other form of PME, nor does it have genes known to be related to cystatin B. This represents a new form of PME and we have designated the locus as EPM1B.

  3. Molecular cloning and chromosomal localization of human holocarboxylase synthetase, a gene responsible for biotin dependency

    SciTech Connect

    Suzuki, Y.; Aoki, Y.; Ishida, Y.

    1994-09-01

    Holocarboxylase synthetase (HCS) catalyzes biotin incorporation into various carboxylases that require biotin as a prosthetic group. They are acetyl-CoA carboxylase, a rate-limiting enzyme of fatty acid synthesis; pyruvate carboxylase, a key enzyme of gluconeogenesis; propionyl-CoA carboxylase and 3-methylcrotonyl-CoA carboxylase, enzymes involved in amino acid catabolism. HCS is therefore involved in various metabolic processes and is a key enzyme for biotin utilization by mammalian cells. Deficiency of HCS in man is known to cause biotin-responsive multiple carboxylase deficiency. Isolation of cDNA clones for the enzyme is essential to understand HCS and its deficiency at the molecular level. We purified bovine liver HCS and sequenced its proteolytic peptides. Degenerative oligonucleotide primers were synthesized from the two peptide sequences and used to amplify a putative HCS cDNA fragment from human liver by PCR. Using the amplified DNA fragment as a probe, we screened {lambda}gt10 human liver cDNA library and isolated 12 positive clones. The isolated cDNAs encoded a protein of 726 amino acids with molecular mass of 80,759. The protein contained several sequences identical or similar to those of peptides derived from the bovine liver HCS. The predicted protein had a homologous region with BirA which acts as both a biotin-[acetyl-CoA-carboxylase] ligase and a biotin repressor in E. coli, suggesting a functional relationship between the two proteins. We expressed the protein using pET3 a vector in E. coli (BL21 strain) and raised antiserum against the expressed protein. The antiserum immunoprecipitated HCS activities of human lymphoblasts and bovine liver. A one-base deletion and a missense mutation were found in cells from siblings with HCS deficiency. The human HCS gene was assigned to chromosome 21, region 21q22.1 by fluorescence in situ hybridization analysis.

  4. Molecular cloning, functional characterization, and subcellular localization of soybean nodule dihydrolipoamide reductase.

    PubMed

    Moran, Jose F; Sun, Zhaohui; Sarath, Gautam; Arredondo-Peter, Raúl; James, Euan K; Becana, Manuel; Klucas, Robert V

    2002-01-01

    Nodule ferric leghemoglobin reductase (FLbR) and leaf dihydrolipoamide reductase (DLDH) belong to the same family of pyridine nucleotide-disulfide oxidoreductases. We report here the cloning, expression, and characterization of a second protein with FLbR activity, FLbR-2, from soybean (Glycine max) nodules. The cDNA is 1,779 bp in length and codes for a precursor protein comprising a 30-residue mitochondrial transit peptide and a 470-residue mature protein of 50 kD. The derived protein has considerable homology with soybean nodule FLbR-1 (93% identity) and pea (Pisum sativum) leaf mitochondria DLDH (89% identity). The cDNA encoding the mature protein was overexpressed in Escherichia coli. The recombinant enzyme showed Km and kcat values for ferric leghemoglobin that were very similar to those of DLDH. The transcripts of FLbR-2 were more abundant in stems and roots than in nodules and leaves. Immunoblots of nodule fractions revealed that an antibody raised against pea leaf DLDH cross-reacted with recombinant FLbR-2, native FLbR-2 of soybean nodule mitochondria, DLDH from bacteroids, and an unknown protein of approximately 70 kD localized in the nodule cytosol. Immunogold labeling was also observed in the mitochondria, cytosol, and bacteroids of soybean nodules. The similar biochemical, kinetic, and immunological properties, as well as the high amino acid sequence identity and mitochondrial localization, draw us to conclude that FLbR-2 is soybean DLDH.

  5. Calculation of Local Water Densities in Biological Systems — A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

    PubMed Central

    Stumpe, Martin C.; Blinov, Nikolay; Wishart, David; Kovalenko, Andriy; Pande, Vijay S.

    2010-01-01

    Water plays a unique role in all living organisms. Not only is it nature’s ubiquitous solvent, but it also actively takes part in many cellular processes. In particular, the structure and properties of interfacial water near biomolecules like proteins are often related to the function of the respective molecule. It can therefore be highly instructive to study the local water density around solutes in cellular systems, particularly when solvent-mediated forces like the hydrophobic effect are relevant. Computational methods like molecular dynamics (MD) simulations seem well suited to study these systems at the atomic level. However, due to sampling requirements, it is not clear that MD simulations are indeed the method of choice to obtain converged densities at a given level of precision. We here compare the calculation of local water densities with two different methods, MD simulations and the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). In particular, we investigate the convergence of the local water density to assess the required simulation times for different levels of resolution. Moreover, we provide a quantitative comparison of the densities calculated with MD and with 3D-RISM-KH, and investigate the effect of the choice of the water model for both methods. Our results show that 3D-RISM-KH yields density distributions that are very similar to those from MD up to a 0.5 Å resolution, but for significantly reduced computational cost. The combined use of MD and 3D-RISM-KH emerges as an auspicious perspective for efficient solvent sampling in dynamical systems. PMID:21174421

  6. Molecular Analysis and Localization of CaARA7 a Conventional RAB5 GTPase from Characean Algae

    PubMed Central

    Hoepflinger, Marion C.; Geretschlaeger, Anja; Sommer, Aniela; Hoeftberger, Margit; Hametner, Christina; Ueda, Takashi; Foissner, Ilse

    2015-01-01

    RAB5 GTPases are important regulators of endosomal membrane traffic. Among them Arabidopsis thaliana ARA7/RABF2b is highly conserved and homologues are present in fungal, animal and plant kingdoms. In land plants ARA7 and its homologues are involved in endocytosis and transport towards the vacuole. Here we report on the isolation of an ARA7 homologue (CaARA7/CaRABF2) in the highly evolved characean green alga Chara australis. It encodes a polypeptide of 202 amino acids with a calculated molecular mass of 22.2 kDa and intrinsic GTPase activity. Immunolabelling of internodal cells with a specific antibody reveals CaARA7 epitopes at multivesicular endosomes (MVEs) and at MVE-containing wortmannin (WM) compartments. When transiently expressed in epidermal cells of Nicotiana benthamiana leaves, fluorescently tagged CaARA7 localizes to small organelles (putative MVEs) and WM compartments, and partially colocalizes with AtARA7 and CaARA6, a plant specific RABF1 GTPase. Mutations in membrane anchoring and GTP binding sites alter localization of CaARA7 and affect GTPase activity, respectively. This first detailed study of a conventional RAB5 GTPase in green algae demonstrates that CaARA7 is similar to RAB5 GTPases from land plants and other organisms and shows conserved structure and localization. PMID:25639563

  7. The anatomy of the Orion B giant molecular cloud: A local template for studies of nearby galaxies

    NASA Astrophysics Data System (ADS)

    Pety, Jérôme; Guzmán, Viviana V.; Orkisz, Jan H.; Liszt, Harvey S.; Gerin, Maryvonne; Bron, Emeric; Bardeau, Sébastien; Goicoechea, Javier R.; Gratier, Pierre; Le Petit, Franck; Levrier, François; Öberg, Karin I.; Roueff, Evelyne; Sievers, Albrecht

    2017-03-01

    Context. Molecular lines and line ratios are commonly used to infer properties of extra-galactic star forming regions. The new generation of millimeter receivers almost turns every observation into a line survey. Full exploitation of this technical advancement in extra-galactic study requires detailed bench-marking of available line diagnostics. Aims: We aim to develop the Orion B giant molecular cloud (GMC) as a local template for interpreting extra-galactic molecular line observations. Methods: We use the wide-band receiver at the IRAM-30 m to spatially and spectrally resolve the Orion B GMC. The observations cover almost 1 square degree at 26'' resolution with a bandwidth of 32 GHz from 84 to 116 GHz in only two tunings. Among the mapped spectral lines are the , , C18O, C17O, HCN, HNC, , C2H, HCO+, N2H+(1-0), and , , SiO, c - C3H2, CH3OH (2-1) transitions. Results: We introduce the molecular anatomy of the Orion B GMC, including relationships between line intensities and gas column density or far-UV radiation fields, and correlations between selected line and line ratios. We also obtain a dust-traced gas mass that is less than approximately one third the CO-traced mass, using the standard XCO conversion factor. The presence of over-luminous CO can be traced back to the dependence of the CO intensity on UV illumination. As a matter of fact, while most lines show some dependence on the UV radiation field, CN and C2H are the most sensitive. Moreover, dense cloud cores are almost exclusively traced by N2H+. Other traditional high-density tracers, such as HCN(1-0), are also easily detected in extended translucent regions at a typical density of 500 H2 cm-3. In general, we find no straightforward relationship between line critical density and the fraction of the line luminosity coming from dense gas regions. Conclusions: Our initial findings demonstrate that the relationships between line (ratio) intensities and environment in GMCs are more complicated than often

  8. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    PubMed

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  9. Analysis of electron correlation effects and contributions of NMR J-couplings from occupied localized molecular orbitals.

    PubMed

    Zarycz, Natalia; Aucar, Gustavo A

    2012-02-02

    NMR J-coupling calculations at the second-order of polarization propagator approach, SOPPA, are among the most reliable. They include a high percentage of the total electron correlation effects in saturated and unsaturated molecular systems. Furthermore, J-couplings are quite sensitive to the whole electronic molecular framework. We present in this article the first study of all three response mechanisms, Fermi contact, FC, spin-dipolar, SD and paramagnetic spin-orbital, PSO, for J-couplings with occupied localized molecular orbitals at the SOPPA level of approach. Even though SOPPA results are not invariant under unitary transformations, the difference between results obtained with canonical and localized molecular orbitals, LMOs, are small enough to permit its application with confidence. The following small-size saturated and unsaturated compounds were analyzed: CH(4), CH(3)F, C(2)H(6), NH(3), C(2)H(4), CH(2)NH, H(2)C═CHF, and FHC═CHF. The local character of the FC mechanism that appears in J-couplings of these molecular models is shown through the analysis of contributions from LMOs. The importance of including the electron correlation on the engaged bonding orbitals for one-bond couplings is emphasized. Almost all electron correlation effects are included in such orbitals. Interesting findings were the large contributions by s-type LMOs to the C-H and C-C J-couplings; they are responsible for the variation of (1)J(C-C) when going from ethane to ethene and to 1,2-difluoroethene. The previously proposed hyperconjugative transfer mechanism has been tested. Among other tests we found the difference anti-syn of one-bond (1)J(C-H) in imine as due to both the corresponding σ(C-H) and the lone-pair, LP, contribution. Geminal and vicinal J-couplings were also analyzed. Our findings are in accord with a previous work by Pople and Bothner-by, who considered results taken from calculations or empirical data. For all geminal couplings the pattern of J-couplings, like

  10. Localization microscopy coming of age: from concepts to biological impact.

    PubMed

    Sauer, Markus

    2013-08-15

    Super-resolution fluorescence imaging by single-molecule photoactivation or photoswitching and position determination (localization microscopy) has the potential to fundamentally revolutionize our understanding of how cellular function is encoded at the molecular level. Among all powerful, high-resolution imaging techniques introduced in recent years, localization microscopy excels because it delivers single-molecule information about molecular distributions, even giving absolute numbers of proteins present in subcellular compartments. This provides insight into biological systems at a molecular level that can yield direct experimental feedback for modeling the complexity of biological interactions. In addition, efficient new labeling methods and strategies to improve localization are emerging that promise to achieve true molecular resolution. This raises localization microscopy as a powerful complementary method for correlative light and electron microscopy experiments.

  11. Metallic Glass Wire Based Localization of Kinesin/Microtubule Bio-molecular Motility System

    NASA Astrophysics Data System (ADS)

    Kim, K.; Sikora, A.; Yaginuma, S.; Nakayama, K. S.; Nakazawa, H.; Umetsu, M.; Hwang, W.; Teizer, W.

    2014-03-01

    We report electrophoretic accumulation of microtubules along metallic glass (Pd42.5Cu30Ni7.5P20) wires free-standing in solution. Microtubules are dynamic cytoskeletal filaments. Kinesin is a cytoskeletal motor protein. Functions of these bio-molecules are central to various dynamic cellular processes. Functional artificial organization of bio-molecules is a prerequisite for transferring their native functions into device applications. Fluorescence microscopy at the individual-microtubule level reveals microtubules aligning along the wire axis during the electrophoretic migration. Casein-treated electrodes are effective for releasing trapped microtubules upon removal of the external field. Furthermore, we demonstrate gliding motion of microtubules on kinesin-treated metallic glass wires. The reversible manner in the local adsorption of microtubules, the flexibility of wire electrodes, and the compatibility between the wire electrode and the bio-molecules are beneficial for spatio-temporal manipulation of the motility machinery in 3 dimensions.

  12. Cosmology with negative absolute temperatures

    NASA Astrophysics Data System (ADS)

    Vieira, J. P. P.; Byrnes, Christian T.; Lewis, Antony

    2016-08-01

    Negative absolute temperatures (NAT) are an exotic thermodynamical consequence of quantum physics which has been known since the 1950's (having been achieved in the lab on a number of occasions). Recently, the work of Braun et al. [1] has rekindled interest in negative temperatures and hinted at a possibility of using NAT systems in the lab as dark energy analogues. This paper goes one step further, looking into the cosmological consequences of the existence of a NAT component in the Universe. NAT-dominated expanding Universes experience a borderline phantom expansion (w < -1) with no Big Rip, and their contracting counterparts are forced to bounce after the energy density becomes sufficiently large. Both scenarios might be used to solve horizon and flatness problems analogously to standard inflation and bouncing cosmologies. We discuss the difficulties in obtaining and ending a NAT-dominated epoch, and possible ways of obtaining density perturbations with an acceptable spectrum.

  13. Analysis of local properties during a scratch test on a polymeric surface using molecular dynamics simulations.

    PubMed

    Solar, M; Meyer, H; Gauthier, C

    2013-03-01

    This work demonstrates a possible route to connect a particle (chain) based understanding with continuum mechanical questions about contact mechanics. The bond orientation, chain conformation and stress field of a polymer film were analyzed during scratch tests (tangential contact) using a molecular dynamics (MD) simulation approach. Scratch tests with a conical tip at constant scratching velocity were simulated on linear amorphous polymer surfaces at various temperatures and roughnesses of the tip and for various interactions between the tip and the particles of the polymer chains. The second Legendre polynomial (computed for small domains around the tip) gave the bond orientation inside the polymer film during sliding of the tip. The gyration tensor (layer-resolved in the direction of the polymer film thickness) provided information about the conformation of the polymer chains. These results allowed us to argue in favor of Briscoe's hypothesis (thin film sheared vs. "bulk" compressive behavior) concerning the friction properties of the polymer surfaces. Finally, the first stress measurements of the virial stress tensor (in sub-boxes placed in the MD cell) revealed a complex combination between compressive hydrostatic pressure and shear stress, which may be interpreted as a complex sheared domain at the interface.

  14. Molecular evidence for the localization of Plasmodium falciparum immature gametocytes in bone marrow

    PubMed Central

    Aguilar, Ruth; Magallon-Tejada, Ariel; Achtman, Ariel H.; Moraleda, Cinta; Joice, Regina; Cisteró, Pau; Li Wai Suen, Connie S. N.; Nhabomba, Augusto; Macete, Eusebio; Mueller, Ivo; Marti, Matthias; Alonso, Pedro L.; Menéndez, Clara; Schofield, Louis

    2014-01-01

    Plasmodium falciparum immature gametocytes are not observed in peripheral blood. However, gametocyte stages in organs such as bone marrow have never been assessed by molecular techniques, which are more sensitive than optical microscopy. We quantified P falciparum sexual stages in bone marrow (n = 174) and peripheral blood (n = 70) of Mozambican anemic children by quantitative polymerase chain reaction targeting transcripts specific for early (PF14_0748; PHISTa), intermediate (PF13_0247; Pfs48/45), and mature (PF10_0303; Pfs25) gametocytes. Among children positive for the P falciparum housekeeping gene (PF08_0085; ubiquitin-conjugating enzyme gene) in bone marrow (n = 136) and peripheral blood (n = 25), prevalence of immature gametocytes was higher in bone marrow than peripheral blood (early: 95% vs 20%, P < .001; intermediate: 80% vs 16%; P < .001), as were transcript levels (P < .001 for both stages). In contrast, mature gametocytes were more prevalent (100% vs 51%, P < .001) and abundant (P < .001) in peripheral blood than in the bone marrow. Severe anemia (3.57, 95% confidence interval 1.49-8.53) and dyserythropoiesis (6.21, 95% confidence interval 2.24-17.25) were independently associated with a higher prevalence of mature gametocytes in bone marrow. Our results highlight the high prevalence and abundance of early sexual stages in bone marrow, as well as the relationship between hematological disturbances and gametocyte development in this tissue. PMID:24335496

  15. Molecular characterization and localization of the first tyramine receptor of the American cockroach (Periplaneta americana).

    PubMed

    Rotte, C; Krach, C; Balfanz, S; Baumann, A; Walz, B; Blenau, W

    2009-09-15

    The phenolamines octopamine and tyramine control, regulate, and modulate many physiological and behavioral processes in invertebrates. Vertebrates possess only small amounts of both substances, and thus, octopamine and tyramine, together with other biogenic amines, are referred to as "trace amines." Biogenic amines evoke cellular responses by activating G-protein-coupled receptors. We have isolated a complementary DNA (cDNA) that encodes a biogenic amine receptor from the American cockroach Periplaneta americana, viz., Peatyr1, which shares high sequence similarity to members of the invertebrate tyramine-receptor family. The PeaTYR1 receptor was stably expressed in human embryonic kidney (HEK) 293 cells, and its ligand response has been examined. Receptor activation with tyramine reduces adenylyl cyclase activity in a dose-dependent manner (EC(50) approximately 350 nM). The inhibitory effect of tyramine is abolished by co-incubation with either yohimbine or chlorpromazine. Receptor expression has been investigated by reverse transcription polymerase chain reaction and immunocytochemistry. The mRNA is present in various tissues including brain, salivary glands, midgut, Malpighian tubules, and leg muscles. The effect of tyramine on salivary gland acinar cells has been investigated by intracellular recordings, which have revealed excitatory presynaptic actions of tyramine. This study marks the first comprehensive molecular, pharmacological, and functional characterization of a tyramine receptor in the cockroach.

  16. Advances in Molecular Imaging of Locally Delivered Targeted Therapeutics for Central Nervous System Tumors

    PubMed Central

    Tosi, Umberto; Marnell, Christopher S.; Chang, Raymond; Cho, William C.; Ting, Richard; Maachani, Uday B.; Souweidane, Mark M.

    2017-01-01

    Thanks to the recent advances in the development of chemotherapeutics, the morbidity and mortality of many cancers has decreased significantly. However, compared to oncology in general, the field of neuro-oncology has lagged behind. While new molecularly targeted chemotherapeutics have emerged, the impermeability of the blood–brain barrier (BBB) renders systemic delivery of these clinical agents suboptimal. To circumvent the BBB, novel routes of administration are being applied in the clinic, ranging from intra-arterial infusion and direct infusion into the target tissue (convection enhanced delivery (CED)) to the use of focused ultrasound to temporarily disrupt the BBB. However, the current system depends on a “wait-and-see” approach, whereby drug delivery is deemed successful only when a specific clinical outcome is observed. The shortcomings of this approach are evident, as a failed delivery that needs immediate refinement cannot be observed and corrected. In response to this problem, new theranostic agents, compounds with both imaging and therapeutic potential, are being developed, paving the way for improved and monitored delivery to central nervous system (CNS) malignancies. In this review, we focus on the advances and the challenges to improve early cancer detection, selection of targeted therapy, and evaluation of therapeutic efficacy, brought forth by the development of these new agents. PMID:28208698

  17. Molecular detection and genetic characterization of kobuviruses and astroviruses in asymptomatic local pigs in East Africa

    PubMed Central

    Okoth, Edward; Junga, Joseph O.; Ogara, William O.; Njahira, Moses N.; Wang, Qiuhong; Vlasova, Anastasia N.; Djikeng, Appolinaire

    2014-01-01

    In this study, swine fecal specimens (n = 251) collected from nursing and weaned piglets raised under smallholder production systems were screened for the presence of kobuviruses by RT-PCR. Porcine kobuviruses were detected in 13.1 % (33/251) of the samples. We demonstrated that porcine kobuvirus infections exist in indigenous pigs in Kenya and Uganda and that the prevalence was higher in young piglets than older pigs: nursing piglets (15 %), post-weaning (3-month-old) pigs (17 %), 4-month-old pigs (10 %). Genetic analysis of the partial RNA-dependent RNA polymerase (RdRp) region (690 nt) revealed that kobuviruses circulating in East Africa are diverse, sharing nucleotide sequence identities ranging from 89.7 to 99.1 % and 88 to 92.3 % among them and with known porcine kobuviruses, respectively. The nucleotide sequence identities between our kobuvirus strains and those of human, bovine and canine kobuviruses were 69.4-70.7 %, 73.1-74.4 % and 67-70.7 %, respectively. Additionally, upon sequencing selected samples that showed consistent 720-bp RT-PCR bands while using the same primer set, we detected porcine astroviruses in our samples belonging to type 2 and type 3 mamastroviruses. To our knowledge, this study reports the first detection and molecular analysis of both porcine kobuviruses and astroviruses in an African region. Further studies are required to determine the role of these viruses in gastrointestinal infections of pigs in this region and to determine the genetic diversity of the circulating strains to develop accurate diagnostic tools and implement appropriate control strategies. PMID:24327095

  18. Atom-scale depth localization of biologically important chemical elements in molecular layers

    PubMed Central

    Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

    2016-01-01

    In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers’ global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces. PMID:27503887

  19. Molecular cloning, expression, and chromosome 19 localization of a human Ro/SS-A autoantigen.

    PubMed Central

    McCauliffe, D P; Lux, F A; Lieu, T S; Sanz, I; Hanke, J; Newkirk, M M; Bachinski, L L; Itoh, Y; Siciliano, M J; Reichlin, M

    1990-01-01

    Ro/SS-A antibodies are found in a number of human autoimmune disorders including Sjogren's syndrome and several systemic lupus erythematosus-related disorders. These heterogeneous autoantibodies are known to recognize several distinct cellular antigens. With synthetic oligonucleotides corresponding to amino acid sequence information we have isolated a full-length cDNA clone which encodes a human Ro ribonucleoprotein autoantigen. The 1,890-base pair clone contains an open reading frame that encodes a 417-amino acid, 48-kD polypeptide that migrates aberrantly at 60 kD by SDS-PAGE. Rabbit antibodies raised against this protein's recently described amino-terminal epitope react with a previously identified 52-kD human Ro protein and immunoprecipitate the human cytoplasmic RNAs. Ultraviolet light cross-linking studies suggest that this Ro protein binds each of the four major human cytoplasmic RNAs. The deduced amino acid sequence is 63% homologous to an Onchocerca volvulus antigen. Southern filter hybridization analysis indicates that this gene is not highly polymorphic and exists as a single copy in the human genome. Chromosomal localization studies place this gene on the short arm of chromosome 19 near the gene encoding the low density lipoprotein receptor. Images PMID:2332496

  20. Molecular characterization of Wolbachia infection in bed bugs (Cimex lectularius) collected from several localities in France

    PubMed Central

    Akhoundi, Mohammad; Cannet, Arnaud; Loubatier, Céline; Berenger, Jean-Michel; Izri, Arezki; Marty, Pierre; Delaunay, Pascal

    2016-01-01

    Wolbachia symbionts are maternally inherited intracellular bacteria that have been detected in numerous insects including bed bugs. The objective of this study, the first epidemiological study in Europe, was to screen Wolbachia infection among Cimex lectularius collected in the field, using PCR targeting the surface protein gene (wsp), and to compare obtained Wolbachia strains with those reported from laboratory colonies of C. lectularius as well as other Wolbachia groups. For this purpose, 284 bed bug specimens were caught and studied from eight different regions of France including the suburbs of Paris, Bouches-du-Rhône, Lot-et-Garonne, and five localities in Alpes-Maritimes. Among the samples, 166 were adults and the remaining 118 were considered nymphs. In all, 47 out of 118 nymphs (40%) and 61 out of 166 adults (37%) were found positive on wsp screening. Among the positive cases, 10 samples were selected randomly for sequencing. The sequences had 100% homology with wsp sequences belonging to the F-supergroup strains of Wolbachia. Therefore, we confirm the similarity of Wolbachia strains detected in this epidemiological study to Wolbachia spp. reported from laboratory colonies of C. lectularius. PMID:27492563

  1. The murine ufo receptor: molecular cloning, chromosomal localization and in situ expression analysis.

    PubMed

    Faust, M; Ebensperger, C; Schulz, A S; Schleithoff, L; Hameister, H; Bartram, C R; Janssen, J W

    1992-07-01

    We have cloned the mouse homologue of the ufo oncogene. It encodes a novel tyrosine kinase receptor characterized by a unique extracellular domain containing two immunoglobulin-like and two fibronectin type III repeats. Comparison of the predicted ufo amino acid sequences of mouse and man revealed an overall identity of 87.6%. The ufo locus maps to mouse chromosome 7A3-B1 and thereby extends the known conserved linkage group between mouse chromosome 7 and human chromosome 19. RNA in situ hybridization analysis established the onset of specific ufo expression in the late embryogenesis at day 12.5 post coitum (p.c.) and localized ufo transcription to distinct substructures of a broad spectrum of developing tissues (e.g. subepidermal cells of the skin, mesenchymal cells of the periosteum). In adult animals ufo is expressed in cells forming organ capsules as well as in connective tissue structures. ufo may function as a signal transducer between specific cell types of mesodermal origin.

  2. Cytogenetic and molecular localization of tipE: A gene affecting sodium channels in Drosophila melanogaster

    SciTech Connect

    Feng, G.; Deak, P.; Hall, L.M.

    1995-04-01

    Voltage-sensitive sodium channels play a key role in nerve cells where they are responsible for the increase in sodium permeability during the rising phase of action potentials. In Drosophila melanogaster a subset of temperature-sensitive paralytic mutations affect sodium channel function. One such mutation is temperature-induced paralysis locus E (tipE), which has been shown by electrophysiology and ligand binding studies to reduce sodium channel numbers. Three new {gamma}-ray-induced tipE alleles associated with either visible deletions in 64AB or a translocation breakpoint within 64B2 provide landmarks for positional cloning of tipE. Beginning with the flanking cloned gene Ras2, a 140-kb walk across the translocation breakpoint was completed. Germline transformation using a 42-kb cosmid clone and successively smaller subclones localized the tipE gene within a 7.4-kb genomic DNA segment. Although this chromosome region is rich in transcripts, only three overlapping mRNAs (5.4, 4.4, and 1.7 kb) lie completely within the smallest rescuing construct. The small sizes of the rescuing construct and transcripts suggests that tipE does not encode a standard sodium channel {alpha}-subunit with four homologous repeats. Sequencing these transcripts will elucidate the role of the tipE gene product in sodium channel functional regulation. 55 refs., 4 figs., 2 tabs.

  3. Molecular characterization of Wolbachia infection in bed bugs (Cimex lectularius) collected from several localities in France.

    PubMed

    Akhoundi, Mohammad; Cannet, Arnaud; Loubatier, Céline; Berenger, Jean-Michel; Izri, Arezki; Marty, Pierre; Delaunay, Pascal

    2016-01-01

    Wolbachia symbionts are maternally inherited intracellular bacteria that have been detected in numerous insects including bed bugs. The objective of this study, the first epidemiological study in Europe, was to screen Wolbachia infection among Cimex lectularius collected in the field, using PCR targeting the surface protein gene (wsp), and to compare obtained Wolbachia strains with those reported from laboratory colonies of C. lectularius as well as other Wolbachia groups. For this purpose, 284 bed bug specimens were caught and studied from eight different regions of France including the suburbs of Paris, Bouches-du-Rhône, Lot-et-Garonne, and five localities in Alpes-Maritimes. Among the samples, 166 were adults and the remaining 118 were considered nymphs. In all, 47 out of 118 nymphs (40%) and 61 out of 166 adults (37%) were found positive on wsp screening. Among the positive cases, 10 samples were selected randomly for sequencing. The sequences had 100% homology with wsp sequences belonging to the F-supergroup strains of Wolbachia. Therefore, we confirm the similarity of Wolbachia strains detected in this epidemiological study to Wolbachia spp. reported from laboratory colonies of C. lectularius.

  4. Cytogenetic and molecular localization of tipE: a gene affecting sodium channels in Drosophila melanogaster.

    PubMed

    Feng, G; Deák, P; Kasbekar, D P; Gil, D W; Hall, L M

    1995-04-01

    Voltage-sensitive sodium channels play a key role in nerve cells where they are responsible for the increase in sodium permeability during the rising phase of action potentials. In Drosophila melanogaster a subset of temperature-sensitive paralytic mutations affect sodium channel function. One such mutation is temperature-induced paralysis locus E (tipE), which has been shown by electrophysiology and ligand binding studies to reduce sodium channel numbers. Three new gamma-ray-induced tipE alleles associated with either visible deletions in 64AB or a translocation breakpoint within 64B2 provide landmarks for positional cloning of tipE. Beginning with the flanking cloned gene Ras2, a 140-kb walk across the translocation breakpoint was completed. Germline transformation using a 42-kb cosmid clone and successively smaller subclones localized the tipE gene within a 7.4-kb genomic DNA segment. Although this chromosome region is rich in transcripts, only three overlapping mRNAs (5.4, 4.4, and 1.7 kb) lie completely within the smallest rescuing construct. The small sizes of the rescuing construct and transcripts suggest that tipE does not encode a standard sodium channel alpha-subunit with four homologous repeats. Sequencing these transcripts will elucidate the role of the tipE gene product in sodium channel functional regulation.

  5. Molecular identification and localization of cellular titin, a novel titin isoform in the fibroblast stress fiber.

    PubMed

    Cavnar, Peter J; Olenych, Scott G; Keller, Thomas C S

    2007-06-01

    We previously discovered a large titin-like protein-c-titin-in chicken epithelial brush border and human blood platelet extracts that binds alpha-actinin and organizes arrays of myosin II bipolar filaments in vitro. RT-PCR analysis of total RNA from human megakaryoblastic (CHRF-288-11) and mouse fibroblast (3T3) nonmuscle cells reveal sequences identical to known titin gene exon sequences that encode parts of the Z-line, I-band, PEVK domain, A-band, and M-line regions of striated muscle titins. In the nonmuscle cells, these sequences are differentially spliced in patterns not reported for any striated muscle titin isoform. Rabbit polyclonal antibodies raised against expressed protein fragments encoded by the Z-repeat and kinase domain regions react with the c-titin band in Western blot analysis of platelet extracts and immunoprecipitate c-titin in whole platelet extracts. Immunofluorescent localization demonstrates that the majority of the c-titin colocalizes with alpha-actinin and actin in 3T3 and Indian Muntjac deer skin fibroblast stress fibers. Our results suggest that differential expression of titin gene exons in nonmuscle cells yields multiple novel isoforms of the protein c-titin that are associated with the actin stress fiber structures.

  6. Local structure and molecular motions in imidazolium hydrogen malonate crystal as studied by 2H and 13C NMR

    NASA Astrophysics Data System (ADS)

    Mizuno, M.; Chizuwa, M.; Umiyama, T.; Kumagai, Y.; Miyatou, T.; Ohashi, R.; Ida, T.; Tansho, M.; Shimizu, T.

    2015-04-01

    The local structure and molecular motion of the imidazolium hydrogen malonate crystal were investigated using solid-state 2H and 13C NMR. The imidazolium ion undergoes isotropic rotation, which is correlated with a defect in the crystal, as observed by 2H NMR broadline spectra above 263 K. A 180∘ flip of the imidazolium ion in the regular site was observed from 2H NMR quadrupole Carr-Purcell-Meiboom-Gill (QCPMG) spectra. The Grotthuss mechanism was accompanied by a 180∘ flip of the imidazolium ion in regular sites. Moreover, the proton transfer associated with the imidazolium ion of the defective crystal is important for proton conductivity of the imidazolium hydrogen malonate crystal.

  7. Characterization of the subcellular localization and nuclear import molecular mechanisms of herpes simplex virus 1 UL2.

    PubMed

    Cai, Mingsheng; Huang, Zebin; Liao, Zongmin; Chen, Tao; Wang, Ping; Jiang, Si; Chen, Daixiong; Peng, Tao; Bian, Yun; Hong, Gengde; Yang, Hang; Zeng, Zhancheng; Li, Xiaowei; Li, Meili

    2017-04-01

    As a crucial protein, the herpes simplex virus 1 (HSV-1) UL2 protein has been shown to take part in various stages of viral infection, nonetheless, its exact subcellular localization and transport molecular determinants are not well known thus far. In the present study, by using live cells fluorescent microscopy assay, UL2 tagged with enhanced yellow fluorescent protein was transiently expressed in live cells and showed a completely nuclear accumulation without the presence of other HSV-1 proteins. Moreover, the nuclear transport of UL2 was characterized to be assisted by multiple transport pathways through Ran-, importin α1-, α5-, α7-, β1- and transportin-1 cellular transport receptors. Consequently, these results will improve understanding of UL2-mediated biological functions in HSV-1 infection cycles.

  8. Molecular cloning, expression, and chromosomal localization of the gene encoding a human myeloid membrane antigen (gp150).

    PubMed Central

    Look, A T; Peiper, S C; Rebentisch, M B; Ashmun, R A; Roussel, M F; Lemons, R S; Le Beau, M M; Rubin, C M; Sherr, C J

    1986-01-01

    DNA from a tertiary mouse cell transformant containing amplified human sequences encoding a human myeloid membrane glycoprotein, gp150, was used to construct a bacteriophage lambda library. A single recombinant phage containing 12 kilobases (kb) of human DNA was isolated, and molecular subclones were then used to isolate the complete gp150 gene from a human placental genomic DNA library. The intact gp150 gene, assembled from three recombinant phages, proved to be biologically active when transfected into NIH 3T3 cells. Molecular probes from the gp150 locus annealed with a 4.0-kb polyadenylated RNA transcript derived from human myeloid cell lines and from tertiary mouse cell transformants. The gp150 gene was assigned to human chromosome 15, and was subchromosomally localized to bands q25-26 by in situ hybridization. The chromosomal location of the gp150 gene coincides cytogenetically with the region assigned to the c-fes proto-oncogene, another human gene specifically expressed by myeloid cells. Images PMID:2428842

  9. In vivo seeding and cross-seeding of localized amyloidosis: a molecular link between type 2 diabetes and Alzheimer disease.

    PubMed

    Oskarsson, Marie E; Paulsson, Johan F; Schultz, Sebastian W; Ingelsson, Martin; Westermark, Per; Westermark, Gunilla T

    2015-03-01

    Several proteins have been identified as amyloid forming in humans, and independent of protein origin, the fibrils are morphologically similar. Therefore, there is a potential for structures with amyloid seeding ability to induce both homologous and heterologous fibril growth; thus, molecular interaction can constitute a link between different amyloid forms. Intravenous injection with preformed fibrils from islet amyloid polypeptide (IAPP), proIAPP, or amyloid-beta (Aβ) into human IAPP transgenic mice triggered IAPP amyloid formation in pancreas in 5 of 7 mice in each group, demonstrating that IAPP amyloid could be enhanced through homologous and heterologous seeding with higher efficiency for the former mechanism. Proximity ligation assay was used for colocalization studies of IAPP and Aβ in islet amyloid in type 2 diabetic patients and Aβ deposits in brains of patients with Alzheimer disease. Aβ reactivity was not detected in islet amyloid although islet β cells express AβPP and convertases necessary for Aβ production. By contrast, IAPP and proIAPP were detected in cerebral and vascular Aβ deposits, and presence of proximity ligation signal at both locations showed that the peptides were <40 nm apart. It is not clear whether IAPP present in brain originates from pancreas or is locally produced. Heterologous seeding between IAPP and Aβ shown here may represent a molecular link between type 2 diabetes and Alzheimer disease.

  10. Molecular analysis of human complement component C5: localization of the structural gene to chromosome 9

    SciTech Connect

    Wetsel, R.A.; Lemons, R.S.; Le Beau, M.M.; Barnum, S.R.; Noack, D.; Tack, B.F.

    1988-03-08

    A human C5 clone (pC5HG2) was isolated from a cDNA library constructed from Hep G2 mRNA. he DNA sequence showed that the pC5HG2 insert was comprised of 3309 base pairs of pro-C5 coding sequence and 404 base pairs of 3'-untranslated sequence. The derived amino acid sequence contained the entire coding sequence of the C5 ..cap alpha..-chain, the ..beta..-..cap alpha..-chain junction region, and 100 amino acids (approximately 50%) of the ..beta..-chain. Protein sequences of four C5 tryptic peptides were aligned exactly to this sequence and demonstrated that C5 synthesized and secreted by Hep G2 cells is probably identical with plasma-derived C5. Coding sequence alignment of the human C5 sequences with those of murine C5 indicated that 80% of the nucleotides and 79% of the amino acids were placed identically in the two species. Amino acid sequence alignment of the homologous family members C3, C4, and ..cap alpha../sub 2/-macroglobulin with that of C5 demonstrated 27%, 25%, and 19% identity, respectively. As was found in murine C5, the corresponding thiol ester region of human C5 contained several conserved amino acids, but the critical cysteine and glutamine residues which give rise to the intramolecular thiol ester bond in C3, C4, and ..cap alpha../sub 2/-macroglobulin were absent in C5, having been replaced by serine and alanine, respectively. With the use of a panel of hamster-human somatic cell hybrids, the C5 gene was mapped to human chromosome 9. In situ chromosomal hybridization studies employing metaphase cells further localized the gene to bands 9q32-34, with the largest cluster of grains at 9q34.1.

  11. Absolute cross sections of electron attachment to molecular clusters. Part II: Formation of (H2O) N - , (N2O) N - , and (N2) N -

    NASA Astrophysics Data System (ADS)

    Vostrikov, A. A.; Dubov, D. Yu.

    2006-12-01

    Absolute cross sections σ-( E, N) of electron attachment to clusters (H2O) N , (N2O) N , and (N2) N for varying electron energy E and cluster size N are measured by using crossed electron and cluster beams in a vacuum. Continua of σ-( E) are found that correlate well with the functions of electron impact excitation of molecules’ internal degrees of freedom. The electron is attached through its solvation in a cluster. In the formation of (H2O){/N -}, (N2O){/N -}, and (N2){/N -}, the curves σ-( N) have a well-defined threshold because of a rise in the electron thermalization and solvation probability with N. For (H2O)900, (N2O)350, and (N2)260 clusters at E = 0.2 eV, the energy losses by the slow electron in the cluster are estimated as 3.0 × 107, 2.7 × 107, and 6.0 × 105 eV/m, respectively. It is found that the growth of σ- with N is the fastest for (H2O) N and (N2) N clusters at E → 0 as a result of polarization capture of the s-electron. Specifically, at E = 0.1 eV and N = 260, σ- = 3.0 × 10-13 cm2 for H2O clusters, 8.0 × 10-14 cm2 for N2O clusters, and 1.4 × 10-15 cm2 for N2 clusters; at E = 11 eV, σ- = 9.0 × 10-16 cm2 for (H2O)200 clusters, 2.4 × 10-14 cm2 for (N2O)350 clusters, and 5.0 × 10-17 cm2 for (N2)260 clusters; finally, at E = 30 eV, σ- = 3.6 × 10-17 cm2 for (N2O)10 clusters and 3.0 × 10-17 cm2 for (N2)125 clusters.

  12. A SPITZER SURVEY OF MID-INFRARED MOLECULAR EMISSION FROM PROTOPLANETARY DISKS. II. CORRELATIONS AND LOCAL THERMAL EQUILIBRIUM MODELS

    SciTech Connect

    Salyk, C.; Pontoppidan, K. M.; Blake, G. A.; Najita, J. R.; Carr, J. S.

    2011-04-20

    We present an analysis of Spitzer Infrared Spectrograph observations of H{sub 2}O, OH, HCN, C{sub 2}H{sub 2}, and CO{sub 2} emission, and Keck-NIRSPEC observations of CO emission, from a diverse sample of T Tauri and Herbig Ae/Be circumstellar disks. We find that detections and strengths of most mid-IR molecular emission features are correlated with each other, suggesting a common origin and similar excitation conditions for this mid-infrared line forest. Aside from the remarkable differences in molecular line strengths between T Tauri, Herbig Ae/Be, and transitional disks discussed in Pontoppidan et al., we note that the line detection efficiency is anti-correlated with the 13/30 {mu}m spectral slope, which is a measure of the degree of grain settling in the disk atmosphere. We also note a correlation between detection efficiency and H{alpha} equivalent width, and tentatively with accretion rate, suggesting that accretional heating contributes to line excitation. If detected, H{sub 2}O line fluxes are correlated with the mid-IR continuum flux, and other co-varying system parameters, such as L{sub *}. However, significant sample variation, especially in molecular line ratios, remains, and its origin has yet to be explained. Local thermal equilibrium (LTE) models of the H{sub 2}O emission show that line strength is primarily related to the best-fit emitting area, and this accounts for most source-to-source variation in H{sub 2}O emitted flux. Best-fit temperatures and column densities cover only a small range of parameter space, near {approx}10{sup 18} cm{sup -2} and 450 K for all sources, suggesting a high abundance of H{sub 2}O in many planet-forming regions. Other molecules have a range of excitation temperatures from {approx}500to1500 K, also consistent with an origin in planet-forming regions. We find molecular ratios relative to water of {approx}10{sup -3} for all molecules, with the exception of CO, for which n(CO)/n(H{sub 2}O) {approx} 1. However, LTE

  13. On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes

    SciTech Connect

    Moreira, Rodrigo A.; Melo, Celso P. de

    2014-09-28

    Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

  14. Absolute calibration in the 1750 - 3350 A region

    NASA Technical Reports Server (NTRS)

    Strongylis, G. J.; Bohlin, R. C.

    1977-01-01

    The absolute flux measurements in the rocket ultraviolet made by Bohlin, Frimout, and Lillie (BFL) are revised using a more correct treatment of the air extinction that enters the air calibration of their instrument. The absorption by molecular oxygen and ozone, Rayleigh scattering, and extinction by aerosols is tabulated for general use in ultraviolet calibrations performed in air. The revised absolute flux of eta UMa and final fluxes for alpha Lyr and zeta Oph are presented in the 1750-3350 A region. The absolute flux of the star eta UMa is compared to four other independent determinations in the 1200-3400 A region and a maximum difference of 35% is found near 1500 A between the OAO-2 and Apollo 17 fluxes. The rocket measurements of BFL, the ANS and TD-1 satellite data, and the Apollo 17 data are compared to the ultraviolet fluxes from the OAO-2, demonstrating a photometric reproducibility of about + or - 3 percent. Therefore, all four sets of spectrophotometry can be reduced to a common absolute scale.

  15. Local order and long range correlations in imidazolium halide ionic liquids: a combined molecular dynamics and XAS study.

    PubMed

    Migliorati, Valentina; Serva, Alessandra; Aquilanti, Giuliana; Pascarelli, Sakura; D'Angelo, Paola

    2015-07-07

    A thorough characterization of the structural properties of alkylimidazolium halide ionic liquids (ILs), namely 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br with n = 5, 6, 8, 10) and iodide ([C6mim]I), has been carried out by combining molecular dynamics simulations and EXAFS spectroscopy. The existence of a local order in [Cnmim]Br ILs has been evidenced, with anions and imidazolium head groups forming a local three-dimensional bonding pattern that is common to all the [Cnmim]Br IL family, regardless of the length of the alkyl chain attached to the cation. On the other hand, upon alkyl chain elongation significant differences have been highlighted in the long-range structure of these ILs. Theoretical X-ray structure factors have been calculated from MD simulations and a low q peak has been found for all [Cnmim]Br ILs, indicating the existence of long-range structural correlations. The low q peak moves to smaller q values corresponding to longer distances, increases in intensity and sharpens with increasing alkyl chain length on the cation. Similarities and differences between the ion three-dimensional arrangements in [C6mim]Br and [C6mim]I were highlighted and the structural arrangement of Br(-) and I(-) was found to be different in the proximity of the most acidic hydrogen atom of the imidazolium ring: the I(-) ion is preferentially located above and below the ring plane, while the Br(-) ion has a high probability also to be coplanar with the imidazolium ring. A quantitative analysis of the Br and I K-edge EXAFS spectra of alkylimidazolium halide ILs has been carried out based on the microscopic description of the systems derived from MD simulations. A very good agreement between theoretical and experimental EXAFS signals has been obtained, allowing us to assess the reliability of the MD structural results for all the alkylimidazolium halide ILs investigated in this work.

  16. Molecular cloning, expression analysis and subcellular localization of a Transparent Testa 12 ortholog in brown cotton (Gossypium hirsutum L.).

    PubMed

    Gao, Jun-Shan; Wu, Nan; Shen, Zhi-Lin; Lv, Kai; Qian, Sen-He; Guo, Ning; Sun, Xu; Cai, Yong-Ping; Lin, Yi

    2016-02-01

    Transparent Testa 12 (TT12) is a kind of transmembrane transporter of proanthocyanidins (PAs), which belongs to a membrane-localized multidrug and toxin efflux (MATE) family, but the molecular basis of PAs transport is still poorly understood. Here, we cloned a full-length TT12 cDNA from the fiber of brown cotton (Gossypium hirsutum), named GhTT12 (GenBank accession No. KF240564), which comprised 1733 bp with an open reading frame (ORF) of 1503 bp and encoded a putative protein containing 500 amino acid residues with a typical MATE conserved domain. The GhTT12 gene had 96.8% similarity to AA genome in Gossypium arboretum. Quantitative RT-PCR analysis denoted that the relative expression of GhTT12 in brown cotton was 1-5 folds higher than that in white cotton. The mRNA level was the highest at 5 days post anthesis (DPA) and reduced gradually during the fiber development. Expressing GhTT12-fused green fluorescent protein (GFP) in Nicotiana tabacum showed that GhTT12-GFP was localized in the vacuole membrane. The content of PAs increased firstly and decreased afterwards, and reached the maximum at 15 DPA in brown cotton. But for white cotton, the content of PAs remained at a low level during the fiber development. We speculate that GhTT12 may participate in the transportation of PAs from the cytoplasmic matrix to the vacuole. Taken together, our data revealed that GhTT12 was functional as a PAs transmembrane transporter.

  17. Localized Si enrichment in coherent self-assembled Ge islands grown by molecular beam epitaxy on (001)Si single crystal

    SciTech Connect

    Valvo, M.; Bongiorno, C.; Giannazzo, F.; Terrasi, A.

    2013-01-21

    Transmission electron microscopy (TEM), atomic force microscopy, and Rutherford backscattering spectrometry (RBS) have been used to investigate the morphology, structure, and composition of self-assembled Ge islands grown on Si (001) substrates by molecular beam epitaxy (MBE) at different temperatures. Increasing the temperature from 550 Degree-Sign C to 700 Degree-Sign C causes progressive size and shape uniformity, accompanied by enhanced Si-Ge intermixing within the islands and their wetting layer. Elemental maps obtained by energy filtered-TEM (EF-TEM) clearly show pronounced Si concentration not only in correspondence of island base perimeters, but also along their curved surface boundaries. This phenomenon is strengthened by an increase of the growth temperature, being practically negligible at 550 Degree-Sign C, while very remarkable already at 650 Degree-Sign C. The resulting island shape is affected, since this localized Si enrichment not only provides strain relief near their highly stressed base perimeters but it also influences the cluster surface energy by effective alloying, so as to form Si-enriched SiGe interfaces. Further increase to 700 Degree-Sign C causes a shape transition where more homogenous Si-Ge concentration profiles are observed. The crucial role played by local 'flattened' alloyed clusters, similar to truncated pyramids with larger bases and enhanced Si enrichment at coherently stressed interfaces, has been further clarified by EF-TEM analysis of a multi-layered Ge/Si structure containing stacked Ge islands grown at 650 Degree-Sign C. Sharp accumulation of Si has been here observed not only in proximity of the uncapped island surface in the topmost layer but also at the buried Ge/Si interfaces and even in the core of such capped Ge islands.

  18. Absolute optical metrology : nanometers to kilometers

    NASA Technical Reports Server (NTRS)

    Dubovitsky, Serge; Lay, O. P.; Peters, R. D.; Liebe, C. C.

    2005-01-01

    We provide and overview of the developments in the field of high-accuracy absolute optical metrology with emphasis on space-based applications. Specific work on the Modulation Sideband Technology for Absolute Ranging (MSTAR) sensor is described along with novel applications of the sensor.

  19. ON A SUFFICIENT CONDITION FOR ABSOLUTE CONTINUITY.

    DTIC Science & Technology

    The formulation of a condition which yields absolute continuity when combined with continuity and bounded variation is the problem considered in the...Briefly, the formulation is achieved through a discussion which develops a proof by contradiction of a sufficiently theorem for absolute continuity which uses in its hypothesis the condition of continuity and bounded variation .

  20. Introducing the Mean Absolute Deviation "Effect" Size

    ERIC Educational Resources Information Center

    Gorard, Stephen

    2015-01-01

    This paper revisits the use of effect sizes in the analysis of experimental and similar results, and reminds readers of the relative advantages of the mean absolute deviation as a measure of variation, as opposed to the more complex standard deviation. The mean absolute deviation is easier to use and understand, and more tolerant of extreme…

  1. Monolithically integrated absolute frequency comb laser system

    SciTech Connect

    Wanke, Michael C.

    2016-07-12

    Rather than down-convert optical frequencies, a QCL laser system directly generates a THz frequency comb in a compact monolithically integrated chip that can be locked to an absolute frequency without the need of a frequency-comb synthesizer. The monolithic, absolute frequency comb can provide a THz frequency reference and tool for high-resolution broad band spectroscopy.

  2. Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry.

    PubMed

    Loziuk, Philip L; Sederoff, Ronald R; Chiang, Vincent L; Muddiman, David C

    2014-11-07

    Quantitative mass spectrometry has become central to the field of proteomics and metabolomics. Selected reaction monitoring is a widely used method for the absolute quantification of proteins and metabolites. This method renders high specificity using several product ions measured simultaneously. With growing interest in quantification of molecular species in complex biological samples, confident identification and quantitation has been of particular concern. A method to confirm purity or contamination of product ion spectra has become necessary for achieving accurate and precise quantification. Ion abundance ratio assessments were introduced to alleviate some of these issues. Ion abundance ratios are based on the consistent relative abundance (RA) of specific product ions with respect to the total abundance of all product ions. To date, no standardized method of implementing ion abundance ratios has been established. Thresholds by which product ion contamination is confirmed vary widely and are often arbitrary. This study sought to establish criteria by which the relative abundance of product ions can be evaluated in an absolute quantification experiment. These findings suggest that evaluation of the absolute ion abundance for any given transition is necessary in order to effectively implement RA thresholds. Overall, the variation of the RA value was observed to be relatively constant beyond an absolute threshold ion abundance. Finally, these RA values were observed to fluctuate significantly over a 3 year period, suggesting that these values should be assessed as close as possible to the time at which data is collected for quantification.

  3. Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories.

    PubMed

    Liu, Song; Zhu, Lizhe; Sheong, Fu Kit; Wang, Wei; Huang, Xuhui

    2017-01-30

    We present an efficient density-based adaptive-resolution clustering method APLoD for analyzing large-scale molecular dynamics (MD) trajectories. APLoD performs the k-nearest-neighbors search to estimate the density of MD conformations in a local fashion, which can group MD conformations in the same high-density region into a cluster. APLoD greatly improves the popular density peaks algorithm by reducing the running time and the memory usage by 2-3 orders of magnitude for systems ranging from alanine dipeptide to a 370-residue Maltose-binding protein. In addition, we demonstrate that APLoD can produce clusters with various sizes that are adaptive to the underlying density (i.e., larger clusters at low-density regions, while smaller clusters at high-density regions), which is a clear advantage over other popular clustering algorithms including k-centers and k-medoids. We anticipate that APLoD can be widely applied to split ultra-large MD datasets containing millions of conformations for subsequent construction of Markov State Models. © 2016 Wiley Periodicals, Inc.

  4. Local molecular field theory for effective attractions between like charged objects in systems with strong Coulomb interactions.

    PubMed

    Chen, Yng-Gwei; Weeks, John D

    2006-05-16

    Strong, short-ranged positional correlations involving counterions can induce a net attractive force between negatively charged strands of DNA and lead to the formation of ion pairs in dilute ionic solutions. However, the long range of the Coulomb interactions impedes the development of a simple local picture. We address this general problem by mapping the properties of a nonuniform system with Coulomb interactions onto those of a simpler system with short-ranged intermolecular interactions in an effective external field that accounts for the averaged effects of appropriately chosen long-ranged and slowly varying components of the Coulomb interactions. The remaining short-ranged components combine with the other molecular core interactions and strongly affect pair correlations in dense or strongly coupled systems. We show that pair correlation functions in the effective short-ranged system closely resemble those in the uniform primitive model of ionic solutions and illustrate the formation of ion pairs and clusters at low densities. The theory accurately describes detailed features of the effective attraction between two equally charged walls at strong coupling and intermediate separations of the walls. Analytical results for the minimal coupling strength needed to get any attraction and for the separation at which the attractive force is a maximum are presented.

  5. Absolute Quantification of Rifampicin by MALDI Imaging Mass Spectrometry Using Multiple TOF/TOF Events in a Single Laser Shot.

    PubMed

    Prentice, Boone M; Chumbley, Chad W; Caprioli, Richard M

    2017-01-01

    Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for the visualization of molecular distributions within tissue sections. While providing excellent molecular specificity and spatial information, absolute quantification by MALDI IMS remains challenging. Especially in the low molecular weight region of the spectrum, analysis is complicated by matrix interferences and ionization suppression. Though tandem mass spectrometry (MS/MS) can be used to ensure chemical specificity and improve sensitivity by eliminating chemical noise, typical MALDI MS/MS modalities only scan for a single MS/MS event per laser shot. Herein, we describe TOF/TOF instrumentation that enables multiple fragmentation events to be performed in a single laser shot, allowing the intensity of the analyte to be referenced to the intensity of the internal standard in each laser shot while maintaining the benefits of MS/MS. This approach is illustrated by the quantitative analyses of rifampicin (RIF), an antibiotic used to treat tuberculosis, in pooled human plasma using rifapentine (RPT) as an internal standard. The results show greater than 4-fold improvements in relative standard deviation as well as improved coefficients of determination (R(2)) and accuracy (>93% quality controls, <9% relative errors). This technology is used as an imaging modality to measure absolute RIF concentrations in liver tissue from an animal dosed in vivo. Each microspot in the quantitative image measures the local RIF concentration in the tissue section, providing absolute pixel-to-pixel quantification from different tissue microenvironments. The average concentration determined by IMS is in agreement with the concentration determined by HPLC-MS/MS, showing a percent difference of 10.6%. Graphical Abstract ᅟ.

  6. Absolute Quantification of Rifampicin by MALDI Imaging Mass Spectrometry Using Multiple TOF/TOF Events in a Single Laser Shot

    NASA Astrophysics Data System (ADS)

    Prentice, Boone M.; Chumbley, Chad W.; Caprioli, Richard M.

    2017-01-01

    Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for the visualization of molecular distributions within tissue sections. While providing excellent molecular specificity and spatial information, absolute quantification by MALDI IMS remains challenging. Especially in the low molecular weight region of the spectrum, analysis is complicated by matrix interferences and ionization suppression. Though tandem mass spectrometry (MS/MS) can be used to ensure chemical specificity and improve sensitivity by eliminating chemical noise, typical MALDI MS/MS modalities only scan for a single MS/MS event per laser shot. Herein, we describe TOF/TOF instrumentation that enables multiple fragmentation events to be performed in a single laser shot, allowing the intensity of the analyte to be referenced to the intensity of the internal standard in each laser shot while maintaining the benefits of MS/MS. This approach is illustrated by the quantitative analyses of rifampicin (RIF), an antibiotic used to treat tuberculosis, in pooled human plasma using rifapentine (RPT) as an internal standard. The results show greater than 4-fold improvements in relative standard deviation as well as improved coefficients of determination (R2) and accuracy (>93% quality controls, <9% relative errors). This technology is used as an imaging modality to measure absolute RIF concentrations in liver tissue from an animal dosed in vivo. Each microspot in the quantitative image measures the local RIF concentration in the tissue section, providing absolute pixel-to-pixel quantification from different tissue microenvironments. The average concentration determined by IMS is in agreement with the concentration determined by HPLC-MS/MS, showing a percent difference of 10.6%.

  7. Absolute realization of low BRDF value

    NASA Astrophysics Data System (ADS)

    Liu, Zilong; Liao, Ningfang; Li, Ping; Wang, Yu

    2010-10-01

    Low BRDF value is widespread used in many critical domains such as space and military fairs. These values below 0.1 Sr-1 . So the Absolute realization of these value is the most critical issue in the absolute measurement of BRDF. To develop the Absolute value realization theory of BRDF , defining an arithmetic operators of BRDF , achieving an absolute measurement Eq. of BRDF based on radiance. This is a new theory method to solve the realization problem of low BRDF value. This theory method is realized on a self-designed common double orientation structure in space. By designing an adding structure to extend the range of the measurement system and a control and processing software, Absolute realization of low BRDF value is achieved. A material of low BRDF value is measured in this measurement system and the spectral BRDF value are showed within different angles allover the space. All these values are below 0.4 Sr-1 . This process is a representative procedure about the measurement of low BRDF value. A corresponding uncertainty analysis of this measurement data is given depend on the new theory of absolute realization and the performance of the measurement system. The relative expand uncertainty of the measurement data is 0.078. This uncertainty analysis is suitable for all measurements using the new theory of absolute realization and the corresponding measurement system.

  8. Transport of absolute angular momentum in quasi-axisymmetric equatorial jet streams

    NASA Technical Reports Server (NTRS)

    Read, P. L.

    1986-01-01

    It is well known that prograde equatorial jet stresses cannot occur in an axisymmetric inviscid fluid, owing to the constraints of local angular momentum conservation. For a viscous fluid, the constraints of mass conservation prevent the formation of any local maximum of absolute angular momentum (m) without a means of transferring m against its gradient (delta m) in the meridional plane. The circumstances under which m can be diffused up-gradient by normal molecular viscosity are derived, and illustrated with reference to numerical simulations of axisymmetric flows in a cylindrical annulus. Viscosity is shown to act so as to tend to expel m from the interior outwards from the rotation axis. Such an effect can produce local super-rotation even in a mechanically isolated fluid. The tendency of viscosity to result in the expulsion of m is shown to be analogous in certain respects to a vorticity-mixing hypothesis for the effects of non-axisymmetric eddies of the zonally-averaged flow. It is shown how the advective and diffusive transport of m by non-axisymmetric eddies can be represented by the Transformed Eulerian Mean meridional circulation and the Eliassen-Palm (EP) flux of Andrews and McIntyre respectively, in the zonal mean. Constraints on the form and direction of the EP flux in an advective/diffusive flow for such eddies are derived, by analogy with similar constraints on the diffusive flux of m due to viscosity.

  9. Absolute Gravity Datum in the Age of Cold Atom Gravimeters

    NASA Astrophysics Data System (ADS)

    Childers, V. A.; Eckl, M. C.

    2014-12-01

    The international gravity datum is defined today by the International Gravity Standardization Net of 1971 (IGSN-71). The data supporting this network was measured in the 1950s and 60s using pendulum and spring-based gravimeter ties (plus some new ballistic absolute meters) to replace the prior protocol of referencing all gravity values to the earlier Potsdam value. Since this time, gravimeter technology has advanced significantly with the development and refinement of the FG-5 (the current standard of the industry) and again with the soon-to-be-available cold atom interferometric absolute gravimeters. This latest development is anticipated to provide improvement in the range of two orders of magnitude as compared to the measurement accuracy of technology utilized to develop ISGN-71. In this presentation, we will explore how the IGSN-71 might best be "modernized" given today's requirements and available instruments and resources. The National Geodetic Survey (NGS), along with other relevant US Government agencies, is concerned about establishing gravity control to establish and maintain high order geodetic networks as part of the nation's essential infrastructure. The need to modernize the nation's geodetic infrastructure was highlighted in "Precise Geodetic Infrastructure, National Requirements for a Shared Resource" National Academy of Science, 2010. The NGS mission, as dictated by Congress, is to establish and maintain the National Spatial Reference System, which includes gravity measurements. Absolute gravimeters measure the total gravity field directly and do not involve ties to other measurements. Periodic "intercomparisons" of multiple absolute gravimeters at reference gravity sites are used to constrain the behavior of the instruments to ensure that each would yield reasonably similar measurements of the same location (i.e. yield a sufficiently consistent datum when measured in disparate locales). New atomic interferometric gravimeters promise a significant

  10. Olefin epoxidation by molybdenum peroxo compound: molecular mechanism characterized by the electron localization function and catastrophe theory.

    PubMed

    Berski, Slawomir; Sensato, Fabrício R; Polo, Victor; Andrés, Juan; Safont, V S

    2011-02-03

    The oxygen atom transfer reaction from the Mimoun-type complex MoO(η(2)-O(2))(2)OPH(3) to ethylene C(2)H(4) affording oxirane C(2)H(4)O has been investigated within the framework of the Bonding Evolution Theory in which the corresponding molecular mechanism is characterized by the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT). Topological analysis of ELF and electron density analysis reveals that all Mo-O bonds in MoO(η(2)-O(2))(2)OPH(3) and MoO(2)(η(2)-O(2))OPH(3) belong to closed-shell type interactions though negative values of total energy densities E(e)(r(BCP)) imply some covalent contribution. The peroxo O(i)-O(j) bonds are characterized as charge-shift or protocovalent species in which pairs of monosynaptic basins V(3)(O(i)), V(3)(O(j)) with a small electron population of ~0.25e each, are localized between core basins C(O(i)), C(O(j)). The oxygen transfer reaction from molybdenum diperoxo complex MoO(η(2)-O(2))(2)OPH(3) to C(2)H(4) system can be described by the following consecutive chemical events: (a) protocovalent peroxo O(2)-O(1) bond breaking, (b) reduction of the double C(1)=C(2) bond to single C(1)-C(2) bond in ethylene, (c) displacement of oxygen O(1) with two nonbonding basins, V(i=1,2)(O(1)), (d) increase of a number of the nonbonding basins to three (V(i=1,2,4)(O(1))); (e) reorganization and reduction in the number of nonbonding basis to two basins (V(i=1,4)(O(1))) resembling the ELF-topology of the nonbonding electron density in oxirane, (e) formation of the first O(1)-C(2) bond in oxirane, (f) C(2)-O(1)-C(2) ring closure, (g) formation of singular nonbonding basin V(O(2)) in new Mo=O(2) bond. The oxygen atom is transferred as an anionic moiety carrying a rather small electronic charge ranging from 0.5 to 0.7e.

  11. The Herschel Exploitation of Local Galaxy Andromeda (HELGA). VI. The Distribution and Properties of Molecular Cloud Associations in M31

    NASA Astrophysics Data System (ADS)

    Kirk, J. M.; Gear, W. K.; Fritz, J.; Smith, M. W. L.; Ford, G.; Baes, M.; Bendo, G. J.; De Looze, I.; Eales, S. A.; Gentile, G.; Gomez, H. L.; Gordon, K.; O'Halloran, B.; Madden, S. C.; Roman-Duval, J.; Verstappen, J.; Viaene, S.; Boselli, A.; Cooray, A.; Lebouteiller, V.; Spinoglio, L.

    2015-01-01

    In this paper we present a catalog of giant molecular clouds (GMCs) in the Andromeda (M31) galaxy extracted from the Herschel Exploitation of Local Galaxy Andromeda (HELGA) data set. GMCs are identified from the Herschel maps using a hierarchical source extraction algorithm. We present the results of this new catalog and characterize the spatial distribution and spectral energy properties of its clouds based on the radial dust/gas properties found by Smith et al. A total of 326 GMCs in the mass range 104-107 M ⊙ are identified; their cumulative mass distribution is found to be proportional to M -2.34, in agreement with earlier studies. The GMCs appear to follow the same correlation of cloud mass to L CO observed in the Milky Way. However, comparison between this catalog and interferometry studies also shows that the GMCs are substructured below the Herschel resolution limit, suggesting that we are observing associations of GMCs. Following Gordon et al., we study the spatial structure of M31 by splitting the observed structure into a set of spiral arms and offset rings. We fit radii of 10.3 and 15.5 kpc to the two most prominent rings. We then fit a logarithmic spiral with a pitch angle of 8.°9 to the GMCs not associated with either ring. Last, we comment on the effects of deprojection on our results and investigate the effect different models for M31's inclination will have on the projection of an unperturbed spiral arm system. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  12. Molecular characterization of two small heat shock protein genes in rice: their expression patterns, localizations, networks, and heterogeneous overexpressions.

    PubMed

    Ham, Deok-Jae; Moon, Jun-Chul; Hwang, Sun-Goo; Jang, Cheol Seong

    2013-09-28

    Heat stress is an example of a severe abiotic stress that plants can suffer in the field, causing a significant detrimental effect on their growth and productivity. Understanding the mechanism of plant response to heat stress is important for improving the productivity of crop plants under global warming. We used a microarray dataset that is deposited in the public database to evaluate plant responses to heat stress, and we selected the top 10 genes that are highly expressed under heat stress in rice. Two genes, OsSHSP1 (Os03g16030) and OsSHSP2 (Os01g04380), were selected for further study. These genes were highly induced in response to salt and drought but not in response to cold. In addition, OsSHSP1 and OsSHSP2 gene transcripts were induced under abscisic acid and salicylic acid but not under jasmonic acid and ethylene. Subcellular localization of proteins of 35S::OsSHSP1 were associated with the cytosol, whereas those of and 35S::OsSHSP2 were associated with the cytosol and nucleus. Heterogeneous overexpression of both genes exhibited higher germination rates than those of wild-type plants under the salt treatment, but not under heat or drought stress, supporting a hypothesis regarding functional specialization of members of small heat-shock protein family over evolutionary time. The network of both genes harboring nine sHSPs as well as at least 13 other chaperone genes might support the idea of a role for sHSPs in the chaperone network. Our findings might provide clues to shed light on the molecular functions of OsSHSP1 and OsSHSP2 in response to abiotic stresses, especially heat stress.

  13. Molecular detection of antimicrobial resistance in local isolates of Staphylococcus epidermidis from urinary tract infections in Faisalabad region of Pakistan.

    PubMed

    Farid, Anam; Naz, Iram; Ashraf, Asma; Ali, Aamir; Rehman, Asad-Ur; Sarwar, Yasra; Haque, Abdul

    2015-01-01

    Staphylococci are one of the foremost causes of urinary tract infections (UTIs) in humans. The emergence of multiple drug resistance (MDR) among Staphylococci poses serious challenges in antimicrobial therapy for UTIs. Most work has been done on S. aureus while coagulase negative Staphylococci (mainly S. epidermidis) are often neglected. This study was conducted to establish a baseline profile of drug resistance in local S. epidermidis isolates from UTIs. Eighty urine samples were collected from suspected UTIs cases and screened for S. epidermidis. Twenty isolates were suspected as S. epidermidis based on colony morphology and Gram staining. Molecular detection by polymerase chain reaction (PCR) confirmed 13 isolates as S. epidermidis. Using disc diffusion method, phenotypic drug resistance of the isolates was observed towards erythromycin (100 %), gentamycin, azithromycin and tetracycline (92.3 %), ampicillin and oxytetracyclin (84.6 %), amikacin and srteptomycin (76.9 %), methicillin (69.2 %), cephradine, cefaclor and cefazolin (53.8 %) and vancomycin (15.3 %). Eighteen most commonly reported genes responsible for conferring resistance towards these drugs were targeted by PCR: among these tetM gene was found most prevalent (46.1 %) followed by tetK (30.7 %), aac(6')/aph(2") (30.7 %), aacA-aphD (23 %), ermA (23 %), blaZ (23 %), mecA (23 %) blaTEM-1 (23 %), MeccA (23 %) and mecA (15.3 %). No gene fragment for vancomycin resistance was detected. The salient finding was that all S. epidermidis isolates were multiple drugs resistant as they showed resistance against at least three structurally different antimicrobial agents. It is concluded that in addition to the mostly used antimicrobial agent vancomycin, the cephalosporins including cephradine, cefaclor and cefazolin are also the drugs of choice against UTIs caused by S. epidermidis.

  14. Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

    PubMed

    Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

    2016-07-01

    Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease.

  15. THE HERSCHEL EXPLOITATION OF LOCAL GALAXY ANDROMEDA (HELGA). VI. THE DISTRIBUTION AND PROPERTIES OF MOLECULAR CLOUD ASSOCIATIONS IN M31

    SciTech Connect

    Kirk, J. M.; Gear, W. K.; Smith, M. W. L.; Ford, G.; Eales, S. A.; Gomez, H. L.; Fritz, J.; Baes, M.; De Looze, I.; Gentile, G.; Gordon, K.; Verstappen, J.; Viaene, S.; Bendo, G. J.; O'Halloran, B.; Madden, S. C.; Lebouteiller, V.; Boselli, A.; Cooray, A.; and others

    2015-01-01

    In this paper we present a catalog of giant molecular clouds (GMCs) in the Andromeda (M31) galaxy extracted from the Herschel Exploitation of Local Galaxy Andromeda (HELGA) data set. GMCs are identified from the Herschel maps using a hierarchical source extraction algorithm. We present the results of this new catalog and characterize the spatial distribution and spectral energy properties of its clouds based on the radial dust/gas properties found by Smith et al. A total of 326 GMCs in the mass range 10{sup 4}-10{sup 7} M {sub ☉} are identified; their cumulative mass distribution is found to be proportional to M {sup –2.34}, in agreement with earlier studies. The GMCs appear to follow the same correlation of cloud mass to L {sub CO} observed in the Milky Way. However, comparison between this catalog and interferometry studies also shows that the GMCs are substructured below the Herschel resolution limit, suggesting that we are observing associations of GMCs. Following Gordon et al., we study the spatial structure of M31 by splitting the observed structure into a set of spiral arms and offset rings. We fit radii of 10.3 and 15.5 kpc to the two most prominent rings. We then fit a logarithmic spiral with a pitch angle of 8.°9 to the GMCs not associated with either ring. Last, we comment on the effects of deprojection on our results and investigate the effect different models for M31's inclination will have on the projection of an unperturbed spiral arm system.

  16. Absolute concentration measurements inside a jet plume using video digitization

    NASA Astrophysics Data System (ADS)

    Vauquelin, O.

    An experimental system based on digitized video image analysis is used to measure the local value of the concentration inside a plume. Experiments are carried out in a wind-tunnel for a smoke-seeded turbulent jet plume illuminated with a laser beam. Each test is filmed, subsequently video images are digitized and analysed in order to determine the smoke absolute concentration corresponding to each pixel gray level. This non-intrusive measurement technique is first calibrated and different laws connecting gray level to concentration are established. As a first application, concentration measurements are made inside a turbulent jet plume and compared with measurements conducted using a classic gas analysis method. We finally present and discuss the possibilities offered for the measurements of absolute concentration fluctuations.

  17. Remote ultrasound palpation for robotic interventions using absolute elastography.

    PubMed

    Schneider, Caitlin; Baghani, Ali; Rohling, Robert; Salcudean, Septimiu

    2012-01-01

    Although robotic surgery has addressed many of the challenges presented by minimally invasive surgery, haptic feedback and the lack of knowledge of tissue stiffness is an unsolved problem. This paper presents a system for finding the absolute elastic properties of tissue using a freehand ultrasound scanning technique, which utilizes the da Vinci Surgical robot and a custom 2D ultrasound transducer for intraoperative use. An external exciter creates shear waves in the tissue, and a local frequency estimation method computes the shear modulus. Results are reported for both phantom and in vivo models. This system can be extended to any 6 degree-of-freedom tracking method and any 2D transducer to provide real-time absolute elastic properties of tissue.

  18. A New Gimmick for Assigning Absolute Configuration.

    ERIC Educational Resources Information Center

    Ayorinde, F. O.

    1983-01-01

    A five-step procedure is provided to help students in making the assignment absolute configuration less bothersome. Examples for both single (2-butanol) and multi-chiral carbon (3-chloro-2-butanol) molecules are included. (JN)

  19. Magnifying absolute instruments for optically homogeneous regions

    SciTech Connect

    Tyc, Tomas

    2011-09-15

    We propose a class of magnifying absolute optical instruments with a positive isotropic refractive index. They create magnified stigmatic images, either virtual or real, of optically homogeneous three-dimensional spatial regions within geometrical optics.

  20. The Simplicity Argument and Absolute Morality

    ERIC Educational Resources Information Center

    Mijuskovic, Ben

    1975-01-01

    In this paper the author has maintained that there is a similarity of thought to be found in the writings of Cudworth, Emerson, and Husserl in his investigation of an absolute system of morality. (Author/RK)

  1. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    SciTech Connect

    Zarycz, M. Natalia C. Provasi, Patricio F.; Sauer, Stephan P. A.

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  2. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    NASA Astrophysics Data System (ADS)

    Zarycz, M. Natalia C.; Sauer, Stephan P. A.; Provasi, Patricio F.

    2014-10-01

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the 1J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the 1J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  3. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane.

    PubMed

    Zarycz, M Natalia C; Sauer, Stephan P A; Provasi, Patricio F

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the (1)J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the (1)J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes--SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  4. Absolute cross sections of compound nucleus reactions

    NASA Astrophysics Data System (ADS)

    Capurro, O. A.

    1993-11-01

    The program SEEF is a Fortran IV computer code for the extraction of absolute cross sections of compound nucleus reactions. When the evaporation residue is fed by its parents, only cumulative cross sections will be obtained from off-line gamma ray measurements. But, if one has the parent excitation function (experimental or calculated), this code will make it possible to determine absolute cross sections of any exit channel.

  5. Kelvin and the absolute temperature scale

    NASA Astrophysics Data System (ADS)

    Erlichson, Herman

    2001-07-01

    This paper describes the absolute temperature scale of Kelvin (William Thomson). Kelvin found that Carnot's axiom about heat being a conserved quantity had to be abandoned. Nevertheless, he found that Carnot's fundamental work on heat engines was correct. Using the concept of a Carnot engine Kelvin found that Q1/Q2 = T1/T2. Thermometers are not used to obtain absolute temperatures since they are calculated temperatures.

  6. Measurement of the absolute solar UV irradiance and variability

    NASA Technical Reports Server (NTRS)

    Mentall, James E.

    1990-01-01

    Radiation in the wavelength interval 150-350 nm initiates chemical reactions in the lower mesosphere and the stratosphere through the photodissociation of ambient molecular species. This experiment measures the total solar irradiance, above the Earth's atmosphere, in this wavelength interval, using three spectrometers. Measurements are made from rockets on a once-a-year basis and are used with satellite observations to determine both the absolute irradiance and the long term variability of the sun in the UV. A fourth spectrometer is being added to the payload to measure the emission in the hydrogen Lyman-alpha emission at 121.67 nm.

  7. Investigation of the local structure of mixtures of an ionic liquid with polar molecular species through molecular dynamics: cluster formation and angular distributions.

    PubMed

    Carrete, Jesús; Méndez-Morales, Trinidad; Cabeza, Óscar; Lynden-Bell, Ruth M; Gallego, Luis J; Varela, Luis M

    2012-05-24

    In this work, we used molecular dynamics simulations to analyze in detail the spatial distributions of the different constituents in mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate with three polar molecular species: water and two alcohols of different chain lengths (methanol and ethanol). In particular, we report results regarding the influence of the chosen species and its concentration on the formation of ionic and molecular clusters over the whole miscibility range, as well as on the angular distribution of polar molecules around the anion and the cation in these systems. Both analyses showed that addition of a molecular species breaks down the polar network of the pure ionic liquid in clusters whose mean size decreases progressively as more molecules are added. At very high concentrations of the molecular species, the ions are found to be isolated in mixtures with water and methanol, but they tend to form pairs in ethanol. In mixtures with water we identified large clusters that form a water network at very high water concentrations, while at low water concentrations polar molecules tend to form smaller aggregates. In contrast, in mixtures with alkanols there is no evidence of the formation of large alcohol clusters at any concentration. Spatial order in alcohol was also studied by means of the Kirkwood G factor, reaching the conclusion that the angular correlations which appear in pure alcohols due to dipole interactions are destroyed by the ionic liquid, even when present only in tiny amounts.

  8. Gold Nanoparticle-Quantum Dot Fluorescent Nanohybrid: Application for Localized Surface Plasmon Resonance-induced Molecular Beacon Ultrasensitive DNA Detection

    NASA Astrophysics Data System (ADS)

    Adegoke, Oluwasesan; Park, Enoch Y.

    2016-11-01

    In biosensor design, localized surface plasmon resonance (LSPR)-induced signal from gold nanoparticle (AuNP)-conjugated reporter can produce highly sensitive nanohybrid systems. In order to retain the physicochemical properties of AuNPs upon conjugation, high colloidal stability in aqueous solution is needed. In this work, the colloidal stability with respect to the zeta potential (ZP) of four negatively charged thiol-functionalized AuNPs, thioglycolic (TGA)-AuNPs, 3-mercaptopropionic acid (MPA)-AuNPs, l-cysteine-AuNPs and l-glutathione (GSH)-AuNPs, and a cationic cyteamine-capped AuNPs was studied at various pHs, ionic strength, and NP concentration. A strong dependence of the ZP charge on the nanoparticle (NP) concentration was observed. High colloidal stability was exhibited between pH 3 and 9 for the negatively charged AuNPs and between pH 3 and 7 for the cationic AuNPs. With respect to the ionic strength, high colloidal stability was exhibited at ≤104 μM for TGA-AuNPs, l-cysteine-AuNPs, and GSH-AuNPs, whereas ≤103 μM is recommended for MPA-AuNPs. For the cationic AuNPs, very low ionic strength of ≤10 μM is recommended due to deprotonation at higher concentration. GSH-AuNPs were thereafter bonded to SiO2-functionalized alloyed CdZnSeS/ZnSe1.0S1.3 quantum dots (SiO2-Qdots) to form a plasmon-enhanced AuNP-SiO2-Qdots fluorescent nanohybrid. The AuNP-SiO2-Qdots conjugate was afterward conjugated to a molecular beacon (MB), thus forming an ultrasensitive LSPR-induced SiO2-Qdots-MB biosensor probe that detected a perfect nucleotide DNA sequence at a concentration as low as 10 fg/mL. The limit of detection was 11 fg/mL (1.4 fM) while the biosensor probe efficiently distinguished between single-base mismatch and noncomplementary sequence target.

  9. Investigation of the linear and second-order nonlinear optical properties of molecular crystals within the local field theory.

    PubMed

    Seidler, Tomasz; Stadnicka, Katarzyna; Champagne, Benoît

    2013-09-21

    In this paper it is shown that modest calculations combining first principles evaluations of the molecular properties with electrostatic interaction schemes to account for the crystal environment effects are reliable for predicting and interpreting the experimentally measured electric linear and second-order nonlinear optical susceptibilities of molecular crystals within the experimental error bars. This is illustrated by considering two molecular crystals, namely: 2-methyl-4-nitroaniline and 4-(N,N-dimethylamino)-3-acetamidonitrobenzene. Three types of surrounding effects should be accounted for (i) the polarization due to the surrounding molecules, described here by static electric fields originating from their electric dipoles or charge distributions, (ii) the intermolecular interactions, which affect the geometry and particularly the molecular conformation, and (iii) the screening of the external electric field by the constitutive molecules. This study further highlights the role of electron correlation on the linear and nonlinear responses of molecular crystals and the challenge of describing frequency dispersion.

  10. Jasminum flexile flower absolute from India--a detailed comparison with three other jasmine absolutes.

    PubMed

    Braun, Norbert A; Kohlenberg, Birgit; Sim, Sherina; Meier, Manfred; Hammerschmidt, Franz-Josef

    2009-09-01

    Jasminum flexile flower absolute from the south of India and the corresponding vacuum headspace (VHS) sample of the absolute were analyzed using GC and GC-MS. Three other commercially available Indian jasmine absolutes from the species: J. sambac, J. officinale subsp. grandiflorum, and J. auriculatum and the respective VHS samples were used for comparison purposes. One hundred and twenty-one compounds were characterized in J. flexile flower absolute, with methyl linolate, benzyl salicylate, benzyl benzoate, (2E,6E)-farnesol, and benzyl acetate as the main constituents. A detailed olfactory evaluation was also performed.

  11. Absolute gravity acceleration measurement in atomic sensor laboratories

    NASA Astrophysics Data System (ADS)

    de Angelis, M.; Greco, F.; Pistorio, A.; Poli, N.; Prevedelli, M.; Saccorotti, G.; Sorrentino, F.; Tino, G. M.

    2012-03-01

    This paper reports the results from the accurate measurement of the acceleration of gravity g taken at two separate premises in the Polo Scientifico of the Florence University (Italy). In these laboratories, two separate experiments aiming at measuring the Newtonian constant and testing the measurement of forces with high spatial resolution are in progress. Both experiments require an independent knowledge on the local value of g. Gravity measurements were conducted using an FG5 absolute gravimeter, and accompanied by seismic recordings for evaluating the noise condition at the site. The absolute accelerations of gravity at the two laboratories are ( 980 492 160.6 ± 4.0) μGal and ( 980 492 048.3 ± 3.0) μGal for the European Laboratory for Non-Linear Spectroscopy (LENS) and Dipartimento di Fisica e Astronomia, respectively. Other than for the two referenced experiments, the data here presented will serve as a benchmark for any future study requiring an accurate knowledge of the absolute value of the acceleration of gravity in the study region.

  12. Universal Cosmic Absolute and Modern Science

    NASA Astrophysics Data System (ADS)

    Kostro, Ludwik

    The official Sciences, especially all natural sciences, respect in their researches the principle of methodic naturalism i.e. they consider all phenomena as entirely natural and therefore in their scientific explanations they do never adduce or cite supernatural entities and forces. The purpose of this paper is to show that Modern Science has its own self-existent, self-acting, and self-sufficient Natural All-in Being or Omni-Being i.e. the entire Nature as a Whole that justifies the scientific methodic naturalism. Since this Natural All-in Being is one and only It should be considered as the own scientifically justified Natural Absolute of Science and should be called, in my opinion, the Universal Cosmic Absolute of Modern Science. It will be also shown that the Universal Cosmic Absolute is ontologically enormously stratified and is in its ultimate i.e. in its most fundamental stratum trans-reistic and trans-personal. It means that in its basic stratum. It is neither a Thing or a Person although It contains in Itself all things and persons with all other sentient and conscious individuals as well, On the turn of the 20th century the Science has begun to look for a theory of everything, for a final theory, for a master theory. In my opinion the natural Universal Cosmic Absolute will constitute in such a theory the radical all penetrating Ultimate Basic Reality and will substitute step by step the traditional supernatural personal Absolute.

  13. DISCOVERY OF AN ACTIVE GALACTIC NUCLEUS DRIVEN MOLECULAR OUTFLOW IN THE LOCAL EARLY-TYPE GALAXY NGC 1266

    SciTech Connect

    Alatalo, K.; Blitz, L.; Young, L. M.; Davis, T. A.; Bureau, M.; Cappellari, M.; Scott, N.; Davies, R. L.; Lopez, L. A.; Shapiro, K. L.; Crocker, A. F.; MartIn, S.; Bois, M.; Emsellem, E.; Bournaud, F.; Duc, P.-A.; Falcon-Barroso, J.

    2011-07-10

    We report the discovery of a powerful molecular wind from the nucleus of the non-interacting nearby S0 field galaxy NGC 1266. The single-dish CO profile exhibits emission to {+-}400 km s{sup -1} and requires a nested Gaussian fit to be properly described. Interferometric observations reveal a massive, centrally concentrated molecular component with a mass of 1.1 x 10{sup 9} M{sub sun} and a molecular outflow with a molecular mass of {approx}2.4 x 10{sup 7} M{sub sun}. The molecular gas close to the systemic velocity consists of a rotating, compact nucleus with a mass of about 4.1 x 10{sup 8} M{sub sun} within a radius of {approx}60 pc. This compact molecular nucleus has a surface density of {approx}2.7 x 10{sup 4} M{sub sun} pc{sup -2}, more than two orders of magnitude larger than that of giant molecular clouds in the disk of the Milky Way, and it appears to sit on the Kennicutt-Schmidt relation despite its extreme kinematics and energetic activity. We interpret this nucleus as a disk that confines the outflowing wind. A mass outflow rate of {approx}13 M{sub sun} yr{sup -1} leads to a depletion timescale of {approx}<85 Myr. The star formation in NGC 1266 is insufficient to drive the outflow, and thus it is likely driven by the active galactic nucleus. The concentration of the majority of the molecular gas in the central 100 pc requires an extraordinary loss of angular momentum, but no obvious companion or interacting galaxy is present to enable the transfer. NGC 1266 is the first known outflowing molecular system that does not show any evidence of a recent interaction.

  14. Absolute continuity on paths of spatial open discrete mappings

    NASA Astrophysics Data System (ADS)

    Golberg, Anatoly; Sevost'yanov, Evgeny

    2016-12-01

    We prove that open discrete mappings of Sobolev classes W_loc^{1, p}, p>n-1, with locally integrable inner dilatations admit ACP_p^{ -1} -property, which means that these mappings are absolutely continuous on almost all preimage paths with respect to p-module. In particular, our results extend the well-known Poletskiĭ lemma for quasiregular mappings. We also establish the upper bounds for p-module of such mappings in terms of integrals depending on the inner dilatations and arbitrary admissible functions.

  15. Local vibrational dynamics of hematite (α-Fe{sub 2}O{sub 3}) studied by extended x-ray absorption fine structure and molecular dynamics

    SciTech Connect

    Sanson, A.; Mathon, O.; Pascarelli, S.

    2014-06-14

    The local vibrational dynamics of hematite (α-Fe{sub 2}O{sub 3}) has been investigated by temperature-dependent extended x-ray absorption fine structure spectroscopy and molecular dynamics simulations. The local dynamics of both the short and long nearest-neighbor Fe–O distances has been singled out, i.e., their local thermal expansion and the parallel and perpendicular mean-square relative atomic displacements have been determined, obtaining a partial agreement with molecular dynamics. No evidence of the Morin transition has been observed. More importantly, the strong anisotropy of relative thermal vibrations found for the short Fe–O distance has been related to its negative thermal expansion. The differences between the local dynamics of short and long Fe–O distances are discussed in terms of projection and correlation of atomic motion. As a result, we can conclude that the short Fe–O bond is stiffer to stretching and softer to bending than the long Fe–O bond.

  16. Local vibrational dynamics of hematite (α-Fe₂O₃) studied by extended x-ray absorption fine structure and molecular dynamics.

    PubMed

    Sanson, A; Mathon, O; Pascarelli, S

    2014-06-14

    The local vibrational dynamics of hematite (α-Fe2O3) has been investigated by temperature-dependent extended x-ray absorption fine structure spectroscopy and molecular dynamics simulations. The local dynamics of both the short and long nearest-neighbor Fe-O distances has been singled out, i.e., their local thermal expansion and the parallel and perpendicular mean-square relative atomic displacements have been determined, obtaining a partial agreement with molecular dynamics. No evidence of the Morin transition has been observed. More importantly, the strong anisotropy of relative thermal vibrations found for the short Fe-O distance has been related to its negative thermal expansion. The differences between the local dynamics of short and long Fe-O distances are discussed in terms of projection and correlation of atomic motion. As a result, we can conclude that the short Fe-O bond is stiffer to stretching and softer to bending than the long Fe-O bond.

  17. Quantitative standards for absolute linguistic universals.

    PubMed

    Piantadosi, Steven T; Gibson, Edward

    2014-01-01

    Absolute linguistic universals are often justified by cross-linguistic analysis: If all observed languages exhibit a property, the property is taken to be a likely universal, perhaps specified in the cognitive or linguistic systems of language learners and users. In many cases, these patterns are then taken to motivate linguistic theory. Here, we show that cross-linguistic analysis will very rarely be able to statistically justify absolute, inviolable patterns in language. We formalize two statistical methods--frequentist and Bayesian--and show that in both it is possible to find strict linguistic universals, but that the numbers of independent languages necessary to do so is generally unachievable. This suggests that methods other than typological statistics are necessary to establish absolute properties of human language, and thus that many of the purported universals in linguistics have not received sufficient empirical justification.

  18. Identification of nuclear/nucleolar localization signal in Aplysia learning associated protein of slug with a molecular mass of 18 kDa homologous protein.

    PubMed

    Kim, Hyoung; Chang, Deok-Jin; Lee, Jin-A; Lee, Yong-Seok; Kaang, Bong-Kiun

    2003-06-05

    We isolated a learning associated protein of slug with a molecular mass of 18 kDa (LAPS18) homologue from the expressed sequence tag database of Aplysia kurodai and named it Aplysia LAPS18-like protein (ApLLP). ApLLP encodes 120 amino acids and has 57% identity with LAPS18. To examine the subcellular expression pattern of ApLLP we constructed an EGFP-tagged ApLLP fusion protein and overexpressed it in both Aplysia neurons and COS-7 cells. In contrast to the previous findings, which showed that LAPS18 is secreted by COS-7 cells, ApLLP-EGFP was localized to the nucleus, and most of it to nucleoli. Analysis of deletion mutants of ApLLP-EGFP showed that the N-terminal and the C-terminal nucleolar and nucleus localization signal sequences are important for localization to the nucleus and the nucleoli.

  19. Absolute Distance Measurement with the MSTAR Sensor

    NASA Technical Reports Server (NTRS)

    Lay, Oliver P.; Dubovitsky, Serge; Peters, Robert; Burger, Johan; Ahn, Seh-Won; Steier, William H.; Fetterman, Harrold R.; Chang, Yian

    2003-01-01

    The MSTAR sensor (Modulation Sideband Technology for Absolute Ranging) is a new system for measuring absolute distance, capable of resolving the integer cycle ambiguity of standard interferometers, and making it possible to measure distance with sub-nanometer accuracy. The sensor uses a single laser in conjunction with fast phase modulators and low frequency detectors. We describe the design of the system - the principle of operation, the metrology source, beamlaunching optics, and signal processing - and show results for target distances up to 1 meter. We then demonstrate how the system can be scaled to kilometer-scale distances.

  20. Absolutely relative or relatively absolute: violations of value invariance in human decision making.

    PubMed

    Teodorescu, Andrei R; Moran, Rani; Usher, Marius

    2016-02-01

    Making decisions based on relative rather than absolute information processing is tied to choice optimality via the accumulation of evidence differences and to canonical neural processing via accumulation of evidence ratios. These theoretical frameworks predict invariance of decision latencies to absolute intensities that maintain differences and ratios, respectively. While information about the absolute values of the choice alternatives is not necessary for choosing the best alternative, it may nevertheless hold valuable information about the context of the decision. To test the sensitivity of human decision making to absolute values, we manipulated the intensities of brightness stimuli pairs while preserving either their differences or their ratios. Although asked to choose the brighter alternative relative to the other, participants responded faster to higher absolute values. Thus, our results provide empirical evidence for human sensitivity to task irrelevant absolute values indicating a hard-wired mechanism that precedes executive control. Computational investigations of several modelling architectures reveal two alternative accounts for this phenomenon, which combine absolute and relative processing. One account involves accumulation of differences with activation dependent processing noise and the other emerges from accumulation of absolute values subject to the temporal dynamics of lateral inhibition. The potential adaptive role of such choice mechanisms is discussed.

  1. Comparative vs. Absolute Judgments of Trait Desirability

    ERIC Educational Resources Information Center

    Hofstee, Willem K. B.

    1970-01-01

    Reversals of trait desirability are studied. Terms indicating conservativw behavior appeared to be judged relatively desirable in comparative judgement, while traits indicating dynamic and expansive behavior benefited from absolute judgement. The reversal effect was shown to be a general one, i.e. reversals were not dependent upon the specific…

  2. New Techniques for Absolute Gravity Measurements.

    DTIC Science & Technology

    1983-01-07

    Hammond, J.A. (1978) Bollettino Di Geofisica Teorica ed Applicata Vol. XX. 8. Hammond, J. A., and Iliff, R. L. (1979) The AFGL absolute gravity system...International Gravimetric Bureau, No. L:I-43. 7. Hammond. J.A. (1978) Bollettino Di Geofisica Teorica ed Applicata Vol. XX. 8. Hammond, J.A., and

  3. An Absolute Electrometer for the Physics Laboratory

    ERIC Educational Resources Information Center

    Straulino, S.; Cartacci, A.

    2009-01-01

    A low-cost, easy-to-use absolute electrometer is presented: two thin metallic plates and an electronic balance, usually available in a laboratory, are used. We report on the very good performance of the device that allows precise measurements of the force acting between two charged plates. (Contains 5 footnotes, 2 tables, and 6 figures.)

  4. Stimulus Probability Effects in Absolute Identification

    ERIC Educational Resources Information Center

    Kent, Christopher; Lamberts, Koen

    2016-01-01

    This study investigated the effect of stimulus presentation probability on accuracy and response times in an absolute identification task. Three schedules of presentation were used to investigate the interaction between presentation probability and stimulus position within the set. Data from individual participants indicated strong effects of…

  5. Absolute Positioning Using the Global Positioning System

    DTIC Science & Technology

    1994-04-01

    Global Positioning System ( GPS ) has becom a useful tool In providing relativ survey...Includes the development of a low cost navigator for wheeled vehicles. ABSTRACT The Global Positioning System ( GPS ) has become a useful tool In providing...technique of absolute or point positioning involves the use of a single Global Positioning System ( GPS ) receiver to determine the three-dimenslonal

  6. Absolute Radiation Thermometry in the NIR

    NASA Astrophysics Data System (ADS)

    Bünger, L.; Taubert, R. D.; Gutschwager, B.; Anhalt, K.; Briaudeau, S.; Sadli, M.

    2017-04-01

    A near infrared (NIR) radiation thermometer (RT) for temperature measurements in the range from 773 K up to 1235 K was characterized and calibrated in terms of the "Mise en Pratique for the definition of the Kelvin" (MeP-K) by measuring its absolute spectral radiance responsivity. Using Planck's law of thermal radiation allows the direct measurement of the thermodynamic temperature independently of any ITS-90 fixed-point. To determine the absolute spectral radiance responsivity of the radiation thermometer in the NIR spectral region, an existing PTB monochromator-based calibration setup was upgraded with a supercontinuum laser system (0.45 μm to 2.4 μm) resulting in a significantly improved signal-to-noise ratio. The RT was characterized with respect to its nonlinearity, size-of-source effect, distance effect, and the consistency of its individual temperature measuring ranges. To further improve the calibration setup, a new tool for the aperture alignment and distance measurement was developed. Furthermore, the diffraction correction as well as the impedance correction of the current-to-voltage converter is considered. The calibration scheme and the corresponding uncertainty budget of the absolute spectral responsivity are presented. A relative standard uncertainty of 0.1 % (k=1) for the absolute spectral radiance responsivity was achieved. The absolute radiometric calibration was validated at four temperature values with respect to the ITS-90 via a variable temperature heatpipe blackbody (773 K ...1235 K) and at a gold fixed-point blackbody radiator (1337.33 K).

  7. Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

    2017-04-01

    Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

  8. Molecular localization of the t(11; 22)(q24; q12) translocation of Ewing sarcoma by chromosomal in situ suppression hybridization

    SciTech Connect

    Selleri, L.; Hermanson, G.G.; Eubanks, J.H.; Lewis, K.A.; Evans, G.A. )

    1991-02-01

    Chromosome translocations are associated with a variety of human leukemias, lymphomas, and solid tumors. To localize molecular markers flanking the t(11;22)(q24;q12) breakpoint that occurs in virtually all cases of Ewing sarcoma and peripheral neuroepithelioma, high-resolution chromosomal in situ suppression hybridization was carried out using a panel of cosmid clones localized and ordered on chromosome 11q. The location of the Ewing sarcoma translocation breakpoint was determined relative to the nearest two cosmid markers on 11q, clones 23.2 and 5.8, through the analysis of metaphase chromosome hybridization. By in situ hybridization to interphase nuclei, the approximate physical separation of these two markers was determined. In both Ewing sarcoma and peripheral neuroepithelioma, cosmid clone 5.8 is translocated from chromosome 11q24 to the derivative chromosome 22 and a portion of chromosome 22q12 carrying the leukemia inhibitory factor gene is translocated to the derivative chromosome 11. The physical distance between the flanking cosmid markers on chromosome 11 was determined to be in the range of 1,000 kilobases, and genomic analysis using pulsed-field gel electrophoresis showed no abnormalities over a region of 650 kilobases in the vicinity of the leukemia inhibitory factor gene on chromosome 22. This approach localizes the Ewing sarcoma breakpoint to a small region on chromosome 11q24 and provides a rapid and precise technique for the molecular characterization of chromosomal aberrations.

  9. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

    PubMed

    Ferenczy, György G

    2013-04-05

    The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem.

  10. Sensitive and molecular size-selective detection of proteins using a chip-based and heteroliganded gold nanoisland by localized surface plasmon resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Hong, Surin; Lee, Suseung; Yi, Jongheop

    2011-04-01

    A highly sensitive and molecular size-selective method for the detection of proteins using heteroliganded gold nanoislands and localized surface plasmon resonance (LSPR) is described. Two different heteroligands with different chain lengths (3-mercaptopionicacid and decanethiol) were used in fabricating nanoholes for the size-dependent separation of a protein in comparison with its aggregate. Their ratios on gold nanoisland were optimized for the sensitive detection of superoxide dismutase (SOD1). This protein has been implicated in the pathology of amyotrophic lateral sclerosis (ALS). Upon exposure of the optimized gold nanoisland to a solution of SOD1 and aggregates thereof, changes in the LSPR spectra were observed which are attributed to the size-selective and covalent chemical binding of SOD1 to the nanoholes. With a lower detection limit of 1.0 ng/ml, the method can be used to selectively detect SOD1 in the presence of aggregates at the molecular level.

  11. Ion Coulomb crystals: from quantum technology to chemistry close to the absolute zero point

    NASA Astrophysics Data System (ADS)

    Dulieu, O.; Willitsch, S.

    2017-03-01

    Ion Coulomb crystals are ordered structures of atomic or molecular ions stored in ion traps at temperatures close to the absolute zero point. These unusual "crystals" form the basis of extremely accurate clocks, provide an environment for precise studies of chemical reactions and enable advanced implementations of the technology for a quantum computer. In this article, we discuss the techniques for generating atomic and molecular Coulomb crystals and highlight some of their applications.

  12. Usefulness of Sau-PCR for molecular epidemiology of nosocomial outbreaks due to Burkholderia cepacia which occurred in a local hospital in Guangzhou, China.

    PubMed

    Yan, He; Shi, Lei; Alam, M J; Li, Lin; Yang, Liansheng; Yamasaki, Shinji

    2008-05-01

    The aim of the present study was to determine the source of nosocomial outbreak due to Burkholderia cepacia by molecular techniques. A total of 11 B. cepacia strains were isolated; nine from blood and one from sputum of patients without cystic fibrosis, and one from reverse osmosis water at a local hospital in Guangzhou, China. Analyses of 11 strains by the Sau-PCR assay and pulsed-field gel electrophoresis revealed that nine strains obtained from the blood of outpatients in a hemodialysis unit and one strain from reverse osmosis water had identical DNA profiles, indicating that the reverse osmosis water supply could be a source of infection.

  13. Investigation of the local environment of Eu3+ in a silicophosphate glass using site-selective spectroscopy and Molecular Dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ben Slimen, F.; Haouari, M.; Ben Ouada, H.; Guichaoua, D.; Raso, P.; Bidault, X.; Turlier, J.; Gaumer, N.; Chaussedent, S.

    2017-02-01

    Silicophosphate glasses (SiO2-P2O5) doped with Eu3+ ions were synthesized by the sol-gel process. Optical properties of these glasses were investigated by means of emission spectra and lifetime measurements. The Fluorescence Line Narrowing (FLN) technique was also used to explore the local structure around the Eu3+ ions in this host and to understand the role of phosphate as a codopant. As it is the case for aluminum, the ability of phosphate to avoid the rare earth clustering was investigated, and the role of this codopant in modifying the local order around the rare earth ion was evidenced. The analysis of the FLN spectra and lifetime measurements is consistent with this interpretation. Molecular Dynamics simulations were performed to evaluate and confirm these structural features. Two classes of europium sites were distinguished in agreement with the experimental characterization.

  14. The atomic-to-molecular transition and its relation to the scaling properties of galaxy discs in the local Universe

    NASA Astrophysics Data System (ADS)

    Fu, Jian; Guo, Qi; Kauffmann, Guinevere; Krumholz, Mark R.

    2010-12-01

    We extend the existing semi-analytic models of galaxy formation to track atomic and molecular gas in disc galaxies. Simple recipes for processes such as cooling, star formation, supernova feedback and chemical enrichment of the stars and gas are grafted on to dark matter halo merger trees derived from the Millennium Simulation. Each galactic disc is represented by a series of concentric rings. We assume that the surface density profile of an infalling gas in a dark matter halo is exponential, with scale radius rd that is proportional to the virial radius of the halo times its spin parameter λ. As the dark matter haloes grow through mergers and accretion, disc galaxies assemble from the inside out. We include two simple prescriptions for molecular gas formation processes in our models: one is based on the analytic calculations by Krumholz, McKee & Tumlinson, and the other is a prescription where the H2 fraction is determined by the pressure of the interstellar medium (ISM). Motivated by the observational results of Leroy et al., we adopt a star formation law in which in the regime where the molecular gas dominates the total gas surface density, and where atomic hydrogen dominates. We then fit these models to the radial surface density profiles of stars, HI and H2 drawn from recent high-resolution surveys of stars and gas in nearby galaxies. We explore how the ratios of atomic gas, molecular gas and stellar mass vary as a function of global galaxy scale parameters, including stellar mass, stellar surface density and gas surface density. We elucidate how the trends can be understood in terms of three variables that determine the partition of baryons in discs: the mass of the dark matter halo, the spin parameter of the halo and the amount of gas recently accreted from the external environment.

  15. From Hubble's NGSL to Absolute Fluxes

    NASA Technical Reports Server (NTRS)

    Heap, Sara R.; Lindler, Don

    2012-01-01

    Hubble's Next Generation Spectral Library (NGSL) consists of R-l000 spectra of 374 stars of assorted temperature, gravity, and metallicity. Each spectrum covers the wavelength range, 0.18-1.00 microns. The library can be viewed and/or downloaded from the website, http://archive.stsci.edu/prepds/stisngsll. Stars in the NGSL are now being used as absolute flux standards at ground-based observatories. However, the uncertainty in the absolute flux is about 2%, which does not meet the requirements of dark-energy surveys. We are therefore developing an observing procedure that should yield fluxes with uncertainties less than 1 % and will take part in an HST proposal to observe up to 15 stars using this new procedure.

  16. Consistent thermostatistics forbids negative absolute temperatures

    NASA Astrophysics Data System (ADS)

    Dunkel, Jörn; Hilbert, Stefan

    2014-01-01

    Over the past 60 years, a considerable number of theories and experiments have claimed the existence of negative absolute temperature in spin systems and ultracold quantum gases. This has led to speculation that ultracold gases may be dark-energy analogues and also suggests the feasibility of heat engines with efficiencies larger than one. Here, we prove that all previous negative temperature claims and their implications are invalid as they arise from the use of an entropy definition that is inconsistent both mathematically and thermodynamically. We show that the underlying conceptual deficiencies can be overcome if one adopts a microcanonical entropy functional originally derived by Gibbs. The resulting thermodynamic framework is self-consistent and implies that absolute temperature remains positive even for systems with a bounded spectrum. In addition, we propose a minimal quantum thermometer that can be implemented with available experimental techniques.

  17. Absolute measurement of length with nanometric resolution

    NASA Astrophysics Data System (ADS)

    Apostol, D.; Garoi, F.; Timcu, A.; Damian, V.; Logofatu, P. C.; Nascov, V.

    2005-08-01

    Laser interferometer displacement measuring transducers have a well-defined traceability route to the definition of the meter. The laser interferometer is de-facto length scale for applications in micro and nano technologies. However their physical unit -half lambda is too large for nanometric resolution. Fringe interpolation-usual technique to improve the resolution-lack of reproducibility could be avoided using the principles of absolute distance measurement. Absolute distance refers to the use of interferometric techniques for determining the position of an object without the necessity of measuring continuous displacements between points. The interference pattern as produced by the interference of two point-like coherent sources is fitted to a geometric model so as to determine the longitudinal location of the target by minimizing least square errors. The longitudinal coordinate of the target was measured with accuracy better than 1 nm, for a target position range of 0.4μm.

  18. Asteroid absolute magnitudes and slope parameters

    NASA Technical Reports Server (NTRS)

    Tedesco, Edward F.

    1991-01-01

    A new listing of absolute magnitudes (H) and slope parameters (G) has been created and published in the Minor Planet Circulars; this same listing will appear in the 1992 Ephemerides of Minor Planets. Unlike previous listings, the values of the current list were derived from fits of data at the V band. All observations were reduced in the same fashion using, where appropriate, a single basis default value of 0.15 for the slope parameter. Distances and phase angles were computed for each observation. The data for 113 asteroids was of sufficiently high quality to permit derivation of their H and G. These improved absolute magnitudes and slope parameters will be used to deduce the most reliable bias-corrected asteroid size-frequency distribution yet made.

  19. Computer processing of spectrograms for absolute intensities.

    PubMed

    Guttman, A; Golden, J; Galbraith, H J

    1967-09-01

    A computer program was developed to process photographically recorded spectra for absolute intensity. Test and calibration films are subjected to densitometric scans that provide digitally recorded densities on magnetic tapes. The nonlinear calibration data are fitted by least-squares cubic polynomials to yield a good approximation to the monochromatic H&D curves for commonly used emulsions (2475 recording film, Royal-X, Tri-X, 4-X). Several test cases were made. Results of these cases show that the machine processed absolute intensities are accurate to within 15%o. Arbitrarily raising the sensitivity threshold by 0.1 density units above gross fog yields cubic polynomial fits to the H&D curves that are radiometrically accurate within 10%. In addition, curves of gamma vs wavelength for 2475, Tri-X, and 4-X emulsions were made. These data show slight evidence of the photographic Purkinje effect in the 2475 emulsion.

  20. An absolute measure for a key currency

    NASA Astrophysics Data System (ADS)

    Oya, Shunsuke; Aihara, Kazuyuki; Hirata, Yoshito

    It is generally considered that the US dollar and the euro are the key currencies in the world and in Europe, respectively. However, there is no absolute general measure for a key currency. Here, we investigate the 24-hour periodicity of foreign exchange markets using a recurrence plot, and define an absolute measure for a key currency based on the strength of the periodicity. Moreover, we analyze the time evolution of this measure. The results show that the credibility of the US dollar has not decreased significantly since the Lehman shock, when the Lehman Brothers bankrupted and influenced the economic markets, and has increased even relatively better than that of the euro and that of the Japanese yen.

  1. Absolute and relative dosimetry for ELIMED

    NASA Astrophysics Data System (ADS)

    Cirrone, G. A. P.; Cuttone, G.; Candiano, G.; Carpinelli, M.; Leonora, E.; Lo Presti, D.; Musumarra, A.; Pisciotta, P.; Raffaele, L.; Randazzo, N.; Romano, F.; Schillaci, F.; Scuderi, V.; Tramontana, A.; Cirio, R.; Marchetto, F.; Sacchi, R.; Giordanengo, S.; Monaco, V.

    2013-07-01

    The definition of detectors, methods and procedures for the absolute and relative dosimetry of laser-driven proton beams is a crucial step toward the clinical use of this new kind of beams. Hence, one of the ELIMED task, will be the definition of procedures aiming to obtain an absolute dose measure at the end of the transport beamline with an accuracy as close as possible to the one required for clinical applications (i.e. of the order of 5% or less). Relative dosimetry procedures must be established, as well: they are necessary in order to determine and verify the beam dose distributions and to monitor the beam fluence and the energetic spectra during irradiations. Radiochromic films, CR39, Faraday Cup, Secondary Emission Monitor (SEM) and transmission ionization chamber will be considered, designed and studied in order to perform a fully dosimetric characterization of the ELIMED proton beam.

  2. Silicon Absolute X-Ray Detectors

    SciTech Connect

    Seely, John F.; Korde, Raj; Sprunck, Jacob; Medjoubi, Kadda; Hustache, Stephanie

    2010-06-23

    The responsivity of silicon photodiodes having no loss in the entrance window, measured using synchrotron radiation in the 1.75 to 60 keV range, was compared to the responsivity calculated using the silicon thickness measured using near-infrared light. The measured and calculated responsivities agree with an average difference of 1.3%. This enables their use as absolute x-ray detectors.

  3. System for absolute measurements by interferometric sensors

    NASA Astrophysics Data System (ADS)

    Norton, Douglas A.

    1993-03-01

    The most common problem of interferometric sensors is their inability to measure absolute path imbalance. Presented in this paper is a signal processing system that gives absolute, unambiguous reading of optical path difference for almost any style of interferometric sensor. Key components are a wide band (incoherent) optical source, a polychromator, and FFT electronics. Advantages include no moving parts in the signal processor, no active components at the sensor location, and the use of standard single mode fiber for sensor illumination and signal transmission. Actual absolute path imbalance of the interferometer is determined without using fringe counting or other inferential techniques. The polychromator extracts the interference information that occurs at each discrete wavelength within the spectral band of the optical source. The signal processing consists of analog and digital filtering, Fast Fourier analysis, and a peak detection and interpolation algorithm. This system was originally designed for use in a remote pressure sensing application that employed a totally passive fiber optic interferometer. A performance qualification was made using a Fabry-Perot interferometer and a commercially available laser interferometer to measure the reference displacement.

  4. Chemical composition of French mimosa absolute oil.

    PubMed

    Perriot, Rodolphe; Breme, Katharina; Meierhenrich, Uwe J; Carenini, Elise; Ferrando, Georges; Baldovini, Nicolas

    2010-02-10

    Since decades mimosa (Acacia dealbata) absolute oil has been used in the flavor and perfume industry. Today, it finds an application in over 80 perfumes, and its worldwide industrial production is estimated five tons per year. Here we report on the chemical composition of French mimosa absolute oil. Straight-chain analogues from C6 to C26 with different functional groups (hydrocarbons, esters, aldehydes, diethyl acetals, alcohols, and ketones) were identified in the volatile fraction. Most of them are long-chain molecules: (Z)-heptadec-8-ene, heptadecane, nonadecane, and palmitic acid are the most abundant, and constituents such as 2-phenethyl alcohol, methyl anisate, and ethyl palmitate are present in smaller amounts. The heavier constituents were mainly triterpenoids such as lupenone and lupeol, which were identified as two of the main components. (Z)-Heptadec-8-ene, lupenone, and lupeol were quantified by GC-MS in SIM mode using external standards and represents 6%, 20%, and 7.8% (w/w) of the absolute oil. Moreover, odorant compounds were extracted by SPME and analyzed by GC-sniffing leading to the perception of 57 odorant zones, of which 37 compounds were identified by their odorant description, mass spectrum, retention index, and injection of the reference compound.

  5. Constrained Least Absolute Deviation Neural Networks

    PubMed Central

    Wang, Zhishun; Peterson, Bradley S.

    2008-01-01

    It is well known that least absolute deviation (LAD) criterion or L1-norm used for estimation of parameters is characterized by robustness, i.e., the estimated parameters are totally resistant (insensitive) to large changes in the sampled data. This is an extremely useful feature, especially, when the sampled data are known to be contaminated by occasionally occurring outliers or by spiky noise. In our previous works, we have proposed the least absolute deviation neural network (LADNN) to solve unconstrained LAD problems. The theoretical proofs and numerical simulations have shown that the LADNN is Lyapunov-stable and it can globally converge to the exact solution to a given unconstrained LAD problem. We have also demonstrated its excellent application value in time-delay estimation. More generally, a practical LAD application problem may contain some linear constraints, such as a set of equalities and/or inequalities, which is called constrained LAD problem, whereas the unconstrained LAD can be considered as a special form of the constrained LAD. In this paper, we present a new neural network called constrained least absolute deviation neural network (CLADNN) to solve general constrained LAD problems. Theoretical proofs and numerical simulations demonstrate that the proposed CLADNN is Lyapunov stable and globally converges to the exact solution to a given constrained LAD problem, independent of initial values. The numerical simulations have also illustrated that the proposed CLADNN can be used to robustly estimate parameters for nonlinear curve fitting, which is extensively used in signal and image processing. PMID:18269958

  6. Absolute calibration of Apollo lunar orbital mass spectrometer.

    NASA Technical Reports Server (NTRS)

    Yeager, P. R.; Smith, A.; Jackson, J. J.; Hoffman, J. H.

    1973-01-01

    Recent experiments were conducted in Langley Research Center's molecular beam system to perform an absolute calibration of the lunar orbital mass spectrometer which was flown on the Apollo 15 and 16 missions. Tests were performed with several models of the instrument using two test gases, argon and neon, in the 1 ntorr to .1 picotorr range. Sensitivity to argon at spacecraft orbital velocity was .00028 A/torr enabling partial pressures in the .01-picotorr range to be measured at the spacecraft altitude. Neon sensitivity was nearly a factor of 5 less. Test data support the feasibility of using the lunar orbital mass spectrometer as a tool to gather information about the lunar atmosphere.

  7. What's the meaning of local? Using molecular markers to define seed transfer zones for ecological restoration in Norway.

    PubMed

    Jørgensen, Marte Holten; Elameen, Abdelhameed; Hofman, Nadine; Klemsdal, Sonja; Malaval, Sandra; Fjellheim, Siri

    2016-06-01

    According to the Norwegian Diversity Act, practitioners of restoration in Norway are instructed to use seed mixtures of local provenance. However, there are no guidelines for how local seed should be selected. In this study, we use genetic variation in a set of alpine species (Agrostis mertensii, Avenella flexuosa, Carex bigelowii, Festuca ovina, Poa alpina and Scorzoneroides autumnalis) to define seed transfer zones to reduce confusion about the definition of 'local seeds'. The species selected for the study are common in all parts of Norway and suitable for commercial seed production. The sampling covered the entire alpine region (7-20 populations per species, 3-15 individuals per population). We characterised genetic diversity using amplified fragment length polymorphisms. We identified different spatial genetic diversity structures in the species, most likely related to differences in reproductive strategies, phylogeographic factors and geographic distribution. Based on results from all species, we suggest four general seed transfer zones for alpine Norway. This is likely more conservative than needed for all species, given that no species show more than two genetic groups. Even so, the approach is practical as four seed mixtures will serve the need for restoration of vegetation in alpine regions in Norway.

  8. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

    NASA Astrophysics Data System (ADS)

    Zobač, Vladimír; Lewis, James P.; Abad, Enrique; Mendieta-Moreno, Jesús I.; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-01

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

  9. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

    PubMed

    Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-08

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

  10. Novel serine-based gemini surfactants as chemical permeation enhancers of local anesthetics: A comprehensive study on structure-activity relationships, molecular dynamics and dermal delivery.

    PubMed

    Teixeira, Raquel S; Cova, Tânia F G G; Silva, Sérgio M C; Oliveira, Rita; do Vale, M Luísa C; Marques, Eduardo F; Pais, Alberto A C C; Veiga, Francisco J B

    2015-06-01

    This work aims at studying the efficacy of a series of novel biocompatible, serine-based surfactants as chemical permeation enhancers for two different local anesthetics, tetracaine and ropivacaine, combining an experimental and computational approach. The surfactants consist of gemini molecules structurally related, but with variations in headgroup charge (nonionic vs. cationic) and in the hydrocarbon chain lengths (main and spacer chains). In vitro permeation and molecular dynamics studies combined with cytotoxicity profiles were performed to investigate the permeation of both drugs, probe skin integrity, and rationalize the interactions at molecular level. Results show that these enhancers do not have significant deleterious effects on the skin structure and do not cause relevant changes on cell viability. Permeation across the skin is clearly improved using some of the selected serine-based gemini surfactants, namely the cationic ones with long alkyl chains and shorter spacer. This is noteworthy in the case of ropivacaine hydrochloride, which is not easily administered through the stratum corneum. Molecular dynamics results provide a mechanistic view of the surfactant action on lipid membranes that essentially corroborate the experimental observations. Overall, this study suggests the viability of these serine-based surfactants as suitable and promising delivery agents in pharmaceutical formulations.

  11. Periodic local Møller-Plesset second order perturbation theory method applied to molecular crystals: study of solid NH3 and CO2 using extended basis sets.

    PubMed

    Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Civalleri, Bartolomeo

    2010-04-07

    We have calculated the equilibrium geometry, formation energy, and bulk modulus of two molecular bulk crystals, NH(3) and CO(2), at the periodic post-Hartree-Fock correlated level. The dependence of the results on the basis set has been analyzed, by employing basis sets up to aug-cc-pVQZ quality. In the calculations, we used the periodic local Møller-Plesset second order perturbation theory (LMP2), implemented in the CRYSCOR program. Multipolar expansion techniques, as well as density fitting, are employed in this code to reduce the number of and to factorize the required electron repulsion integrals; as a consequence of that, the computational cost for the correlation part of the calculations is comparable to that of the Hartree-Fock. Auxiliary calculations performed on molecular dimers are also reported to verify the accuracy of the LMP2 approach and of the basis sets used. Furthermore, the effect of spin-component scaling has been investigated for the two crystals. One intention of the present paper is also to lay out and specify the computational setup, which is generally applicable for accurate CRYSCOR calculations on molecular crystals.

  12. Network models provide insights into how oriens-lacunosum-moleculare and bistratified cell interactions influence the power of local hippocampal CA1 theta oscillations.

    PubMed

    Ferguson, Katie A; Huh, Carey Y L; Amilhon, Bénédicte; Manseau, Frédéric; Williams, Sylvain; Skinner, Frances K

    2015-01-01

    Hippocampal theta is a 4-12 Hz rhythm associated with episodic memory, and although it has been studied extensively, the cellular mechanisms underlying its generation are unclear. The complex interactions between different interneuron types, such as those between oriens-lacunosum-moleculare (OLM) interneurons and bistratified cells (BiCs), make their contribution to network rhythms difficult to determine experimentally. We created network models that are tied to experimental work at both cellular and network levels to explore how these interneuron interactions affect the power of local oscillations. Our cellular models were constrained with properties from patch clamp recordings in the CA1 region of an intact hippocampus preparation in vitro. Our network models are composed of three different types of interneurons: parvalbumin-positive (PV+) basket and axo-axonic cells (BC/AACs), PV+ BiCs, and somatostatin-positive OLM cells. Also included is a spatially extended pyramidal cell model to allow for a simplified local field potential representation, as well as experimentally-constrained, theta frequency synaptic inputs to the interneurons. The network size, connectivity, and synaptic properties were constrained with experimental data. To determine how the interactions between OLM cells and BiCs could affect local theta power, we explored how the number of OLM-BiC connections and connection strength affected local theta power. We found that our models operate in regimes that could be distinguished by whether OLM cells minimally or strongly affected the power of network theta oscillations due to balances that, respectively, allow compensatory effects or not. Inactivation of OLM cells could result in no change or even an increase in theta power. We predict that the dis-inhibitory effect of OLM cells to BiCs to pyramidal cell interactions plays a critical role in the resulting power of network theta oscillations. Overall, our network models reveal a dynamic interplay

  13. Network models provide insights into how oriens–lacunosum-moleculare and bistratified cell interactions influence the power of local hippocampal CA1 theta oscillations

    PubMed Central

    Ferguson, Katie A.; Huh, Carey Y. L.; Amilhon, Bénédicte; Manseau, Frédéric; Williams, Sylvain; Skinner, Frances K.

    2015-01-01

    Hippocampal theta is a 4–12 Hz rhythm associated with episodic memory, and although it has been studied extensively, the cellular mechanisms underlying its generation are unclear. The complex interactions between different interneuron types, such as those between oriens–lacunosum-moleculare (OLM) interneurons and bistratified cells (BiCs), make their contribution to network rhythms difficult to determine experimentally. We created network models that are tied to experimental work at both cellular and network levels to explore how these interneuron interactions affect the power of local oscillations. Our cellular models were constrained with properties from patch clamp recordings in the CA1 region of an intact hippocampus preparation in vitro. Our network models are composed of three different types of interneurons: parvalbumin-positive (PV+) basket and axo-axonic cells (BC/AACs), PV+ BiCs, and somatostatin-positive OLM cells. Also included is a spatially extended pyramidal cell model to allow for a simplified local field potential representation, as well as experimentally-constrained, theta frequency synaptic inputs to the interneurons. The network size, connectivity, and synaptic properties were constrained with experimental data. To determine how the interactions between OLM cells and BiCs could affect local theta power, we explored how the number of OLM-BiC connections and connection strength affected local theta power. We found that our models operate in regimes that could be distinguished by whether OLM cells minimally or strongly affected the power of network theta oscillations due to balances that, respectively, allow compensatory effects or not. Inactivation of OLM cells could result in no change or even an increase in theta power. We predict that the dis-inhibitory effect of OLM cells to BiCs to pyramidal cell interactions plays a critical role in the resulting power of network theta oscillations. Overall, our network models reveal a dynamic interplay

  14. Electron Localization in Molecular Fragmentation of H{sub 2} by Carrier-Envelope Phase Stabilized Laser Pulses

    SciTech Connect

    Kremer, Manuel; Fischer, Bettina; Feuerstein, Bernold; Sharma, Vandana; Hofrichter, Christian; Schroeter, Claus Dieter; Moshammer, Robert; Ullrich, Joachim; Jesus, Vitor L. B. de; Rudenko, Artem; Thumm, Uwe

    2009-11-20

    Fully differential data for H{sub 2} dissociation in ultrashort (6 fs, 760 nm), linearly polarized, intense (0.44 PW/cm{sup 2}) laser pulses with a stabilized carrier-envelope phase (CEP) were recorded with a reaction microscope. Depending on the CEP, the molecular orientation, and the kinetic energy release (KER), we find asymmetric proton emission at low KERs (0-3 eV), basically predicted by Roudnev and Esry, and much stronger than reported by Kling et al. Wave packet propagation calculations reproduce the salient features and discard, together with the observed KER-independent electron asymmetry, the first ionization step to be the reason for the asymmetric proton emission.

  15. Local segmental dynamics of cis-1,4-polybutadiene, polypropylene, and polyethylene terephthalate via molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Whitley, David; Adolf, David

    2011-03-01

    NPT molecular dynamics simulations of cis-1,4-polybutadiene, polypropylene, and polyethylene terephthalate have been performed. The simulation pressure was 1 atmosphere for all systems, with all simulation temperatures being well above each polymer's glass transition temperature. The trajectories have been analysed via autocorrelation functions (ACFs) of chord vectors spanning different numbers of chain backbone bonds. Inverse Laplace transformations of these ACFs using the CONTIN algorithm afforded the corresponding distributions of relaxation times (DRTs) for the simulated dynamics. All DRTs illustrated a peak on fast time scales corresponding to short length scale segmental motion and a peak at longer time scales corresponding to longer length scale relaxations. An intermediate peak between the fast and slow peaks appears as the relaxation dynamics of longer chord vectors are analysed. The temperature dependence of the relaxation dynamics has also been investigated.

  16. Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO2-H2O systems.

    PubMed

    Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang

    2014-01-28

    In view of the important implications of excess electrons (EEs) interacting with CO2-H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2-H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π(*) orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2 (-) oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n](-) systems. Interestingly, hydration occurs not only on the O atoms of the core CO2 (-) through formation of O⋯H-O H-bond(s), but also on the C atom, through formation of a C⋯H-O H-bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H-O H-bonds, and vice versa. The number of water molecules associated with the CO2 (-) anion in the first hydration shell is about 4∼7. No dimer-core (C2O4 (-)) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2-H2O media.

  17. Molecular Cloning, mRNA Expression, and Localization of the G-protein Subunit Galphaq in Sheep Testis and Epididymis

    PubMed Central

    Li, Zhen; Lu, Jieli; Sun, Xiaowei; Pang, Quanhai; Zhao, Yiwen

    2016-01-01

    The reproductive function of G-protein subunit Galphaq (GNAQ), a member of the G protein alpha subunit family, has been extensively studied in humans and rats. However, no data is available on its status in ruminants. The objectives of this study were to evaluate the expression pattern of the GNAQ in the testis and epididymis of sheep by polymerase chain reaction (PCR). The mRNA expression levels were detected by real-time fluorescent quantitative PCR, and cellular localization of GNAQ in the testis and epididymis was examined by immunohistochemistry. Additionally, GNAQ protein was qualitatively evaluated via western blot, with the results indicating that similarities between GNAQ mRNA levels from sheep was highly conserved with those observed in Bos taurus and Sus scrofa. Our results also indicated that GNAQ exists in the caput and cauda epididymis of sheep, while GNAQ in the testis and epididymis was localized to Leydig cells, spermatogonial stem cells, spermatocytes, Sertoli cells, spermatid, principal cells, and epididymis interstitial cells. The concentrations of GNAQ mRNA and protein in the caput and cauda epididymis were significantly greater than those observed in the corpus epididymis (p<0.01) and testis (p<0.05). Our results indicated that GNAQ exists at high concentrations in the caput and cauda epididymis of sheep, suggesting that GNAQ may play an important role in gonad development and sperm maturation. PMID:27004818

  18. Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential.

    PubMed

    Matta, Chérif F

    2014-06-15

    The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pK(a)'s, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme-substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as "interacting quantum atoms (IQA)" energies which are expressible into an interaction matrix of two body terms (and diagonal one body "self" terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established.

  19. Modeling Biophysical and Biological Properties From the Characteristics of the Molecular Electron Density, Electron Localization and Delocalization Matrices, and the Electrostatic Potential

    PubMed Central

    Matta*, Chérif F

    2014-01-01

    The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pKa's, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme–substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as “interacting quantum atoms (IQA)” energies which are expressible into an interaction matrix of two body terms (and diagonal one body “self” terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established. © 2014 The Author and the Journal of Computational Chemistry Published

  20. Conserving the linear momentum in stochastic dynamics: Dissipative particle dynamics as a general strategy to achieve local thermostatization in molecular dynamics simulations.

    PubMed

    Passler, Peter P; Hofer, Thomas S

    2017-02-15

    Stochastic dynamics is a widely employed strategy to achieve local thermostatization in molecular dynamics simulation studies; however, it suffers from an inherent violation of momentum conservation. Although this short-coming has little impact on structural and short-time dynamic properties, it can be shown that dynamics in the long-time limit such as diffusion is strongly dependent on the respective thermostat setting. Application of the methodically similar dissipative particle dynamics (DPD) provides a simple, effective strategy to ensure the advantages of local, stochastic thermostatization while at the same time the linear momentum of the system remains conserved. In this work, the key parameters to employ the DPD thermostats in the framework of periodic boundary conditions are investigated, in particular the dependence of the system properties on the size of the DPD-region as well as the treatment of forces near the cutoff. Structural and dynamical data for light and heavy water as well as a Lennard-Jones fluid have been compared to simulations executed via stochastic dynamics as well as via use of the widely employed Nose-Hoover chain and Berendsen thermostats. It is demonstrated that a small size of the DPD region is sufficient to achieve local thermalization, while at the same time artifacts in the self-diffusion characteristic for stochastic dynamics are eliminated. © 2016 Wiley Periodicals, Inc.

  1. An unambiguous signature in molecular frame photoelectron angular distributions of core hole localization in fluorine K-edge photoionization of CF4

    NASA Astrophysics Data System (ADS)

    McCurdy, C. W.; Rescigno, T. N.; Trevisan, C. S.; Lucchese, R. R.

    2016-05-01

    Molecular Frame Photoelectron Angular Distributions (MFPADs) are calculated using the Complex Kohn variational method for core-hole ionization of the carbon and fluorines in CF4 at photoelectron energies below 15 eV. The angular distributions for localized versus delocalized core-hole creation on the four equivalent fluorines are radically different. A strong propensity for the dissociation to take place via the mechanism hν +CF4 -->CF 4 + +e- -->CF 3 + +F(1s-1) -->CF 3 + +F+ + 2e- in which a core excited neutral fluorine atom ionizes during or after dissociation creates the conditions for experimental observation of core hole localization. Comparison with recent unpublished experiments at the Advanced Light Source that measured the Recoil Frame Photoelectron Angular Distributions (averaged over CF3 rotations around the recoil axis) for fluorine K-edge ionization gives unambiguous evidence that these experiments directly observed the creation of an almost completely localized core hole on the dissociating fluorine atom when the molecule was initially photoionized. Work supported by USDOE, OBES Chemical Sciences, Geosciences, and Biosciences Division.

  2. In Situ Molecular Identification of the Plastid ω3 Fatty Acid Desaturase FAD7 from Soybean: Evidence of Thylakoid Membrane Localization1

    PubMed Central

    Andreu, Vanesa; Collados, Raquel; Testillano, Pilar S.; Risueño, María del Carmen; Picorel, Rafael; Alfonso, Miguel

    2007-01-01

    ω3 fatty acid desaturases are the enzymes responsible for the synthesis of trienoic fatty acids in plants. These enzymes have been mainly investigated using molecular, biochemical, and genetic approaches but very little is known about their subcellular distribution in plant cells. In this work, the precise subcellular localization of the ω3 desaturase FAD7 was elucidated by immunofluorescence and immunogold labeling using a monospecific GmFAD7 polyclonal antibody in soybean (Glycine max) photoautotrophic cell suspension cultures. Confocal analysis revealed the localization of the GmFAD7 protein within the chloroplast; i.e. signals from FAD7 and chlorophyll autofluorescence showed specific colocalization. Immunogold labeling was pursued on cryofixed and freeze-substituted samples for convenient preservation of antigenicity and ultrastructure of membrane subcompartments. Our data revealed that the FAD7 protein was preferentially localized in the thylakoid membranes. Biochemical fractionation of purified chloroplasts and western analysis of the subfractions further confirmed these results. These findings suggest that not only the envelope, but also the thylakoid membranes could be sites of lipid desaturation in higher plants. PMID:17951449

  3. Clock time is absolute and universal

    NASA Astrophysics Data System (ADS)

    Shen, Xinhang

    2015-09-01

    A critical error is found in the Special Theory of Relativity (STR): mixing up the concepts of the STR abstract time of a reference frame and the displayed time of a physical clock, which leads to use the properties of the abstract time to predict time dilation on physical clocks and all other physical processes. Actually, a clock can never directly measure the abstract time, but can only record the result of a physical process during a period of the abstract time such as the number of cycles of oscillation which is the multiplication of the abstract time and the frequency of oscillation. After Lorentz Transformation, the abstract time of a reference frame expands by a factor gamma, but the frequency of a clock decreases by the same factor gamma, and the resulting multiplication i.e. the displayed time of a moving clock remains unchanged. That is, the displayed time of any physical clock is an invariant of Lorentz Transformation. The Lorentz invariance of the displayed times of clocks can further prove within the framework of STR our earth based standard physical time is absolute, universal and independent of inertial reference frames as confirmed by both the physical fact of the universal synchronization of clocks on the GPS satellites and clocks on the earth, and the theoretical existence of the absolute and universal Galilean time in STR which has proved that time dilation and space contraction are pure illusions of STR. The existence of the absolute and universal time in STR has directly denied that the reference frame dependent abstract time of STR is the physical time, and therefore, STR is wrong and all its predictions can never happen in the physical world.

  4. Absolute Radiometric Calibration of EUNIS-06

    NASA Technical Reports Server (NTRS)

    Thomas, R. J.; Rabin, D. M.; Kent, B. J.; Paustian, W.

    2007-01-01

    The Extreme-Ultraviolet Normal-Incidence Spectrometer (EUNIS) is a soundingrocket payload that obtains imaged high-resolution spectra of individual solar features, providing information about the Sun's corona and upper transition region. Shortly after its successful initial flight last year, a complete end-to-end calibration was carried out to determine the instrument's absolute radiometric response over its Longwave bandpass of 300 - 370A. The measurements were done at the Rutherford-Appleton Laboratory (RAL) in England, using the same vacuum facility and EUV radiation source used in the pre-flight calibrations of both SOHO/CDS and Hinode/EIS, as well as in three post-flight calibrations of our SERTS sounding rocket payload, the precursor to EUNIS. The unique radiation source provided by the Physikalisch-Technische Bundesanstalt (PTB) had been calibrated to an absolute accuracy of 7% (l-sigma) at 12 wavelengths covering our bandpass directly against the Berlin electron storage ring BESSY, which is itself a primary radiometric source standard. Scans of the EUNIS aperture were made to determine the instrument's absolute spectral sensitivity to +- 25%, considering all sources of error, and demonstrate that EUNIS-06 was the most sensitive solar E W spectrometer yet flown. The results will be matched against prior calibrations which relied on combining measurements of individual optical components, and on comparisons with theoretically predicted 'insensitive' line ratios. Coordinated observations were made during the EUNIS-06 flight by SOHO/CDS and EIT that will allow re-calibrations of those instruments as well. In addition, future EUNIS flights will provide similar calibration updates for TRACE, Hinode/EIS, and STEREO/SECCHI/EUVI.

  5. Achieving Climate Change Absolute Accuracy in Orbit

    NASA Technical Reports Server (NTRS)

    Wielicki, Bruce A.; Young, D. F.; Mlynczak, M. G.; Thome, K. J; Leroy, S.; Corliss, J.; Anderson, J. G.; Ao, C. O.; Bantges, R.; Best, F.; Bowman, K.; Brindley, H.; Butler, J. J.; Collins, W.; Dykema, J. A.; Doelling, D. R.; Feldman, D. R.; Fox, N.; Huang, X.; Holz, R.; Huang, Y.; Jennings, D.; Jin, Z.; Johnson, D. G.; Jucks, K.; Kato, S.; Kratz, D. P.; Liu, X.; Lukashin, C.; Mannucci, A. J.; Phojanamongkolkij, N.; Roithmayr, C. M.; Sandford, S.; Taylor, P. C.; Xiong, X.

    2013-01-01

    The Climate Absolute Radiance and Refractivity Observatory (CLARREO) mission will provide a calibration laboratory in orbit for the purpose of accurately measuring and attributing climate change. CLARREO measurements establish new climate change benchmarks with high absolute radiometric accuracy and high statistical confidence across a wide range of essential climate variables. CLARREO's inherently high absolute accuracy will be verified and traceable on orbit to Système Internationale (SI) units. The benchmarks established by CLARREO will be critical for assessing changes in the Earth system and climate model predictive capabilities for decades into the future as society works to meet the challenge of optimizing strategies for mitigating and adapting to climate change. The CLARREO benchmarks are derived from measurements of the Earth's thermal infrared spectrum (5-50 micron), the spectrum of solar radiation reflected by the Earth and its atmosphere (320-2300 nm), and radio occultation refractivity from which accurate temperature profiles are derived. The mission has the ability to provide new spectral fingerprints of climate change, as well as to provide the first orbiting radiometer with accuracy sufficient to serve as the reference transfer standard for other space sensors, in essence serving as a "NIST [National Institute of Standards and Technology] in orbit." CLARREO will greatly improve the accuracy and relevance of a wide range of space-borne instruments for decadal climate change. Finally, CLARREO has developed new metrics and methods for determining the accuracy requirements of climate observations for a wide range of climate variables and uncertainty sources. These methods should be useful for improving our understanding of observing requirements for most climate change observations.

  6. Negative absolute temperature for motional degrees of freedom.

    PubMed

    Braun, S; Ronzheimer, J P; Schreiber, M; Hodgman, S S; Rom, T; Bloch, I; Schneider, U

    2013-01-04

    Absolute temperature is usually bound to be positive. Under special conditions, however, negative temperatures-in which high-energy states are more occupied than low-energy states-are also possible. Such states have been demonstrated in localized systems with finite, discrete spectra. Here, we prepared a negative temperature state for motional degrees of freedom. By tailoring the Bose-Hubbard Hamiltonian, we created an attractively interacting ensemble of ultracold bosons at negative temperature that is stable against collapse for arbitrary atom numbers. The quasimomentum distribution develops sharp peaks at the upper band edge, revealing thermal equilibrium and bosonic coherence over several lattice sites. Negative temperatures imply negative pressures and open up new parameter regimes for cold atoms, enabling fundamentally new many-body states.

  7. Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies.

    PubMed

    Khaliullin, Rustam Z; Kühne, Thomas D

    2013-10-14

    The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

  8. Brownian motion: Absolute negative particle mobility

    NASA Astrophysics Data System (ADS)

    Ros, Alexandra; Eichhorn, Ralf; Regtmeier, Jan; Duong, Thanh Tu; Reimann, Peter; Anselmetti, Dario

    2005-08-01

    Noise effects in technological applications, far from being a nuisance, can be exploited with advantage - for example, unavoidable thermal fluctuations have found application in the transport and sorting of colloidal particles and biomolecules. Here we use a microfluidic system to demonstrate a paradoxical migration mechanism in which particles always move in a direction opposite to the net acting force (`absolute negative mobility') as a result of an interplay between thermal noise, a periodic and symmetric microstructure, and a biased alternating-current electric field. This counterintuitive phenomenon could be used for bioanalytical purposes, for example in the separation and fractionation of colloids, biological molecules and cells.

  9. Arbitrary segments of absolute negative mobility

    NASA Astrophysics Data System (ADS)

    Chen, Ruyin; Nie, Linru; Chen, Chongyang; Wang, Chaojie

    2017-01-01

    In previous research work, investigators have reported only one or two segments of absolute negative mobility (ANM) in a periodic potential. In fact, many segments of ANM also occur in the system considered here. We investigate transport of an inertial particle in a gating ratchet periodic potential subjected to a constant bias force. Our numerical results show that its mean velocity can decrease with the bias force increasing, i.e. ANM phenomenon. Furthermore, the ANM can take place arbitrary segments, even up to more than thirty. Intrinsic physical mechanism and conditions for arbitrary segments of ANM to occur are discussed in detail.

  10. Absolute quantification of myocardial blood flow.

    PubMed

    Yoshinaga, Keiichiro; Manabe, Osamu; Tamaki, Nagara

    2016-07-21

    With the increasing availability of positron emission tomography (PET) myocardial perfusion imaging, the absolute quantification of myocardial blood flow (MBF) has become popular in clinical settings. Quantitative MBF provides an important additional diagnostic or prognostic information over conventional visual assessment. The success of MBF quantification using PET/computed tomography (CT) has increased the demand for this quantitative diagnostic approach to be more accessible. In this regard, MBF quantification approaches have been developed using several other diagnostic imaging modalities including single-photon emission computed tomography, CT, and cardiac magnetic resonance. This review will address the clinical aspects of PET MBF quantification and the new approaches to MBF quantification.

  11. An absolute radius scale for Saturn's rings

    NASA Technical Reports Server (NTRS)

    Nicholson, Philip D.; Cooke, Maren L.; Pelton, Emily

    1990-01-01

    Radio and stellar occultation observations of Saturn's rings made by the Voyager spacecraft are discussed. The data reveal systematic discrepancies of almost 10 km in some parts of the rings, limiting some of the investigations. A revised solution for Saturn's rotation pole has been proposed which removes the discrepancies between the stellar and radio occultation profiles. Corrections to previously published radii vary from -2 to -10 km for the radio occultation, and +5 to -6 km for the stellar occultation. An examination of spiral density waves in the outer A Ring supports that the revised absolute radii are in error by no more than 2 km.

  12. Absolute Rate Theories of Epigenetic Stability

    NASA Astrophysics Data System (ADS)

    Walczak, Aleksandra M.; Onuchic, Jose N.; Wolynes, Peter G.

    2006-03-01

    Spontaneous switching events in most characterized genetic switches are rare, resulting in extremely stable epigenetic properties. We show how simple arguments lead to theories of the rate of such events much like the absolute rate theory of chemical reactions corrected by a transmission factor. Both the probability of the rare cellular states that allow epigenetic escape, and the transmission factor, depend on the rates of DNA binding and unbinding events and on the rates of protein synthesis and degradation. Different mechanisms of escape from the stable attractors occur in the nonadiabatic, weakly adiabatic and strictly adiabatic regimes, characterized by the relative values of those input rates.

  13. Absolute rate theories of epigenetic stability

    NASA Astrophysics Data System (ADS)

    Walczak, Aleksandra M.; Onuchic, José N.; Wolynes, Peter G.

    2005-12-01

    Spontaneous switching events in most characterized genetic switches are rare, resulting in extremely stable epigenetic properties. We show how simple arguments lead to theories of the rate of such events much like the absolute rate theory of chemical reactions corrected by a transmission factor. Both the probability of the rare cellular states that allow epigenetic escape and the transmission factor depend on the rates of DNA binding and unbinding events and on the rates of protein synthesis and degradation. Different mechanisms of escape from the stable attractors occur in the nonadiabatic, weakly adiabatic, and strictly adiabatic regimes, characterized by the relative values of those input rates. rate theory | stochastic gene expression | gene switches

  14. Absolute method of measuring magnetic susceptibility

    USGS Publications Warehouse

    Thorpe, A.; Senftle, F.E.

    1959-01-01

    An absolute method of standardization and measurement of the magnetic susceptibility of small samples is presented which can be applied to most techniques based on the Faraday method. The fact that the susceptibility is a function of the area under the curve of sample displacement versus distance of the magnet from the sample, offers a simple method of measuring the susceptibility without recourse to a standard sample. Typical results on a few substances are compared with reported values, and an error of less than 2% can be achieved. ?? 1959 The American Institute of Physics.

  15. Absolute Priority for a Vehicle in VANET

    NASA Astrophysics Data System (ADS)

    Shirani, Rostam; Hendessi, Faramarz; Montazeri, Mohammad Ali; Sheikh Zefreh, Mohammad

    In today's world, traffic jams waste hundreds of hours of our life. This causes many researchers try to resolve the problem with the idea of Intelligent Transportation System. For some applications like a travelling ambulance, it is important to reduce delay even for a second. In this paper, we propose a completely infrastructure-less approach for finding shortest path and controlling traffic light to provide absolute priority for an emergency vehicle. We use the idea of vehicular ad-hoc networking to reduce the imposed travelling time. Then, we simulate our proposed protocol and compare it with a centrally controlled traffic light system.

  16. Genuine multipartite entanglement of symmetric Gaussian states: Strong monogamy, unitary localization, scaling behavior, and molecular sharing structure

    NASA Astrophysics Data System (ADS)

    Adesso, Gerardo; Illuminati, Fabrizio

    2008-10-01

    We investigate the structural aspects of genuine multipartite entanglement in Gaussian states of continuous variable systems. Generalizing the results of Adesso and Illuminati [Phys. Rev. Lett. 99, 150501 (2007)], we analyze whether the entanglement shared by blocks of modes distributes according to a strong monogamy law. This property, once established, allows us to quantify the genuine N -partite entanglement not encoded into 2,…,K,…,(N-1) -partite quantum correlations. Strong monogamy is numerically verified, and the explicit expression of the measure of residual genuine multipartite entanglement is analytically derived, by a recursive formula, for a subclass of Gaussian states. These are fully symmetric (permutation-invariant) states that are multipartitioned into blocks, each consisting of an arbitrarily assigned number of modes. We compute the genuine multipartite entanglement shared by the blocks of modes and investigate its scaling properties with the number and size of the blocks, the total number of modes, the global mixedness of the state, and the squeezed resources needed for state engineering. To achieve the exact computation of the block entanglement, we introduce and prove a general result of symplectic analysis: Correlations among K blocks in N -mode multisymmetric and multipartite Gaussian states, which are locally invariant under permutation of modes within each block, can be transformed by a local (with respect to the partition) unitary operation into correlations shared by K single modes, one per block, in effective nonsymmetric states where N-K modes are completely uncorrelated. Due to this theorem, the above results, such as the derivation of the explicit expression for the residual multipartite entanglement, its nonnegativity, and its scaling properties, extend to the subclass of non-symmetric Gaussian states that are obtained by the unitary localization of the multipartite entanglement of symmetric states. These findings provide strong

  17. Molecular cloning and sequence analysis of a human 372-kDA protein localized in the Golgi complex.

    PubMed

    Sohda, M; Misumi, Y; Fujiwara, T; Nishioka, M; Ikehara, Y

    1994-12-15

    Autoantibodies from a patient with chronic rheumatoid arthritis recognized an antigen localized in the Golgi complex of various cells from different tissues and species. The autoantibodies were used as a probe for screening human QGP-1 cDNA library, resulting in identification of a 10.3-kb cDNA. The cDNA insert contained an open reading frame which encodes a 3225-residue protein with a calculated mass of 372 kDa. The predicted protein was found to have no NH2-terminal signal sequence but a single hydrophobic domain at the COOH terminus. These results indicate that the 372-kDa antigen is cytoplasmically disposed and anchored to the Golgi membrane by the COOH-terminal hydrophobic domain.

  18. Density functional theory study of the local molecular properties of acetamide derivatives as anti-HIV drugs

    PubMed Central

    Oftadeh, M.; Mahani, N. Madadi; Hamadanian, M.

    2013-01-01

    Accurate quantum chemical computations based on density functional theory (DFT) were performed on the series of 2-(4-(naphthalen-2-yl)-1,2,3-thiadiazol-5-ylthio)-N-acetamide (TTA) derivatives. The local reactivity of the acetamide derivatives as anti-HIV drugs were studied in terms of Fukui functions in the framework of DFT. The results based on the basis set superposition error (BSSE) corrections showed that the mechanism of bond formation between the acetamide derivatives and tyrosine as a biological molecule occurs mainly through nitrogen atoms. The intramolecular interaction energies between the acetamide derivatives and tyrosine were calculated and the nature of the intermolecular interaction was revealed by natural bond orbital charge (NBO) analysis. The results suggest that acetamide derivatives with bromophenyl and nitrophenyl substitutions are the most potent as anti-HIV drugs. PMID:24082898

  19. Molecular characterization of the gonadal kisspeptin system: Cloning, tissue distribution, gene expression analysis and localization in sablefish (Anoplopoma fimbria).

    PubMed

    Fairgrieve, Marian R; Shibata, Yasushi; Smith, Elizabeth K; Hayman, Edward S; Luckenbach, J Adam

    2016-01-01

    The kisspeptin system plays pivotal roles in the regulation of vertebrate reproduction. Classically, kisspeptin produced in the brain stimulates brain gonadotropin-releasing hormone signaling, which in turn activates the pituitary-gonad axis. Expression of the kisspeptin system has also been documented in peripheral tissues, including gonads of mammals and fishes. However, the fish gonadal kisspeptin system remained uncharacterized. Herein we report identification and characterization of four kisspeptin system mRNAs (kisspeptin 1 (kiss1), kiss2, and G protein-coupled receptor 54-1 (gpr54-1) and gpr54-2) in sablefish, Anoplopoma fimbria. Sablefish predicted protein sequences were highly similar to those of other marine teleosts, but less so to freshwater teleosts. Tissue distribution analyses revealed that all four kisspeptin-system transcripts were expressed in both brain and gonad. However, kiss2 was the predominant transcript in the gonads and the only transcript detected in ovulated eggs. Ontogenetic analysis of kiss2 expression in juvenile sablefish gonads demonstrated that levels were low during sex differentiation but increased with fish size and gonadal development. Dramatic increases in kiss2 mRNA occurred during primary oocyte growth, while levels remained relatively low in testes. In situ hybridization revealed that kiss2 mRNA was localized to cytoplasm of perinucleolus stage oocytes, suggesting it could play a local role in oogenesis or could be synthesized and stored within oocytes as maternal mRNA. This represents the first study to focus on the gonadal kisspeptin system in fishes and provides important tools for further investigation of both the gonadal and brain kisspeptin systems in sablefish.

  20. Cadherin-8 expression, synaptic localization and molecular control of neuronal form in prefrontal cortico-striatal circuits

    PubMed Central

    Friedman, Lauren G.; Riemslagh, Fréderike W.; Sullivan, Josefa M.; Mesias, Roxana; Williams, Frances M.; Huntley, George W.; Benson, Deanna L.

    2014-01-01

    Neocortical interactions with dorsal striatum support many motor and executive functions, and such underlying functional networks are particularly vulnerable to a variety of developmental, neurological, and psychiatric brain disorders, including autism spectrum disorders, Parkinson’s disease, and Huntington’s disease. Relatively little is known about the development of functional corticostriatal interactions, and in particular, virtually nothing is known of molecular mechanisms that control generation of prefrontal cortex-striatal circuits. Here, we used regional and cellular in situ hybridization techniques coupled with neuronal tract tracing to show that Cadherin 8 (Cdh8), a homophilic adhesion protein encoded by a gene associated with autism spectrum disorders and learning disability susceptibility, is enriched within striatal projection neurons in medial prefrontal cortex and in striatal medium spiny neurons forming the direct- or indirect-pathways. Developmental analysis of quantitative RTPCR and Western blot data show that Cdh8 expression peaks in prefrontal cortex and striatum at P10, when cortical projections start to form synapses in the striatum. High-resolution immunoelectron-microscopy shows Cdh8 is concentrated at excitatory synapses in dorsal striatum, and Cdh8 knockdown in cortical neurons impairs dendritic arborization and dendrite self-avoidance. Taken together our findings indicate that Cdh8 delineates developing corticostriatal circuits where it is a strong candidate for regulating the generation of normal cortical projections, neuronal morphology, and corticostriatal synapses. PMID:25158904

  1. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations.

    PubMed

    Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M

    2016-09-21

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5-(B2O3)10-(Na2O)15-(CaO)15-(MoO3)2.5 and (SiO2)57.3-(B2O3)20-(Na2O)6.8-(Li2O)13.4-(MoO3)2.5, were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.

  2. Absolute Spectrophotometry of 237 Open Cluster Stars

    NASA Astrophysics Data System (ADS)

    Clampitt, L.; Burstein, D.

    1994-12-01

    We present absolute spectrophotometry of 237 stars in 7 nearby open clusters: Hyades, Pleiades, Alpha Persei, Praesepe, Coma Berenices, IC 4665, and M 39. The observations were taken using the Wampler single-channel scanner (Wampler 1966) on the Crossley 0.9m telescope at Lick Observatory from July 1973 through December 1974. 21 bandpasses spanning the spectral range 3500 Angstroms to 7780 Angstroms were observed for each star, with bandwiths ranging from 32Angstroms to 64 Angstroms. Data are standardized to the Hayes--Latham (1975) system. Our measurements are compared to filter colors on the Johnson BV, Stromgren ubvy, and Geneva U V B_1 B_2 V_1 G systems, as well as to spectrophotometry of a few stars published by Gunn, Stryker & Tinsley and in the Spectrophotometric Standards Catalog (Adelman; as distributed by the NSSDC). Both internal and external comparisons to the filter systems indicate a formal statistical accuracy per bandpass of 0.01 to 0.02 mag, with apparent larger ( ~ 0.03 mag) differences in absolute calibration between this data set and existing spectrophotometry. These data will comprise part of the spectrophotometry that will be used to calibrate the Beijing-Arizona-Taipei-Connecticut Color Survey of the Sky (see separate paper by Burstein et al. at this meeting).

  3. Linear ultrasonic motor for absolute gravimeter.

    PubMed

    Jian, Yue; Yao, Zhiyuan; Silberschmidt, Vadim V

    2017-02-01

    Thanks to their compactness and suitability for vacuum applications, linear ultrasonic motors are considered as substitutes for classical electromagnetic motors as driving elements in absolute gravimeters. Still, their application is prevented by relatively low power output. To overcome this limitation and provide better stability, a V-type linear ultrasonic motor with a new clamping method is proposed for a gravimeter. In this paper, a mechanical model of stators with flexible clamping components is suggested, according to a design criterion for clamps of linear ultrasonic motors. After that, an effect of tangential and normal rigidity of the clamping components on mechanical output is studied. It is followed by discussion of a new clamping method with sufficient tangential rigidity and a capability to facilitate pre-load. Additionally, a prototype of the motor with the proposed clamping method was fabricated and the performance tests in vertical direction were implemented. Experimental results show that the suggested motor has structural stability and high dynamic performance, such as no-load speed of 1.4m/s and maximal thrust of 43N, meeting the requirements for absolute gravimeters.

  4. The absolute threshold of cone vision

    PubMed Central

    Koeing, Darran; Hofer, Heidi

    2013-01-01

    We report measurements of the absolute threshold of cone vision, which has been previously underestimated due to sub-optimal conditions or overly strict subjective response criteria. We avoided these limitations by using optimized stimuli and experimental conditions while having subjects respond within a rating scale framework. Small (1′ fwhm), brief (34 msec), monochromatic (550 nm) stimuli were foveally presented at multiple intensities in dark-adapted retina for 5 subjects. For comparison, 4 subjects underwent similar testing with rod-optimized stimuli. Cone absolute threshold, that is, the minimum light energy for which subjects were just able to detect a visual stimulus with any response criterion, was 203 ± 38 photons at the cornea, ∼0.47 log units lower than previously reported. Two-alternative forced-choice measurements in a subset of subjects yielded consistent results. Cone thresholds were less responsive to criterion changes than rod thresholds, suggesting a limit to the stimulus information recoverable from the cone mosaic in addition to the limit imposed by Poisson noise. Results were consistent with expectations for detection in the face of stimulus uncertainty. We discuss implications of these findings for modeling the first stages of human cone vision and interpreting psychophysical data acquired with adaptive optics at the spatial scale of the receptor mosaic. PMID:21270115

  5. [Estimation of absolute risk for fracture].

    PubMed

    Fujiwara, Saeko

    2009-03-01

    Osteoporosis treatment aims to prevent fractures and maintain the QOL of the elderly. However, persons at high risk of future fracture cannot be effectively identified on the basis of bone density (BMD) alone, although BMD is used as an diagnostic criterion. Therefore, the WHO recommended that absolute risk for fracture (10-year probability of fracture) for each individual be evaluated and used as an index for intervention threshold. The 10-year probability of fracture is calculated based on age, sex, BMD at the femoral neck (body mass index if BMD is not available), history of previous fractures, parental hip fracture history, smoking, steroid use, rheumatoid arthritis, secondary osteoporosis and alcohol consumption. The WHO has just announced the development of a calculation tool (FRAX: WHO Fracture Risk Assessment Tool) in February this year. Fractures could be prevented more effectively if, based on each country's medical circumstances, an absolute risk value for fracture to determine when to start medical treatment is established and persons at high risk of fracture are identified and treated accordingly.

  6. Absolute stereochemistry of altersolanol A and alterporriols.

    PubMed

    Kanamaru, Saki; Honma, Miho; Murakami, Takanori; Tsushima, Taro; Kudo, Shinji; Tanaka, Kazuaki; Nihei, Ken-Ichi; Nehira, Tatsuo; Hashimoto, Masaru

    2012-02-01

    The absolute stereochemistry of altersolanol A (1) was established by observing a positive exciton couplet in the circular dichroism (CD) spectrum of the C3,C4-O-bis(2-naphthoyl) derivative 10 and by chemical correlations with known compound 8. Before the discussion, the relative stereochemistry of 1 was confirmed by X-ray crystallographic analysis. The shielding effect at C7'-OMe group by C1-O-benzoylation established the relative stereochemical relationship between the C8-C8' axial bonding and the C1-C4/C1'-C4' polyol moieties of alterporriols E (3), an atropisomer of the C8-C8' dimer of 1. As 3 could be obtained by dimerization of 1 in vitro, the absolute configuration of its central chirality elements (C1-C4) must be identical to those of 1. Spectral comparison between the experimental and theoretical CD spectra supported the above conclusion. Axial stereochemistry of novel C4-O-deoxy dimeric derivatives, alterporriols F (4) and G (5), were also revealed by comparison of their CD spectra to those of 2 and 3.

  7. Absolute Electron Extraction Efficiency of Liquid Xenon

    NASA Astrophysics Data System (ADS)

    Kamdin, Katayun; Mizrachi, Eli; Morad, James; Sorensen, Peter

    2016-03-01

    Dual phase liquid/gas xenon time projection chambers (TPCs) currently set the world's most sensitive limits on weakly interacting massive particles (WIMPs), a favored dark matter candidate. These detectors rely on extracting electrons from liquid xenon into gaseous xenon, where they produce proportional scintillation. The proportional scintillation from the extracted electrons serves to internally amplify the WIMP signal; even a single extracted electron is detectable. Credible dark matter searches can proceed with electron extraction efficiency (EEE) lower than 100%. However, electrons systematically left at the liquid/gas boundary are a concern. Possible effects include spontaneous single or multi-electron proportional scintillation signals in the gas, or charging of the liquid/gas interface or detector materials. Understanding EEE is consequently a serious concern for this class of rare event search detectors. Previous EEE measurements have mostly been relative, not absolute, assuming efficiency plateaus at 100%. I will present an absolute EEE measurement with a small liquid/gas xenon TPC test bed located at Lawrence Berkeley National Laboratory.

  8. Standardization of the cumulative absolute velocity

    SciTech Connect

    O'Hara, T.F.; Jacobson, J.P. )

    1991-12-01

    EPRI NP-5930, A Criterion for Determining Exceedance of the Operating Basis Earthquake,'' was published in July 1988. As defined in that report, the Operating Basis Earthquake (OBE) is exceeded when both a response spectrum parameter and a second damage parameter, referred to as the Cumulative Absolute Velocity (CAV), are exceeded. In the review process of the above report, it was noted that the calculation of CAV could be confounded by time history records of long duration containing low (nondamaging) acceleration. Therefore, it is necessary to standardize the method of calculating CAV to account for record length. This standardized methodology allows consistent comparisons between future CAV calculations and the adjusted CAV threshold value based upon applying the standardized methodology to the data set presented in EPRI NP-5930. The recommended method to standardize the CAV calculation is to window its calculation on a second-by-second basis for a given time history. If the absolute acceleration exceeds 0.025g at any time during each one second interval, the earthquake records used in EPRI NP-5930 have been reanalyzed and the adjusted threshold of damage for CAV was found to be 0.16g-set.

  9. Swarm's Absolute Scalar Magnetometers Burst Mode Results

    NASA Astrophysics Data System (ADS)

    Coisson, P.; Vigneron, P.; Hulot, G.; Crespo Grau, R.; Brocco, L.; Lalanne, X.; Sirol, O.; Leger, J. M.; Jager, T.; Bertrand, F.; Boness, A.; Fratter, I.

    2014-12-01

    Each of the three Swarm satellites embarks an Absolute Scalar Magnetometer (ASM) to provide absolute scalar measurements of the magnetic field with high accuracy and stability. Nominal data acquisition of these ASMs is 1 Hz. But they can also run in a so-called "burst mode" and provide data at 250 Hz. During the commissioning phase of the mission, seven burst mode acquisition campaigns have been run simultaneously for all satellites, obtaining a total of ten days of burs-mode data. These campaigns allowed the identification of issues related to the operations of the piezo-electric motor and the heaters connected to the ASM, that do not impact the nominal 1 Hz scalar data. We analyze the burst mode data to identify high frequency geomagnetic signals, focusing the analysis in two regions: the low latitudes, where we seek signatures of ionospheric irregularities, and the high latitudes, to identify high frequency signals related to polar region currents. Since these campaigns have been conducted during the initial months of the mission, the three satellites where still close to each other, allowing to analyze the spatial coherency of the signals. Wavelet analysis have revealed 31 Hz signals appearing in the night-side in the equatorial region.

  10. Extracting infrared absolute reflectance from relative reflectance measurements.

    PubMed

    Berets, Susan L; Milosevic, Milan

    2012-06-01

    Absolute reflectance measurements are valuable to the optics industry for development of new materials and optical coatings. Yet, absolute reflectance measurements are notoriously difficult to make. In this paper, we investigate the feasibility of extracting the absolute reflectance from a relative reflectance measurement using a reference material with known refractive index.

  11. A Conceptual Approach to Absolute Value Equations and Inequalities

    ERIC Educational Resources Information Center

    Ellis, Mark W.; Bryson, Janet L.

    2011-01-01

    The absolute value learning objective in high school mathematics requires students to solve far more complex absolute value equations and inequalities. When absolute value problems become more complex, students often do not have sufficient conceptual understanding to make any sense of what is happening mathematically. The authors suggest that the…

  12. A novel sequence-based approach to localize translocation breakpoints identifies the molecular basis of a t(4;22).

    PubMed

    Nimmakayalu, Manjunath A; Gotter, Anthony L; Shaikh, Tamim H; Emanuel, Beverly S

    2003-11-01

    Low copy repeats (LCRs) located in 22q11.2, especially LCR-B, are susceptible to rearrangements associated with several relatively common constitutional disorders. These include DiGeorge syndrome, Velocardiofacial syndrome, Cat-eye syndrome and recurrent translocations of 22q11 including the constitutional t(11;22) and t(17;22). The presence of palindromic AT-rich repeats (PATRRs) within LCR-B of 22q11.2, as well as within the 11q23 and 17q11 regions, has suggested a palindrome-mediated, stem-loop mechanism for the generation of such recurring constitutional 22q11.2 translocations. The mechanism responsible for non-recurrent 22q11.2 rearrangements is presently unknown due to the extensive effort required for breakpoint cloning. Thus, we have developed a novel fluorescence in-situ hybridization and primed in-situ hybridization (PRINS) approach and rapidly localized the breakpoint of a non-recurrent 22q11.2 translocation, a t(4;22). Multiple primer pairs were designed from the sequence of a 200 kb, chromosome 4, breakpoint-spanning BAC to generate PRINS probes. Amplification of adjacent primer pairs, labeled in two colors, allowed us to narrow the 4q35.1 breakpoint to a 6.7 kb clonable region. Application of our improved PRINS protocol facilitated fine-mapping the translocation breakpoints within 4q35.1 and 22q11.2, and permitted rapid cloning and analysis of translocation junction fragments. To confirm the PRINS localization results, PCR mapping of t(4;22) somatic cell hybrid DNA was employed. Analysis of the breakpoints demonstrates the presence of a 554 bp palindromic sequence at the chromosome 4 breakpoint and a 22q11.2 location within the same PATRR as the recurrent t(11;22) and t(17;22). The sequence of this breakpoint further suggests that a stem-loop secondary structure mechanism is responsible for the formation of other, non-recurrent translocations involving LCR-B of 22q11.2.

  13. Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers.

    PubMed

    Murat, C; Riccioni, C; Belfiori, B; Cichocki, N; Labbé, J; Morin, E; Tisserant, E; Paolocci, F; Rubini, A; Martin, F

    2011-06-01

    The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexa-nucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system.

  14. Interplay between spin-density wave and 3 d local moments with random exchange in a molecular conductor

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Genta; Maesato, Mitsuhiko; Komatsu, Tokutaro; Imakubo, Tatsuro; Kitagawa, Hiroshi

    2016-02-01

    We present the results of high-pressure transport measurements on the anion-mixed molecular conductors (DIETSe)2M Br2Cl2 [DIETSe = diiodo(ethylenedithio)tetraselenafulvalene; M =Fe , Ga]. They undergo a metal-insulator (M-I) transition below 9 K at ambient pressure, which is suppressed by applying pressure, indicating a spin-density-wave (SDW) transition caused by a nesting instability of the quasi-one-dimensional (Q1D) Fermi surface, as observed in the parent compounds (DIETSe)2M Cl4 (M =Fe , Ga). In the metallic state, the existence of the Q1D Fermi surface is confirmed by observing the Lebed resonance. The critical pressures of the SDW, Pc, of the M Br2Cl2 (M =Fe , Ga) salts are significantly lower than those of the the M Cl4 (M = Fe, Ga) salts, suggesting chemical pressure effects. Above Pc, field-induced SDW transitions appear, as evidenced by kink structures in the magnetoresistance (MR) in both salts. The FeBr2Cl2 salt also shows antiferromagnetic (AF) ordering of d spins at 4 K, below which significant spin-charge coupling is observed. A large positive MR change up to 150% appears above the spin-flop field at high pressure. At low pressure, in particular below Pc, a dip or kink structure appears in MR at the spin-flop field, which shows unconventionally large hysteresis at low temperature (T <1 K). The hysteresis region clearly decreases with increasing pressure towards Pc, strongly indicating that the coexisting SDW plays an important role in the enhancement of magnetic hysteresis besides the random exchange interaction.

  15. PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

    PubMed Central

    Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G.; Kihara, Daisuke

    2014-01-01

    Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets. PMID:25167137

  16. Localization and molecular interactions of mitoxantrone within living K562 cells as probed by confocal spectral imaging analysis.

    PubMed Central

    Feofanov, A; Sharonov, S; Kudelina, I; Fleury, F; Nabiev, I

    1997-01-01

    Studying mechanisms of drug antitumor action is complicated by the lack of noninvasive methods enabling direct monitoring of the state and interactions of the drugs within intact viable cells. Here we present a confocal spectral imaging (CSI) technique as a method of overcoming this problem. We applied this method to the examination of localization and interactions of mitoxantrone (1, 4-dihydroxy-5, 8-bis-[([2-(2-hydroxyethyl)-amino]ethyl)amino]-9,10-anthracenedione dihydrochloride), a potent antitumor drug, in living K562 cells. A two-dimensional set of fluorescence spectra of mitoxantrone (MITOX) recorded with micron resolution within a drug-treated cell was analyzed to reveal formation of drug-target complexes and to create the maps of their intracellular distribution. The analysis was based on detailed in vitro modeling of drug-target (DNA, RNA, DNA topoisomerase II) interactions and environmental effects affecting drug fluorescence. MITOX exposed to aqueous intracellular environment, MITOX bound to hydrophobic cellular structures, complexes of MITOX with nucleic acids, as well as the naphtoquinoxaline metabolite of MITOX were simultaneously detected and mapped in K562 cells. These states and complexes are known to be immediately related to the antitumor action of the drug. The results obtained present a basis for the subsequent quantitative analysis of concentration and time-dependent accumulation of free and bound MITOX within different compartments of living cancer cells. Images FIGURE 3 FIGURE 5 FIGURE 6 PMID:9414242

  17. General characterization of Tityus fasciolatus scorpion venom. Molecular identification of toxins and localization of linear B-cell epitopes.

    PubMed

    Mendes, T M; Guimarães-Okamoto, P T C; Machado-de-Avila, R A; Oliveira, D; Melo, M M; Lobato, Z I; Kalapothakis, E; Chávez-Olórtegui, C

    2015-06-01

    This communication describes the general characteristics of the venom from the Brazilian scorpion Tityus fasciolatus, which is an endemic species found in the central Brazil (States of Goiás and Minas Gerais), being responsible for sting accidents in this area. The soluble venom obtained from this scorpion is toxic to mice being the LD50 is 2.984 mg/kg (subcutaneally). SDS-PAGE of the soluble venom resulted in 10 fractions ranged in size from 6 to 10-80 kDa. Sheep were employed for anti-T. fasciolatus venom serum production. Western blotting analysis showed that most of these venom proteins are immunogenic. T. fasciolatus anti-venom revealed consistent cross-reactivity with venom antigens from Tityus serrulatus. Using known primers for T. serrulatus toxins, we have identified three toxins sequences from T. fasciolatus venom. Linear epitopes of these toxins were localized and fifty-five overlapping pentadecapeptides covering complete amino acid sequence of the three toxins were synthesized in cellulose membrane (spot-synthesis technique). The epitopes were located on the 3D structures and some important residues for structure/function were identified.

  18. Molecular cloning, subcellular localization and characterization of two adenylate kinases from cassava, Manihot esculenta Crantz cv. KU50.

    PubMed

    Boonrueng, Channarong; Tangpranomkorn, Surachat; Yazhisai, Uthaman; Sirikantaramas, Supaart

    2016-10-01

    Adenylate kinase (ADK) is a phosphotransferase that plays an important role in cellular energy homeostasis. Many isozymes located in different subcellular compartments have been reported. In this study, we focus on the characterization of cassava (Manihot esculenta) ADKs. We found 15 ADKs that are publicly available in the African cassava genome database. We cloned two ADKs, namely MeADK1 and MeADK2, which are phylogenetically grouped together with the plastidial ADK in potato. Both MeADK1 and MeADK2 showed 66% identity in the amino acid sequences with plastidial ADK in potato. However, we demonstrated that they are localized to mitochondria using GFP fusions of MeADK1 and MeADK2. The Escherichia coli-produced recombinant MeADK1 and MeADK2 preferred forward reactions that produce ATP. They exhibited similar specific activities. The semi-quantitative RT-PCR analysis showed that MeADK1 and MeADK2 in 2-month-old leaves have similar expression patterns under a diurnal light-dark cycle. However, MeADK2 transcripts were expressed at much higher levels than MeADK1 in 5-month-old leaves and roots. Thus, we conclude that MeADK2 might play a vital role in energy homeostasis in cassava mitochondria.

  19. Molecular dynamics simulations of self-emulsifying drug-delivery systems (SEDDS): influence of excipients on droplet nanostructure and drug localization.

    PubMed

    Benson, Sven P; Pleiss, Jürgen

    2014-07-22

    In this study, molecular dynamics (MD) simulations were applied to model the lipidic nanoscale droplets that form when self-emulsifying drug-delivery systems (SEDDS) disperse into microemulsions in the gastrointestinal (GI) tract. The influence of the excipient composition on the droplet nanostructure and on the localization of drug molecules was monitored by the drug immersion depth and the molecular association bias between hydrophilic and hydrophobic moieties. A SEDDS standard system consisting of capric (C10) fatty acid chain length triglycerides and drug molecule cyclosporin A (CyA) was compared to systematic excipient variations. Investigating the drug-loading capacity of droplets yielded a negligible influence of drug molecules on the droplet nanostructure; increasing the drug load merely resulted in increased drug exposure to the aqueous environment. The variation of triglyceride fatty acid chain lengths yielded clearly distinguishable droplet association patterns (random, lamellar-like, and vesicle-like), which could prove beneficial for predicting and engineering drug solubilization in SEDDS. The addition of surfactant poly(ethylene glycol) (PEG-6) revealed the formation of an encapsulating surfactant shell with a negligible impact on the droplet interior triglyceride nanostructure, which could potentially be utilized to protect drug molecules from digestion. Mono- and diglyceride molecules displayed an increased tendency to accumulate at the droplet surface as well, in accordance with their capacity to act as surfactants, while also significantly interfering with the interior droplet nanostructure. The addition of monoglyceride molecules in particular caused the CyA molecule to be solubilized in a hydrophilic droplet core region consisting of polar triglyceride moieties. This mode of drug localization was in stark contrast to that of other systems, where CyA was predominantly found in the interfacial region of the aqueous environment.

  20. ROBO1, a tumor suppressor and critical molecular barrier for localized tumor cells to acquire invasive phenotype: study in African-American and Caucasian prostate cancer models.

    PubMed

    Parray, Aijaz; Siddique, Hifzur R; Kuriger, Jacquelyn K; Mishra, Shrawan K; Rhim, Johng S; Nelson, Heather H; Aburatani, Hiroyuki; Konety, Badrinath R; Koochekpour, Shahriar; Saleem, Mohammad

    2014-12-01

    High-risk populations exhibit early transformation of localized prostate cancer (CaP) disease to metastasis which results in the mortality of such patients. The paucity of knowledge about the molecular mechanism involved in acquiring of metastatic behavior by primary tumor cells and non-availability of reliable phenotype-discriminating biomarkers are stumbling blocks in the management of CaP disease. Here, we determine the role and translational relevance of ROBO1 (an organogenesis-associated gene) in human CaP. Employing CaP-progression models and prostatic tissues of Caucasian and African-American patients, we show that ROBO1 expression is localized to cell-membrane and significantly lost in primary and metastatic tumors. While Caucasians exhibited similar ROBO1 levels in primary and metastatic phenotype, a significant difference was observed between tumor phenotypes in African-Americans. Epigenetic assays identified promoter methylation of ROBO1 specific to African-American metastatic CaP cells. Using African-American CaP models for further studies, we show that ROBO1 negatively regulates motility and invasiveness of primary CaP cells, and its loss causes these cells to acquire invasive trait. To understand the underlying mechanism, we employed ROBO1-expressing/ROBO1-C2C3-mutant constructs, immunoprecipitation, confocal-microscopy and luciferase-reporter techniques. We show that ROBO1 through its interaction with DOCK1 (at SH3-SH2-domain) controls the Rac-activation. However, loss of ROBO1 results in Rac1-activation which in turn causes E-Cadherin/β-catenin cytoskeleton destabilization and induction of cell migration. We suggest that ROBO1 is a predictive biomarker that has potential to discriminate among CaP types, and could be exploited as a molecular target to inhibit the progression of disease as well as treat metastasis in high-risk populations such as African-Americans.

  1. ROBO1, a tumor suppressor and critical molecular barrier for localized tumor cells to acquire invasive phenotype: Study in African-American and Caucasian prostate cancer models

    PubMed Central

    Parray, Aijaz; Siddique, Hifzur R.; Kuriger, Jacquelyn K.; Mishra, Shrawan K.; Rhim, Johng S.; Nelson, Heather H.; Aburatani, Hiroyuki; Konety, Badrinath R.; Koochekpour, Shahriar; Saleem, Mohammad

    2015-01-01

    High-risk populations exhibit early transformation of localized prostate cancer (CaP) disease to metastasis which results in the mortality of such patients. The paucity of knowledge about the molecular mechanism involved in acquiring of metastatic behavior by primary tumor cells and non-availability of reliable phenotype-discriminating biomarkers are stumbling blocks in the management of CaP disease. Here, we determine the role and translational relevance of ROBO1 (an organogenesis-associated gene) in human CaP. Employing CaP-progression models and prostatic tissues of Caucasian and African-American patients, we show that ROBO1 expression is localized to cell-membrane and significantly lost in primary and metastatic tumors. While Caucasians exhibited similar ROBO1 levels in primary and metastatic phenotype, a significant difference was observed between tumor phenotypes in African-Americans. Epigenetic assays identified promoter methylation of ROBO1 specific to African-American metastatic CaP cells. Using African-American CaP models for further studies, we show that ROBO1 negatively regulates motility and invasiveness of primary CaP cells, and its loss causes these cells to acquire invasive trait. To understand the underlying mechanism, we employed ROBO1-expressing/ROBO1-C2C3-mutant constructs, immunoprecipitation, confocal-microscopy and luciferase-reporter techniques. We show that ROBO1 through its interaction with DOCK1 (at SH3-SH2-domain) controls the Rac-activation. However, loss of ROBO1 results in Rac1-activation which in turn causes E-Cadherin/β-catenin cytoskeleton destabilization and induction of cell migration. We suggest that ROBO1 is a predictive biomarker that has potential to discriminate among CaP types, and could be exploited as a molecular target to inhibit the progression of disease as well as treat metastasis in high-risk populations such as African-Americans. PMID:24752651

  2. Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations.

    PubMed

    Paluch, Piotr; Pawlak, Tomasz; Jeziorna, Agata; Trébosc, Julien; Hou, Guangjin; Vega, Alexander J; Amoureux, Jean-Paul; Dracinsky, Martin; Polenova, Tatyana; Potrzebowski, Marek J

    2015-11-21

    We report a new multidimensional magic angle spinning NMR methodology, which provides an accurate and detailed probe of molecular motions occurring on timescales of nano- to microseconds, in sidechains of proteins. The approach is based on a 3D CPVC-RFDR correlation experiment recorded under fast MAS conditions (ν(R) = 62 kHz), where (13)C-(1)H CPVC dipolar lineshapes are recorded in a chemical shift resolved manner. The power of the technique is demonstrated in model tripeptide Tyr-(d)Ala-Phe and two nanocrystalline proteins, GB1 and LC8. We demonstrate that, through numerical simulations of dipolar lineshapes of aromatic sidechains, their detailed dynamic profile, i.e., the motional modes, is obtained. In GB1 and LC8 the results unequivocally indicate that a number of aromatic residues are dynamic, and using quantum mechanical calculations, we correlate the molecular motions of aromatic groups to their local environment in the crystal lattice. The approach presented here is general and can be readily extended to other biological systems.

  3. Modeling and predicting pKa values of mono-hydroxylated polychlorinated biphenyls (HO-PCBs) and polybrominated diphenyl ethers (HO-PBDEs) by local molecular descriptors.

    PubMed

    Yu, Haiying; Wondrousch, Dominik; Yuan, Quan; Lin, Hongjun; Chen, Jianrong; Hong, Huachang; Schüürmann, Gerrit

    2015-11-01

    Hydroxylated polychlorinated biphenyls (HO-PCBs) and polybrominated diphenyl ethers (HO-PBDEs) are attracting considerable concerns because of their multiple endocrine-disrupting effects and wide existence in environment and organisms. The hydroxyl groups enable these chemicals to be ionizable, and dissociation constant, pKa, becomes an important parameter for investigating their environmental behavior and biological activities. In this study, a new pKa prediction model was developed using local molecular descriptors. The dataset contains 21 experimental pKa values of HO-PCBs and HO-PBDEs. The optimized geometries by ab initio HF/6-31G(∗∗) algorithm were used to calculate the site-specific molecular readiness to accept or donate electron charges. The developed model obtained good statistical performance, which significantly outperformed commercial software ACD and SPARC. Mechanism analysis indicates that pKa values increase with the charge-limited donor energy EQocc on hydroxyl oxygen atom and decrease with the energy-limited acceptor charge QEvac on hydroxyl hydrogen atom. The regression model was also applied to calculate pKa values for all 837 mono-hydroxylated PCBs and PBDEs in each class, aiming to provide basic data for the ecological risk assessment of these chemicals.

  4. Molecular characterization, functional expression, tissue localization and protective potential of a Taenia solium fatty acid-binding protein.

    PubMed

    Illescas, Oscar; Carrero, Julio C; Bobes, Raúl J; Flisser, Ana; Rosas, Gabriela; Laclette, Juan P

    2012-12-01

    The fatty acid-binding proteins (FABPs) comprise a family of proteins that are widely expressed in animal cells and perform a variety of vital functions. Here, we report the identification, characterization, recombinant expression, tissue localization and protective potential of a Taenia solium FABP (TsFABP1). The TsFABP1 primary structure showed all the conserved residues characteristic of the subfamily iv of the intracellular Lipid-Binding Proteins (iLBPs), including those involved in the binding stabilization of the fatty acid molecule. Through a competitive binding assay we found that TsFABP1 is able to bind at least six different fatty acids with preference toward palmitic and stearic acid, suggesting that TsFABP1 is a member of the iLBP subfamily iv. Immunolocalization assays carried out on larval and adult tissues of four species of taeniids using anti-TsFABP1 hyperimmune sera produced in mice and rabbit, showed intense labeling in the tegument of the spiral canal and in subtegumental cytons of the larvae. These findings suggest that the spiral canal might be a major place for FA uptake in the developing scolex. In contrast, only subtegumental cytons in the adult worms stained positive. We propose that TsFABP1 is involved in the mechanism to mobilize fatty acids between compartments in the extensive syncytial tissue of taeniids. Protection assays carried out in a murine model of cysticercosis showed that subcutaneous immunization with TsFABP1 resulted in about 45% reduction of parasite load against an intraperitoneal challenge with Taenia crassiceps cysts. This reduction in parasite load correlated with the level of cellular and humoral immune responses against TsFABP1, as determined in spleen lymphocyte proliferation and ELISA testing.

  5. Molecular structure, expression patterns, and localization of the circadian transcription modulator CYCLE in the cricket, Dianemobius nigrofasciatus.

    PubMed

    Shao, Qi-Miao; Bembenek, Jadwiga; Trang, Le Thi Dieu; Hiragaki, Susumu; Takeda, Makio

    2008-02-01

    CYCLE (CYC), also known as BMAL1 in vertebrate nomenclature, is a transcription modulator of the circadian genes period and timeless of Drosophila melanogaster. We cloned a cDNA encoding a CYC homologue from the head of the ground cricket, Dianemobius nigrofasciatus (Dncyc), the first CYC from Hemimetabola. The deduced sequence corresponded to a 601 amino-acid polypeptide, with well-defined bHLH, PAS-A, PAS-B, PAC, and BTCR domains. The amino-acid sequence showed 70.7% identity with the CYC protein of Athalia rosae, 63.8% with D. melanogaster, and 52% identity with the human homologue. A cyc transcript of around 3.6kb occurs in the brain, midgut, testis, fatbody, and muscle. An additional band of around 1.1kb gave a hybridization signal in the head. No temporal oscillation in cyc mRNA abundance was observed in the head of the adult cricket when investigated by Northern blot analysis. CYC-like immunohistochemical reactivity (ir) and its dimerization partner CLOCK (CLK)-ir appeared in the pars intercerebralis (PI), tritocerebrum, dorsolateral protocerebrum, and subesophageal ganglion (SOG), but no CYC-ir was observed in the optic lobe (OL) that showed CLK-ir. The deutocerebrum showed a unique CLK-ir but no CYC-ir pattern. Double-labelling experiments showed that both antigens were co-localized in the mandibular and maxillary neuromeres of the SOG. CYC-ir showed no daily oscillation in intensity and the staining pattern was always cytoplasmic. CLK-ir occurred in the nucleus at ZT 16, but was cytoplasmic at other ZT times. A neuronal network equivalent to adult system occurred in the second nymphal stadium.

  6. Molecular cloning, functional characterization and localization of an annexin from a fish gill fluke Microcotyle sebastis (Platyhelminthes: Monogenea).

    PubMed

    Choi, Seung Hyuk; Kwon, Se Ryun; Lee, Eun Hye; Kim, Ki Hong

    2009-01-01

    The full cDNA of an annexin gene from Microcotyle sebastis (MsANX) was cloned for the first time in monogeneans. The cDNA of MsANX comprises 1199bp with a 29bp 5' untranslated region, an open reading frame of 1062bp, and a 108bp 3' untranslated region. The recombinantly produced MsANX bound phosphatidylserine vesicles in the presence of Ca2+, whereas no MsANX was precipitated in the absence of free Ca2+. Phylogenetically, MsANX formed a cluster with human annexin A13, known as the earliest annexin in vertebrates and expressed mainly in the intestine. The localization of MsANX in M. sebastis was analyzed by Western blotting and immunohistochemistry using the antiserum raised against the recombinant MsANX. In Western blot analysis, rat antiserum bound to a protein corresponding to the MsANX in size when worm crude extracts were used as antigens, but no bands were detected by the antiserum when the excretory/secretory proteins of worms were used as antigens. In immunohistochemistry analysis, significant antibody binding annexin was found in the ovarian region, the pharynx and the intestinal caecum of the worm. Interestingly, the alimentary canal location of MsANX was similar to the location of human annexin A13, and further research is needed to trace evolutionary relationship among helminthic annexins and human annexin A13. Also it remains to be investigated whether immunization of naïve fish with the recombinant MsANX can induce protective immune responses against M. sebastis infection.

  7. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations

    SciTech Connect

    None, None

    2016-01-01

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).

  8. Use of Absolute and Comparative Performance Feedback in Absolute and Comparative Judgments and Decisions

    ERIC Educational Resources Information Center

    Moore, Don A.; Klein, William M. P.

    2008-01-01

    Which matters more--beliefs about absolute ability or ability relative to others? This study set out to compare the effects of such beliefs on satisfaction with performance, self-evaluations, and bets on future performance. In Experiment 1, undergraduate participants were told they had answered 20% correct, 80% correct, or were not given their…

  9. Absolute nonlocality via distributed computing without communication

    NASA Astrophysics Data System (ADS)

    Czekaj, Ł.; Pawłowski, M.; Vértesi, T.; Grudka, A.; Horodecki, M.; Horodecki, R.

    2015-09-01

    Understanding the role that quantum entanglement plays as a resource in various information processing tasks is one of the crucial goals of quantum information theory. Here we propose an alternative perspective for studying quantum entanglement: distributed computation of functions without communication between nodes. To formalize this approach, we propose identity games. Surprisingly, despite no signaling, we obtain that nonlocal quantum strategies beat classical ones in terms of winning probability for identity games originating from certain bipartite and multipartite functions. Moreover we show that, for a majority of functions, access to general nonsignaling resources boosts success probability two times in comparison to classical ones for a number of large enough outputs. Because there are no constraints on the inputs and no processing of the outputs in the identity games, they detect very strong types of correlations: absolute nonlocality.

  10. In vivo absorption spectroscopy for absolute measurement.

    PubMed

    Furukawa, Hiromitsu; Fukuda, Takashi

    2012-10-01

    In in vivo spectroscopy, there are differences between individual subjects in parameters such as tissue scattering and sample concentration. We propose a method that can provide the absolute value of a particular substance concentration, independent of these individual differences. Thus, it is not necessary to use the typical statistical calibration curve, which assumes an average level of scattering and an averaged concentration over individual subjects. This method is expected to greatly reduce the difficulties encountered during in vivo measurements. As an example, for in vivo absorption spectroscopy, the method was applied to the reflectance measurement in retinal vessels to monitor their oxygen saturation levels. This method was then validated by applying it to the tissue phantom under a variety of absorbance values and scattering efficiencies.

  11. Determining Absolute Zero Using a Tuning Fork

    NASA Astrophysics Data System (ADS)

    Goldader, Jeffrey D.

    2008-04-01

    The Celsius and Kelvin temperature scales, we tell our students, are related. We explain that a change in temperature of 1°C corresponds to a change of 1 Kelvin and that atoms and molecules have zero kinetic energy at zero Kelvin, -273°C. In this paper, we will show how students can derive the relationship between the Celsius and Kelvin temperature scales using a simple, well-known physics experiment. By making multiple measurements of the speed of sound at different temperatures, using the classic physics experiment of determining the speed of sound with a tuning fork and variable-length tube, they can determine the temperature at which the speed of sound is zero—absolute zero.

  12. MAGSAT: Vector magnetometer absolute sensor alignment determination

    NASA Technical Reports Server (NTRS)

    Acuna, M. H.

    1981-01-01

    A procedure is described for accurately determining the absolute alignment of the magnetic axes of a triaxial magnetometer sensor with respect to an external, fixed, reference coordinate system. The method does not require that the magnetic field vector orientation, as generated by a triaxial calibration coil system, be known to better than a few degrees from its true position, and minimizes the number of positions through which a sensor assembly must be rotated to obtain a solution. Computer simulations show that accuracies of better than 0.4 seconds of arc can be achieved under typical test conditions associated with existing magnetic test facilities. The basic approach is similar in nature to that presented by McPherron and Snare (1978) except that only three sensor positions are required and the system of equations to be solved is considerably simplified. Applications of the method to the case of the MAGSAT Vector Magnetometer are presented and the problems encountered discussed.

  13. An estimate of global absolute dynamic topography

    NASA Technical Reports Server (NTRS)

    Tai, C.-K.; Wunsch, C.

    1984-01-01

    The absolute dynamic topography of the world ocean is estimated from the largest scales to a short-wavelength cutoff of about 6700 km for the period July through September, 1978. The data base consisted of the time-averaged sea-surface topography determined by Seasat and geoid estimates made at the Goddard Space Flight Center. The issues are those of accuracy and resolution. Use of the altimetric surface as a geoid estimate beyond the short-wavelength cutoff reduces the spectral leakage in the estimated dynamic topography from erroneous small-scale geoid estimates without contaminating the low wavenumbers. Comparison of the result with a similarly filtered version of Levitus' (1982) historical average dynamic topography shows good qualitative agreement. There is quantitative disagreement, but it is within the estimated errors of both methods of calculation.

  14. Micron Accurate Absolute Ranging System: Range Extension

    NASA Technical Reports Server (NTRS)

    Smalley, Larry L.; Smith, Kely L.

    1999-01-01

    The purpose of this research is to investigate Fresnel diffraction as a means of obtaining absolute distance measurements with micron or greater accuracy. It is believed that such a system would prove useful to the Next Generation Space Telescope (NGST) as a non-intrusive, non-contact measuring system for use with secondary concentrator station-keeping systems. The present research attempts to validate past experiments and develop ways to apply the phenomena of Fresnel diffraction to micron accurate measurement. This report discusses past research on the phenomena, and the basis of the use Fresnel diffraction distance metrology. The apparatus used in the recent investigations, experimental procedures used, preliminary results are discussed in detail. Continued research and equipment requirements on the extension of the effective range of the Fresnel diffraction systems is also described.

  15. Absolute measurements of fast neutrons using yttrium.

    PubMed

    Roshan, M V; Springham, S V; Rawat, R S; Lee, P; Krishnan, M

    2010-08-01

    Yttrium is presented as an absolute neutron detector for pulsed neutron sources. It has high sensitivity for detecting fast neutrons. Yttrium has the property of generating a monoenergetic secondary radiation in the form of a 909 keV gamma-ray caused by inelastic neutron interaction. It was calibrated numerically using MCNPX and does not need periodic recalibration. The total yttrium efficiency for detecting 2.45 MeV neutrons was determined to be f(n) approximately 4.1x10(-4) with an uncertainty of about 0.27%. The yttrium detector was employed in the NX2 plasma focus experiments and showed the neutron yield of the order of 10(8) neutrons per discharge.

  16. Local structure and intermolecular dynamics of an equimolar benzene and 1,3-dimethylimidazolium bis[(trifluoromethane)sulfonyl]amide mixture: Molecular dynamics simulations and OKE spectroscopic measurements

    NASA Astrophysics Data System (ADS)

    Lynden-Bell, Ruth M.; Xue, Lianjie; Tamas, George; Quitevis, Edward L.

    2014-07-01

    The local structure and intermolecular dynamics of an equimolar mixture of benzene and 1,3-dimethylimidazolium bis[(trifluoromethane)sulfonyl]amide ([dmim][NTf2]) were studied using molecular dynamics (MD) simulations and femtosecond optical Kerr effect (OKE) spectroscopy. The OKE spectrum of the benzene/[dmim][NTf2] mixture at 295 K was analyzed by comparing it to an ideal mixture spectrum obtained by taking the volume-fraction weighted sum of the OKE spectra of the pure liquids. The experimental mixture spectrum is higher in frequency and broader than that of the ideal mixture spectrum. These spectral differences are rationalized in terms of the local structure around benzene molecules in the mixture and the intermolecular dynamics as reflected in the density of states from the MD simulations. Specifically, we attribute the deviation of the OKE spectrum of the mixture from ideal behavior to benzene molecules seeing a stiffer intermolecular potential due to their being trapped in cages comprised of ions in the first solvation shell.

  17. Ring polymer molecular dynamics fast computation of rate coefficients on accurate potential energy surfaces in local configuration space: Application to the abstraction of hydrogen from methane.

    PubMed

    Meng, Qingyong; Chen, Jun; Zhang, Dong H

    2016-04-21

    To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ∼20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.

  18. Ring polymer molecular dynamics fast computation of rate coefficients on accurate potential energy surfaces in local configuration space: Application to the abstraction of hydrogen from methane

    NASA Astrophysics Data System (ADS)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2016-04-01

    To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3 reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ˜20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.

  19. Molecular cloning, expression, and localization of a brain-specific phosphodiesterase I/nucleotide pyrophosphatase (PD-I alpha) from rat brain.

    PubMed

    Narita, M; Goji, J; Nakamura, H; Sano, K

    1994-11-11

    We have isolated cDNA clones encoding the rat brain phosphodiesterase I/nucleotide pyrophosphatase (PD-I alpha), a novel member of the membrane phosphodiesterase I gene family. PD-I alpha cDNA has a 2,655-nucleotide open reading frame encoding a polypeptide of 885 amino acids with a calculated M(r) of 101,302. Northern blot analysis revealed that PD-I alpha transcript was abundantly present in cerebrum and cerebellum while its level was quite low in other tissues. In situ hybridization analysis revealed that PD-I alpha mRNA is localized in secretory epithelial cells in the brain and the eye including choroid plexus epithelial cells, ciliary epithelial cells, iris pigment epithelial cells, and retinal pigment cells. Localization of PD-I alpha mRNA was also observed in glial cells in the molecular layer of the cerebellum. These results indicate that this protein might be involved in the synthesis of adenosine as well as in the regulation of the secretion/transport of epithelial cells and glial cells in the central nervous system.

  20. Base damage, local sequence context and TP53 mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability

    PubMed Central

    Menzies, Georgina E.; Reed, Simon H.; Brancale, Andrea; Lewis, Paul D.

    2015-01-01

    The mutational pattern for the TP53 tumour suppressor gene in lung tumours differs to other cancer types by having a higher frequency of G:C>T:A transversions. The aetiology of this differing mutation pattern is still unknown. Benzo[a]pyrene,diol epoxide (BPDE) is a potent cigarette smoke carcinogen that forms guanine adducts at TP53 CpG mutation hotspot sites including codons 157, 158, 245, 248 and 273. We performed molecular modelling of BPDE-adducted TP53 duplex sequences to determine the degree of local distortion caused by adducts which could influence the ability of nucleotide excision repair. We show that BPDE adducted codon 157 has greater structural distortion than other TP53 G:C>T:A hotspot sites and that sequence context more distal to adjacent bases must influence local distortion. Using TP53 trinucleotide mutation signatures for lung cancer in smokers and non-smokers we further show that codons 157 and 273 have the highest mutation probability in smokers. Combining this information with adduct structural data we predict that G:C>T:A mutations at codon 157 in lung tumours of smokers are predominantly caused by BPDE. Our results provide insight into how different DNA sequence contexts show variability in DNA distortion at mutagen adduct sites that could compromise DNA repair at well characterized cancer related mutation hotspots. PMID:26400171

  1. Measured and modelled absolute gravity in Greenland

    NASA Astrophysics Data System (ADS)

    Nielsen, E.; Forsberg, R.; Strykowski, G.

    2012-12-01

    Present day changes in the ice volume in glaciated areas like Greenland will change the load on the Earth and to this change the lithosphere will respond elastically. The Earth also responds to changes in the ice volume over a millennial time scale. This response is due to the viscous properties of the mantle and is known as Glaical Isostatic Adjustment (GIA). Both signals are present in GPS and absolute gravity (AG) measurements and they will give an uncertainty in mass balance estimates calculated from these data types. It is possible to separate the two signals if both gravity and Global Positioning System (GPS) time series are available. DTU Space acquired an A10 absolute gravimeter in 2008. One purpose of this instrument is to establish AG time series in Greenland and the first measurements were conducted in 2009. Since then are 18 different Greenland GPS Network (GNET) stations visited and six of these are visited more then once. The gravity signal consists of three signals; the elastic signal, the viscous signal and the direct attraction from the ice masses. All of these signals can be modelled using various techniques. The viscous signal is modelled by solving the Sea Level Equation with an appropriate ice history and Earth model. The free code SELEN is used for this. The elastic signal is modelled as a convolution of the elastic Greens function for gravity and a model of present day ice mass changes. The direct attraction is the same as the Newtonian attraction and is calculated as this. Here we will present the preliminary results of the AG measurements in Greenland. We will also present modelled estimates of the direct attraction, the elastic and the viscous signals.

  2. Absolute bioavailability of quinine formulations in Nigeria.

    PubMed

    Babalola, C P; Bolaji, O O; Ogunbona, F A; Ezeomah, E

    2004-09-01

    This study compared the absolute bioavailability of quinine sulphate as capsule and as tablet against the intravenous (i.v.) infusion of the drug in twelve male volunteers. Six of the volunteers received intravenous infusion over 4 h as well as the capsule formulation of the drug in a cross-over manner, while the other six received the tablet formulation. Blood samples were taken at predetermined time intervals and plasma analysed for quinine (QN) using reversed-phase HPLC method. QN was rapidly absorbed after the two oral formulations with average t(max) of 2.67 h for both capsule and tablet. The mean elimination half-life of QN from the i.v. and oral dosage forms varied between 10 and 13.5 hr and were not statistically different (P > 0.05). On the contrary, the maximum plasma concentration (C(max)) and area under the curve (AUC) from capsule were comparable to those from i.v. (P > 0.05), while these values were markedly higher than values from tablet formulation (P < 0.05). The therapeutic QN plasma levels were not achieved with the tablet formulation. The absolute bioavailability (F) were 73% (C.l., 53.3 - 92.4%) and 39 % (C.I., 21.7 - 56.6%) for the capsule and tablet respectively and the difference was significant (P < 0.05). The subtherapeutic levels obtained from the tablet form used in this study may cause treatment failure during malaria and caution should be taken when predictions are made from results obtained from different formulations of QN.

  3. Absolute GPS Positioning Using Genetic Algorithms

    NASA Astrophysics Data System (ADS)

    Ramillien, G.

    A new inverse approach for restoring the absolute coordinates of a ground -based station from three or four observed GPS pseudo-ranges is proposed. This stochastic method is based on simulations of natural evolution named genetic algorithms (GA). These iterative procedures provide fairly good and robust estimates of the absolute positions in the Earth's geocentric reference system. For comparison/validation, GA results are compared to the ones obtained using the classical linearized least-square scheme for the determination of the XYZ location proposed by Bancroft (1985) which is strongly limited by the number of available observations (i.e. here, the number of input pseudo-ranges must be four). The r.m.s. accuracy of the non -linear cost function reached by this latter method is typically ~10-4 m2 corresponding to ~300-500-m accuracies for each geocentric coordinate. However, GA can provide more acceptable solutions (r.m.s. errors < 10-5 m2), even when only three instantaneous pseudo-ranges are used, such as a lost of lock during a GPS survey. Tuned GA parameters used in different simulations are N=1000 starting individuals, as well as Pc=60-70% and Pm=30-40% for the crossover probability and mutation rate, respectively. Statistical tests on the ability of GA to recover acceptable coordinates in presence of important levels of noise are made simulating nearly 3000 random samples of erroneous pseudo-ranges. Here, two main sources of measurement errors are considered in the inversion: (1) typical satellite-clock errors and/or 300-metre variance atmospheric delays, and (2) Geometrical Dilution of Precision (GDOP) due to the particular GPS satellite configuration at the time of acquisition. Extracting valuable information and even from low-quality starting range observations, GA offer an interesting alternative for high -precision GPS positioning.

  4. Relative Stereochemistry and Absolute Configuration of Farinosin, a Eudesmanolide From Encelia farinosa.

    PubMed

    Ortega, Alfredo R; Sánchez-Castellanos, Mariano; Pérez-Hernández, Nury; Robles-Zepeda, Ramón E; Joseph-Nathan, Pedro; Quijano, Leovigildo

    2016-05-01

    The naturally occurring eudesmanolide farinosin () is now fully characterized for the first time despite its original isolation almost half a century ago. The early assumed relative stereochemistry and absolute configuration were confirmed by vibrational circular dichroism together with evaluation of the Hooft X-ray parameters. The molecular conformation is very similar in the gas stage and in the solid state. Chirality 28:415-419, 2016. © 2016 Wiley Periodicals, Inc.

  5. Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Schmitz, Christian; Bachert, Peter

    2004-12-01

    Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model

  6. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions.

    PubMed

    Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A

    2008-12-07

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

  7. Discovery of (2-aminophenyl)methanol as a new molecular chaperone that rescues the localization of P123S mutant pendrin stably expressed in HEK293 cells.

    PubMed

    Nabeyama, Wataru; Ishihara, Kenji; Ban, Hyun Seung; Wada, Hiroshi; Nakamura, Hiroyuki

    2017-05-01

    Pendred syndrome is the most common form of syndromic deafness. It is associated with a mutation in the SLC26A4 gene that encodes pendrin, which is thought to maintain the ion concentration of endolymph in the inner ear most likely by acting as a chloride/bicarbonate transporter. Mutations in the SLC26A4 gene are responsible for sensorineural hearing loss. In this study, we established a stable HEK293 cell line expressing P123S mutant pendrin and developed screening methods for compounds that show pharmacological chaperone activity by image analysis using CellInsight™. Morphological analysis of stained cells in each well of 96-well plates yielded six compounds in the compound library. Furthermore, fluorescence intensity analysis of the intracellular localization of P123S mutant pendrin in HEK293 cells using FLUOVIEW™ and cytotoxicity experiments revealed that (2-aminophenyl)methanol 8 is the most promising molecular chaperone to rescue P123S mutant pendrin: the plasma membrane (M)/cytoplasm (C) ratios are 1.5 and 0.9 at the concentrations of 0.3 and 0.1mM, respectively, and a sustained effect was observed 12h after removal of the compound from the cell medium. Because the M/C ratio of salicylate, which was previously discovered as a molecular chaperone of P123S mutant pendrin, was approximately 1 at 10mM concentration and a sustained effect was not observed even at 6h, (2-aminophenyl)methanol 8 was 100 times more potent and exhibited a longer sustained effect than salicylate. These findings suggest that (2-aminophenyl)methanol 8 is an attractive candidate for therapeutic agent for Pendred syndrome patients.

  8. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

    PubMed Central

    Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

    2008-01-01

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner , J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT’s inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G*, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal∕mol [obtained with B3LYP∕6-311++G(3df,3pd)] to 0.8 kcal∕mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies. PMID:19063542

  9. Structure, Topology and Tilt of Cell-Signaling Peptides Containing Nuclear Localization Sequences in Membrane Bilayers Determined by Solid-State NMR and Molecular Dynamics Simulation Studies

    PubMed Central

    Ramamoorthy, Ayyalusamy; Kandasamy, Senthil K.; Lee, Dong-Kuk; Kidambi, Srikanth; Larson, Ronald G.

    2008-01-01

    Cell-signaling peptides have been extensively used to transport functional molecules across the plasma membrane into living cells. These peptides consist of a hydrophobic sequence and a cationic nuclear localization sequence (NLS). It has been assumed that the hydrophobic region penetrates through the hydrophobic lipid bilayer and delivers the NLS inside the cell. To better understand the transport mechanism of these peptides, in this study, we investigated the structure, orientation, tilt of the peptide relative to the bilayer normal, and the membraneinteraction of two cell-signaling peptides, SA and SKP. Results from CD and solid-state NMR experiments combined with molecular dynamics simulations suggest that the hydrophobic region is helical and has a transmembrane orientation with the helical axis tilted away from the bilayer normal. The influence of the hydrophobic mismatch, between the hydrophobic length of the peptide and the hydrophobic thickness of the bilayer, on the tilt angle of the peptides was investigated using thicker POPC and thinner DMPC bilayers. NMR experiments showed that the hydrophobic domain of each peptide has a tilt angle of 15±3° in POPC, while in DMPC 25±3° and 30±3° tilts were observed for SA and SKP peptides respectively. These results are in good agreement with molecular dynamics simulations, which predicts a tilt angle of 13.3° (SA in POPC), 16.4° (SKP in POPC), 22.3° (SA in DMPC) and 31.7° (SKP in POPC). These results and simulations on the hydrophobic fragment of SA or SKP suggest that the tilt of helices increases with a decrease in the bilayer thickness without changing the phase, order, and structure of the lipid bilayers. PMID:17240980

  10. Structural study of the effects of mutations in proteins to identify the molecular basis of the loss of local structural fluidity leading to the onset of autoimmune diseases.

    PubMed

    Ali, Ananya; Ghosh, Semanti; Bagchi, Angshuman

    2017-02-26

    Protein-Protein Interactions (PPIs) are crucial in most of the biological processes and PPI dysfunctions are known to be associated with the onsets of various diseases. One of such diseases is the auto-immune disease. Auto-immune diseases are one among the less studied group of diseases with very high mortality rates. Thus, we tried to correlate the appearances of mutations with their probable biochemical basis of the molecular mechanisms leading to the onset of the disease phenotypes. We compared the effects of the Single Amino Acid Variants (SAVs) in the wild type and mutated proteins to identify any structural deformities that might lead to altered PPIs leading ultimately to disease onset. For this we used Relative Solvent Accessibility (RSA) as a spatial parameter to compare the structural perturbation in mutated and wild type proteins. We observed that the mutations were capable to increase intra-chain PPIs whereas inter-chain PPIs would remain mostly unaltered. This might lead to more intra-molecular friction causing a deleterious alteration of protein's normal function. A Lyapunov exponent analysis, using the altered RSA values due to polymorphic and disease causing mutations, revealed polymorphic mutations have a positive mean value for the Lyapunov exponent while disease causing mutations have a negative mean value. Thus, local spatial stochasticity has been lost due to disease causing mutations, indicating a loss of structural fluidity. The amino acid conversion plot also showed a clear tendency of altered surface patch residue conversion propensity than polymorphic conversions. So far, this is the first report that compares the effects of different kinds of mutations (disease and non-disease causing polymorphic mutations) in the onset of autoimmune diseases.

  11. Absolute calibration of forces in optical tweezers

    NASA Astrophysics Data System (ADS)

    Dutra, R. S.; Viana, N. B.; Maia Neto, P. A.; Nussenzveig, H. M.

    2014-07-01

    Optical tweezers are highly versatile laser traps for neutral microparticles, with fundamental applications in physics and in single molecule cell biology. Force measurements are performed by converting the stiffness response to displacement of trapped transparent microspheres, employed as force transducers. Usually, calibration is indirect, by comparison with fluid drag forces. This can lead to discrepancies by sizable factors. Progress achieved in a program aiming at absolute calibration, conducted over the past 15 years, is briefly reviewed. Here we overcome its last major obstacle, a theoretical overestimation of the peak stiffness, within the most employed range for applications, and we perform experimental validation. The discrepancy is traced to the effect of primary aberrations of the optical system, which are now included in the theory. All required experimental parameters are readily accessible. Astigmatism, the dominant effect, is measured by analyzing reflected images of the focused laser spot, adapting frequently employed video microscopy techniques. Combined with interface spherical aberration, it reveals a previously unknown window of instability for trapping. Comparison with experimental data leads to an overall agreement within error bars, with no fitting, for a broad range of microsphere radii, from the Rayleigh regime to the ray optics one, for different polarizations and trapping heights, including all commonly employed parameter domains. Besides signaling full first-principles theoretical understanding of optical tweezers operation, the results may lead to improved instrument design and control over experiments, as well as to an extended domain of applicability, allowing reliable force measurements, in principle, from femtonewtons to nanonewtons.

  12. Elevation correction factor for absolute pressure measurements

    NASA Technical Reports Server (NTRS)

    Panek, Joseph W.; Sorrells, Mark R.

    1996-01-01

    With the arrival of highly accurate multi-port pressure measurement systems, conditions that previously did not affect overall system accuracy must now be scrutinized closely. Errors caused by elevation differences between pressure sensing elements and model pressure taps can be quantified and corrected. With multi-port pressure measurement systems, the sensing elements are connected to pressure taps that may be many feet away. The measurement system may be at a different elevation than the pressure taps due to laboratory space or test article constraints. This difference produces a pressure gradient that is inversely proportional to height within the interface tube. The pressure at the bottom of the tube will be higher than the pressure at the top due to the weight of the tube's column of air. Tubes with higher pressures will exhibit larger absolute errors due to the higher air density. The above effect is well documented but has generally been taken into account with large elevations only. With error analysis techniques, the loss in accuracy from elevation can be easily quantified. Correction factors can be applied to maintain the high accuracies of new pressure measurement systems.

  13. What is Needed for Absolute Paleointensity?

    NASA Astrophysics Data System (ADS)

    Valet, J. P.

    2015-12-01

    Many alternative approaches to the Thellier and Thellier technique for absolute paleointensity have been proposed during the past twenty years. One reason is the time consuming aspect of the experiments. Another reason is to avoid uncertainties in determinations of the paleofield which are mostly linked to the presence of multidomain grains. Despite great care taken by these new techniques, there is no indication that they always provide the right answer and in fact sometimes fail. We are convinced that the most valid approach remains the original double heating Thellier protocol provided that natural remanence is controlled by pure magnetite with a narrow distribution of small grain sizes, mostly single domains. The presence of titanium, even in small amount generates biases which yield incorrect field values. Single domain grains frequently dominate the magnetization of glass samples, which explains the success of this selective approach. They are also present in volcanic lava flows but much less frequently, and therefore contribute to the low success rate of most experiments. However the loss of at least 70% of the magnetization at very high temperatures prior to the Curie point appears to be an essential prerequisite that increases the success rate to almost 100% and has been validated from historical flows and from recent studies. This requirement can easily be tested by thermal demagnetization while low temperature experiments can document the detection of single domain magnetite using the δFC/δZFC parameter as suggested (Moskowitz et al, 1993) for biogenic magnetite.

  14. Gyrokinetic Statistical Absolute Equilibrium and Turbulence

    SciTech Connect

    Jian-Zhou Zhu and Gregory W. Hammett

    2011-01-10

    A paradigm based on the absolute equilibrium of Galerkin-truncated inviscid systems to aid in understanding turbulence [T.-D. Lee, "On some statistical properties of hydrodynamical and magnetohydrodynamical fields," Q. Appl. Math. 10, 69 (1952)] is taken to study gyrokinetic plasma turbulence: A finite set of Fourier modes of the collisionless gyrokinetic equations are kept and the statistical equilibria are calculated; possible implications for plasma turbulence in various situations are discussed. For the case of two spatial and one velocity dimension, in the calculation with discretization also of velocity v with N grid points (where N + 1 quantities are conserved, corresponding to an energy invariant and N entropy-related invariants), the negative temperature states, corresponding to the condensation of the generalized energy into the lowest modes, are found. This indicates a generic feature of inverse energy cascade. Comparisons are made with some classical results, such as those of Charney-Hasegawa-Mima in the cold-ion limit. There is a universal shape for statistical equilibrium of gyrokinetics in three spatial and two velocity dimensions with just one conserved quantity. Possible physical relevance to turbulence, such as ITG zonal flows, and to a critical balance hypothesis are also discussed.

  15. Climate Absolute Radiance and Refractivity Observatory (CLARREO)

    NASA Technical Reports Server (NTRS)

    Leckey, John P.

    2015-01-01

    The Climate Absolute Radiance and Refractivity Observatory (CLARREO) is a mission, led and developed by NASA, that will measure a variety of climate variables with an unprecedented accuracy to quantify and attribute climate change. CLARREO consists of three separate instruments: an infrared (IR) spectrometer, a reflected solar (RS) spectrometer, and a radio occultation (RO) instrument. The mission will contain orbiting radiometers with sufficient accuracy, including on orbit verification, to calibrate other space-based instrumentation, increasing their respective accuracy by as much as an order of magnitude. The IR spectrometer is a Fourier Transform spectrometer (FTS) working in the 5 to 50 microns wavelength region with a goal of 0.1 K (k = 3) accuracy. The FTS will achieve this accuracy using phase change cells to verify thermistor accuracy and heated halos to verify blackbody emissivity, both on orbit. The RS spectrometer will measure the reflectance of the atmosphere in the 0.32 to 2.3 microns wavelength region with an accuracy of 0.3% (k = 2). The status of the instrumentation packages and potential mission options will be presented.

  16. Absolute flux measurements for swift atoms

    NASA Technical Reports Server (NTRS)

    Fink, M.; Kohl, D. A.; Keto, J. W.; Antoniewicz, P.

    1987-01-01

    While a torsion balance in vacuum can easily measure the momentum transfer from a gas beam impinging on a surface attached to the balance, this measurement depends on the accommodation coefficients of the atoms with the surface and the distribution of the recoil. A torsion balance is described for making absolute flux measurements independent of recoil effects. The torsion balance is a conventional taut suspension wire design and the Young modulus of the wire determines the relationship between the displacement and the applied torque. A compensating magnetic field is applied to maintain zero displacement and provide critical damping. The unique feature is to couple the impinging gas beam to the torsion balance via a Wood's horn, i.e., a thin wall tube with a gradual 90 deg bend. Just as light is trapped in a Wood's horn by specular reflection from the curved surfaces, the gas beam diffuses through the tube. Instead of trapping the beam, the end of the tube is open so that the atoms exit the tube at 90 deg to their original direction. Therefore, all of the forward momentum of the gas beam is transferred to the torsion balance independent of the angle of reflection from the surfaces inside the tube.

  17. Modulation of bone ingrowth and tissue differentiation by local infusion of interleukin-10 in the presence of ultra-high molecular weight polyethylene (UHMWPE) wear particles.

    PubMed

    Goodman, Stuart; Trindade, Michael; Ma, Ting; Lee, Mel; Wang, Neal; Ikenou, Takashi; Matsuura, Ippe; Miyanishi, Keita; Fox, Nora; Regula, Donald; Genovese, Mark; Klein, John; Bloch, Dan; Smith, R Lane

    2003-04-01

    Interleukin-10 (IL-10) is a cytokine that plays a major role in suppressing the inflammatory response, particularly cell-mediated immunity that is characteristic of the TH1 response. The purpose of this study was to determine whether local infusion of IL-10 could mitigate the suppression of bone ingrowth associated with polyethylene wear particles. Drug test chambers were implanted in the proximal tibia of 20 mature New Zealand White rabbits. The DTC provided a continuous 1 x 1 x 5-mm canal for tissue ingrowth. After a 6-week period for osseointegration, the DTC was then connected to an osmotic diffusion pump. IL-10 at doses of 0.1-100 ng/mL (0.25 microL/h) was infused with or without ultra-high molecular weight polyethylene particles (0.5 +/- 0.2 microm diameter, 10(12) particles/mL) present in the chamber for a 3- or 6-week period. The tissue in the chamber was harvested after each treatment; sections were stained with hematoxylin and eosin for morphometric analysis. Osteoclast-like cells were identified by immunohistochemical staining using a monoclonal antibody directed against the alpha chain of the vitronectin receptor, CD51. Osteoblasts were identified using alkaline phosphatase staining. In dose-response studies, infusion of 1 ng/mL IL-10 yielded the greatest bone ingrowth in the presence of particles. The addition of polyethylene particles evoked a marked foreign body reaction and fibrosis; bone ingrowth was significantly suppressed (p = 0.0003). Bone ingrowth was increased by over 48% with infusion of IL-10 for the final 3 weeks of a 6-week ultra-high molecular weight polyethylene particle exposure compared with particles alone (p = 0.027). IL-10 is a cytokine that plays a major role in suppressing the inflammatory response, especially cell-mediated immunity that is characteristic of the TH1 response. Local infusion of immune-modulating cytokines such as IL-10 may prove to be useful in abating particle-induced periprosthetic osteolysis.

  18. Absolute objects and counterexamples: Jones-Geroch dust, Torretti constant curvature, tetrad-spinor, and scalar density

    NASA Astrophysics Data System (ADS)

    Brian Pitts, J.

    James L. Anderson analyzed the novelty of Einstein's theory of gravity as its lack of "absolute objects." Michael Friedman's related work has been criticized by Roger Jones and Robert Geroch for implausibly admitting as absolute the timelike 4-velocity field of dust in cosmological models in Einstein's theory. Using Rosen-Sorkin Lagrange multiplier trick, I complete Anna Maidens's argument that the problem is not solved by prohibiting variation of absolute objects in an action principle. Recalling Anderson's proscription of "irrelevant" variables, I generalize that proscription to locally irrelevant variables that do no work in some places in some models. This move vindicates Friedman's intuitions and removes the Jones-Geroch counterexample: some regions of some models of gravity with dust are dust-free and so naturally lack a timelike 4-velocity, so diffeomorphic equivalence to (1,0,0,0) is spoiled. Torretti's example involving constant curvature spaces is shown to have an absolute object on Anderson's analysis, viz., the conformal spatial metric density. The previously neglected threat of an absolute object from an orthonormal tetrad used for coupling spinors to gravity appears resolvable by eliminating irrelevant fields. However, given Anderson's definition, GTR itself has an absolute object (as Robert Geroch has observed recently): a change of variables to a conformal metric density and a scalar density shows that the latter is absolute.

  19. Anti-peptide antibodies for examining the conformation, molecular assembly and localization of an intracellular protein, ribosomal protein S6, in vivo.

    PubMed

    Nakagawa, Masatoshi; Ohmido, Nobuko; Ishikawa, Katsumi; Uchiyama, Susumu; Fukui, Kiichi; Azuma, Takachika

    2008-03-01

    Ribosomal protein S6 (rpS6) is known to relate to cell proliferation. Our recent proteome analysis of human metaphase chromosomes revealed the enrichment of rpS6 during mitosis. Here, structure, localization and molecular assembly in vitro and in vivo of a human rpS6, were examined using antibodies (Abs) prepared by immunizing rabbits with synthetic peptides. Five peptides, Ser6-Asp20 (S6-1), Ile52-Gly66 (S6-2), Asp103-Gly117 (S6-3), Asn146-Lys160 (S6-4) and Arg178-Ile192 (S6-5) were chosen as epitopes of human rpS6. These peptides except for S6-3 induced strong Ab production, and with an enzyme-linked immunosorbent assay, anti-S6-2, anti-S6-4 and anti-S6-5, showed high reactivity to recombinant rpS6 (r-rpS6), while anti-S6-1 did not, suggesting that S6-2, S6-4 and S6-5 were exposed on the r-rpS6 surface, while S6-1 was less exposed or possessed a different conformation. The immunostaining of HeLa cells as well as isolated chromosomes suggested that rpS6 occurs in endoplasmic reticulum (ER) but less possible on chromosomes since no Abs showed localization of rpS6 to chromosomes. In addition, the immunostaining suggested that only S6-4 is exposed on the protein surface, while S6-2 and S6-5 are buried by the interaction with other macromolecules in HeLa cells. Present our result shows new possibility of antibodies as tools for structure-oriented cell biology.

  20. Absolute nuclear material assay using count distribution (LAMBDA) space

    DOEpatents

    Prasad, Mano K.; Snyderman, Neal J.; Rowland, Mark S.

    2015-12-01

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  1. Absolute nuclear material assay using count distribution (LAMBDA) space

    DOEpatents

    Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

    2012-06-05

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  2. Positioning, alignment and absolute pointing of the ANTARES neutrino telescope

    NASA Astrophysics Data System (ADS)

    Fehr, F.; Distefano, C.; Antares Collaboration

    2010-01-01

    A precise detector alignment and absolute pointing is crucial for point-source searches. The ANTARES neutrino telescope utilises an array of hydrophones, tiltmeters and compasses for the relative positioning of the optical sensors. The absolute calibration is accomplished by long-baseline low-frequency triangulation of the acoustic reference devices in the deep-sea with a differential GPS system at the sea surface. The absolute pointing can be independently verified by detecting the shadow of the Moon in cosmic rays.

  3. Absolute calibration for complex-geometry biomedical diffuse optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Mastanduno, Michael A.; Jiang, Shudong; El-Ghussein, Fadi; diFlorio-Alexander, Roberta; Pogue, Brian W.; Paulsen, Keith D.

    2013-03-01

    We have presented methodology to calibrate data in NIRS/MRI imaging versus an absolute reference phantom and results in both phantoms and healthy volunteers. This method directly calibrates data to a diffusion-based model, takes advantage of patient specific geometry from MRI prior information, and generates an initial guess without the need for a large data set. This method of calibration allows for more accurate quantification of total hemoglobin, oxygen saturation, water content, scattering, and lipid concentration as compared with other, slope-based methods. We found the main source of error in the method to be derived from incorrect assignment of reference phantom optical properties rather than initial guess in reconstruction. We also present examples of phantom and breast images from a combined frequency domain and continuous wave MRI-coupled NIRS system. We were able to recover phantom data within 10% of expected contrast and within 10% of the actual value using this method and compare these results with slope-based calibration methods. Finally, we were able to use this technique to calibrate and reconstruct images from healthy volunteers. Representative images are shown and discussion is provided for comparison with existing literature. These methods work towards fully combining the synergistic attributes of MRI and NIRS for in-vivo imaging of breast cancer. Complete software and hardware integration in dual modality instruments is especially important due to the complexity of the technology and success will contribute to complex anatomical and molecular prognostic information that can be readily obtained in clinical use.

  4. Surface Characterization of pNIPAM Under Varying Absolute Humidity

    NASA Astrophysics Data System (ADS)

    Chhabra, Arnav; Kanapuram, Ravitej; Leva, Harrison; Trejo, Juan; Kim, Tae Jin; Hidrovo, Carlos

    2012-11-01

    Poly(N-isopropylacrylamide) has become ubiquitously known as a ``smart'' polymer, showing many promising applications in tissue engineering and drug delivery systems. These applications are particularly reliant on its trenchant, thermally induced hydrophilic-hydrophobic transition that occurs at the lower critical solution temperature (LCST). This feature imparts the pNIPAM programmable adsorption and release capabilities, thus eliminating the need for additional enzymes when removing cells from pNIPAM coated surfaces and leaving the extracellular matrix proteins of the cells largely untouched. The dependence of the LCST on molecular weight, solvent systems, and various salts has been studied extensively. However, what has not been explored is the effect of humidity on the characteristic properties of the polymer, specifically the LCST and the magnitude of the hydrophilic-hydrophobic transition. We studied the surface energy variation of pNIPAM as a function of humidity by altering the absolute humidity and keeping the ambient temperature constant. Our experiments were conducted inside a cuboidal environmental chamber with control over the temperature and humidity inside the chamber. A controlled needle was employed to dispense size-regulated droplets. Throughout this process, a CCD camera was used to image the droplet and the static contact angle was determined using image processing techniques. The behavior of pNIPAM as a function of humidity is presented and discussed.

  5. Scanning micro-resonator direct-comb absolute spectroscopy

    NASA Astrophysics Data System (ADS)

    Gambetta, Alessio; Cassinerio, Marco; Gatti, Davide; Laporta, Paolo; Galzerano, Gianluca

    2016-10-01

    Direct optical Frequency Comb Spectroscopy (DFCS) is proving to be a fundamental tool in many areas of science and technology thanks to its unique performance in terms of ultra-broadband, high-speed detection and frequency accuracy, allowing for high-fidelity mapping of atomic and molecular energy structure. Here we present a novel DFCS approach based on a scanning Fabry-Pérot micro-cavity resonator (SMART) providing a simple, compact and accurate method to resolve the mode structure of an optical frequency comb. The SMART approach, while drastically reducing system complexity, allows for a straightforward absolute calibration of the optical-frequency axis with an ultimate resolution limited by the micro-resonator resonance linewidth and can be used in any spectral region from UV to THz. We present an application to high-precision spectroscopy of acetylene at 1.54 μm, demonstrating performances comparable or even better than current state-of-the-art DFCS systems in terms of sensitivity, optical bandwidth and frequency-resolution.

  6. Scanning micro-resonator direct-comb absolute spectroscopy

    PubMed Central

    Gambetta, Alessio; Cassinerio, Marco; Gatti, Davide; Laporta, Paolo; Galzerano, Gianluca

    2016-01-01

    Direct optical Frequency Comb Spectroscopy (DFCS) is proving to be a fundamental tool in many areas of science and technology thanks to its unique performance in terms of ultra-broadband, high-speed detection and frequency accuracy, allowing for high-fidelity mapping of atomic and molecular energy structure. Here we present a novel DFCS approach based on a scanning Fabry-Pérot micro-cavity resonator (SMART) providing a simple, compact and accurate method to resolve the mode structure of an optical frequency comb. The SMART approach, while drastically reducing system complexity, allows for a straightforward absolute calibration of the optical-frequency axis with an ultimate resolution limited by the micro-resonator resonance linewidth and can be used in any spectral region from UV to THz. We present an application to high-precision spectroscopy of acetylene at 1.54 μm, demonstrating performances comparable or even better than current state-of-the-art DFCS systems in terms of sensitivity, optical bandwidth and frequency-resolution. PMID:27752132

  7. Absolute and Convective Instability of a Liquid Jet

    NASA Technical Reports Server (NTRS)

    Lin, S. P.; Hudman, M.; Chen, J. N.

    1999-01-01

    The existence of absolute instability in a liquid jet has been predicted for some time. The disturbance grows in time and propagates both upstream and downstream in an absolutely unstable liquid jet. The image of absolute instability is captured in the NASA 2.2 sec drop tower and reported here. The transition from convective to absolute instability is observed experimentally. The experimental results are compared with the theoretical predictions on the transition Weber number as functions of the Reynolds number. The role of interfacial shear relative to all other relevant forces which cause the onset of jet breakup is explained.

  8. Absolute Plate Velocities from Seismic Anisotropy

    NASA Astrophysics Data System (ADS)

    Kreemer, Corné; Zheng, Lin; Gordon, Richard

    2015-04-01

    The orientation of seismic anisotropy inferred beneath plate interiors may provide a means to estimate the motions of the plate relative to the sub-asthenospheric mantle. Here we analyze two global sets of shear-wave splitting data, that of Kreemer [2009] and an updated and expanded data set, to estimate plate motions and to better understand the dispersion of the data, correlations in the errors, and their relation to plate speed. We also explore the effect of using geologically current plate velocities (i.e., the MORVEL set of angular velocities [DeMets et al. 2010]) compared with geodetically current plate velocities (i.e., the GSRM v1.2 angular velocities [Kreemer et al. 2014]). We demonstrate that the errors in plate motion azimuths inferred from shear-wave splitting beneath any one tectonic plate are correlated with the errors of other azimuths from the same plate. To account for these correlations, we adopt a two-tier analysis: First, find the pole of rotation and confidence limits for each plate individually. Second, solve for the best fit to these poles while constraining relative plate angular velocities to consistency with the MORVEL relative plate angular velocities. The SKS-MORVEL absolute plate angular velocities (based on the Kreemer [2009] data set) are determined from the poles from eight plates weighted proportionally to the root-mean-square velocity of each plate. SKS-MORVEL indicates that eight plates (Amur, Antarctica, Caribbean, Eurasia, Lwandle, Somalia, Sundaland, and Yangtze) have angular velocities that differ insignificantly from zero. The net rotation of the lithosphere is 0.25±0.11° Ma-1 (95% confidence limits) right-handed about 57.1°S, 68.6°E. The within-plate dispersion of seismic anisotropy for oceanic lithosphere (σ=19.2° ) differs insignificantly from that for continental lithosphere (σ=21.6° ). The between-plate dispersion, however, is significantly smaller for oceanic lithosphere (σ=7.4° ) than for continental

  9. Molecular analysis of 24 Alagille syndrome families identifies a single submicroscopic deletion and further localizes the Alagille region within 20p12

    SciTech Connect

    Rand, E.B.; Piccoli, D.A.; Spinner, N.B.

    1995-11-01

    Alagille syndrome (AGS) is a clinically defined disorder characterized by cholestatic liver disease with bile duct paucity, peculiar facies, structural heart defects, vertebral anomalies, and ocular abnormalities. Multiple patients with various cytogenetic abnormalities involving 20p12 have been identified, allowing the assignment of AGS to this region. The presence of interstitial deletions of varying size led to the hypothesis that AGS is a contiguous gene deletion syndrome. This molecular analysis of cytogenetically normal AGS patients was performed in order to test this hypothesis and to refine the localization of the known AGS region. Investigation of inheritance of simple tandem repeat polymorphism alleles in 67 members of 24 cytogenetically normal Alagille families led to the identification of a single submicroscopic deletion. The deletion included loci D20S61, D20S41, D20S186, and D20S188 and presumably intervening uninformative loci D20S189 and D20S27. The six deleted loci are contained in a single YAC of 1.9 Mb. The additional finding of multiple unrelated probands who are heterozygous at each locus demonstrates that microdeletions at known loci within the AGS region are rare in cytogenetically normal patients with this disorder. This suggests that the majority of cases of AGS may be the result of a single gene defect rather than a contiguous gene deletion syndrome. 29 refs., 4 figs., 1 tab.

  10. Molecular cloning, immunochemical localization to the vacuole, and expression in transgenic yeast and tobacco of a putative sugar transporter from sugar beet.

    PubMed

    Chiou, T J; Bush, D R

    1996-02-01

    Several plant genes have been cloned that encode members of the sugar transporter subgroup of the major facilitator superfamily of transporters. Here we report the cloning, expression, and membrane localization of one of these porters found in sugar beet (Beta vulgaris L.). This clone, cDNA-1, codes for a protein with 490 amino acids and an estimated molecular mass of 54 kD. The predicted membrane topology and sequence homology suggest that cDNA-1 is a member of the sugar transporter family. RNA gel blot analysis revealed that this putative sugar transporter is expressed in all vegetative tissues and expression increases with development in leaves. DNA gel blot analysis indicated that multiple gene copies exist for this putative sugar transporter in the sugar beet genome. Antibodies directed against small peptides representing the N- and C-terminal domains of the cDNA1 protein identified a 40-kD polypeptide in microsomes isolated from cDNA-1-transformed yeast (Saccharomyces cerevisiae). Moreover, the same protein was identified in sugar beet and transgenic tobacco (Nicotaina tobacum L.) membrane fractions. Detailed analysis of the transporter's distribution across linear sucrose gradients and flotation centrifugations showed that it co-migrates with tonoplast membrane markers. We conclude that this carrier is located on the tonoplast membrane and that it may mediate sugar partitioning between the vacuole and cytoplasmic compartments.

  11. Orion Absolute Navigation System Progress and Challenge

    NASA Technical Reports Server (NTRS)

    Holt, Greg N.; D'Souza, Christopher

    2012-01-01

    The absolute navigation design of NASA's Orion vehicle is described. It has undergone several iterations and modifications since its inception, and continues as a work-in-progress. This paper seeks to benchmark the current state of the design and some of the rationale and analysis behind it. There are specific challenges to address when preparing a timely and effective design for the Exploration Flight Test (EFT-1), while still looking ahead and providing software extensibility for future exploration missions. The primary onboard measurements in a Near-Earth or Mid-Earth environment consist of GPS pseudo-range and delta-range, but for future explorations missions the use of star-tracker and optical navigation sources need to be considered. Discussions are presented for state size and composition, processing techniques, and consider states. A presentation is given for the processing technique using the computationally stable and robust UDU formulation with an Agee-Turner Rank-One update. This allows for computational savings when dealing with many parameters which are modeled as slowly varying Gauss-Markov processes. Preliminary analysis shows up to a 50% reduction in computation versus a more traditional formulation. Several state elements are discussed and evaluated, including position, velocity, attitude, clock bias/drift, and GPS measurement biases in addition to bias, scale factor, misalignment, and non-orthogonalities of the accelerometers and gyroscopes. Another consideration is the initialization of the EKF in various scenarios. Scenarios such as single-event upset, ground command, and cold start are discussed as are strategies for whole and partial state updates as well as covariance considerations. Strategies are given for dealing with latent measurements and high-rate propagation using multi-rate architecture. The details of the rate groups and the data ow between the elements is discussed and evaluated.

  12. Evaluation of the Absolute Regional Temperature Potential

    NASA Technical Reports Server (NTRS)

    Shindell, D. T.

    2012-01-01

    The Absolute Regional Temperature Potential (ARTP) is one of the few climate metrics that provides estimates of impacts at a sub-global scale. The ARTP presented here gives the time-dependent temperature response in four latitude bands (90-28degS, 28degS-28degN, 28-60degN and 60-90degN) as a function of emissions based on the forcing in those bands caused by the emissions. It is based on a large set of simulations performed with a single atmosphere-ocean climate model to derive regional forcing/response relationships. Here I evaluate the robustness of those relationships using the forcing/response portion of the ARTP to estimate regional temperature responses to the historic aerosol forcing in three independent climate models. These ARTP results are in good accord with the actual responses in those models. Nearly all ARTP estimates fall within +/-20%of the actual responses, though there are some exceptions for 90-28degS and the Arctic, and in the latter the ARTP may vary with forcing agent. However, for the tropics and the Northern Hemisphere mid-latitudes in particular, the +/-20% range appears to be roughly consistent with the 95% confidence interval. Land areas within these two bands respond 39-45% and 9-39% more than the latitude band as a whole. The ARTP, presented here in a slightly revised form, thus appears to provide a relatively robust estimate for the responses of large-scale latitude bands and land areas within those bands to inhomogeneous radiative forcing and thus potentially to emissions as well. Hence this metric could allow rapid evaluation of the effects of emissions policies at a finer scale than global metrics without requiring use of a full climate model.

  13. Absolute Radiometric Calibration of KOMPSAT-3A

    NASA Astrophysics Data System (ADS)

    Ahn, H. Y.; Shin, D. Y.; Kim, J. S.; Seo, D. C.; Choi, C. U.

    2016-06-01

    This paper presents a vicarious radiometric calibration of the Korea Multi-Purpose Satellite-3A (KOMPSAT-3A) performed by the Korea Aerospace Research Institute (KARI) and the Pukyong National University Remote Sensing Group (PKNU RSG) in 2015.The primary stages of this study are summarized as follows: (1) A field campaign to determine radiometric calibrated target fields was undertaken in Mongolia and South Korea. Surface reflectance data obtained in the campaign were input to a radiative transfer code that predicted at-sensor radiance. Through this process, equations and parameters were derived for the KOMPSAT-3A sensor to enable the conversion of calibrated DN to physical units, such as at-sensor radiance or TOA reflectance. (2) To validate the absolute calibration coefficients for the KOMPSAT-3A sensor, we performed a radiometric validation with a comparison of KOMPSAT-3A and Landsat-8 TOA reflectance using one of the six PICS (Libya 4). Correlations between top-of-atmosphere (TOA) radiances and the spectral band responses of the KOMPSAT-3A sensors at the Zuunmod, Mongolia and Goheung, South Korea sites were significant for multispectral bands. The average difference in TOA reflectance between KOMPSAT-3A and Landsat-8 image over the Libya 4, Libya site in the red-green-blue (RGB) region was under 3%, whereas in the NIR band, the TOA reflectance of KOMPSAT-3A was lower than the that of Landsat-8 due to the difference in the band passes of two sensors. The KOMPSAT-3Aensor includes a band pass near 940 nm that can be strongly absorbed by water vapor and therefore displayed low reflectance. Toovercome this, we need to undertake a detailed analysis using rescale methods, such as the spectral bandwidth adjustment factor.

  14. Weighted Wilcoxon-type Smoothly Clipped Absolute Deviation Method

    PubMed Central

    Wang, Lan; Li, Runze

    2009-01-01

    Summary Shrinkage-type variable selection procedures have recently seen increasing applications in biomedical research. However, their performance can be adversely influenced by outliers in either the response or the covariate space. This paper proposes a weighted Wilcoxon-type smoothly clipped absolute deviation (WW-SCAD) method, which deals with robust variable selection and robust estimation simultaneously. The new procedure can be conveniently implemented with the statistical software R. We establish that the WW-SCAD correctly identifies the set of zero coefficients with probability approaching one and estimates the nonzero coefficients with the rate n−1/2. Moreover, with appropriately chosen weights the WW-SCAD is robust with respect to outliers in both the x and y directions. The important special case with constant weights yields an oracle-type estimator with high efficiency at the presence of heavier-tailed random errors. The robustness of the WW-SCAD is partly justified by its asymptotic performance under local shrinking contamination. We propose a BIC-type tuning parameter selector for the WW-SCAD. The performance of the WW-SCAD is demonstrated via simulations and by an application to a study that investigates the effects of personal characteristics and dietary factors on plasma beta-carotene level. PMID:18647294

  15. Near-infrared absolute magnitudes of Type Ia Supernovae

    NASA Astrophysics Data System (ADS)

    Avelino, Arturo; Friedman, Andrew S.; Mandel, Kaisey; Kirshner, Robert; Challis, Peter

    2017-01-01

    Type Ia Supernovae light curves (SN Ia) in the near infrared (NIR) exhibit low dispersion in their peak luminosities and are less vulnerable to extinction by interstellar dust in their host galaxies. The increasing number of high quality NIR SNe Ia light curves, including the recent CfAIR2 sample obtained with PAIRITEL, provides updated evidence for their utility as standard candles for cosmology. Using NIR YJHKs light curves of ~150 nearby SNe Ia from the CfAIR2 and CSP samples, and from the literature, we determine the mean value and dispersion of the absolute magnitude in the range between -10 to 50 rest-frame days after the maximum luminosity in B band. We present the mean light-curve templates and Hubble diagram for YJHKs bands. This work contributes to a firm local anchor for supernova cosmology studies in the NIR which will help to reduce the systematic uncertainties due to host galaxy dust present in optical-only studies. This research is supported by NSF grants AST-156854, AST-1211196, Fundacion Mexico en Harvard, and CONACyT.

  16. Old and new research on the Absolute Parallelism theory

    NASA Astrophysics Data System (ADS)

    Zhogin, I. L.

    2004-12-01

    Compatible equations, Singularities of solutions, Topological charges and quasi-charges. PhD thesis (translated frorm Russian). The book shows the sights of Absolute Parallelism (AP), and contains useful information on the problem of singularities, compatibility theory, homotopy groups (also relative and k-ad), topological quasi-charge groups and their morphisms. AP is a single (frame) field theory proposed by Einstein some 80 years ago; it embraces symmetries of both Special and General Relativity. The compatibility theory, if applied to the cases when the frame matrix degenerates, gives a covariant test on singularities of solutions. This gives a single variant (missed in Einstein-Mayer's list of compatible equations), the unique 5D equation (nothing, nor D, can be changed), which solutions are free of emerging singularities. SO4-symmetrical nonstationary solutions give rise to a cosmological model (relativistic surfing; anti-Milne model in FRW framework) with a specific reduction of the extra-dimension. Topological classification of localized field configurations, combinatorics of topological quasi-charges (quanta), is discussed in an attempt to imagine the Standard Model (and quantum theory itself; and, perhaps, to make some qualitative predictions, like the absence of spin zero elementary quanta).

  17. Alignment and absolute wavelength calibration of imaging Bragg spectrometers

    NASA Astrophysics Data System (ADS)

    Bertschinger, G.; Marchuk, O.; Barnsley, R.

    2016-11-01

    In the present and the next generation of fusion devices, imaging Bragg spectrometers are key diagnostics to measure plasma parameters in the hot core, especially ion temperature and plasma rotation. The latter quantities are routinely obtained using the Doppler-width and -shift of the emitted spectral lines, respectively. Line shift measurements require absolute accuracies Δλ/λ of about 10 ppm, where λ-is the observed wavelength. For ITER and the present fusion devices, spectral lines of He-and H-like argon, iron, and krypton as well as Ne-like tungsten are foreseen for the measurements. For these lines, Kα lines can be found, some in higher order, which fit into the narrow energy window of the spectrometers. For arbitrary wavelength settings, Kα lines are also used to measure the miscut of the spherical crystals; afterwards the spectrometers can be set according to the geometrical imaging properties using coordinate measurement machines. For the spectrometers measuring Lyα lines of H-like ions, fluorescence targets can provide in situ localized calibration lines on the spectra. The fluorescence targets are used best in transmission and are excited by the thermal x-ray radiation of the plasma. An analytic theory of fluorescence is worked out.

  18. Determination of Absolute Zero Using a Computer-Based Laboratory

    ERIC Educational Resources Information Center

    Amrani, D.

    2007-01-01

    We present a simple computer-based laboratory experiment for evaluating absolute zero in degrees Celsius, which can be performed in college and undergraduate physical sciences laboratory courses. With a computer, absolute zero apparatus can help demonstrators or students to observe the relationship between temperature and pressure and use…

  19. A Global Forecast of Absolute Poverty and Employment.

    ERIC Educational Resources Information Center

    Hopkins, M. J. D.

    1980-01-01

    Estimates are made of absolute poverty and employment under the hypothesis that existing trends continue. Concludes that while the number of people in absolute poverty is not likely to decline by 2000, the proportion will fall. Jobs will have to grow 3.9% per year in developing countries to achieve full employment. (JOW)

  20. Absolute Humidity and the Seasonality of Influenza (Invited)

    NASA Astrophysics Data System (ADS)

    Shaman, J. L.; Pitzer, V.; Viboud, C.; Grenfell, B.; Goldstein, E.; Lipsitch, M.

    2010-12-01

    Much of the observed wintertime increase of mortality in temperate regions is attributed to seasonal influenza. A recent re-analysis of laboratory experiments indicates that absolute humidity strongly modulates the airborne survival and transmission of the influenza virus. Here we show that the onset of increased wintertime influenza-related mortality in the United States is associated with anomalously low absolute humidity levels during the prior weeks. We then use an epidemiological model, in which observed absolute humidity conditions temper influenza transmission rates, to successfully simulate the seasonal cycle of observed influenza-related mortality. The model results indicate that direct modulation of influenza transmissibility by absolute humidity alone is sufficient to produce this observed seasonality. These findings provide epidemiological support for the hypothesis that absolute humidity drives seasonal variations of influenza transmission in temperate regions. In addition, we show that variations of the basic and effective reproductive numbers for influenza, caused by seasonal changes in absolute humidity, are consistent with the general timing of pandemic influenza outbreaks observed for 2009 A/H1N1 in temperate regions. Indeed, absolute humidity conditions correctly identify the region of the United States vulnerable to a third, wintertime wave of pandemic influenza. These findings suggest that the timing of pandemic influenza outbreaks is controlled by a combination of absolute humidity conditions, levels of susceptibility and changes in population mixing and contact rates.

  1. Novalis' Poetic Uncertainty: A "Bildung" with the Absolute

    ERIC Educational Resources Information Center

    Mika, Carl

    2016-01-01

    Novalis, the Early German Romantic poet and philosopher, had at the core of his work a mysterious depiction of the "absolute." The absolute is Novalis' name for a substance that defies precise knowledge yet calls for a tentative and sensitive speculation. How one asserts a truth, represents an object, and sets about encountering things…

  2. Absolute radiometric calibration of advanced remote sensing systems

    NASA Technical Reports Server (NTRS)

    Slater, P. N.

    1982-01-01

    The distinction between the uses of relative and absolute spectroradiometric calibration of remote sensing systems is discussed. The advantages of detector-based absolute calibration are described, and the categories of relative and absolute system calibrations are listed. The limitations and problems associated with three common methods used for the absolute calibration of remote sensing systems are addressed. Two methods are proposed for the in-flight absolute calibration of advanced multispectral linear array systems. One makes use of a sun-illuminated panel in front of the sensor, the radiance of which is monitored by a spectrally flat pyroelectric radiometer. The other uses a large, uniform, high-radiance reference ground surface. The ground and atmospheric measurements required as input to a radiative transfer program to predict the radiance level at the entrance pupil of the orbital sensor are discussed, and the ground instrumentation is described.

  3. A developmental study of latent absolute pitch memory.

    PubMed

    Jakubowski, Kelly; Müllensiefen, Daniel; Stewart, Lauren

    2017-03-01

    The ability to recall the absolute pitch level of familiar music (latent absolute pitch memory) is widespread in adults, in contrast to the rare ability to label single pitches without a reference tone (overt absolute pitch memory). The present research investigated the developmental profile of latent absolute pitch (AP) memory and explored individual differences related to this ability. In two experiments, 288 children from 4 to12 years of age performed significantly above chance at recognizing the absolute pitch level of familiar melodies. No age-related improvement or decline, nor effects of musical training, gender, or familiarity with the stimuli were found in regard to latent AP task performance. These findings suggest that latent AP memory is a stable ability that is developed from as early as age 4 and persists into adulthood.

  4. Fully distributed absolute blood flow velocity measurement for middle cerebral arteries using Doppler optical coherence tomography

    PubMed Central

    Qi, Li; Zhu, Jiang; Hancock, Aneeka M.; Dai, Cuixia; Zhang, Xuping; Frostig, Ron D.; Chen, Zhongping

    2016-01-01

    Doppler optical coherence tomography (DOCT) is considered one of the most promising functional imaging modalities for neuro biology research and has demonstrated the ability to quantify cerebral blood flow velocity at a high accuracy. However, the measurement of total absolute blood flow velocity (BFV) of major cerebral arteries is still a difficult problem since it is related to vessel geometry. In this paper, we present a volumetric vessel reconstruction approach that is capable of measuring the absolute BFV distributed along the entire middle cerebral artery (MCA) within a large field-of-view. The Doppler angle at each point of the MCA, representing the vessel geometry, is derived analytically by localizing the artery from pure DOCT images through vessel segmentation and skeletonization. Our approach could achieve automatic quantification of the fully distributed absolute BFV across different vessel branches. Experiments on rodents using swept-source optical coherence tomography showed that our approach was able to reveal the consequences of permanent MCA occlusion with absolute BFV measurement. PMID:26977365

  5. Absolute configuration assignment of a chiral molecule in the gas phase using foil-induced Coulomb explosion imaging

    NASA Astrophysics Data System (ADS)

    Herwig, Philipp; Zawatzky, Kerstin; Schwalm, Dirk; Grieser, Manfred; Heber, Oded; Jordon-Thaden, Brandon; Krantz, Claude; Novotný, Oldřich; Repnow, Roland; Schurig, Volker; Vager, Zeev; Wolf, Andreas; Trapp, Oliver; Kreckel, Holger

    2014-11-01

    Chiral molecules exist in two configurations that are nonsuperposable mirror images of one another. The underlying molecular structure is referred to as the absolute configuration. In chiral environments, the handedness of molecules influences their chemical characteristics dramatically, and therefore the determination of absolute configurations is of fundamental interest in organic chemistry and biology. Commonly applied techniques to assign absolute configuration are anomalous single-crystal x-ray diffraction and vibrational circular dichroism. However, these techniques become increasingly more challenging when applied to molecules that are made out of light atoms exclusively. Furthermore, there is no established method to determine the absolute handedness of gas-phase molecules that are not optically active. In this work, we apply the foil-induced Coulomb explosion imaging technique to determine directly the absolute configuration of the chiral molecule trans-2,3-dideuterooxirane (C2OD2H2) in the gas phase. The experiment leads to the definitive assignment of the (R ,R ) configuration to an enantio-selected dideuterooxirane sample with a statistical confidence of 5 σ . As the handedness of trans-2,3-dideuterooxirane is unambiguously linked by chemical synthesis to the stereochemical key reference glyceraldehyde, our results provide an independent verification of the absolute configuration of the stereochemical reference standard.

  6. Absolute Thermal SST Measurements over the Deepwater Horizon Oil Spill

    NASA Astrophysics Data System (ADS)

    Good, W. S.; Warden, R.; Kaptchen, P. F.; Finch, T.; Emery, W. J.

    2010-12-01

    Climate monitoring and natural disaster rapid assessment require baseline measurements that can be tracked over time to distinguish anthropogenic versus natural changes to the Earth system. Disasters like the Deepwater Horizon Oil Spill require constant monitoring to assess the potential environmental and economic impacts. Absolute calibration and validation of Earth-observing sensors is needed to allow for comparison of temporally separated data sets and provide accurate information to policy makers. The Ball Experimental Sea Surface Temperature (BESST) radiometer was designed and built by Ball Aerospace to provide a well calibrated measure of sea surface temperature (SST) from an unmanned aerial system (UAS). Currently, emissive skin SST observed by satellite infrared radiometers is validated by shipborne instruments that are expensive to deploy and can only take a few data samples along the ship track to overlap within a single satellite pixel. Implementation on a UAS will allow BESST to map the full footprint of a satellite pixel and perform averaging to remove any local variability due to the difference in footprint size of the instruments. It also enables the capability to study this sub-pixel variability to determine if smaller scale effects need to be accounted for in models to improve forecasting of ocean events. In addition to satellite sensor validation, BESST can distinguish meter scale variations in SST which could be used to remotely monitor and assess thermal pollution in rivers and coastal areas as well as study diurnal and seasonal changes to bodies of water that impact the ocean ecosystem. BESST was recently deployed on a conventional Twin Otter airplane for measurements over the Gulf of Mexico to access the thermal properties of the ocean surface being affected by the oil spill. Results of these measurements will be presented along with ancillary sensor data used to eliminate false signals including UV and Synthetic Aperture Radar (SAR

  7. A localized and propagating SPR, and molecular imprinting based fiber-optic ascorbic acid sensor using an in situ polymerized polyaniline-Ag nanocomposite

    NASA Astrophysics Data System (ADS)

    Shrivastav, Anand M.; Usha, Sruthi P.; Gupta, Banshi D.

    2016-08-01

    We report a successful approach for the fabrication and characterization of a fiber-optic sensor for ascorbic acid (AA) detection, using a molecularly imprinted polyaniline-Ag (PANI-Ag) nanocomposite layer based on the combined phenomena of surface plasmon resonance (SPR) and localized SPR (LSPR). The PANI-Ag nanocomposite is synthesized by an in situ polymerization process and AA imprints are prepared on the polymeric composite. The confirmation of the PANI-Ag nanocomposite and AA imprinting is performed using various characterization methods such as x-ray diffraction (XRD), UV-vis, Fourier transform infrared spectroscopy and scanning electron microscopy. From XRD, the size of Ag nanoparticles is analyzed. The absorbance spectra are recorded for samples of different concentrations of AA around the sensing region of the probe. An increase in peak absorbance wavelength with the increase in AA concentration is observed with a linear response for the concentration range from 10-8 M to 10-6 M. The sensor possesses a high sensitivity of 45.1 nm log-1 M near an AA concentration of 10-8 M. The limit of detection (LOD) and limit of quantification of the sensor are found to be 7.383 × 10-11 M and 4.16 × 10-10 M, respectively. The LOD of the sensor is compared to studies reported in the literature and is found to be the lowest. The sensor possesses several other advantages such as cost effectiveness, selectivity, and low response time (<5 s), along with abilities of remote sensing and online monitoring.

  8. A new immunoreactive recombinant protein designated as rBoSA2 from Babesia ovis: Its molecular characterization, subcellular localization and antibody recognition by infected sheep.

    PubMed

    Sevinc, Ferda; Cao, Shinuo; Zhou, Mo; Sevinc, Mutlu; Ceylan, Onur; Xuan, Xuenan

    2015-11-30

    Ovine babesiosis, caused by the intra-erythrocytic protozoan parasite Babesia ovis, is an infectious and economically important tick-borne disease of sheep. Diagnostic testing is an essential tool used for the control of the disease. In order to identify and characterize the immunoreactive proteins which are useful in serological diagnosis of the disease, a complementary DNA (cDNA) expression library was constructed from B. ovis merozoite mRNA. A cDNA clone designated as BoSA2 was identified by immunoscreening of a cDNA library using immune sheep serum. The sequence of the BoSA2 cDNA had a partial open reading frame of 1156 nucleotides encoding a polypeptide of 384 amino acid residues. Theoretical molecular mass for the mature protein was 43.5 kDa. The sequence of the BoSA2 was inserted into the expression vector pGEX-4T-1 and then expressed in Escherichia coli DH5α cells as a glutathione S-transferase (GST)-tagged fusion protein. This recombinant fusion protein (rBoSA2) was purified by GST-affinity chromatography. Immunoreactivity of the rBoSA2 was evaluated by indirect enzyme-linked immunosorbent assay (ELISA) using the sera from the animals naturally and experimentally infected with B. ovis. ELISA results demonstrated that this antigen was useful for the diagnosis of ovine babesiosis. The localization of the BoSA2 protein was shown in and on the parasite and in the cytoplasm of the infected erythrocyte by confocal laser microscope. To our knowledge, rBoSA2 is the second immunoreactive recombinant protein of B. ovis until the present.

  9. Uroporphyrinogen-III synthase: Molecular cloning, nucleotide sequence, expression of a mouse full-length cDNA, and its localization on mouse chromosome 7

    SciTech Connect

    Xu, W.; Desnick, R.J.; Kozak, C.A.

    1995-04-10

    Uroporphyrinogen-III synthase, the fourth enzyme in the heme biosynthetic pathway, is responsible for the conversion of hydroxymethylbilane to the cyclic tetrapyrrole, uroporphyrinogen III. The deficient activity of URO-S is the enzymatic defect in congenital erythropoietic porphyria (CEP), an autosomal recessive disorder. For the generation of a mouse model of CEP, the human URO-S cDNA was used to screen 2 X 10{sup 6} recombinants from a mouse adult liver cDNA library. Ten positive clones were isolated, and dideoxy sequencing of the entire 1.6-kb insert of clone pmUROS-1 revealed 5{prime} and 3{prime} untranslated sequences of 144 and 623 bp, respectively, and an open reading frame of 798 bp encoding a 265-amino-acid polypeptide with a predicted molecular mass of 28,501 Da. The mouse and human coding sequences had 80.5 and 77.8% nucleotide and amino acid identity, respectively. The authenticity of the mouse cDNA was established by expression of the active monomeric enzyme in Escherichia coli. In addition, the analysis of two multilocus genetic crosses localized the mouse gene on chromosome 7, consistent with the mapping of the human gene to a position of conserved synteny on chromosome 10. The isolation, expression, and chromosomal mapping of this full-length cDNA should facilitate studies of the structure and organization of the mouse genomic sequence and the development of a mouse model of CEP for characterization of the disease pathogenesis and evaluation of gene therapy. 38 refs., 1 tab.

  10. Characterization of Xenopus egg membrane microdomains containing uroplakin Ib/III complex: roles of their molecular interactions for subcellular localization and signal transduction.

    PubMed

    Mahbub Hasan, A K M; Ou, Zhize; Sakakibara, Keiichi; Hirahara, Shino; Iwasaki, Tetsushi; Sato, Ken-ichi; Fukami, Yasuo

    2007-02-01

    A single-transmembrane protein uroplakin III (UPIII) and its tetraspanin binding-partner uroplakin Ib (UPIb) are members of the UP proteins that were originally identified in mammalian urothelium. In Xenopus laevis eggs, these proteins: xUPIII and xUPIb, are components of the cholesterol-enriched membrane microdomains or "rafts" and involved in the sperm-egg membrane interaction and subsequent egg activation signaling via Src tyrosine kinase at fertilization. Here, we investigate whether the xUPIII-xUPIb complex is in close proximity to CD9, a tetraspanin that has been implicated in the sperm-egg fusion in the mouse and GM1, a ganglioside typically enriched in egg rafts. Preparation of the egg membrane microdomains using different non-ionic detergents (Brij 98 and Triton X-100), chemical cross-linking, co-immunoprecipitation, in vitro kinase assay and in vitro fertilization experiments demonstrated that GM1, but not CD9, is in association with the xUPIII-xUPIb complex and contributes to the sperm-dependent egg activation. Transfection experiments using HEK293 cells demonstrated that xUPIII and xUPIb localized efficiently to the cholesterol-dependent membrane microdomains when they were co-expressed, whereas co-expression of xUPIII and CD9, instead of xUPIb, did not show this effect. Furthermore, xUPIII and xUPIb were shown to suppress kinase activity of the wild type, but not a constitutively active form of, Xenopus Src protein co-expressed in HEK293 cells. These results provide novel insight into the molecular architecture of the egg membrane microdomains containing xUPIII, xUPIb and Src, which may contribute to the understanding of sperm-egg interaction and signaling during Xenopus fertilization.

  11. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition.

    PubMed

    Silva, Jeffrey C; Gorenstein, Marc V; Li, Guo-Zhong; Vissers, Johannes P C; Geromanos, Scott J

    2006-01-01

    Relative quantification methods have dominated the quantitative proteomics field. There is a need, however, to conduct absolute quantification studies to accurately model and understand the complex molecular biology that results in proteome variability among biological samples. A new method of absolute quantification of proteins is described. This method is based on the discovery of an unexpected relationship between MS signal response and protein concentration: the average MS signal response for the three most intense tryptic peptides per mole of protein is constant within a coefficient of variation of less than +/-10%. Given an internal standard, this relationship is used to calculate a universal signal response factor. The universal signal response factor (counts/mol) was shown to be the same for all proteins tested in this study. A controlled set of six exogenous proteins of varying concentrations was studied in the absence and presence of human serum. The absolute quantity of the standard proteins was determined with a relative error of less than +/-15%. The average MS signal responses of the three most intense peptides from each protein were plotted against their calculated protein concentrations, and this plot resulted in a linear relationship with an R(2) value of 0.9939. The analyses were applied to determine the absolute concentration of 11 common serum proteins, and these concentrations were then compared with known values available in the literature. Additionally within an unfractionated Escherichia coli lysate, a subset of identified proteins known to exist as functional complexes was studied. The calculated absolute quantities were used to accurately determine their stoichiometry.

  12. Communication: Probing the absolute configuration of chiral molecules at aqueous interfaces

    SciTech Connect

    Lotze, Stephan Versluis, Jan; Olijve, Luuk L. C.; Schijndel, Luuk van; Milroy, Lech G.; Voets, Ilja K.; Bakker, Huib J.

    2015-11-28

    We demonstrate that the enantiomers of chiral macromolecules at an aqueous interface can be distinguished with monolayer sensitivity using heterodyne-detected vibrational sum-frequency generation (VSFG). We perform VSFG spectroscopy with a polarization combination that selectively probes chiral molecular structures. By using frequencies far detuned from electronic resonances, we probe the chiral macromolecular structures with high surface specificity. The phase of the sum-frequency light generated by the chiral molecules is determined using heterodyne detection. With this approach, we can distinguish right-handed and left-handed helical peptides at a water-air interface. We thus show that heterodyne-detected VSFG is sensitive to the absolute configuration of complex, interfacial macromolecules and has the potential to determine the absolute configuration of enantiomers at interfaces.

  13. Communication: Probing the absolute configuration of chiral molecules at aqueous interfaces.

    PubMed

    Lotze, Stephan; Versluis, Jan; Olijve, Luuk L C; van Schijndel, Luuk; Milroy, Lech G; Voets, Ilja K; Bakker, Huib J

    2015-11-28

    We demonstrate that the enantiomers of chiral macromolecules at an aqueous interface can be distinguished with monolayer sensitivity using heterodyne-detected vibrational sum-frequency generation (VSFG). We perform VSFG spectroscopy with a polarization combination that selectively probes chiral molecular structures. By using frequencies far detuned from electronic resonances, we probe the chiral macromolecular structures with high surface specificity. The phase of the sum-frequency light generated by the chiral molecules is determined using heterodyne detection. With this approach, we can distinguish right-handed and left-handed helical peptides at a water-air interface. We thus show that heterodyne-detected VSFG is sensitive to the absolute configuration of complex, interfacial macromolecules and has the potential to determine the absolute configuration of enantiomers at interfaces.

  14. Absolute Binding Free Energy Calculations: On the Accuracy of Computational Scoring of Protein-ligand Interactions

    PubMed Central

    Singh, Nidhi; Warshel, Arieh

    2010-01-01

    Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer-aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic Linear Response Approximation (LRA/β version) and its variants including the Linear Interaction Energy (LIE) to the more approximated and considerably faster scaled Protein Dipoles Langevin Dipoles (PDLD/S-LRA version), as well as the less rigorous Molecular Mechanics Poisson–Boltzmann/Surface Area (MM/PBSA) and Generalized Born/Surface Area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/β, the LIE, the PDLD/S-LRA/β and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the non-electrostatic term. On the average, the PDLD/S-LRA/β performs effectively. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies due to its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S-LRA/β appears to offer an appealing option for the final stages of massive screening approaches. PMID:20186976

  15. Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics.

    PubMed

    Meirovitch, Hagai

    2010-01-01

    The commonly used simulation techniques, Metropolis Monte Carlo (MC) and molecular dynamics (MD) are of a dynamical type which enables one to sample system configurations i correctly with the Boltzmann probability, P(i)(B), while the value of P(i)(B) is not provided directly; therefore, it is difficult to obtain the absolute entropy, S approximately -ln P(i)(B), and the Helmholtz free energy, F. With a different simulation approach developed in polymer physics, a chain is grown step-by-step with transition probabilities (TPs), and thus their product is the value of the construction probability; therefore, the entropy is known. Because all exact simulation methods are equivalent, i.e. they lead to the same averages and fluctuations of physical properties, one can treat an MC or MD sample as if its members have rather been generated step-by-step. Thus, each configuration i of the sample can be reconstructed (from nothing) by calculating the TPs with which it could have been constructed. This idea applies also to bulk systems such as fluids or magnets. This approach has led earlier to the "local states" (LS) and the "hypothetical scanning" (HS) methods, which are approximate in nature. A recent development is the hypothetical scanning Monte Carlo (HSMC) (or molecular dynamics, HSMD) method which is based on stochastic TPs where all interactions are taken into account. In this respect, HSMC(D) can be viewed as exact and the only approximation involved is due to insufficient MC(MD) sampling for calculating the TPs. The validity of HSMC has been established by applying it first to liquid argon, TIP3P water, self-avoiding walks (SAW), and polyglycine models, where the results for F were found to agree with those obtained by other methods. Subsequently, HSMD was applied to mobile loops of the enzymes porcine pancreatic alpha-amylase and acetylcholinesterase in explicit water, where the difference in F between the bound and free states of the loop was calculated. Currently

  16. Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

    PubMed Central

    2016-01-01

    Binding selectivity is a requirement for the development of a safe drug, and it is a critical property for chemical probes used in preclinical target validation. Engineering selectivity adds considerable complexity to the rational design of new drugs, as it involves the optimization of multiple binding affinities. Computationally, the prediction of binding selectivity is a challenge, and generally applicable methodologies are still not available to the computational and medicinal chemistry communities. Absolute binding free energy calculations based on alchemical pathways provide a rigorous framework for affinity predictions and could thus offer a general approach to the problem. We evaluated the performance of free energy calculations based on molecular dynamics for the prediction of selectivity by estimating the affinity profile of three bromodomain inhibitors across multiple bromodomain families, and by comparing the results to isothermal titration calorimetry data. Two case studies were considered. In the first one, the affinities of two similar ligands for seven bromodomains were calculated and returned excellent agreement with experiment (mean unsigned error of 0.81 kcal/mol and Pearson correlation of 0.75). In this test case, we also show how the preferred binding orientation of a ligand for different proteins can be estimated via free energy calculations. In the second case, the affinities of a broad-spectrum inhibitor for 22 bromodomains were calculated and returned a more modest accuracy (mean unsigned error of 1.76 kcal/mol and Pearson correlation of 0.48); however, the reparametrization of a sulfonamide moiety improved the agreement with experiment. PMID:28009512

  17. Upscaling of absolute permeability for a super element model of petroleum reservoir

    NASA Astrophysics Data System (ADS)

    Mazo, A. B.; Potashev, K. A.

    2016-11-01

    This paper presents a new method of local upscaling of absolute permeability for super element simulation of an oil reservoir. Upscaling was performed for each block of a super element unstructured grid. For this purpose, a set of problems of a one-phase steady-state flow was solved on a fine computational grid with the initial scalar field of absolute permeability with various boundary conditions. These conditions reflect the specific variants of filtrational flow through the super element and take into account the presence or absence of boreholes in the coarse block. The resulting components of the effective permeability tensor in each super element were found from the solution of the problem of minimizing the deviations of the normal flows through the super element faces, averaged on a detailed computational grid, from those approximated on a coarse super element grid. The results of using the method are demonstrated for reservoirs with river-type absolute permeability. The method is compared with the traditional methods of local upscaling.

  18. Mini-implants and miniplates generate sub-absolute and absolute anchorage.

    PubMed

    Consolaro, Alberto

    2014-01-01

    The functional demand imposed on bone promotes changes in the spatial properties of osteocytes as well as in their extensions uniformly distributed throughout the mineralized surface. Once spatial deformation is established, osteocytes create the need for structural adaptations that result in bone formation and resorption that happen to meet the functional demands. The endosteum and the periosteum are the effectors responsible for stimulating adaptive osteocytes in the inner and outer surfaces. Changes in shape, volume and position of the jaws as a result of skeletal correction of the maxilla and mandible require anchorage to allow bone remodeling to redefine morphology, esthetics and function as a result of spatial deformation conducted by orthodontic appliances. Examining the degree of changes in shape, volume and structural relationship of areas where mini-implants and miniplates are placed allows us to classify mini-implants as devices of subabsolute anchorage and miniplates as devices of absolute anchorage.

  19. Absolute dose verifications in small photon fields using BANGTM gel

    NASA Astrophysics Data System (ADS)

    Scheib, S. G.; Schenkel, Y.; Gianolini, S.

    2004-01-01

    Polymer gel dosimeters change their magnetic resonance (MR) and optical properties with the absorbed dose when irradiated and are suitable for narrow photon beam dosimetry in radiosurgery. Such dosimeters enable relative and absolute 3D dose verifications in order to check the entire treatment chain from imaging to dose application during commissioning and quality assurance. For absolute 3D dose verifications in radiosurgery using Gamma Knife B, commercially available BANGTM Gels (BANG 25 Gy and BANG 3 Gy) together with dedicated phantoms were chosen in order to determine the potential of absolute gel dosimetry in radiosurgery.

  20. Measuring the absolute magnetic field using high-Tc SQUID

    NASA Astrophysics Data System (ADS)

    He, D. F.; Itozaki, H.

    2006-06-01

    SQUID normally can only measure the change of magnetic field instead of the absolute value of magnetic field. Using a compensation method, a mobile SQUID, which could keep locked when moving in the earth's magnetic field, was developed. Using the mobile SQUID, it was possible to measure the absolute magnetic field. The absolute value of magnetic field could be calculated from the change of the compensation output when changing the direction of the SQUID in a magnetic field. Using this method and the mobile SQUID, we successfully measured the earth's magnetic field in our laboratory.

  1. Absolute Antenna Calibration at the US National Geodetic Survey

    NASA Astrophysics Data System (ADS)

    Mader, G. L.; Bilich, A. L.

    2012-12-01

    Geodetic GNSS applications routinely demand millimeter precision and extremely high levels of accuracy. To achieve these accuracies, measurement and instrument biases at the centimeter to millimeter level must be understood. One of these biases is the antenna phase center, the apparent point of signal reception for a GNSS antenna. It has been well established that phase center patterns differ between antenna models and manufacturers; additional research suggests that the addition of a radome or the choice of antenna mount can significantly alter those a priori phase center patterns. For the more demanding GNSS positioning applications and especially in cases of mixed-antenna networks, it is all the more important to know antenna phase center variations as a function of both elevation and azimuth in the antenna reference frame and incorporate these models into analysis software. Determination of antenna phase center behavior is known as "antenna calibration". Since 1994, NGS has computed relative antenna calibrations for more than 350 antennas. In recent years, the geodetic community has moved to absolute calibrations - the IGS adopted absolute antenna phase center calibrations in 2006 for use in their orbit and clock products, and NGS's CORS group began using absolute antenna calibration upon the release of the new CORS coordinates in IGS08 epoch 2005.00 and NAD 83(2011,MA11,PA11) epoch 2010.00. Although NGS relative calibrations can be and have been converted to absolute, it is considered best practice to independently measure phase center characteristics in an absolute sense. Consequently, NGS has developed and operates an absolute calibration system. These absolute antenna calibrations accommodate the demand for greater accuracy and for 2-dimensional (elevation and azimuth) parameterization. NGS will continue to provide calibration values via the NGS web site www.ngs.noaa.gov/ANTCAL, and will publish calibrations in the ANTEX format as well as the legacy ANTINFO

  2. Absolute frequency measurement at 10-16 level based on the international atomic time

    NASA Astrophysics Data System (ADS)

    Hachisu, H.; Fujieda, M.; Kumagai, M.; Ido, T.

    2016-06-01

    Referring to International Atomic Time (TAI), we measured the absolute frequency of the 87Sr lattice clock with its uncertainty of 1.1 x 10-15. Unless an optical clock is continuously operated for the five days of the TAI grid, it is required to evaluate dead time uncertainty in order to use the available five-day average of the local frequency reference. We homogeneously distributed intermittent measurements over the five-day grid of TAI, by which the dead time uncertainty was reduced to low 10-16 level. Three campaigns of the five (or four)-day consecutive measurements have resulted in the absolute frequency of the 87Sr clock transition of 429 228 004 229 872.85 (47) Hz, where the systematic uncertainty of the 87Sr optical frequency standard amounts to 8.6 x 10-17.

  3. Monochromator-Based Absolute Calibration of Radiation Thermometers

    NASA Astrophysics Data System (ADS)

    Keawprasert, T.; Anhalt, K.; Taubert, D. R.; Hartmann, J.

    2011-08-01

    A monochromator integrating-sphere-based spectral comparator facility has been developed to calibrate standard radiation thermometers in terms of the absolute spectral radiance responsivity, traceable to the PTB cryogenic radiometer. The absolute responsivity calibration has been improved using a 75 W xenon lamp with a reflective mirror and imaging optics to a relative standard uncertainty at the peak wavelength of approximately 0.17 % ( k = 1). Via a relative measurement of the out-of-band responsivity, the spectral responsivity of radiation thermometers can be fully characterized. To verify the calibration accuracy, the absolutely calibrated radiation thermometer is used to measure Au and Cu freezing-point temperatures and then to compare the obtained results with the values obtained by absolute methods, resulting in T - T 90 values of +52 mK and -50 mK for the gold and copper fixed points, respectively.

  4. Gibbs Paradox Revisited from the Fluctuation Theorem with Absolute Irreversibility

    NASA Astrophysics Data System (ADS)

    Murashita, Yûto; Ueda, Masahito

    2017-02-01

    The inclusion of the factor ln (1 /N !) in the thermodynamic entropy proposed by Gibbs is shown to be equivalent to the validity of the fluctuation theorem with absolute irreversibility for gas mixing.

  5. Absolute Value Boundedness, Operator Decomposition, and Stochastic Media and Equations

    NASA Technical Reports Server (NTRS)

    Adomian, G.; Miao, C. C.

    1973-01-01

    The research accomplished during this period is reported. Published abstracts and technical reports are listed. Articles presented include: boundedness of absolute values of generalized Fourier coefficients, propagation in stochastic media, and stationary conditions for stochastic differential equations.

  6. A critical residue for isoform difference in tetrodotoxin affinity is a molecular determinant of the external access path for local anesthetics in the cardiac sodium channel

    PubMed Central

    Sunami, Akihiko; Glaaser, Ian W.; Fozzard, Harry A.

    2000-01-01

    Membrane-impermeant quaternary derivatives of lidocaine (QX222 and QX314) block cardiac Na+ channels when applied from either side of the membrane, but they block neuronal and skeletal muscle channels poorly from the outside. To find the molecular determinants of the cardiac external QX access path, mutations of adult rat skeletal muscle (μ1) and rat heart (rH1) Na+ channels were studied by two-electrode voltage clamp in Xenopus oocytes. Mutating the μ1 domain I P-loop Y401, which is the critical residue for isoform differences in tetrodotoxin block, to the heart sequence (Y401C) allowed outside QX222 block, but its mutation to brain type (Y401F) showed little block. μ1-Y401C accelerated recovery from block by internal QX222. Block by external QX222 in μ1-Y401C was diminished by chemical modification with methanethiosulfonate ethylammonium (MTSEA) to the outer vestibule or by a double mutant (μ1-Y401C/F1579A), which altered the putative local anesthetic binding site. The reverse mutation in heart rH1-C374Y reduced outside QX314 block and slowed dissociation of internal QX222. Mutation of μ1-C1572 in IVS6 to Thr, the cardiac isoform residue (C1572T), allowed external QX222 block, and accelerated recovery from internal QX222 block, as reported. Blocking efficacy of outside QX222 in μ1-Y401C was more than that in μ1-C1572T, and the double mutant (μ1-Y401C/C1572T) accelerated internal QX recovery more than μ1-Y401C or μ1-C1572T alone. We conclude that the isoform-specific residue (Tyr/Phe/Cys) in the P-loop of domain I plays an important role in drug access as well as in tetrodotoxin binding. Isoform-specific residues in the IP-loop and IVS6 determine outside drug access to an internal binding site. PMID:10681444

  7. Microfabricated Collector-Generator Electrode Sensor for Measuring Absolute pH and Oxygen Concentrations.

    PubMed

    Dengler, Adam K; Wightman, R Mark; McCarty, Gregory S

    2015-10-20

    Fast-scan cyclic voltammetry (FSCV) has attracted attention for studying in vivo neurotransmission due to its subsecond temporal resolution, selectivity, and sensitivity. Traditional FSCV measurements use background subtraction to isolate changes in the local electrochemical environment, providing detailed information on fluctuations in the concentration of electroactive species. This background subtraction removes information about constant or slowly changing concentrations. However, determination of background concentrations is still important for understanding functioning brain tissue. For example, neural activity is known to consume oxygen and produce carbon dioxide which affects local levels of oxygen and pH. Here, we present a microfabricated microelectrode array which uses FSCV to detect the absolute levels of oxygen and pH in vitro. The sensor is a collector-generator electrode array with carbon microelectrodes spaced 5 μm apart. In this work, a periodic potential step is applied at the generator producing transient local changes in the electrochemical environment. The collector electrode continuously performs FSCV enabling these induced changes in concentration to be recorded with the sensitivity and selectivity of FSCV. A negative potential step applied at the generator produces a transient local pH shift at the collector. The generator-induced pH signal is detected using FSCV at the collector and correlated to absolute solution pH by postcalibration of the anodic peak position. In addition, in oxygenated solutions a negative potential step at the generator produces hydrogen peroxide by reducing oxygen. Hydrogen peroxide is detected with FSCV at the collector electrode, and the magnitude of the oxidative peak is proportional to absolute oxygen concentrations. Oxygen interference on the pH signal is minimal and can be accounted for with a postcalibration.

  8. Absolute flux calibration of optical spectrophotometric standard stars

    NASA Technical Reports Server (NTRS)

    Colina, Luis; Bohlin, Ralph C.

    1994-01-01

    A method based on Landolt photometry in B and V is developed to correct for a wavelength independent offset of the absolute flux level of optical spectrophotometric standards. The method is based on synthetic photometry techniques in B and V and is accurate to approximately 1%. The correction method is verified by Hubble Space Telescope Faint Object Spectrograph absolute fluxes for five calibration stars, which agree with Landolt photometry to 0.5% in B and V.

  9. Absolute cross sections for electronic excitation of condensed tetrahydrofuran (THF) by 11-16 eV electrons.

    PubMed

    Lemelin, V; Bass, A D; Cloutier, P; Sanche, L

    2016-11-07

    Absolute cross section (CS) data on the interaction of low energy electrons with DNA and its molecular constituents are required as input parameters in Monte-Carlo type simulations, for several radiobiological applications. Previously [V. Lemelin et al., J. Chem. Phys. 144, 074701 (2016)], we measured absolute vibrational CSs for low-energy electron scattering from condensed tetrahydrofuran, a convenient surrogate for the deoxyribose. Here we report absolute electronic CSs for energy losses of between 6 and 11.5 eV, by electrons with energies between 11 and 16 eV. The variation of these CSs with incident electron energy shows no evidence of transient anion states, consistent with theoretical and other experimental results, indicating that initial electron capture leading to DNA strand breaks occurs primarily on DNA bases or the phosphate group.

  10. Absolute cross sections for electronic excitation of condensed tetrahydrofuran (THF) by 11-16 eV electrons

    NASA Astrophysics Data System (ADS)

    Lemelin, V.; Bass, A. D.; Cloutier, P.; Sanche, L.

    2016-11-01

    Absolute cross section (CS) data on the interaction of low energy electrons with DNA and its molecular constituents are required as input parameters in Monte-Carlo type simulations, for several radiobiological applications. Previously [V. Lemelin et al., J. Chem. Phys. 144, 074701 (2016)], we measured absolute vibrational CSs for low-energy electron scattering from condensed tetrahydrofuran, a convenient surrogate for the deoxyribose. Here we report absolute electronic CSs for energy losses of between 6 and 11.5 eV, by electrons with energies between 11 and 16 eV. The variation of these CSs with incident electron energy shows no evidence of transient anion states, consistent with theoretical and other experimental results, indicating that initial electron capture leading to DNA strand breaks occurs primarily on DNA bases or the phosphate group.

  11. Absolute cross sections for electronic excitation of condensed tetrahydrofuran (THF) by 11–16 eV electrons

    PubMed Central

    Lemelin, V.; Bass, A. D.; Cloutier, P.; Sanche, L.

    2016-01-01

    Absolute cross section (CS) data on the interaction of low energy electrons with DNA and its molecular constituents are required as input parameters in Monte-Carlo type simulations, for several radiobiological applications. Previously [V. Lemelin et al., J. Chem. Phys. 144, 074701 (2016)], we measured absolute vibrational CSs for low-energy electron scattering from condensed tetrahydrofuran, a convenient surrogate for the deoxyribose. Here we report absolute electronic CSs for energy losses of between 6 and 11.5 eV, by electrons with energies between 11 and 16 eV. The variation of these CSs with incident electron energy shows no evidence of transient anion states, consistent with theoretical and other experimental results, indicating that initial electron capture leading to DNA strand breaks occurs primarily on DNA bases or the phosphate group. PMID:27825202

  12. Absolute Measurements of Methane on Mars

    NASA Astrophysics Data System (ADS)

    Mumma, M. J.; Villanueva, G. L.; Novak, R. E.

    2009-12-01

    On Mars, methane has been sought for nearly 40 years because of its potential biological significance, but it was detected only recently [1-5]. Its distribution on the planet is found to be patchy and to vary with time [1,2,4,5], suggesting that methane is released from the subsurface in localized areas, and is then rapidly destroyed [1,6]. To date, we have detected four spectral lines of the CH4 ν3 band near 3.3 µm, along with H2O and HDO [1,5,7]. Our observational campaign resumed in August 2009, now using CRIRES/VLT along with CSHELL/NASA-IRTF and NIRSPEC/Keck. Our study of methane on Mars now extends over four Mars years, sampling a wide range of seasons (Ls) with significant spatial coverage. For a typical observation, the spectrometer's long entrance slit is held to the central meridian of Mars while spectra are taken sequentially in time. For each snapshot in time, spectra are acquired simultaneously at contiguous positions along the entire slit length, sampling latitudinally resolved spatial footprints on the planet (35 footprints along the N-S meridian, when Mars is 7 arc-sec in diameter). Successive longitudes are presented as the planet rotates, and the combination then permits partial mapping of the planet. In Northern summer 2003, methane was notably enriched over several localized areas: A (East of Arabia Terra, where water vapor is also greatly enriched), B1 (Nili Fossae), and B2 (southeast quadrant of Syrtis Major) [1,5]. The combined plume contained ~19,000 metric tons of methane, and the estimated source strength (≥ 0.6 kilogram per second) was comparable to that of the massive hydrocarbon seep at Coal Oil Point in Santa Barbara, California. By vernal equinox about one-half the released methane had been lost. When averaged over latitude and season, spectral data from Mars Express also imply an enhancement in methane in this longitude range [4]. The most compelling results from these searches are: 1) the unambiguous detection of multiple

  13. The Molecular Structures of the Local Arm and Perseus Arm in the Galactic Region of l = [139.°75, 149.°75], b = [‑5.°25, 5.°25

    NASA Astrophysics Data System (ADS)

    Du, Xinyu; Xu, Ye; Yang, Ji; Sun, Yan

    2017-04-01

    Using the Purple Mountain Observatory Delingha (PMODLH) 13.7 m telescope, we report a 96 deg2 12CO/13CO/C18O mapping observation toward the Galactic region of l = [139.°75,149.°75], b = [‑5.°25, 5.°25]. The molecular structures of the Local Arm and Perseus Arm are presented. Combining H i data and part of the Outer Arm results, we obtain that the warp structure of both atomic and molecular gas is obvious, while the flare structure only exists in atomic gas in this observing region. In addition, five filamentary giant molecular clouds on the Perseus Arm are identified. Among them, four are newly identified. Their relations with the Milky Way large-scale structure are discussed.

  14. Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.

    PubMed

    Shivakumar, Devleena; Harder, Edward; Damm, Wolfgang; Friesner, Richard A; Sherman, Woody

    2012-08-14

    Explicit solvent molecular dynamics free energy perturbation simulations were performed to predict absolute solvation free energies of 239 diverse small molecules. We use OPLS2.0, the next generation OPLS force field, and compare the results with popular small molecule force fields-OPLS_2005, GAFF, and CHARMm-MSI. OPLS2.0 produces the best correlation with experimental data (R(2) = 0.95, slope = 0.96) and the lowest average unsigned errors (0.7 kcal/mol). Important classes of compounds that performed suboptimally with OPLS_2005 show significant improvements.

  15. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.

    PubMed

    Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil

    2013-01-28

    Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder ( http://www.charmm-gui.org/input/gbinding ), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently set up the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three nonpolar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). Therefore, CHARMM-GUI Ligand Binder provides a convenient and reliable way to set up the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems.

  16. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

    PubMed Central

    Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil

    2013-01-01

    Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly web interface, CHARMM-GUI Ligand Binder (http://www.charmm-gui.org/input/gbinding), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently setup the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three non-polar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). CHARMM-GUI Ligand Binder provides a convenient and reliable way to setup the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems. PMID:23205773

  17. Auditory working memory predicts individual differences in absolute pitch learning.

    PubMed

    Van Hedger, Stephen C; Heald, Shannon L M; Koch, Rachelle; Nusbaum, Howard C

    2015-07-01

    Absolute pitch (AP) is typically defined as the ability to label an isolated tone as a musical note in the absence of a reference tone. At first glance the acquisition of AP note categories seems like a perceptual learning task, since individuals must assign a category label to a stimulus based on a single perceptual dimension (pitch) while ignoring other perceptual dimensions (e.g., loudness, octave, instrument). AP, however, is rarely discussed in terms of domain-general perceptual learning mechanisms. This is because AP is typically assumed to depend on a critical period of development, in which early exposure to pitches and musical labels is thought to be necessary for the development of AP precluding the possibility of adult acquisition of AP. Despite this view of AP, several previous studies have found evidence that absolute pitch category learning is, to an extent, trainable in a post-critical period adult population, even if the performance typically achieved by this population is below the performance of a "true" AP possessor. The current studies attempt to understand the individual differences in learning to categorize notes using absolute pitch cues by testing a specific prediction regarding cognitive capacity related to categorization - to what extent does an individual's general auditory working memory capacity (WMC) predict the success of absolute pitch category acquisition. Since WMC has been shown to predict performance on a wide variety of other perceptual and category learning tasks, we predict that individuals with higher WMC should be better at learning absolute pitch note categories than individuals with lower WMC. Across two studies, we demonstrate that auditory WMC predicts the efficacy of learning absolute pitch note categories. These results suggest that a higher general auditory WMC might underlie the formation of absolute pitch categories for post-critical period adults. Implications for understanding the mechanisms that underlie the

  18. Near-Infrared Absolute Photometric Imaging of the Uranian System

    NASA Astrophysics Data System (ADS)

    Baines, Kevin H.; Yanamandra-Fisher, Padmavati A.; Lebofsky, Larry A.; Momary, Thomas W.; Golisch, William; Kaminski, Charles; Wild, Walter J.

    1998-04-01

    We report the first multifilter set of absolutely calibrated near-infrared images of Uranus, its rings, and three major satellites-Titania, Ariel, and Miranda. Along with imagery utilizing the canonical K filter bandpass (effective wavelength 2.20 μm), absolutely calibrated images of the uranian system are presented for the first time for three additional filter bandpasses: J (1.27 μm), H (1.62 μm), and in a narrow bandpass (0.1 μm full-width-at-half-maximum) centered at 1.73 μm (hereafter designated H‧) particularly diagnostic of C-H stretch vibrational absorptions common in hydrocarbons. Multifilter-derived spectra of the southern ring ansa including the bright apoapse of the dominant ɛ ring show no absorptions due to condensable volatiles, including water, ammonia, and light (high H:C) hydrocarbons. Plausible near-infrared spherical geometric and single-scattering particle albedos consistent with Voyager-derived phase functions range from 0.069 to 0.102 and from 0.030 to 0.037, respectively. These are approximately 50% greater than visible values, consistent with the optical properties of charcoal, carbonaceous chondrite material, and the darkside of Iapetus, and consistent with the hypothesis that a primary component of the ring particles is high stoichiometric ratio C:H organics produced by charged-particle and/or photochemical weathering of methane clathrate and/or hydrocarbon ice material originating from nearby moonlets. Additional components consistent with the ring spectrum include silicates such as pyroxene, but not olivine. Analytical modeling of the ring structure indicates ɛ-ring near-infrared opacities of 0.37 ± 0.05 and 1.8 ± 0.3 at apoapsis and periapsis, respectively. Ariel is more than 25% brighter than Miranda and 15% brighter than Titania at all near-infrared wavelengths. Comparisons with UV-visible spectra by Karkoschka (1997,Icarus125, 348-363) show consistency with the hypothesis that the water-ice surfaces of Titania and Ariel

  19. Physical localization of molecular markers and assignment of the 15th linkage group to chromosome 11 of the karyotype in cassava (Manihot esculenta Crantz) by primed in situ labeling.

    PubMed

    Wang, Y; Wang, J F; Yin, H; Gao, H Q; Zhuang, N S; Liu, J P

    2015-07-28

    Physical localization of molecular markers and assignment of the 15th linkage group to chromosome 11 of the karyotype in cassava (Manihot esculenta Crantz) were achieved using primed in situ labeling. Amplified signals for both the EST507-1 and SSRY13-5 markers were consistently observed in different stages of cell division. A comparison of the length, arm ratio, and other morphological characteristics of somatic metaphase chromosomes in karyotype analysis indicated that the EST507-1 and SSRY13-5 markers were localized on the short and long arm of cassava chromosome 11 with the relative map positions of 41.67 and 23.07, respectively. The physical localization of the 2 markers on chromosome 11 of the karyotype corresponds to their positions on the 15th linkage group in cassava.

  20. Principle of relative locality

    SciTech Connect

    Amelino-Camelia, Giovanni; Freidel, Laurent; Smolin, Lee; Kowalski-Glikman, Jerzy

    2011-10-15

    We propose a deepening of the relativity principle according to which the invariant arena for nonquantum physics is a phase space rather than spacetime. Descriptions of particles propagating and interacting in spacetimes are constructed by observers, but different observers, separated from each other by translations, construct different spacetime projections from the invariant phase space. Nonetheless, all observers agree that interactions are local in the spacetime coordinates constructed by observers local to them. This framework, in which absolute locality is replaced by relative locality, results from deforming energy-momentum space, just as the passage from absolute to relative simultaneity results from deforming the linear addition of velocities. Different aspects of energy-momentum space geometry, such as its curvature, torsion and nonmetricity, are reflected in different kinds of deformations of the energy-momentum conservation laws. These are in principle all measurable by appropriate experiments. We also discuss a natural set of physical hypotheses which singles out the cases of energy-momentum space with a metric compatible connection and constant curvature.

  1. Synchronous absolute EIT in three thoracic planes at different gravity levels

    NASA Astrophysics Data System (ADS)

    Hahn, G.; Just, A.; Dittmar, J.; Fromm, K. H.; Quintel, M.

    2013-04-01

    The validity of absolute Electrical Impedance Tomography (a-EIT) for assessment of local lung volume has been investigated far less than the well evaluated ventilation monitoring by functional EIT (f-EIT). To achieve progress in a-EIT we investigated 10 healthy volunteers in an upright sitting position by using a-EIT at normal gravity (1 g), weightlessness (0 g) and approx. double gravity (1.8 g) during parabolic flight manoeuvres. Lung resistivity in three thoracic planes was determined by a-EIT using a multiple-plane synchronised Goe-MF II EIT system. Tomograms of resistivity at end-expiration in normal spontaneous breathing were reconstructed by a modified SIRT algorithm. Local lung resistivity was determined separately for both lungs. The respective resistivity values at 1 g and 1.8 g before and after weightlessness show an almost reversible behaviour along the sequence of gravity changes with a tendency to be lower after occurrence of weightlessness. The results reveal not only the expected varying resistivity of lung tissue in cranio-caudal direction but also a clear difference in these cranio-caudal stratifications of local lung volume between the left and right lung. The resolution and stability of absolute EIT seem to be valid and expressive for future investigations of unilateral lung volume under different physiological and pathological conditions.

  2. Zero absolute vorticity: insight from experiments in rotating laminar plane Couette flow.

    PubMed

    Suryadi, Alexandre; Segalini, Antonio; Alfredsson, P Henrik

    2014-03-01

    For pressure-driven turbulent channel flows undergoing spanwise system rotation, it has been observed that the absolute vorticity, i.e., the sum of the averaged spanwise flow vorticity and system rotation, tends to zero in the central region of the channel. This observation has so far eluded a convincing theoretical explanation, despite experimental and numerical evidence reported in the literature. Here we show experimentally that three-dimensional laminar structures in plane Couette flow, which appear under anticyclonic system rotation, give the same effect, namely, that the absolute vorticity tends to zero if the rotation rate is high enough. It is shown that this is equivalent to a local Richardson number of approximately zero, which would indicate a stable condition. We also offer an explanation based on Kelvin's circulation theorem to demonstrate that the absolute vorticity should remain constant and approximately equal to zero in the central region of the channel when going from the nonrotating fully turbulent state to any state with sufficiently high rotation.

  3. Absolute and relative family affluence and psychosomatic symptoms in adolescents.

    PubMed

    Elgar, Frank J; De Clercq, Bart; Schnohr, Christina W; Bird, Phillippa; Pickett, Kate E; Torsheim, Torbjørn; Hofmann, Felix; Currie, Candace

    2013-08-01

    Previous research on the links between income inequality and health and socioeconomic differences in health suggests that relative differences in affluence impact health and well-being more than absolute affluence. This study explored whether self-reported psychosomatic symptoms in adolescents relate more closely to relative affluence (i.e., relative deprivation or rank affluence within regions or schools) than to absolute affluence. Data on family material assets and psychosomatic symptoms were collected from 48,523 adolescents in eight countries (Austria, Belgium, Canada, Norway, Scotland, Poland, Turkey, and Ukraine) as part of the 2009/10 Health Behaviour in School-aged Children study. Multilevel regression analyses of the data showed that relative deprivation (Yitzhaki Index, calculated in regions and in schools) and rank affluence (in regions) (1) related more closely to symptoms than absolute affluence, and (2) related to symptoms after differences in absolute affluence were held constant. However, differences in family material assets, whether they are measured in absolute or relative terms, account for a significant variation in adolescent psychosomatic symptoms. Conceptual and empirical issues relating to the use of material affluence indices to estimate socioeconomic position are discussed.

  4. High speed image acquisition system of absolute encoder

    NASA Astrophysics Data System (ADS)

    Liao, Jianxiang; Chen, Xin; Chen, Xindu; Zhang, Fangjian; Wang, Han

    2017-01-01

    Absolute optical encoder as a product of optical, mechanical and electronic integration has been widely used in displacement measuring fields. However, how to improve the measurement velocity and reduce the manufacturing cost of absolute optical encoder is the key problem to be solved. To improve the measurement speed, a novel absolute optical encoder image acquisition system is proposed. The proposed acquisition system includes a linear CCD sensor is applied for capturing coding pattern images, an optical magnifying system is used for enlarging the grating stripes, an analog-digital conversion(ADC) module is used for processing the CCD analogy signal, a field programmable gate array(FPGA) device and other peripherals perform driving task. An absolute position measurement experiment was set up to verify and evaluate the proposed image acquisition system. The experimental result indicates that the proposed absolute optical encoder image acquisition system has the image acquisition speed of more than 9500fp/s with well reliability and lower manufacture cost.

  5. Absolute irradiance of the Moon for on-orbit calibration

    USGS Publications Warehouse

    Stone, T.C.; Kieffer, H.H.; ,

    2002-01-01

    The recognized need for on-orbit calibration of remote sensing imaging instruments drives the ROLO project effort to characterize the Moon for use as an absolute radiance source. For over 5 years the ground-based ROLO telescopes have acquired spatially-resolved lunar images in 23 VNIR (Moon diameter ???500 pixels) and 9 SWIR (???250 pixels) passbands at phase angles within ??90 degrees. A numerical model for lunar irradiance has been developed which fits hundreds of ROLO images in each band, corrected for atmospheric extinction and calibrated to absolute radiance, then integrated to irradiance. The band-coupled extinction algorithm uses absorption spectra of several gases and aerosols derived from MODTRAN to fit time-dependent component abundances to nightly observations of standard stars. The absolute radiance scale is based upon independent telescopic measurements of the star Vega. The fitting process yields uncertainties in lunar relative irradiance over small ranges of phase angle and the full range of lunar libration well under 0.5%. A larger source of uncertainty enters in the absolute solar spectral irradiance, especially in the SWIR, where solar models disagree by up to 6%. Results of ROLO model direct comparisons to spacecraft observations demonstrate the ability of the technique to track sensor responsivity drifts to sub-percent precision. Intercomparisons among instruments provide key insights into both calibration issues and the absolute scale for lunar irradiance.

  6. Accurate absolute GPS positioning through satellite clock error estimation

    NASA Astrophysics Data System (ADS)

    Han, S.-C.; Kwon, J. H.; Jekeli, C.

    2001-05-01

    An algorithm for very accurate absolute positioning through Global Positioning System (GPS) satellite clock estimation has been developed. Using International GPS Service (IGS) precise orbits and measurements, GPS clock errors were estimated at 30-s intervals. Compared to values determined by the Jet Propulsion Laboratory, the agreement was at the level of about 0.1 ns (3 cm). The clock error estimates were then applied to an absolute positioning algorithm in both static and kinematic modes. For the static case, an IGS station was selected and the coordinates were estimated every 30 s. The estimated absolute position coordinates and the known values had a mean difference of up to 18 cm with standard deviation less than 2 cm. For the kinematic case, data obtained every second from a GPS buoy were tested and the result from the absolute positioning was compared to a differential GPS (DGPS) solution. The mean differences between the coordinates estimated by the two methods are less than 40 cm and the standard deviations are less than 25 cm. It was verified that this poorer standard deviation on 1-s position results is due to the clock error interpolation from 30-s estimates with Selective Availability (SA). After SA was turned off, higher-rate clock error estimates (such as 1 s) could be obtained by a simple interpolation with negligible corruption. Therefore, the proposed absolute positioning technique can be used to within a few centimeters' precision at any rate by estimating 30-s satellite clock errors and interpolating them.

  7. Absolute Instability in Swept Leading-Edge Boundary Layers

    NASA Astrophysics Data System (ADS)

    Lin, R.-S.; Li, F.; Malik, M. R.

    1997-11-01

    Absolute instabilities in the swept Hiemenz flow and flows over Poll's swept cylinder are studied. It is assumed that the span is infinite and the laminar flow field is subjected to a line impulsive excitation so that the spanwise wavenumber (β) is taken to be real, which is akin to the rotating disk study made by Lingwood.footnote Lingwood, R. J., J. Fluid Mech., 299, 17, 1995. We found that these flows can be absolutely unstable in the chordwise (x) direction. The pinch-point singularities formed by the coalescence of two distinct spatial branches can lie either below or above the real α-axis. The pinch points with a positive αi imply the existence of an unstable disturbance propagating against the mainstream, which has never been observed before. It is found that singularities of pinch type occur in a region very close to the leading edge, therefore the attachment-line Reynolds number is used to correlate the onset of absolute instability. The critical Reynolds number for absolute instability is found to be about R=540 compared to 583 for the attachment-line instability. Provided the non-linear behavior of this absolute instability is sufficient to trigger the laminar to turbulent transition, then it would cause a complete loss of laminar flow on a swept wing as does the attachment-line instability.

  8. The Interplay Between Conformation and Absolute Configuration in Chiral Electron Dynamics of Small Diols.

    PubMed

    Daly, Steven; Tia, Maurice; Garcia, Gustavo A; Nahon, Laurent; Powis, Ivan

    2016-09-05

    A competition between chiral characteristics alternatively attributable to either conformation or to absolute configuration is identified. Circular dichroism associated with photoexcitation of the outer orbital of configurational enantiomers of 1,3- and 2,3-butanediols has been examined with a focus on the large changes in electron chiral asymmetry produced by different molecular conformations. Experimental gas-phase measurements offer support for the theoretical modeling of this chiroptical effect. A surprising prediction is that a conformationally produced pseudo-enantiomerism in 1,3-butanediol generates a chiral response in the frontier electron dynamics that outweighs the influence of the permanent configurational handedness established at the asymmetrically substituted carbon. Induced conformation, and specifically induced conformational chirality, may thus be a dominating factor in chiral molecular recognition in such systems.

  9. Near-threshold absolute photoionization cross-sections of some reaction intermediates in combustion

    NASA Astrophysics Data System (ADS)

    Wang, Juan; Yang, Bin; Cool, Terrill A.; Hansen, Nils; Kasper, Tina

    2008-02-01

    The use of photoionization mass spectrometry for the development of quantitative kinetic models for the complex combustion chemistry of both conventional hydrocarbon fuels and oxygenated biofuels requires near-threshold measurements of absolute photoionization cross-sections for numerous reaction intermediates. Near-threshold absolute cross-sections for molecular and dissociative photoionization for 20 stable reaction intermediates (methane, ethane, propane, n-butane, cyclopropane, methylcyclopentane, 1-butene, cis-2-butene, isobutene, 1-pentene, cyclohexene, 3,3-dimethyl-1-butene, 1,3-hexadiene, 1,3-cyclohexadiene, methyl acetate, ethyl acetate, tetrahydrofuran, propanal, 1-butyne, 2-butyne) are presented. Previously measured total photoionization cross-sections for 9 of these molecules are in good agreement with the present results. The measurements are performed with photoionization mass spectrometry (PIMS) using a monochromated VUV synchrotron light source with an energy resolution of 40 meV (fwhm) comparable to that used for flame-sampling molecular beam PIMS studies of flame chemistry and reaction kinetics.

  10. System and method for calibrating a rotary absolute position sensor

    NASA Technical Reports Server (NTRS)

    Davis, Donald R. (Inventor); Permenter, Frank Noble (Inventor); Radford, Nicolaus A (Inventor)

    2012-01-01

    A system includes a rotary device, a rotary absolute position (RAP) sensor generating encoded pairs of voltage signals describing positional data of the rotary device, a host machine, and an algorithm. The algorithm calculates calibration parameters usable to determine an absolute position of the rotary device using the encoded pairs, and is adapted for linearly-mapping an ellipse defined by the encoded pairs to thereby calculate the calibration parameters. A method of calibrating the RAP sensor includes measuring the rotary position as encoded pairs of voltage signals, linearly-mapping an ellipse defined by the encoded pairs to thereby calculate the calibration parameters, and calculating an absolute position of the rotary device using the calibration parameters. The calibration parameters include a positive definite matrix (A) and a center point (q) of the ellipse. The voltage signals may include an encoded sine and cosine of a rotary angle of the rotary device.

  11. Absolute distance sensing by two laser optical interferometry.

    PubMed

    Thurner, Klaus; Braun, Pierre-François; Karrai, Khaled

    2013-11-01

    We have developed a method for absolute distance sensing by two laser optical interferometry. A particularity of this technique is that a target distance is determined in absolute and is no longer limited to within an ambiguity range affecting usually multiple wavelength interferometers. We implemented the technique in a low-finesse Fabry-Pérot miniature fiber based interferometer. We used two diode lasers, both operating in the 1550 nm wavelength range. The wavelength difference is chosen to create a 25 μm long periodic beating interferometric pattern allowing a nanometer precise position measurement but limited to within an ambiguity range of 25 μm. The ambiguity is then eliminated by scanning one of the wavelengths over a small range (3.4 nm). We measured absolute distances in the sub-meter range and this with just few nanometer repeatability.

  12. Method and apparatus for two-dimensional absolute optical encoding

    NASA Technical Reports Server (NTRS)

    Leviton, Douglas B. (Inventor)

    2004-01-01

    This invention presents a two-dimensional absolute optical encoder and a method for determining position of an object in accordance with information from the encoder. The encoder of the present invention comprises a scale having a pattern being predetermined to indicate an absolute location on the scale, means for illuminating the scale, means for forming an image of the pattern; and detector means for outputting signals derived from the portion of the image of the pattern which lies within a field of view of the detector means, the field of view defining an image reference coordinate system, and analyzing means, receiving the signals from the detector means, for determining the absolute location of the object. There are two types of scale patterns presented in this invention: grid type and starfield type.

  13. PHASES: A Project to Perform Absolute Spectrophotometry from Space

    NASA Astrophysics Data System (ADS)

    del Burgo, C.; Vather, D.; Allende Prieto, C.; Murphy, N.

    2013-04-01

    This paper presents the current status of the opto-mechanical design of PHASES (Planet Hunting and AsteroSeismology Explorer Spectrophotometer), which is a project to develop a space-borne telescope to obtain absolute flux calibrated spectra of bright stars. The science payload is intended to be housed in a micro-satellite launched into a low-earth Sun-synchronous orbit with an inclination to the equator of 98.7° and a local time ascending node LTAN of 6:00 AM. PHASES will be able to measure micromagnitude photometric variations due to stellar oscillations/activity and planet/moon transits. It consists of a 20 cm aperture modified Baker telescope feeding two detectors: the tracking detector provides the fine telescope guidance system with a required pointing stability of 0.2″, and the science detector performs spectrophotometry in the wavelength range 370-960 nm with a resolving power between 200 and 900. The spectrograph is designed to provide 1% RMS flux calibrated spectra with signal-to-noise ratios > 100 for stars with V < 10 in short integration times. Our strategy to calibrate the system using A type stars is explained. From comparison with model atmospheres it would be possible to determine the stellar angular diameters with an uncertainty of approximately 0.5%. In the case of a star hosting a transiting planet it would be possible to derive its light curve, and then the planet to stellar radius ratio. Bright stars have high precision Hipparcos parallaxes and the expected level of accuracy for their fluxes will be propagated to the stellar radii, and more significantly to the planetary radii. The scientific drivers for PHASES give rise to some design challenges, which are particularly related to the opto-mechanics for extreme environmental conditions. The optical design has been developed with the primary goal of avoiding stray light reaching the science detector. Three different proposals for the opto-mechanical design are under investigation.

  14. The Absolute Gravimeter FG5 - Adjustment and Residual Data Evaluation

    NASA Astrophysics Data System (ADS)

    Orlob, M.; Braun, A.; Henton, J.; Courtier, N.; Liard, J.

    2009-05-01

    The most widely used method of direct terrestrial gravity determination is performed by using a ballistic absolute gravimeter. Today, the FG5 (Micro-g LaCoste; Lafayette, CO) is the most common free-fall absolute gravimeter. It uses the Michelson-type interferometer to determine the absolute gravity value with accuracies up to one part- per-billion of g. Furthermore, absolute gravimeter measurements can be used to assist in the validation and interpretation of temporal variations of the global gravity field, e.g. from the GRACE mission. In addition, absolute gravimetry allows for monitoring gravity changes which are caused by subsurface mass redistributions and/or vertical displacements. In this study,adjustment software was developed and applied to the raw data sets of FG5#106 and FG5#236, made available by Natural Resources Canada. Both data sets have been collected at the same time and place which leads to an intercomparison of the instruments performance. The adjustment software was validated against the official FG5 software package developed by Micro-g Lacoste. In order to identify potential environmental or instrument disturbances in the observed time series, a Lomb- Scargle periodogram analysis was employed. The absolute gravimeter FG5 is particularly sensitive to low frequencies between 0-3Hz. Hence, the focus of the analysis is to detect signals in the band of 0-100 Hz. An artificial signal was added to the measurements for demonstration purposes. Both the performance of the adjustment software and the Lomb-Scargle analysis will be discussed.

  15. Absolute configuration and crystal packing for three chiral drugs prone to spontaneous resolution: Guaifenesin, methocarbamol and mephenesin

    NASA Astrophysics Data System (ADS)

    Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Krivolapov, Dmitry B.; Pashagin, Alexander V.; Litvinov, Igor A.

    2009-02-01

    Popular chiral drugs, guaifenesin, methocarbamol, and mephenesin were investigated by single-crystal X-ray analysis both for enantiopure and racemic samples. The absolute configurations for all substances were established through Flack parameter method. The conglomerate-forming nature for the compounds was confirmed by equivalence of crystal characteristics of enantiopure and racemic samples. The molecular structures and crystal packing details were evaluated and compared with one another for all three investigated substances.

  16. Measurements of the reactor neutron power in absolute units

    SciTech Connect

    Lebedev, G. V.

    2015-12-15

    The neutron power of the reactor of the Yenisei space nuclear power plant is measured in absolute units using the modernized method of correlation analysis during the ground-based tests of the Yenisei prototypes. Results of the experiments are given. The desired result is obtained in a series of experiments carried out at the stage of the plant preparation for tests. The acceptability of experimental data is confirmed by the results of measuring the reactor neutron power in absolute units at the nominal level by the thermal balance during the life cycle tests of the ground prototypes.

  17. STS-9 Shuttle grow - Ram angle effect and absolute intensities

    NASA Technical Reports Server (NTRS)

    Swenson, G. R.; Mende, S. B.; Clifton, K. S.

    1986-01-01

    Visible imagery from Space Shuttle mission STS-9 (Spacelab 1) has been analyzed for the ram angle effect and the absolute intensity of glow. The data are compared with earlier measurements and the anomalous high intensities at large ram angles are confirmed. Absolute intensities of the ram glow on the shuttle tile, at 6563 A, are observed to be about 20 times more intense than those measured on the AE-E spacecraft. Implications of these observations for an existing theory of glow involving NO2 are presented.

  18. Absolute integrated intensity for the nu-1 sulfur dioxide band

    NASA Technical Reports Server (NTRS)

    Pilon, P. J.; Young, C.

    1976-01-01

    The absolute integrated intensity of the IR vibration-rotation nu-1 SO2 band was measured using the linear portion of the curve of growth. Infrared spectroscopic-absorption cell measurements were performed on sulfur dioxide at partial pressures less than 0.15 torr with nitrogen added to give a total pressure of 705 torr, the path length being 4 mm. The absolute integrated intensity was determined to be 112.0 plus or minus 2.6/cm/sq (atm cm) at 296 K at the 95% confidence level.

  19. From Hubble's Next Generation Spectral Library (NGSL) to Absolute Fluxes

    NASA Astrophysics Data System (ADS)

    Heap, S. R.; Lindler, D.

    2016-05-01

    Hubble's Next Generation Spectral Library (NGSL) consists of R˜1000 spectra of 374 stars of assorted temperature, gravity, and metallicity. Each spectrum covers the wavelength range, 0.18-1.03 μ. The library can be viewed and/or downloaded from the website, http://archive.stsci.edu/prepds/stisngsl/. Stars in the NGSL are now being used as absolute flux standards at ground-based observatories. However, the uncertainty in the absolute flux is about 2%, which does not meet the requirements of dark-energy surveys. We have therefore developed an observing procedure, data-reduction procedure, and correction algorithms that should yield fluxes with uncertainties less than 1%.

  20. Absolute configuration determination of angular dihydrocoumarins from Peucedanum praeruptorum.

    PubMed

    Lou, Hong-Xiang; Sun, Long-Ru; Yu, Wen-Tao; Fan, Pei-Hong; Cui, Lei; Gao, Yan-Hui; Ma, Bin; Ren, Dong-Mei; Ji, Mei

    2004-09-01

    From Peucedanum praeruptorum, one new khellactone ester (3'R)-O-acetyl-(4'S)-O-angeloylkhellactone (3), as well as four known angular dihydropyranocoumarins (1, 2, 4, 5) have been isolated. On the basis of NMR spectra and X-ray crystallography, their structures were determined. We have elucidated their absolute configuration by either chiral separation of their alkaline hydrolysis products with Rp-18 HPLC eluted with 5% hydroxypropyl-beta-cyclodextrin (beta-HCD) or by measurement of their CD spectra. A general rule relating the position and absolute streochemistry of the khellactone esters to the sign of their Cotton effects in CD curves is proposed.

  1. Absolute, Extreme-Ultraviolet, Solar Spectral Irradiance Monitor (AESSIM)

    NASA Technical Reports Server (NTRS)

    Huber, Martin C. E.; Smith, Peter L.; Parkinson, W. H.; Kuehne, M.; Kock, M.

    1988-01-01

    AESSIM, the Absolute, Extreme-Ultraviolet, Solar Spectral Irradiance Monitor, is designed to measure the absolute solar spectral irradiance at extreme-ultraviolet (EUV) wavelengths. The data are required for studies of the processes that occur in the earth's upper atmosphere and for predictions of atmospheric drag on space vehicles. AESSIM is comprised of sun-pointed spectrometers and newly-developed, secondary standards of spectral irradiance for the EUV. Use of the in-orbit standard sources will eliminate the uncertainties caused by changes in spectrometer efficiency that have plagued all previous measurements of the solar spectral EUV flux.

  2. Large-Scale Measurement of Absolute Protein Glycosylation Stoichiometry.

    PubMed

    Sun, Shisheng; Zhang, Hui

    2015-07-07

    Protein glycosylation is one of the most important protein modifications. Glycosylation site occupancy alteration has been implicated in human diseases and cancers. However, current glycoproteomic methods focus on the identification and quantification of glycosylated peptides and glycosylation sites but not glycosylation occupancy or glycoform stoichiometry. Here we describe a method for large-scale determination of the absolute glycosylation stoichiometry using three independent relative ratios. Using this method, we determined 117 absolute N-glycosylation occupancies in OVCAR-3 cells. Finally, we investigated the possible functions and the determinants for partial glycosylation.

  3. Non-Invasive Method of Determining Absolute Intracranial Pressure

    NASA Technical Reports Server (NTRS)

    Yost, William T. (Inventor); Cantrell, John H., Jr. (Inventor); Hargens, Alan E. (Inventor)

    2004-01-01

    A method is presented for determining absolute intracranial pressure (ICP) in a patient. Skull expansion is monitored while changes in ICP are induced. The patient's blood pressure is measured when skull expansion is approximately zero. The measured blood pressure is indicative of a reference ICP value. Subsequently, the method causes a known change in ICP and measured the change in skull expansion associated therewith. The absolute ICP is a function of the reference ICP value, the known change in ICP and its associated change in skull expansion; and a measured change in skull expansion.

  4. Absolute gain measurement by the image method under mismatched condition

    NASA Technical Reports Server (NTRS)

    Lee, Richard Q.; Baddour, Maurice F.

    1987-01-01

    Purcell's image method for measuring the absolute gain of an antenna is particularly attractive for small test antennas. The method is simple to use and utilizes only one antenna with a reflecting plane to provide an image for the receiving antenna. However, the method provides accurate results only if the antenna is matched to its waveguide. In this paper, a waveguide junction analysis is developed to determine the gain of an antenna under mismatched condition. Absolute gain measurements for two standard gain horn antennas have been carried out. Experimental results agree closely with published data.

  5. Absolute photon-flux measurements in the vacuum ultraviolet

    NASA Technical Reports Server (NTRS)

    Samson, J. A. R.; Haddad, G. N.

    1974-01-01

    Absolute photon-flux measurements in the vacuum ultraviolet have extended to short wavelengths by use of rare-gas ionization chambers. The technique involves the measurement of the ion current as a function of the gas pressure in the ion chamber. The true value of the ion current, and hence the absolute photon flux, is obtained by extrapolating the ion current to zero gas pressure. Examples are given at 162 and 266 A. The short-wavelength limit is determined only by the sensitivity of the current-measuring apparatus and by present knowledge of the photoionization processes that occur in the rate gases.

  6. Nonexistence of equilibrium states at absolute negative temperatures

    NASA Astrophysics Data System (ADS)

    Romero-Rochín, Víctor

    2013-08-01

    We show that states of macroscopic systems with purported absolute negative temperatures are not stable under small, yet arbitrary, perturbations. We prove the previous statement using the fact that, in equilibrium, the entropy takes its maximum value. We discuss that, while Ramsey theoretical reformulation of the second law for systems with negative temperatures is logically correct, it must be a priori assumed that those states are in thermodynamic equilibrium. Since we argue that those states cannot occur, reversible processes are impossible, and, thus, Ramsey identification of absolute negative temperatures is untenable.

  7. Absolute Stability Analysis of a Phase Plane Controlled Spacecraft

    NASA Technical Reports Server (NTRS)

    Jang, Jiann-Woei; Plummer, Michael; Bedrossian, Nazareth; Hall, Charles; Jackson, Mark; Spanos, Pol

    2010-01-01

    Many aerospace attitude control systems utilize phase plane control schemes that include nonlinear elements such as dead zone and ideal relay. To evaluate phase plane control robustness, stability margin prediction methods must be developed. Absolute stability is extended to predict stability margins and to define an abort condition. A constrained optimization approach is also used to design flex filters for roll control. The design goal is to optimize vehicle tracking performance while maintaining adequate stability margins. Absolute stability is shown to provide satisfactory stability constraints for the optimization.

  8. Bone mineralization is regulated by signaling cross talk between molecular factors of local and systemic origin: the role of fibroblast growth factor 23.

    PubMed

    Sapir-Koren, Rony; Livshits, Gregory

    2014-01-01

    Body phosphate homeostasis is regulated by a hormonal counter-balanced intestine-bone-kidney axis. The major systemic hormones involved in this axis are parathyroid hormone (PTH), 1,25-dihydroxyvitamin-D, and fibroblast growth factor-23 (FGF23). FGF23, produced almost exclusively by the osteocytes, is a phosphaturic hormone that plays a major role in regulation of the bone remodeling process. Remodeling composite components, bone mineralization and resorption cycles create a continuous influx-efflux loop of the inorganic phosphate (Pi) through the skeleton. This "bone Pi loop," which is formed, is controlled by local and systemic factors according to phosphate homeostasis demands. Although FGF23 systemic actions in the kidney, and for the production of PTH and 1,25-dihydroxyvitamin-D are well established, its direct involvement in bone metabolism is currently poorly understood. This review presents the latest available evidence suggesting two aspects of FGF23 bone local activity: (a) Regulation of FGF23 production by both local and systemic factors. The suggested local factors include extracellular levels of Pi and pyrophosphate (PPi), (the Pi/PPi ratio), and another osteocyte-derived protein, sclerostin. In addition, 1,25-dihydroxyvitamin-D, synthesized locally by bone cells, may contribute to regulation of FGF23 production. The systemic control is achieved via PTH and 1,25-dihydroxyvitamin-D endocrine functions. (b) FGF23 acts as a local agent, directly affecting bone mineralization. We support the assumption that under balanced physiological conditions, sclerostin, by para- autocrine signaling, upregulates FGF23 production by the osteocyte. FGF23, in turn, acts as a mineralization inhibitor, by stimulating the generation of the major mineralization antagonist-PPi.

  9. Two methods for absolute calibration of dynamic pressure transducers

    NASA Astrophysics Data System (ADS)

    Swift, G. W.; Migliori, A.; Garrett, S. L.; Wheatley, J. C.

    1982-12-01

    Two techniques are described for absolute calibration of a dynamic pressure transducer from 0 to 400 Hz in 1-MPa helium gas. One technique is based on a comparison to a mercury manometer; the other is based on the principle of reciprocity. The two techniques agree within the instrumental uncertainties of 1%.

  10. Toward The Absolute Age of M92 With MIST

    NASA Astrophysics Data System (ADS)

    Choi, Jieun; Conroy, Charlie; Dotter, Aaron; Weisz, Daniel; Rosenfield, Philip; Dolphin, Andrew

    2016-08-01

    Globular clusters provide a fundamental link between stars and galaxies. For example, it has been suggested that ultra faint dwarf galaxies formed all of their stars prior to the epoch of reionization, but this conclusion hinges entirely on the striking similarity of their stellar populations to the ancient, metal-poor globular cluster M92. The accurate measurement of absolute ages of ancient globular clusters therefore has direct implications for the formation histories of the smallest galaxies in the Universe. However, a reliable determination of the absolute ages of globular clusters has proven to be a challenge due to uncertainties in stellar physics and complications in how the models are compared to observations. I will present preliminary results from a comprehensive study to measure the absolute age of M92 using high-quality HST archival imaging data. We pair our new MESA Isochrones and Stellar Tracks (MIST) models with a full CMD fitting framework to jointly fit multi-color CMDs, taking into account the uncertainties in abundances, distance, and stellar physics. The goal of this project is two-fold. First, we aim to provide the most secure absolute age of M92 to date with robustly estimated uncertainties. Second, we explore and quantify the degeneracies between uncertain physical quantities and model variables, such as the distance, mixing-length-alpha parameter, and helium abundance, with the ultimate goal of better constraining these unknowns with data from ongoing and future surveys such as K2, Gaia, TESS, JWST, and WFIRST.

  11. Individual Differences in Absolute and Relative Metacomprehension Accuracy

    ERIC Educational Resources Information Center

    Maki, Ruth H.; Shields, Micheal; Wheeler, Amanda Easton; Zacchilli, Tammy Lowery

    2005-01-01

    The authors investigated absolute and relative metacomprehension accuracy as a function of verbal ability in college students. Students read hard texts, revised texts, or a mixed set of texts. They then predicted their performance, took a multiple-choice test on the texts, and made posttest judgments about their performance. With hard texts,…

  12. Absolute Value Inequalities: High School Students' Solutions and Misconceptions

    ERIC Educational Resources Information Center

    Almog, Nava; Ilany, Bat-Sheva

    2012-01-01

    Inequalities are one of the foundational subjects in high school math curricula, but there is a lack of academic research into how students learn certain types of inequalities. This article fills part of the research gap by presenting the findings of a study that examined high school students' methods of approaching absolute value inequalities,…

  13. Is There a Rule of Absolute Neutralization in Nupe?

    ERIC Educational Resources Information Center

    Krohn, Robert

    1975-01-01

    A previously prosed rule of absolute neutralization (merging underlying low vowels) is eliminated in an alternative analysis including instead a rule that "breaks" the feature matrix of certain low vowels and redistributes the features of each vowel as a sequence of vowel-like transition plus (a). (Author/RM)

  14. A mathematical biologist's guide to absolute and convective instability.

    PubMed

    Sherratt, Jonathan A; Dagbovie, Ayawoa S; Hilker, Frank M

    2014-01-01

    Mathematical models have been highly successful at reproducing the complex spatiotemporal phenomena seen in many biological systems. However, the ability to numerically simulate such phenomena currently far outstrips detailed mathematical understanding. This paper reviews the theory of absolute and convective instability, which has the potential to redress this inbalance in some cases. In spatiotemporal systems, unstable steady states subdivide into two categories. Those that are absolutely unstable are not relevant in applications except as generators of spatial or spatiotemporal patterns, but convectively unstable steady states can occur as persistent features of solutions. The authors explain the concepts of absolute and convective instability, and also the related concepts of remnant and transient instability. They give examples of their use in explaining qualitative transitions in solution behaviour. They then describe how to distinguish different types of instability, focussing on the relatively new approach of the absolute spectrum. They also discuss the use of the theory for making quantitative predictions on how spatiotemporal solutions change with model parameters. The discussion is illustrated throughout by numerical simulations of a model for river-based predator-prey systems.

  15. Ophthalmoplegic migraine. Two patients with an absolute response to indomethacin.

    PubMed

    Pareja, J A; Churruca, J; de la Casa Fages, B; de Silanes, C López; Sánchez, C; Barriga, F J

    2010-06-01

    Two patients suffering from ophthalmoplegic migraine had a strictly unilateral headache absolutely responsive to indomethacin, but not to other non-steroidal anti-inflammatory drugs, analgesics or corticosteroids. Such observations raise a therapeutic alternative and suggest that ophthalmoplegic migraine may present with different headache phenotypes.

  16. Absolute Interrogative Intonation Patterns in Buenos Aires Spanish

    ERIC Educational Resources Information Center

    Lee, Su Ar

    2010-01-01

    In Spanish, each uttered phrase, depending on its use, has one of a variety of intonation patterns. For example, a phrase such as "Maria viene manana" "Mary is coming tomorrow" can be used as a declarative or as an absolute interrogative (a yes/no question) depending on the intonation pattern that a speaker produces. …

  17. Absolute configurations of zingiberenols isolated from ginger (Zingiber officinale) rhizomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The sesquiterpene alcohol zingiberenol, or 1,10-bisaboladien-3-ol, was isolated some time ago from ginger, Zingiber officinale, rhizomes, but its absolute configuration had not been determined. With three chiral centers present in the molecule, zingiberenol can exist in eight stereoisomeric forms. ...

  18. Lyman alpha SMM/UVSP absolute calibration and geocoronal correction

    NASA Technical Reports Server (NTRS)

    Fontenla, Juan M.; Reichmann, Edwin J.

    1987-01-01

    Lyman alpha observations from the Ultraviolet Spectrometer Polarimeter (UVSP) instrument of the Solar Maximum Mission (SMM) spacecraft were analyzed and provide instrumental calibration details. Specific values of the instrument quantum efficiency, Lyman alpha absolute intensity, and correction for geocoronal absorption are presented.

  19. Urey: to measure the absolute age of Mars

    NASA Technical Reports Server (NTRS)

    Randolph, J. E.; Plescia, J.; Bar-Cohen, Y.; Bartlett, P.; Bickler, D.; Carlson, R.; Carr, G.; Fong, M.; Gronroos, H.; Guske, P. J.; Herring, M.; Javadi, H.; Johnson, D. W.; Larson, T.; Malaviarachchi, K.; Sherrit, S.; Stride, S.; Trebi-Ollennu, A.; Warwick, R.

    2003-01-01

    UREY, a proposed NASA Mars Scout mission will, for the first time, measure the absolute age of an identified igneous rock formation on Mars. By extension to relatively older and younger rock formations dated by remote sensing, these results will enable a new and better understanding of Martian geologic history.

  20. Relative versus Absolute Stimulus Control in the Temporal Bisection Task

    ERIC Educational Resources Information Center

    de Carvalho, Marilia Pinhiero; Machado, Armando

    2012-01-01

    When subjects learn to associate two sample durations with two comparison keys, do they learn to associate the keys with the short and long samples (relational hypothesis), or with the specific sample durations (absolute hypothesis)? We exposed 16 pigeons to an ABA design in which phases A and B corresponded to tasks using samples of 1 s and 4 s,…

  1. Mechanism for an absolute parametric instability of an inhomogeneous plasma

    NASA Astrophysics Data System (ADS)

    Arkhipenko, V. I.; Budnikov, V. N.; Gusakov, E. Z.; Romanchuk, I. A.; Simonchik, L. V.

    1984-05-01

    The structure of plasma oscillations in a region of parametric spatial amplification has been studied experimentally for the first time. A new mechanism for an absolute parametric instability has been observed. This mechanism operates when a pump wave with a spatial structure more complicated than a plane wave propagates through a plasma which is inhomogeneous along more than one dimension.

  2. Mathematical Model for Absolute Magnetic Measuring Systems in Industrial Applications

    NASA Astrophysics Data System (ADS)

    Fügenschuh, Armin; Fügenschuh, Marzena; Ludszuweit, Marina; Mojsic, Aleksandar; Sokół, Joanna

    2015-09-01

    Scales for measuring systems are either based on incremental or absolute measuring methods. Incremental scales need to initialize a measurement cycle at a reference point. From there, the position is computed by counting increments of a periodic graduation. Absolute methods do not need reference points, since the position can be read directly from the scale. The positions on the complete scales are encoded using two incremental tracks with different graduation. We present a new method for absolute measuring using only one track for position encoding up to micrometre range. Instead of the common perpendicular magnetic areas, we use a pattern of trapezoidal magnetic areas, to store more complex information. For positioning, we use the magnetic field where every position is characterized by a set of values measured by a hall sensor array. We implement a method for reconstruction of absolute positions from the set of unique measured values. We compare two patterns with respect to uniqueness, accuracy, stability and robustness of positioning. We discuss how stability and robustness are influenced by different errors during the measurement in real applications and how those errors can be compensated.

  3. Series that Converge Absolutely but Don't Converge

    ERIC Educational Resources Information Center

    Kantrowitz, Robert; Schramm, Michael

    2012-01-01

    If a series of real numbers converges absolutely, then it converges. The usual proof requires completeness in the form of the Cauchy criterion. Failing completeness, the result is false. We provide examples of rational series that illustrate this point. The Cantor set appears in connection with one of the examples.

  4. Analysis of standard reference materials by absolute INAA

    SciTech Connect

    Heft, R.E.; Koszykowski, R.F.

    1981-07-01

    Three standard reference materials, flyash, soil, and ASI 4340 steel, were analyzed by a method of absolute instrumental neutron activation analysis (INAA). Two different light water pool-type reactors were used to produce equivalent analytical results even though the epithermal to thermal flux ratio in one reactor was higher than that in the other by a factor of two.

  5. Compositional dependence of the local structure of Se{sub x}Te{sub 1-x} alloys: Electron energy-loss spectra, real-space multiple-scattering calculations, and first-principles molecular dynamics

    SciTech Connect

    Katcho, N. A.; Lomba, E.; Urones-Garrote, E.; Otero-Diaz, L. C.; Landa-Canovas, A. R.

    2006-06-01

    In this work we present an investigation on the composition dependence of the local structure in Se{sub x}Te{sub 1-x} crystalline alloys analyzing their experimental energy-loss spectra with the aid of a real-space multiple-scattering modeling approach and first-principles molecular dynamics. The concourse of this latter technique is essential for a proper modeling of the alloy spectra. From our results, it can be inferred that Se{sub x}Te{sub 1-x} alloys exhibit a high degree of substitutional disorder ruling out the existence of fully ordered alternating copolymer chains of Se and Te atoms.

  6. Enhanced Cortical Connectivity in Absolute Pitch Musicians: A Model for Local Hyperconnectivity

    ERIC Educational Resources Information Center

    Loui, Psyche; Li, H. Charles; Hohmann, Anja; Schlaug, Gottfried

    2011-01-01

    Connectivity in the human brain has received increased scientific interest in recent years. Although connection disorders can affect perception, production, learning, and memory, few studies have associated brain connectivity with graded variations in human behavior, especially among normal individuals. One group of normal individuals who possess…

  7. The EM-POGO: A simple, absolute velocity profiler

    NASA Astrophysics Data System (ADS)

    Terker, S. R.; Sanford, T. B.; Dunlap, J. H.; Girton, J. B.

    2013-01-01

    Electromagnetic current instrumentation has been added to the Bathy Systems, Inc. POGO transport sondes to produce a free-falling absolute velocity profiler called EM-POGO. The POGO is a free-fall profiler that measures a depth-averaged velocity using GPS fixes at the beginning and end of a round trip to the ocean floor (or a preset depth). The EM-POGO adds a velocity profile determined from measurements of motionally induced electric fields generated by the ocean current moving through the vertical component of the Earth's magnetic field. In addition to providing information about the vertical structure of the velocity, the depth-dependent measurements improve transport measurements by correcting for the non-constant fall-rate. Neglecting the variable fall rate results in errors O (1 cm s-1). The transition from POGO to EM-POGO included electrically isolating the POGO and electric-field-measuring circuits, installing a functional GPS receiver, finding a pressure case that provided an optimal balance among crush-depth, price and size, and incorporating the electrodes, electrode collar, and the circuitry required for the electric field measurement. The first EM-POGO sea-trial was in July 1999. In August 2006 a refurbished EM-POGO collected 15 absolute velocity profiles; relative and absolute velocity uncertainty was ˜1cms-1 and 0.5-5 cm s-1, respectively, at a vertical resolution of 25 m. Absolute velocity from the EM-POGO compared to shipboard ADCP measurements differed by ˜ 1-2 cm s-1, comparable to the uncertainty in absolute velocity from the ADCP. The EM-POGO is thus a low-cost, easy to deploy and recover, and accurate velocity profiler.

  8. Networks of Absolute Calibration Stars for SST, AKARI, and WISE

    NASA Astrophysics Data System (ADS)

    Cohen, M.

    2007-04-01

    I describe the Cohen-Walker-Witteborn (CWW) network of absolute calibration stars built to support ground-based, airborne, and space-based sensors, and how they are used to calibrate instruments on the SPITZER Space Telescope (SST and Japan's AKARI (formerly ASTRO-F), and to support NASA's planned MidEx WISE (the Wide-field Infrared Survey Explorer). All missions using this common calibration share a self-consistent framework embracing photometry and low-resolution spectroscopy. CWW also underpins COBE/DIRBE several instruments used on the Kuiper Airborne Observatory ({KAO}), the joint Japan-USA ``IR Telescope in Space" (IRTS) Near-IR and Mid-IR spectrometers, the European Space Agency's IR Space Observatory (ISO), and the US Department of Defense's Midcourse Space eXperiment (MSX). This calibration now spans the far-UV to mid-infrared range with Sirius (one specific Kurucz synthetic spectrum) as basis, and zero magnitude defined from another Kurucz spectrum intended to represent an ideal Vega (not the actual star with its pole-on orientation and mid-infrared dust excess emission). Precision 4-29 μm radiometric measurements on MSX validate CWW's absolute Kurucz spectrum of Sirius, the primary, and a set of bright K/MIII secondary standards. Sirius is measured to be 1.0% higher than predicted. CWW's definitions of IR zero magnitudes lie within 1.1% absolute of MSX measurements. The US Air Force Research Laboratory's independent analysis of on-orbit {MSX} stellar observations compared with emissive reference spheres show CWW primary and empirical secondary spectra lie well within the ±1.45% absolute uncertainty associated with this 15-year effort. Our associated absolute calibration for the InfraRed Array Camera (IRAC) on the SST lies within ˜2% of the recent extension of the calibration of the Hubble Space Telescope's STIS instrument to NICMOS (Bohlin, these Proceedings), showing the closeness of these two independent approaches to calibration.

  9. Resolution of high molecular weight proteins in dependence on electric field strength in polyacrylamide gel electrophoresis.

    PubMed

    Starita-Geribaldi, M; Houri, A

    1997-01-01

    Resolution of high molecular weight proteins, in the upper region of polyacrylamide gels, was studied in relation to the type of electric field. Separations by constant field gel electrophoresis (CFGE) were compared to those in pulsed oscillatory high-performance electrophoresis (POPE), a novel technique which allows electrophoresis at high field strengths owing to a novel local field distribution. This distribution contributes to structural and mechanical stability of the gel with resultant well-reproducible separation, enhanced resolution, and higher absolute mobility of proteins in POPE.

  10. Modern management of locally advanced cervical carcinoma.

    PubMed

    Dueñas-Gonzalez, Alfonso; Cetina, Lucely; Mariscal, Ignacio; de la Garza, Jaime

    2003-10-01

    Radiation was until recently the key and only modality for the routine treatment of locally advanced cervical carcinoma. However after years of studying multi-modality treatments as an alternative to radiation alone in randomized phase III trials, the standard treatment has changed to chemo-radiation based on cisplatin. Three recent meta-analyses have confirmed that cisplatin-based chemo-radiation adds an absolute 12% benefit in five-year survival over radiation therapy alone. Neoadjuvant chemotherapy followed by radiation has not been of proven benefit, but when neoadjuvant chemotherapy is followed by surgery, an absolute increase of 15% in five-year survival over radiation alone is seen. This benefit in survival is comparable to that obtained with the current chemo-radiation schedules based on cisplatin. Despite these encouraging results there remains room for improvement as the five-year survival of patients treated with chemo-radiation ranges from nearly 80% in bulky IB tumours to only 25% in stage IVA disease. Other therapeutic approaches need to be fully evaluated including the use of chemo-radiation after neoadjuvant chemotherapy; the use of new drug combinations and the multi-modality combination of neoadjuvant chemotherapy followed by radical surgery plus adjuvant chemo-radiation. Likewise, the addition of radiosensitizers to cisplatin, preoperative chemo-radiation and/or adjuvant chemotherapy may eventually improve the currents results of cisplatin-based chemo-radiation. Nevertheless, it is hard to foresee a dramatic increase in cure rate, even with the most optimal combination of cytotoxic drugs, surgery and radiation, and thus the testing of molecular targeted therapies against cervical cancer is a logical step to follow.

  11. Potential energy hypersurface and molecular flexibility

    NASA Astrophysics Data System (ADS)

    Koča, Jaroslav

    1993-02-01

    The molecular flexibility phenomenon is discussed from the conformational potential energy(hyper) surface (PES) point of view. Flexibility is considered as a product of three terms: thermodynamic, kinetic and geometrical. Several expressions characterizing absolute and relative molecular flexibility are introduced, depending on a subspace studied of the entire conformational space, energy level E of PES as well as absolute temperature. Results obtained by programs DAISY, CICADA and PANIC in conjunction with molecular mechanics program MMX for flexibility analysis of isopentane, 2,2-dimethylpentane and isohexane molecules are introduced.

  12. Molecular Thermometry

    PubMed Central

    McCabe, Kevin M.; Hernandez, Mark

    2010-01-01

    Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients’ temperatures could be measured, recorded and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nano-scale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even sub-cellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry moved into the clinic, so too will these molecular thermometers. PMID:20139796

  13. Molecular typing of the recently expanding subtype B HIV-1 epidemic in Romania: evidence for local spread among MSMs in Bucharest area.

    PubMed

    Paraschiv, Simona; Otelea, Dan; Batan, Ionelia; Baicus, Cristian; Magiorkinis, Gkikas; Paraskevis, Dimitrios

    2012-07-01

    HIV-1 subtype B is predominant in Europe except in some countries from Eastern Europe which are characterized by a high prevalence of non-B subtypes and circulating recombinant forms (CRFs). Romania is a particular case: the HIV-1 epidemic started with subtype F1 which is still the most prevalent. Previous studies have shown an increasing prevalence of subtype B which is the second most frequent one among the newly diagnosed individuals, followed by subtype C and several CRFs as well as unique recombinant forms (URFs). Our objective was to analyze in detail the characteristics (way of dispersal, association with transmission risk groups) of the subtype B infections in Romania by means of phylogenetic analysis. Among all the individuals sampled during 2003-2010, 71 out of 1127 patients (6.3%) have been identified to be infected with subtype B strains. The most frequent route of infection identified in HIV-1 subtype B patients in Romania was MSM transmission (39.6%), followed by the heterosexual route (35.2%). Many of the patients acquired the infection abroad, mainly in Western European countries. Phylogenetic analysis indicated the existence of a local transmission network (monophyletic clade) including 14 patients, mainly MSM living in the Bucharest area. We estimate the origin of the local transmission network that dates at the beginning of the 90s; the introduction of the F1 and C subtypes occurred earlier. The rest of the sequences were intermixed with reference strains sampled across Europe suggesting that single infection were not followed by subsequent dispersal within the local population. Although HIV-1 subtype B epidemic in Romania is recent, there is evidence for local spread among the MSMs, in addition to multiple introductions.

  14. Molecular typing of the recently expanding subtype B HIV-1 epidemic in Romania: Evidence for local spread among MSMs in Bucharest area☆☆☆

    PubMed Central

    Paraschiv, Simona; Otelea, Dan; Batan, Ionelia; Baicus, Cristian; Magiorkinis, Gkikas; Paraskevis, Dimitrios

    2012-01-01

    HIV-1 subtype B is predominant in Europe except in some countries from Eastern Europe which are characterized by a high prevalence of non-B subtypes and circulating recombinant forms (CRFs). Romania is a particular case: the HIV-1 epidemic started with subtype F1 which is still the most prevalent. Previous studies have shown an increasing prevalence of subtype B which is the second most frequent one among the newly diagnosed individuals, followed by subtype C and several CRFs as well as unique recombinant forms (URFs). Our objective was to analyze in detail the characteristics (way of dispersal, association with transmission risk groups) of the subtype B infections in Romania by means of phylogenetic analysis. Among all the individuals sampled during 2003–2010, 71 out of 1127 patients (6.3%) have been identified to be infected with subtype B strains. The most frequent route of infection identified in HIV-1 subtype B patients in Romania was MSM transmission (39.6%), followed by the heterosexual route (35.2%). Many of the patients acquired the infection abroad, mainly in Western European countries. Phylogenetic analysis indicated the existence of a local transmission network (monophyletic clade) including 14 patients, mainly MSM living in the Bucharest area. We estimate the origin of the local transmission network that dates at the beginning of the 90s; the introduction of the F1 and C subtypes occurred earlier. The rest of the sequences were intermixed with reference strains sampled across Europe suggesting that single infection were not followed by subsequent dispersal within the local population. Although HIV-1 subtype B epidemic in Romania is recent, there is evidence for local spread among the MSMs, in addition to multiple introductions. PMID:22430050

  15. Greater absolute risk for all subtypes of breast cancer in the US than Malaysia.

    PubMed

    Horne, Hisani N; Beena Devi, C R; Sung, Hyuna; Tang, Tieng Swee; Rosenberg, Philip S; Hewitt, Stephen M; Sherman, Mark E; Anderson, William F; Yang, Xiaohong R

    2015-01-01

    Hormone receptor (HR) negative breast cancers are relatively more common in low-risk than high-risk countries and/or populations. However, the absolute variations between these different populations are not well established given the limited number of cancer registries with incidence rate data by breast cancer subtype. We, therefore, used two unique population-based resources with molecular data to compare incidence rates for the 'intrinsic' breast cancer subtypes between a low-risk Asian population in Malaysia and high-risk non-Hispanic white population in the National Cancer Institute's surveillance, epidemiology, and end results 18 registries database (SEER 18). The intrinsic breast cancer subtypes were recapitulated with the joint expression of the HRs (estrogen receptor and progesterone receptor) and human epidermal growth factor receptor-2 (HER2). Invasive breast cancer incidence rates overall were fivefold greater in SEER 18 than in Malaysia. The majority of breast cancers were HR-positive in SEER 18 and HR-negative in Malaysia. Notwithstanding the greater relative distribution for HR-negative cancers in Malaysia, there was a greater absolute risk for all subtypes in SEER 18; incidence rates were nearly 7-fold higher for HR-positive and 2-fold higher for HR-negative cancers in SEER 18. Despite the well-established relative breast cancer differences between low-risk and high-risk countries and/or populations, there was a greater absolute risk for HR-positive and HR-negative subtypes in the US than Malaysia. Additional analytical studies are sorely needed to determine the factors responsible for the elevated risk of all subtypes of breast cancer in high-risk countries like the United States.

  16. Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry*

    PubMed Central

    Ludwig, Christina; Claassen, Manfred; Schmidt, Alexander; Aebersold, Ruedi

    2012-01-01

    For many research questions in modern molecular and systems biology, information about absolute protein quantities is imperative. This information includes, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes, or quantitative comparisons of different proteins within one sample or across samples. To date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers of samples. Here we describe and demonstrate the utility of a targeting MS technique for the estimation of absolute protein abundance in unlabeled and nonfractionated cell lysates. The method is based on selected reaction monitoring (SRM) mass spectrometry and the “best flyer” hypothesis, which assumes that the specific MS signal intensity of the most intense tryptic peptides per protein is approximately constant throughout a whole proteome. SRM-targeted best flyer peptides were selected for each protein from the peptide precursor ion signal intensities from directed MS data. The most intense transitions per peptide were selected from full MS/MS scans of crude synthetic analogs. We used Monte Carlo cross-validation to systematically investigate the accuracy of the technique as a function of the number of measured best flyer peptides and the number of SRM transitions per peptide. We found that a linear model based on the two most intense transitions of the three best flying peptides per proteins (TopPep3/TopTra2) generated optimal results with a cross-correlated mean fold error of 1.8 and a squared Pearson coefficient R2 of 0.88. Applying the optimized model to lysates of the microbe Leptospira interrogans, we detected significant protein abundance changes of 39 target proteins upon antibiotic treatment, which correlate well with literature values. The described method is generally applicable and exploits the inherent performance advantages of SRM

  17. Determination of absolute configuration of chiral molecules using vibrational optical activity: a review.

    PubMed

    He, Yanan; Wang, Bo; Dukor, Rina K; Nafie, Laurence A

    2011-07-01

    Determination of the absolute handedness, known as absolute configuration (AC), of chiral molecules is an important step in any field related to chirality, especially in the pharmaceutical industry. Vibrational optical activity (VOA) has become a powerful tool for the determination of the AC of chiral molecules in the solution state after nearly forty years of evolution. VOA offers a novel alternative, or supplement, to X-ray crystallography, permitting AC determinations on neat liquid, oil, and solution samples without the need to grow single crystals of the pure chiral sample molecules as required for X-ray analysis. By comparing the sign and intensity of the measured VOA spectrum with the corresponding ab initio density functional theory (DFT) calculated VOA spectrum of a chosen configuration, one can unambiguously assign the AC of a chiral molecule. Comparing measured VOA spectra with calculated VOA spectra of all the conformers can also provide solution-state conformational populations. VOA consists of infrared vibrational circular dichroism (VCD) and vibrational Raman optical activity (ROA). Currently, VCD is used routinely by researchers in a variety of backgrounds, including molecular chirality, asymmetric synthesis, chiral catalysis, drug screening, pharmacology, and natural products. Although the application of ROA in AC determination lags behind that of VCD, with the recent implementation of ROA subroutines in commercial quantum chemistry software, ROA will in the future complement VCD for AC determination. In this review, the basic principles of the application of VCD to the determination of absolute configuration in chiral molecules are described. The steps required for VCD spectral measurement and calculation are outlined, followed by brief descriptions of recently published papers reporting the determination of AC in small organic, pharmaceutical, and natural product molecules.

  18. Evaluation of the Linear and Second-Order NLO Properties of Molecular Crystals within the Local Field Theory: Electron Correlation Effects, Choice of XC Functional, ZPVA Contributions, and Impact of the Geometry in the Case of 2-Methyl-4-nitroaniline.

    PubMed

    Seidler, Tomasz; Stadnicka, Katarzyna; Champagne, Benoît

    2014-05-13

    The linear [χ((1))] and second-order nonlinear [χ((2))] optical susceptibilities of the 2-methyl-4-nitroaniline (MNA) crystal are calculated within the local field theory, which consists of first computing the molecular properties, accounting for the dressing effects of the surroundings, and then taking into account the local field effects. Several aspects of these calculations are tackled with the aim of monitoring the convergence of the χ((1)) and χ((2)) predictions with respect to experiment by accounting for the effects of (i) the dressing field within successive approximations, of (ii) the first-order ZPVA corrections, and of (iii) the geometry. With respect to the reference CCSD-based results, besides double hybrid functionals, the most reliable exchange-correlation functionals are LC-BLYP for the static χ((1)) and CAM-B3LYP (and M05-2X, to a lesser extent) for the dynamic χ((1)) but they strongly underestimate χ((2)). Double hybrids perform better for χ((2)) but not necessarily for χ((1)), and, moreover, their performances are much similar to MP2, which is known to slightly overestimate β, with respect to high-level coupled-clusters calculations and, therefore, χ((2)). Other XC functionals with less HF exchange perform poorly with overestimations/underestimations of χ((1))/χ((2)), whereas the HF method leads to underestimations of both. The first-order ZPVA corrections, estimated at the B3LYP level, are usually small but not negligible. Indeed, after ZPVA corrections, the molecular polarizabilities and first hyperpolarizabilities increase by 2% and 5%, respectively, whereas their impact is magnified on the macroscopic responses with enhancements of χ((1)) by up to 5% and of χ((2)) by as much as 10%-12% at λ = 1064 nm. The geometry plays also a key role in view of predicting accurate susceptibilities, particularly for push-pull π-conjugated compounds such as MNA. So, the geometry optimized using periodic boundary conditions is characterized

  19. Molecular characterization of a sarco(endo)plasmic reticulum Ca2+-ATPase gene from Paramecium tetraurelia and localization of its gene product to sub-plasmalemmal calcium stores.

    PubMed Central

    Hauser, K; Pavlovic, N; Kissmehl, R; Plattner, H

    1998-01-01

    A cDNA encoding the gene for a sarco(endo)plasmic reticulum-type Ca2+-ATPase (SERCA) was isolated from a cDNA library of Paramecium tetraurelia by using degenerated primers according to conserved domains of SERCA-type ATPases. The identified nucleotide sequence (PtSERCA) is 3114 nucleotides in length with an open reading frame of 1037 amino acids. An intron of only 22 nucleotides occurs. Homology searches for the deduced amino acid sequence revealed 38-49% similarity to SERCA-type ATPases from organisms ranging from protozoans to mammals, with no more similarity to some parasitic protozoa of the same phylum. The calculated molecular mass of the encoded protein is 114.7 kDa. It contains the typical 10 transmembrane domains of SERCA-type ATPases and other conserved domains, such as the phosphorylation site and the ATP binding site. However, there are no binding sites for phospholamban and thapsigargin present in the PtSERCA. Antibodies raised against a cytoplasmic loop peptide between the phosphorylation site and the ATP binding site recognize on Western blots a protein of 106 kDa, exclusively in the fraction of sub-plasmalemmal calcium stores ('alveolar sacs'). In immunofluorescence studies the antibodies show labelling exclusively in the cell cortex of permeabilized cells in a pattern characteristic of the arrangement of alveolar sacs. When alveolar sacs where tested for phosphoenzyme-intermediate formation a phosphoprotein of the same molecular mass (106 kDa) could be identified. PMID:9693098

  20. Absolute calibration of vacuum ultraviolet spectrograph system for plasma diagnostics

    SciTech Connect

    Yoshikawa, M.; Kubota, Y.; Kobayashi, T.; Saito, M.; Numada, N.; Nakashima, Y.; Cho, T.; Koguchi, H.; Yagi, Y.; Yamaguchi, N.

    2004-10-01

    A space- and time-resolving vacuum ultraviolet (VUV) spectrograph system has been applied to diagnose impurity ions behavior in plasmas produced in the tandem mirror GAMMA 10 and the reversed field pinch TPE-RX. We have carried out ray tracing calculations for obtaining the characteristics of the VUV spectrograph and calibration experiments to measure the absolute sensitivities of the VUV spectrograph system for the wavelength range from 100 to 1100 A. By changing the incident angle, 50.6 deg. -51.4 deg., to the spectrograph whose nominal incident angle is 51 deg., we can change the observing spectral range of the VUV spectrograph. In this article, we show the ray tracing calculation results and absolute sensitivities when the angle of incidence into the VUV spectrograph is changed, and the results of VUV spectroscopic measurement in both GAMMA 10 and TPE-RX plasmas.