Leveling the field: The role of training, safety programs, and knowledge management systems in fostering inclusive field settings

NASA Astrophysics Data System (ADS)

Starkweather, S.; Crain, R.; Derry, K. R.

2016-12-01

Knowledge is empowering in all settings, but plays an elevated role in empowering under-represented groups in field research. Field research, particularly polar field research, has deep roots in masculinized and colonial traditions, which can lead to high barriers for women and minorities (e.g. Carey et al., 2016). While recruitment of underrepresented groups into polar field research has improved through the efforts of organizations like the Association of Polar Early Career Scientists (APECS), the experiences and successes of these participants is often contingent on the availability of specialized training opportunities or the quality of explicitly documented information about how to survive Arctic conditions or how to establish successful measurement protocols in harsh environments. In Arctic field research, knowledge is often not explicitly documented or conveyed, but learned through "experience" or informally through ad hoc advice. The advancement of field training programs and knowledge management systems suggest two means for unleashing more explicit forms of knowledge about field work. Examples will be presented along with a case for how they level the playing field and improve the experience of field work for all participants.

Leveling the field: The role of training, safety programs, and knowledge management systems in fostering inclusive field settings

NASA Astrophysics Data System (ADS)

Starkweather, S.; Crain, R.; Derry, K. R.

2017-12-01

Knowledge is empowering in all settings, but plays an elevated role in empowering under-represented groups in field research. Field research, particularly polar field research, has deep roots in masculinized and colonial traditions, which can lead to high barriers for women and minorities (e.g. Carey et al., 2016). While recruitment of underrepresented groups into polar field research has improved through the efforts of organizations like the Association of Polar Early Career Scientists (APECS), the experiences and successes of these participants is often contingent on the availability of specialized training opportunities or the quality of explicitly documented information about how to survive Arctic conditions or how to establish successful measurement protocols in harsh environments. In Arctic field research, knowledge is often not explicitly documented or conveyed, but learned through "experience" or informally through ad hoc advice. The advancement of field training programs and knowledge management systems suggest two means for unleashing more explicit forms of knowledge about field work. Examples will be presented along with a case for how they level the playing field and improve the experience of field work for all participants.

Beta Regression Finite Mixture Models of Polarization and Priming

ERIC Educational Resources Information Center

Smithson, Michael; Merkle, Edgar C.; Verkuilen, Jay

2011-01-01

This paper describes the application of finite-mixture general linear models based on the beta distribution to modeling response styles, polarization, anchoring, and priming effects in probability judgments. These models, in turn, enhance our capacity for explicitly testing models and theories regarding the aforementioned phenomena. The mixture…

On push-forward representations in the standard gyrokinetic model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyato, N., E-mail: miyato.naoaki@jaea.go.jp; Yagi, M.; Scott, B. D.

2015-01-15

Two representations of fluid moments in terms of a gyro-center distribution function and gyro-center coordinates, which are called push-forward representations, are compared in the standard electrostatic gyrokinetic model. In the representation conventionally used to derive the gyrokinetic Poisson equation, the pull-back transformation of the gyro-center distribution function contains effects of the gyro-center transformation and therefore electrostatic potential fluctuations, which is described by the Poisson brackets between the distribution function and scalar functions generating the gyro-center transformation. Usually, only the lowest order solution of the generating function at first order is considered to explicitly derive the gyrokinetic Poisson equation. This ismore » true in explicitly deriving representations of scalar fluid moments with polarization terms. One also recovers the particle diamagnetic flux at this order because it is associated with the guiding-center transformation. However, higher-order solutions are needed to derive finite Larmor radius terms of particle flux including the polarization drift flux from the conventional representation. On the other hand, the lowest order solution is sufficient for the other representation, in which the gyro-center transformation part is combined with the guiding-center one and the pull-back transformation of the distribution function does not appear.« less

Three-dimensional polarization algebra.

PubMed

R Sheppard, Colin J; Castello, Marco; Diaspro, Alberto

2016-10-01

If light is focused or collected with a high numerical aperture lens, as may occur in imaging and optical encryption applications, polarization should be considered in three dimensions (3D). The matrix algebra of polarization behavior in 3D is discussed. It is useful to convert between the Mueller matrix and two different Hermitian matrices, representing an optical material or system, which are in the literature. Explicit transformation matrices for converting the column vector form of these different matrices are extended to the 3D case, where they are large (81×81) but can be generated using simple rules. It is found that there is some advantage in using a generalization of the Chandrasekhar phase matrix treatment, rather than that based on Gell-Mann matrices, as the resultant matrices are of simpler form and reduce to the two-dimensional case more easily. Explicit expressions are given for 3D complex field components in terms of Chandrasekhar-Stokes parameters.

On the Wiener Polarity Index of Lattice Networks

PubMed Central

Chen, Lin; Li, Tao; Liu, Jinfeng; Shi, Yongtang; Wang, Hua

2016-01-01

Network structures are everywhere, including but not limited to applications in biological, physical and social sciences, information technology, and optimization. Network robustness is of crucial importance in all such applications. Research on this topic relies on finding a suitable measure and use this measure to quantify network robustness. A number of distance-based graph invariants, also known as topological indices, have recently been incorporated as descriptors of complex networks. Among them the Wiener type indices are the most well known and commonly used such descriptors. As one of the fundamental variants of the original Wiener index, the Wiener polarity index has been introduced for a long time and known to be related to the cluster coefficient of networks. In this paper, we consider the value of the Wiener polarity index of lattice networks, a common network structure known for its simplicity and symmetric structure. We first present a simple general formula for computing the Wiener polarity index of any graph. Using this formula, together with the symmetric and recursive topology of lattice networks, we provide explicit formulas of the Wiener polarity index of the square lattices, the hexagonal lattices, the triangular lattices, and the 33 ⋅ 42 lattices. We also comment on potential future research topics. PMID:27930705

Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory.

PubMed

Isegawa, Miho; Gao, Jiali; Truhlar, Donald G

2011-08-28

Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi-Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi-Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred. © 2011 American Institute of Physics

Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory

PubMed Central

Isegawa, Miho; Gao, Jiali; Truhlar, Donald G.

2011-01-01

Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi–Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi–Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred. PMID:21895159

Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

NASA Astrophysics Data System (ADS)

Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.

2011-01-01

Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

Emergence of a coherent and cohesive swarm based on mutual anticipation

PubMed Central

Murakami, Hisashi; Niizato, Takayuki; Gunji, Yukio-Pegio

2017-01-01

Collective behavior emerging out of self-organization is one of the most striking properties of an animal group. Typically, it is hypothesized that each individual in an animal group tends to align its direction of motion with those of its neighbors. Most previous models for collective behavior assume an explicit alignment rule, by which an agent matches its velocity with that of neighbors in a certain neighborhood, to reproduce a collective order pattern by simple interactions. Recent empirical studies, however, suggest that there is no evidence for explicit matching of velocity, and that collective polarization arises from interactions other than those that follow the explicit alignment rule. We here propose a new lattice-based computational model that does not incorporate the explicit alignment rule but is based instead on mutual anticipation and asynchronous updating. Moreover, we show that this model can realize densely collective motion with high polarity. Furthermore, we focus on the behavior of a pair of individuals, and find that the turning response is drastically changed depending on the distance between two individuals rather than the relative heading, and is consistent with the empirical observations. Therefore, the present results suggest that our approach provides an alternative model for collective behavior. PMID:28406173

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

PubMed

Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali

2009-02-17

A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.

Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.

PubMed

Chakravorty, Arghya; Jia, Zhe; Li, Lin; Zhao, Shan; Alexov, Emil

2018-02-13

Typically, the ensemble average polar component of solvation energy (ΔG polar solv ) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each snapshot. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB)-based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al. J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) can reproduce that ensemble average (ΔG polar solv ) of a protein from a single structure. We show that the Gaussian-based dielectric model reproduces the ensemble average ΔG polar solv (⟨ΔG polar solv ⟩) from an energy-minimized structure of a protein regardless of the minimization environment (structure minimized in vacuo, implicit or explicit waters, or crystal structure); the best case, however, is when it is paired with an in vacuo-minimized structure. In other minimization environments (implicit or explicit waters or crystal structure), the traditional two-dielectric model can still be selected with which the model produces correct solvation energies. Our observations from this work reflect how the ability to appropriately mimic the motion of residues, especially the salt bridge residues, influences a dielectric model's ability to reproduce the ensemble average value of polar solvation free energy from a single in vacuo-minimized structure.

Coherent nonlinear optical response of single-layer black phosphorus: third-harmonic generation

NASA Astrophysics Data System (ADS)

Margulis, Vladimir A.; Muryumin, Evgeny E.; Gaiduk, Evgeny A.

2017-10-01

We theoretically calculate the nonlinear optical (NLO) response of phosphorene (a black phosphorus monolayer) to a normally incident and linearly polarized coherent laser radiation of frequency ω, resulting in the generation of radiation at frequency 3ω. We derive explicit analytic expressions for four independent nonvanishing elements of the third-order NLO susceptibility tensor, describing the third-harmonic generation (THG) from phosphorene. The final formulas are numerically evaluated for typical values of the system's parameters to explore how the efficiency of the THG varies with both the frequency and the polarization direction of the incident radiation. The results obtained show a resonant enhancement of the THG efficiency when the pump photon energy ℏω approaches a value of one third of the bandgap energy Eg (≈1.5 eV) of phosphorene. It is also shown that the THG efficiency exhibits a specific polarization dependence, allowing the THG to be used for determining the orientation of phosphorene's crystallographic axes. Our findings highlight the material's potential for practical application in nanoscale photonic devices such as frequency convertors operating in the near-infrared spectral range.

Vacuum polarization near a distorted black hole

NASA Astrophysics Data System (ADS)

Frolov, V. P.; Alberto García, D.

1983-12-01

The vacuum polarization near a black hole distorted by the axially symmetric gravitational field of external matter is studied. The explicit expression for <φ2> at the pole of the distorted horizon is obtained. Also at Sección de Graduados, Escuela Superior de Ingeniería Mecánica y Eléctrica del IPN, México DF, México.

Numerical solution of the full potential equation using a chimera grid approach

NASA Technical Reports Server (NTRS)

Holst, Terry L.

1995-01-01

A numerical scheme utilizing a chimera zonal grid approach for solving the full potential equation in two spatial dimensions is described. Within each grid zone a fully-implicit approximate factorization scheme is used to advance the solution one interaction. This is followed by the explicit advance of all common zonal grid boundaries using a bilinear interpolation of the velocity potential. The presentation is highlighted with numerical results simulating the flow about a two-dimensional, nonlifting, circular cylinder. For this problem, the flow domain is divided into two parts: an inner portion covered by a polar grid and an outer portion covered by a Cartesian grid. Both incompressible and compressible (transonic) flow solutions are included. Comparisons made with an analytic solution as well as single grid results indicate that the chimera zonal grid approach is a viable technique for solving the full potential equation.

Linking Spectral Induced Polarization (SIP) and Subsurface Microbial Processes: Results from Sand Column Incubation Experiments.

PubMed

Mellage, Adrian; Smeaton, Christina M; Furman, Alex; Atekwana, Estella A; Rezanezhad, Fereidoun; Van Cappellen, Philippe

2018-02-20

Geophysical techniques, such as spectral induced polarization (SIP), offer potentially powerful approaches for in situ monitoring of subsurface biogeochemistry. The successful implementation of these techniques as monitoring tools for reactive transport phenomena, however, requires the deconvolution of multiple contributions to measured signals. Here, we present SIP spectra and complementary biogeochemical data obtained in saturated columns packed with alternating layers of ferrihydrite-coated and pure quartz sand, and inoculated with Shewanella oneidensis supplemented with lactate and nitrate. A biomass-explicit diffusion-reaction model is fitted to the experimental biogeochemical data. Overall, the results highlight that (1) the temporal response of the measured imaginary conductivity peaks parallels the microbial growth and decay dynamics in the columns, and (2) SIP is sensitive to changes in microbial abundance and cell surface charging properties, even at relatively low cell densities (<10 8 cells mL -1 ). Relaxation times (τ) derived using the Cole-Cole model vary with the dominant electron accepting process, nitrate or ferric iron reduction. The observed range of τ values, 0.012-0.107 s, yields effective polarization diameters in the range 1-3 μm, that is, 2 orders of magnitude smaller than the smallest quartz grains in the columns, suggesting that polarization of the bacterial cells controls the observed chargeability and relaxation dynamics in the experiments.

Non-inverse-square force-distance law for long thin magnets-revisited.

PubMed

Darvell, Brian W; Gilding, Brian H

2012-05-01

It had previously been shown that the inverse-square law does not apply to the force-distance relationship in the case of a long, thin magnet with one end in close proximity to its image in a permeable plane when simple point-like poles are assumed. Treating the system instead as having a 'polar disc', arising from an assumed bundle of dipoles, led to a double integral that could only be evaluated numerically, and a relationship that still did not match observed behavior. Using an elaborate 'stretched' exponential polynomial to represent the position of an 'elastic' polar disc resulted in a fair representation of the physical response, but this was essentially merely the fitting of an arbitrary function. The present purpose was therefore to find an explicit formula for the force-distance relationship in the polar-disc problem and assess its fit to the previously obtained experimental data. Starting from Coulomb's law a corrected integral formula for the force-distance relationship was derived. The integral in this formula was evaluated explicitly using rescaling, changes of order of integration, reduction by symmetry, and change of variables. The resulting formula was then fitted to data that had been obtained for the force exerted by eighty-five rod-shaped magnets (Alnico V, 3 mm diameter, 170 mm long) perpendicular to a large steel plate, as a function of distance, at small separations (<5 mm). Subsequently, the fit of alternative functions was explored. An explicit formula in terms of elliptic integrals was obtained for the polar-disc problem. Despite the greater fidelity, this too was found not to fit the observed physical behavior. Given that failure, nevertheless a simple formula that conforms closely and parsimoniously to the actual magnet data was found. A key feature remains the marked departure from inverse-square behavior. The failure of the explicit formula to fit the data indicates an inadequate model of the physical system. Nonetheless it constitutes a useful tool for quantifying the force-distance relationship on the premise of polar discs. Given these insights, it may now be possible to address the original motivating problem of the behavior of real dental magnets. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Solvent electronic polarization effects on a charge transfer excitation studied by the mean-field QM/MM method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakano, Hiroshi; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8245

2015-12-31

Electronic polarization effects of a medium can have a significant impact on a chemical reaction in condensed phases. We discuss the effects on the charge transfer excitation of a chromophore, N,N-dimethyl-4-nitroaniline, in various solvents using the mean-field QM/MM method with a polarizable force field. The results show that the explicit consideration of the solvent electronic polarization effects is important especially for a solvent with a low dielectric constant when we study the solvatochromism of the chromophore.

Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water.

PubMed

Yonezawa, Yasushige; Nakata, Kazuto; Sakakura, Kota; Takada, Toshikazu; Nakamura, Haruki

2009-04-01

The cis-trans isomerization of the peptide bond preceding a proline plays important roles in protein folding and biological function. Although many experimental and theoretical studies have been done, the mechanism has not yet been clearly elucidated. We studied the cis-trans isomerization of the proline dipeptide (Ace-Pro-NMe) in explicit water by molecular dynamics simulations using a combined potential derived from ab initio quantum mechanics and empirical molecular mechanics. We obtained the free energy landscape during the isomerization by using the umbrella sampling method. The free energy landscape is in good accordance with previous experimental and theoretical values. We observed that in the middle of the isomerization, the prolyl nitrogen transiently takes pyramidal conformations in two polarized directions and that, simultaneously, the prolyl C-N bond extends. We show that these geometrical changes cooperatively transform the prolyl nitrogen from a sp(2)-hybridized electronic state into a sp(3)-hybridized one, and thus realize a transition state that reduces the rotational barriers separating the cis- and trans-states. We also found that the hydration of the prolyl nitrogen stabilizes the negative pyramidal conformation, while an intramolecular interaction mainly stabilizes the positive one. Fluctuations in the polarity and magnitude of the pyramidal conformation during the isomerization are interpreted as a competition between the hydrogen-bonding partners for the prolyl nitrogen between different sides of the pyrrolidine ring.

Localized states in advanced dielectrics from the vantage of spin- and symmetry-polarized tunnelling across MgO.

PubMed

Schleicher, F; Halisdemir, U; Lacour, D; Gallart, M; Boukari, S; Schmerber, G; Davesne, V; Panissod, P; Halley, D; Majjad, H; Henry, Y; Leconte, B; Boulard, A; Spor, D; Beyer, N; Kieber, C; Sternitzky, E; Cregut, O; Ziegler, M; Montaigne, F; Beaurepaire, E; Gilliot, P; Hehn, M; Bowen, M

2014-08-04

Research on advanced materials such as multiferroic perovskites underscores promising applications, yet studies on these materials rarely address the impact of defects on the nominally expected materials property. Here, we revisit the comparatively simple oxide MgO as the model material system for spin-polarized solid-state tunnelling studies. We present a defect-mediated tunnelling potential landscape of localized states owing to explicitly identified defect species, against which we examine the bias and temperature dependence of magnetotransport. By mixing symmetry-resolved transport channels, a localized state may alter the effective barrier height for symmetry-resolved charge carriers, such that tunnelling magnetoresistance decreases most with increasing temperature when that state is addressed electrically. Thermal excitation promotes an occupancy switchover from the ground to the excited state of a defect, which impacts these magnetotransport characteristics. We thus resolve contradictions between experiment and theory in this otherwise canonical spintronics system, and propose a new perspective on defects in dielectrics.

A new numerical model of the middle atmosphere. I - Dynamics and transport of tropospheric source gases

NASA Technical Reports Server (NTRS)

Garcia, Rolando R.; Stordal, Frode; Solomon, Susan; Kiehl, Jeffrey T.

1992-01-01

Attention is given to a new model of the middle atmosphere which includes, in addition to the equations governing the zonal mean state, a potential vorticity equation for a single planetary-scale Rossby wave, and an IR radiative transfer code for the stratosphere and lower mesosphere, which replaces the Newtonian cooling parameterization used previously. It is shown that explicit computation of the planetary-scale wave field yields a more realistic representation of the zonal mean dynamics and the distribution of trace chemical species. Wave breaking produces a well-mixed 'surf zone' equatorward of the polar night vortex and drives a meridional circulation with downwelling on the poleward side of the vortex. This combination of mixing and downwelling produces shallow meridional gradients of trace gases in the subtropics and middle latitudes, and very steep gradients at the edge of the polar vortex. Computed distributions of methane and nitrous oxide are shown to agree well with observations.

Density functional perturbational orbital theory of spin polarization in electronic systems. II. Transition metal dimer complexes.

PubMed

Seo, Dong-Kyun

2007-11-14

We present a theoretical scheme for a semiquantitative analysis of electronic structures of magnetic transition metal dimer complexes within spin density functional theory (DFT). Based on the spin polarization perturbational orbital theory [D.-K. Seo, J. Chem. Phys. 125, 154105 (2006)], explicit spin-dependent expressions of the spin orbital energies and coefficients are derived, which allows to understand how spin orbitals form and change their energies and shapes when two magnetic sites are coupled either ferromagnetically or antiferromagnetically. Upon employment of the concept of magnetic orbitals in the active-electron approximation, a general mathematical formula is obtained for the magnetic coupling constant J from the analytical expression for the electronic energy difference between low-spin broken-symmetry and high-spin states. The origin of the potential exchange and kinetic exchange terms based on the one-electron picture is also elucidated. In addition, we provide a general account of the DFT analysis of the magnetic exchange interactions in compounds for which the active-electron approximation is not appropriate.

Making maps of cosmic microwave background polarization for B-mode studies: the POLARBEAR example

DOE PAGES

Poletti, Davide; Fabbian, Giulio; Le Jeune, Maude; ...

2017-03-30

Analysis of cosmic microwave background (CMB) datasets typically requires some filtering of the raw time-ordered data. For instance, in the context of ground-based observations, filtering is frequently used to minimize the impact of low frequency noise, atmospheric contributions and/or scan synchronous signals on the resulting maps. In this paper, we have explicitly constructed a general filtering operator, which can unambiguously remove any set of unwanted modes in the data, and then amend the map-making procedure in order to incorporate and correct for it. We show that such an approach is mathematically equivalent to the solution of a problem in whichmore » the sky signal and unwanted modes are estimated simultaneously and the latter are marginalized over. We investigated the conditions under which this amended map-making procedure can render an unbiased estimate of the sky signal in realistic circumstances. We then discuss the potential implications of these observations on the choice of map-making and power spectrum estimation approaches in the context of B-mode polarization studies. Specifically, we have studied the effects of time-domain filtering on the noise correlation structure in the map domain, as well as impact it may haveon the performance of the popular pseudo-spectrum estimators. We conclude that although maps produced by the proposed estimators arguably provide the most faithful representation of the sky possible given the data, they may not straightforwardly lead to the best constraints on the power spectra of the underlying sky signal and special care may need to be taken to ensure this is the case. By contrast, simplified map-makers which do not explicitly correct for time-domain filtering, but leave it to subsequent steps in the data analysis, may perform equally well and be easier and faster to implement. We focused on polarization-sensitive measurements targeting the B-mode component of the CMB signal and apply the proposed methods to realistic simulations based on characteristics of an actual CMB polarization experiment, POLARBEAR. Finally, our analysis and conclusions are however more generally applicable.« less

Making maps of cosmic microwave background polarization for B-mode studies: the POLARBEAR example

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poletti, Davide; Fabbian, Giulio; Le Jeune, Maude

Analysis of cosmic microwave background (CMB) datasets typically requires some filtering of the raw time-ordered data. For instance, in the context of ground-based observations, filtering is frequently used to minimize the impact of low frequency noise, atmospheric contributions and/or scan synchronous signals on the resulting maps. In this paper, we have explicitly constructed a general filtering operator, which can unambiguously remove any set of unwanted modes in the data, and then amend the map-making procedure in order to incorporate and correct for it. We show that such an approach is mathematically equivalent to the solution of a problem in whichmore » the sky signal and unwanted modes are estimated simultaneously and the latter are marginalized over. We investigated the conditions under which this amended map-making procedure can render an unbiased estimate of the sky signal in realistic circumstances. We then discuss the potential implications of these observations on the choice of map-making and power spectrum estimation approaches in the context of B-mode polarization studies. Specifically, we have studied the effects of time-domain filtering on the noise correlation structure in the map domain, as well as impact it may haveon the performance of the popular pseudo-spectrum estimators. We conclude that although maps produced by the proposed estimators arguably provide the most faithful representation of the sky possible given the data, they may not straightforwardly lead to the best constraints on the power spectra of the underlying sky signal and special care may need to be taken to ensure this is the case. By contrast, simplified map-makers which do not explicitly correct for time-domain filtering, but leave it to subsequent steps in the data analysis, may perform equally well and be easier and faster to implement. We focused on polarization-sensitive measurements targeting the B-mode component of the CMB signal and apply the proposed methods to realistic simulations based on characteristics of an actual CMB polarization experiment, POLARBEAR. Finally, our analysis and conclusions are however more generally applicable.« less

Explicit symplectic orbit and spin tracking method for electric storage ring

DOE PAGES

Hwang, Kilean; Lee, S. Y.

2016-08-18

We develop a symplectic charged particle tracking method for phase space coordinates and polarization in all electric storage rings. Near the magic energy, the spin precession tune is proportional to the fractional momentum deviation δ m from the magic energy, and the amplitude of the radial and longitudinal spin precession is proportional to η/δ m, where η is the electric dipole moment for an initially vertically polarized beam. As a result, the method can be used to extract the electron electric dipole moment of a charged particle by employing narrow band frequency analysis of polarization around the magic energy.

Electrode effects in dielectric spectroscopy of colloidal suspensions

NASA Astrophysics Data System (ADS)

Cirkel, P. A.; van der Ploeg, J. P. M.; Koper, G. J. M.

1997-02-01

We present a simple model to account for electrode polarization in colloidal suspensions. Apart from correctly predicting the ω {-3}/{2} dependence for the dielectric permittivity at low frequencies ω, the model provides an explicit dependence of the effect on electrode spacing. The predictions are tested for the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) water-in-oil microemulsion with iso-octane as continuous phase. In particular, the dependence of electrode polarization effects on electrode spacing has been measured and is found to be in accordance with the model prediction. Methods to reduce or account for electrode polarization are briefly discussed.

Projected polar bear sea ice habitat in the Canadian Arctic Archipelago.

PubMed

Hamilton, Stephen G; Castro de la Guardia, Laura; Derocher, Andrew E; Sahanatien, Vicki; Tremblay, Bruno; Huard, David

2014-01-01

Sea ice across the Arctic is declining and altering physical characteristics of marine ecosystems. Polar bears (Ursus maritimus) have been identified as vulnerable to changes in sea ice conditions. We use sea ice projections for the Canadian Arctic Archipelago from 2006 - 2100 to gain insight into the conservation challenges for polar bears with respect to habitat loss using metrics developed from polar bear energetics modeling. Shifts away from multiyear ice to annual ice cover throughout the region, as well as lengthening ice-free periods, may become critical for polar bears before the end of the 21st century with projected warming. Each polar bear population in the Archipelago may undergo 2-5 months of ice-free conditions, where no such conditions exist presently. We identify spatially and temporally explicit ice-free periods that extend beyond what polar bears require for nutritional and reproductive demands. Under business-as-usual climate projections, polar bears may face starvation and reproductive failure across the entire Archipelago by the year 2100.

Photodetection and Photoswitch Based On Polarized Optical Response of Macroscopically Aligned Carbon Nanotubes.

PubMed

Zhang, Ling; Wu, Yang; Deng, Lei; Zhou, Yi; Liu, Changhong; Fan, Shoushan

2016-10-12

Light polarization is extensively applied in optical detection, industry processing and telecommunication. Although aligned carbon nanotube naturally suppresses the transmittance of light polarized parallel to its axial direction, there is little application regarding the photodetection of carbon nanotube based on this anisotropic interaction with linearly polarized light. Here, we report a photodetection device realized by aligned carbon nanotube. Because of the different absorption behavior of polarized light with respect to polarization angles, such device delivers an explicit response to specific light wavelength regardless of its intensity. Furthermore, combining both experimental and mathematical analysis, we found that the light absorption of different wavelength causes characteristic thermoelectric voltage generation, which makes aligned carbon nanotube promising in optical detection. This work can also be utilized directly in developing new types of photoswitch that features a broad spectrum application from near-ultraviolet to intermediate infrared with easy integration into practical electric devices, for instance, a "wavelength lock".

Stellar occultation of polarized light from circumstellar electrons. I - Flat envelopes viewed edge on

NASA Technical Reports Server (NTRS)

Brown, John C.; Fox, Geoffrey K.

1989-01-01

The depolarizing and occultation effects of a finite spherical light source on the polarization of light Thomson-scattered from a flat circumstellar envelope seen edge-on are analyzed. The analysis shows that neglect of the finite size of the light source leads to a gross overestimate of the polarization for a given disk geometry. By including occultation and depolarization, it is found that B-star envelopes are necessarily highly flattened disk-type structures. For a disk viewed edge-on, the effect of occultation reduces the polarization more than the inclusion of the depolarization factor alone. Analysis of a one-dimensional plume leads to a powerful technique that permits the electron density distribution to be explicitly obtained from the polarimetric data.

TRANSPORT EQUATION OF A PLASMA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balescu, R.

1960-10-01

It is shown that the many-body problem in plasmas can be handled explicitly. An equation describing the collective effects of the problem is derived. For simplicity, a onecomponent gas is considered in a continuous neutralizing background. The tool for handling the problem is provided by the general theory of irreversible processes in gases. The equation derived describes the interaction of electrons which are"dressed" by a polarization cloud. The polarization cloud differs from the Debye cloud. (B.O.G.)

Two charges on a plane in a magnetic field: hidden algebra, (particular) integrability, polynomial eigenfunctions

NASA Astrophysics Data System (ADS)

Turbiner, A. V.; Escobar-Ruiz, M. A.

2013-07-01

The quantum mechanics of two Coulomb charges on a plane (e1, m1) and (e2, m2) subject to a constant magnetic field B perpendicular to the plane is considered. Four integrals of motion are explicitly indicated. It is shown that for two physically important particular cases, namely that of two particles of equal Larmor frequencies, {e_c} \\propto \\frac{e_1}{m_1}-\\frac{e_2}{m_2}=0 (e.g. two electrons) and one of a neutral system (e.g. the electron-positron pair, hydrogen atom) at rest (the center-of-mass momentum is zero) some outstanding properties occur. They are the most visible in double polar coordinates in CMS (R, ϕ) and relative (ρ, φ) coordinate systems: (i) eigenfunctions are factorizable, all factors except one with the explicit ρ-dependence are found analytically, they have definite relative angular momentum, (ii) dynamics in the ρ-direction is the same for both systems, it corresponds to a funnel-type potential and it has hidden sl(2) algebra, at some discrete values of dimensionless magnetic fields b ⩽ 1, (iii) particular integral(s) occur, (iv) the hidden sl(2) algebra emerges in finite-dimensional representation, thus, the system becomes quasi-exactly-solvable and (v) a finite number of polynomial eigenfunctions in ρ appear. Nine families of eigenfunctions are presented explicitly.

Debunking Climate Change Myths in the College Classroom

NASA Astrophysics Data System (ADS)

Bedford, D. P.

2012-12-01

Research in sociology (e.g. Hamilton, 2011) and social psychology (e.g. Kahan et al., 2012) suggests that there is no basis to an assumption common among educators that higher education levels lead to more rational decision making. Indeed, there is growing evidence that views on climate change, for just one significant example, become more polarized at higher education levels, rather than converging on the scientific consensus. Some research points to improved facility at filtering information according to preconceptions at higher education levels as a possible explanation for this phenomenon. Misinformation about subjects that are perceived to be contentious, such as anthropogenic climate change, is therefore potentially easily accepted despite-- or even because of-- higher levels of education. Thus, explicitly addressing misinformation about climate change may be an important strategy for use in the classroom. Fortunately, misinformation provides a valuable opportunity to turn a challenging situation to educational advantage and, in effect, make lemonade out of lemons. This presentation provides a case study of efforts explicitly to debunk climate change myths in the college classroom. The approach outlined here utilizes material on the psychology of the acceptance of misinformation for the popular audience, combined with examples of misinformation itself. Qualitative assessment of the effectiveness of these efforts is also presented. Hamilton, L. 2011. Education, political and opinions about climate change: evidence for interaction effects. Climatic Change vol. 104 no. 2, 231-242.. Kahan, D.M., E. Peters, M. Wittlin, P. Slovic, L. Larrimore Ouellette, D. Braman and G. Mandel. 2012. The polarizing impact of science literacy and numeracy on perceived climate change risks. Nature Climate Change. doi:10.1038/nclimate1547.

Roles of urea and TMAO on the interaction between extended non-polar peptides

NASA Astrophysics Data System (ADS)

Su, Zhaoqian; Dias, Cristiano

Urea and trimethylamine n-oxide (TMAO) are small molecules known to destabilize and stabilize, respectively, the structure of proteins when added to aqueous solution. To unravel the molecular mechanisms of these cosolvents on protein structure we perform explicit all-atom molecular dynamics simulations of extended poly-alanine and polyleucine dimers. We use an umbrella sampling protocol to compute the potential of mean force (PMF) of dimers at different concentrations of urea and TMAO. We find that the large non-polar side chain of leucine is affected by urea whereas backbone atoms and alanine's side chain are not. Urea is found to occupy positions between leucine's side chains that are not accessible to water. This accounts for extra Lennard-Jones bonds between urea and side chains that favors the unfolded state. These bonds compete with urea-solvent interactions that favor the folded state. The sum of these two energetic terms provide the enthalpic driving force for unfolding. We show here that this enthalpy correlate with the potential of mean force of poly-leucine dimers. Moreover, the framework developed here is general and may be used to provide insights into effects of other small molecules on protein interactions. The effect of the TMAO will be in the presentation. Department of Physics, University Heights, Newark, New Jersey, 07102-1982.

Theoretical analysis of uranium-doped thorium dioxide: Introduction of a thoria force field with explicit polarization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shields, A. E.; Ruiz Hernandez, S. E.; Leeuw, N. H. de, E-mail: DeLeeuwN@Cardiff.ac.uk

2015-08-15

Thorium dioxide is used industrially in high temperature applications, but more insight is needed into the behavior of the material as part of a mixed-oxide (MOX) nuclear fuel, incorporating uranium. We have developed a new interatomic potential model including polarizability via a shell model, and commensurate with a prominent existing UO{sub 2} potential, to conduct configurational analyses and to investigate the thermophysical properties of uranium-doped ThO{sub 2}. Using the GULP and Site Occupancy Disorder (SOD) computational codes, we have analyzed the distribution of low concentrations of uranium in the bulk material, where we have not observed the formation of uraniummore » clusters or the dominance of a single preferred configuration. We have calculated thermophysical properties of pure thorium dioxide and Th{sub (1−x)}U{sub x}O{sub 2} which generated values in very good agreement with experimental data.« less

A premodern legacy: the "easy" criminalization of homosexual acts between women in the Finnish Penal Code of 1889.

PubMed

Löfström, J

1998-01-01

Homosexual acts between women were criminalized in Finland in the 1889 Penal Code which also criminalized men's homosexual acts for the first time explicitly in Finnish legislation. The inclusion of women in the Penal Code took place without much ado. In the article it is argued that the uncomplicated juxtaposing of men and women was due to the legacy of a cultural pattern where man and woman, as categories, were not in an all-pervasive polarity to each other, for example, in sexual subjectivity. A cultural pattern of low gender polarization was typical of preindustrial rural culture, and it can help us apprehend also certain other features in contemporary Finnish social and political life, for example, women obtaining a general franchise and eligibility for the parliament first in the world, in 1906. A modern image of "public man" and "private woman" was only making its way in Finnish society; hence, there was not much anxiety at women's entry in politics, or, for that matter, at their potential for (homo)sexual subjectivity becoming recognized publicly in criminal law.

Oceanic signals in rapid polar motion: results from a barotropic forward model with explicit consideration of self-attraction and loading effects

NASA Astrophysics Data System (ADS)

Schindelegger, Michael; Quinn, Katherine J.; Ponte, Rui M.

2017-04-01

Numerical modeling of non-tidal variations in ocean currents and bottom pressure has played a key role in closing the excitation budget of Earth's polar motion for a wide range of periodicities. Non-negligible discrepancies between observations and model accounts of pole position changes prevail, however, on sub-monthly time scales and call for examination of hydrodynamic effects usually omitted in general circulation models. Specifically, complete hydrodynamic cores must incorporate self-attraction and loading (SAL) feedbacks on redistributed water masses, effects that produces ocean bottom pressure perturbations of typically about 10% relative to the computed mass variations. Here, we report on a benchmark simulation with a near-global, barotropic forward model forced by wind stress, atmospheric pressure, and a properly calculated SAL term. The latter is obtained by decomposing ocean mass anomalies on a 30-minute grid into spherical harmonics at each time step and applying Love numbers to account for seafloor deformation and changed gravitational attraction. The increase in computational time at each time step is on the order of 50%. Preliminary results indicate that the explicit consideration of SAL in the forward runs increases the fidelity of modeled polar motion excitations, in particular on time scales shorter than 5 days as evident from cross spectral comparisons with geodetic excitation. Definite conclusions regarding the relevance of SAL in simulating rapid polar motion are, however, still hampered by the model's incomplete domain representation that excludes parts of the highly energetic Arctic Ocean.

Excited state electronic polarization and reappraisal of the n ← π∗ emission of acetone in water

NASA Astrophysics Data System (ADS)

Orozco-González, Yoelvis; Coutinho, Kaline; Canuto, Sylvio

2010-10-01

Electronic polarization of the acetone molecule in the excited n → π∗ state is considered and its influence on the solvent shift in the emission spectrum is analyzed. Using an iterative procedure the electronic polarizations of both the ground and the excited states are included and compared with previous results obtained with Car-Parrinello dynamics. Analysis of the emission transition obtained using CIS(D)/aug-cc-pVDZ on statistically uncorrelated solute-solvent structures, composed of acetone and twelve explicit water molecules embedded in the electrostatic field of remaining 263 water molecules, corroborates that the solvent effect is mild, calculated here between 80 and 380 cm -1.

Explicit polarization: a quantum mechanical framework for developing next generation force fields.

PubMed

Gao, Jiali; Truhlar, Donald G; Wang, Yingjie; Mazack, Michael J M; Löffler, Patrick; Provorse, Makenzie R; Rehak, Pavel

2014-09-16

Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples involving water clusters (which show the power of two-body corrections), ethylmethylimidazolium acetate ionic liquids (which reveal that the amount of charge transfer between anion and cation is much smaller than what has been assumed in some classical simulations), and a solvated protein in aqueous solution (which shows that the average charge distribution of carbonyl groups along the polypeptide chain depends strongly on their position in the sequence, whereas they are fixed in most classical force fields). The development of QMFFs also offers an opportunity to extend the accuracy of biochemical simulations to areas where classical force fields are often insufficient, especially in the areas of spectroscopy, reactivity, and enzyme catalysis.

[Emotional processes in schizophrenia: investigation of the evaluative component].

PubMed

Sander, D; Koenig, O; Georgieff, N; Terra, J-L; Franck, N

2005-01-01

Schizophrenia is a disease that constitutes a particularly relevant way to investigate emotional processing. Indeed, major clinical signs of emotional disturbance (eg, anhedonia) suggest that some emotional mechanisms are defective in patients with schizophrenia. Evaluation can be considered as a fundamental component of the emotional system (28) and the first aim of the present study was to test the polarity hypothesis according to which different mechanisms are involved in the evaluation of positive vs negative emotional events. The second aim was to disentangle a -paradox emerging from the schizophrenia literature. On one hand, the tendency that schizophrenic patients have to under-evaluate the level of unpleasantness of negative stimuli suggests a deficit in the evaluation of negative events. For instance, it was proposed that patients with schizophrenia show a major deficit in the recognition of negative emotions, but a preserved recognition of positive emotions. On the other hand, the fact that anhedonia constitutes a critical cli-nical feature of schizophrenia suggests a deficit in the eva-luation of positive events. For instance, Crespo-Facorro et al. showed that patients with schizophrenia had a tendency to under-evaluate the level of pleasantness of positive stimuli but correctly evaluated the level of unpleasantness of negative stimuli. Given the importance of the social component in the analysis of deficits in patients with schizophrenia, we hypothesized that the variation of this component in stimuli used in the literature could explain the apparently inconsistent results described above. For example, the Bell et al. study used social stimuli whereas the Crespo-Facorro et al. study used non-social stimuli. Therefore, in our study, we have decided to manipulate the social component of stimuli. Another research issue of the present experiment was to study the explicit and/or implicit mode of processing of eva-luation in schizophrenic patients. In general, the experimental logic was to expect interaction effects between the factors polarity (negative vs positive) and participants (schizophrenic patients vs controls). Moreover, given the potential importance of the social component, a three-way interaction of the factors polarity, participants, and social component was expected. Finally, the experimental paradigm allowed us to search for dissociations in the context of both explicit and implicit evaluation. Stimuli used were negative and positive emotional pictures from the International Affective Picture System. Stimuli were chosen so that the mean valence -ratings of negative and positive pictures were at the same distance from neutrality. The factor arousal was controlled so that negative and positive pictures had equivalent mean arousal ratings. The social component factor was operatio-nalized by selecting pictures that either depicted or not a social scene. A fundamental criterion was that all social pictures were depicting at least one human being (eg, a wedding or a funeral), whereas non-social pictures never depicted any human being (eg, animals and landscapes). An upper and a lower border, that were either identical or different, were added to each picture. In a first experiment (the "implicit-task experiment"), patients with schizophrenia and matched controls were requested to decide whether the two borders surrounding the pictures were identical or different. Asking participants to process the borders was an experimental ruse to test if emotional processing takes place even when it is not task-relevant, and therefore if it is implicit. In a second experiment (the "explicit-task experiment"), the same participants were requested to evaluate whether the pictures were pleasant or unpleasant. Analyses of variance (ANOVA) were computed on response time and number of correct responses for both tasks. An important result was the observation of the expected three-way interaction effect of the factors polarity, participants, and social component on response time in the explicit task F(1, 19)=4.8, p<0.05. Critically, we observed that, for non-social stimuli, the interaction effect of the factors participants and polarity on response time was significant in the explicit task, F(1, 8)=4.9, p<0.05. These results are consistent with the polarity hypothesis and suggest a deficit in the processing of non-social positive stimuli in patients with schizophrenia. The expected three-way interaction effect was also observed on the number of correct responses in the explicit task F(1, 19)=5, p<0.04. For this task, we critically observed that, for social stimuli, the interaction effect of the factors participants and polarity on the number of correct responses was significant F(1, 19)=8.4, p<0.04. These results are also consistent with the polarity hypothesis and suggest a deficit in the processing of social negative stimuli in patients with schizophrenia. Moreover, let us notice that a comparison of the performances of the two groups revealed that patients made significantly more errors than controls for the evaluation of non-social positive stimuli, F(1, 19)=10,5, p<0.001, but not for the evaluation of non-social negative stimuli, F<1. In the implicit-task experiment, the analysis revealed that patients had a tendency to make more errors in the judgment of borders configuration for negative than for positive stimuli, whereas control participants showed the opposite tendency F(1, 19)=5.7, p<0.03, for the interaction of the factors polarity and participants. This result is consistent with the idea that distinct cognitive mechanisms are involved in the evaluation of positive vs negative emotional events even in the context of implicit processing. In conclusion, results obtained support the hypothesis according to which different cognitive mechanisms are involved in the evaluation of positive vs negative emotional events. Moreover, results suggest that patients with schizophrenia show a deficit in hedonic judgment of social negative and non-social positive stimuli. The later result indicates that the paradox described above becomes clearer whenever the social component of emotional stimuli happens to be taken into account. Results suggest that the polarity and the social component of events evaluated by patients with schizophrenia are critical parameters that should be considered in forthcoming studies that investigate affect disorders in schizophrenia.

A new ab initio potential energy surface for the Ne-H 2 interaction

NASA Astrophysics Data System (ADS)

Lique, François

2009-03-01

A new accurate three-dimensional potential energy surface for the Ne-H 2 system, which explicitly takes into account the r-dependence of the H 2 vibration, was determined from ab initio calculations. It was obtained with the single and double excitation coupled-cluster method with noniterative perturbational treatment of triple excitation [CCSD(T)]. Calculations was been performed using the augmented correlation-consistent polarized quintuple zeta basis set (aug-cc-pV5Z) for the three atoms. We checked the accuracy of the present ab initio calculations. We have determined, using the new Ne-H 2 potential energy surface, differential cross-sections for the rotational excitation of the H 2 and D 2 molecules in collision with Ne and we have compared them with experimental results of Faubel et al. [M. Faubel, F.A. Gianturco, F. Ragnetti, L.Y. Rusin, F. Sondermann, U. Tappe, J.P. Toennies, J. Chem. Phys. 101 (1994) 8800]. The overall agreement confirms that the new potential energy surface can be used for the simulation of molecular collisions and/or molecular spectroscopy of the van der Waals complex Ne-H 2.

Vacuum-polarization effects in global monopole space-times

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mazzitelli, F.D.; Lousto, C.O.

1991-01-15

The gravitational effect produced by a global monopole may be approximated by a solid deficit angle. As a consequence, the energy-momentum tensor of a quantum field will have a nonzero vacuum expectation value. Here we study this vacuum-polarization effect'' around the monopole. We find explicit expressions for both {l angle}{phi}{sup 2}{r angle}{sub ren} and {l angle}{ital T}{sub {mu}{nu}}{r angle}{sub ren} for a massless scalar field. The back reaction of the quantum field on the monopole metric is also investigated.

Polarized 3-folds in a codimension 10 weighted homogeneous F4 variety

NASA Astrophysics Data System (ADS)

Qureshi, Muhammad Imran

2017-10-01

We describe the construction of a codimension 10 weighted homogeneous variety wΣF4(μ , u) corresponding to the exceptional Lie group F4 by explicit computation of its graded ring structure. We give a formula for the Hilbert series of the generic weighted wΣF4(μ , u) in terms of representation theoretic data of F4. We also construct some families of polarized 3-folds in codimension 10 whose general member is a weighted complete intersection of some wΣF4(μ , u) .

Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

PubMed

Tahan, A; Monajjemi, M

2011-12-01

Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.

Dielectric constant and low-frequency infrared spectra for liquid water and ice Ih within the E3B model.

PubMed

Shi, L; Ni, Y; Drews, S E P; Skinner, J L

2014-08-28

Two intrinsic difficulties in modeling condensed-phase water with conventional rigid non-polarizable water models are: reproducing the static dielectric constants for liquid water and ice Ih, and generating the peak at about 200 cm(-1) in the low-frequency infrared spectrum for liquid water. The primary physical reason for these failures is believed to be the missing polarization effect in these models, and consequently various sophisticated polarizable water models have been developed. However, in this work we pursue a different strategy and propose a simple empirical scheme to include the polarization effect only on the dipole surface (without modifying a model's intermolecular interaction potential). We implement this strategy for our explicit three-body (E3B) model. Our calculated static dielectric constants and low-frequency infrared spectra are in good agreement with experiment for both liquid water and ice Ih over wide temperature ranges, albeit with one fitting parameter for each phase. The success of our modeling also suggests that thermal fluctuations about local minima and the energy differences between different proton-disordered configurations play minor roles in the static dielectric constant of ice Ih. Our analysis shows that the polarization effect is important in resolving the two difficulties mentioned above and sheds some light on the origin of several features in the low-frequency infrared spectra for liquid water and ice Ih.

Discrete and continuum modeling of solvent effects in a twisted intramolecular charge transfer system: The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule.

PubMed

Modesto-Costa, Lucas; Borges, Itamar

2018-08-05

The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule is a prototypical system displaying twisted intramolecular (TICT) charge transfer effects. The ground and the first four electronic excited states (S 1 -S 4 ) in gas phase and upon solvation were studied. Charge transfer values as function of the torsion angle between the donor group (dimethylamine) and the acceptor moiety (benzonitrile) were explicitly computed. Potential energy curves were also obtained. The algebraic diagrammatic construction method at the second-order [ADC(2)] ab initio wave function was employed. Three solvents of increased polarities (benzene, DMSO and water) were investigated using discrete (average solvent electrostatic configuration - ASEC) and continuum (conductor-like screening model - COSMO) models. The results for the S 3 and S 4 excited states and the S 1 -S 4 charge transfer curves were not previously available in the literature. Electronic gas phase and solvent vertical spectra are in good agreement with previous theoretical and experimental results. In the twisted (90°) geometry the optical oscillator strengths have negligible values even for the S 2 bright state. Potential energy curves show two distinct pairs of curves intersecting at decreasing angles or not crossing in the more polar solvents. Charge transfer and electric dipole values allowed the rationalization of these results. The former effects are mostly independent of the solvent model and polarity. Although COSMO and ASEC solvent models mostly lead to similar results, there is an important difference: some crossings of the excitation energy curves appear only in the ASEC solvation model, which has important implications to the photochemistry of DMABN. Copyright © 2018 Elsevier B.V. All rights reserved.

Kinetic attractor phase diagrams of active nematic suspensions: the dilute regime.

PubMed

Forest, M Gregory; Wang, Qi; Zhou, Ruhai

2015-08-28

Large-scale simulations by the authors of the kinetic-hydrodynamic equations for active polar nematics revealed a variety of spatio-temporal attractors, including steady and unsteady, banded (1d) and cellular (2d) spatial patterns. These particle scale activation-induced attractors arise at dilute nanorod volume fractions where the passive equilibrium phase is isotropic, whereas all previous model simulations have focused on the semi-dilute, nematic equilibrium regime and mostly on low-moment orientation tensor and polarity vector models. Here we extend our previous results to complete attractor phase diagrams for active nematics, with and without an explicit polar potential, to map out novel spatial and dynamic transitions, and to identify some new attractors, over the parameter space of dilute nanorod volume fraction and nanorod activation strength. The particle-scale activation parameter corresponds experimentally to a tunable force dipole strength (so-called pushers with propulsion from the rod tail) generated by active rod macromolecules, e.g., catalysis with the solvent phase, ATP-induced propulsion, or light-activated propulsion. The simulations allow 2d spatial variations in all flow and orientational variables and full spherical orientational degrees of freedom; the attractors correspond to numerical integration of a coupled system of 125 nonlinear PDEs in 2d plus time. The phase diagrams with and without the polar interaction potential are remarkably similar, implying that polar interactions among the rodlike particles are not essential to long-range spatial and temporal correlations in flow, polarity, and nematic order. As a general rule, above a threshold, low volume fractions induce 1d banded patterns, whereas higher yet still dilute volume fractions yield 2d patterns. Again as a general rule, varying activation strength at fixed volume fraction induces novel dynamic transitions. First, stationary patterns saturate the instability of the isotropic state, consisting of discrete 1d banded or 2d cellular patterns depending on nanorod volume fraction. Increasing activation strength further induces a sequence of attractor bifurcations, including oscillations superimposed on the 1d and 2d stationary patterns, a uniform translational motion of 1d and 2d oscillating patterns, and periodic switching between 1d and 2d patterns. These results imply that active macromolecular suspensions are capable of long-range spatial and dynamic organization at isotropic equilibrium concentrations, provided particle-scale activation is sufficiently strong.

Magnetic Nulls and Super-radial Expansion in the Solar Corona

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibson, Sarah E.; Dalmasse, Kevin; Tomczyk, Steven

Magnetic fields in the Sun’s outer atmosphere—the corona—control both solar-wind acceleration and the dynamics of solar eruptions. We present the first clear observational evidence of coronal magnetic nulls in off-limb linearly polarized observations of pseudostreamers, taken by the Coronal Multichannel Polarimeter (CoMP) telescope. These nulls represent regions where magnetic reconnection is likely to act as a catalyst for solar activity. CoMP linear-polarization observations also provide an independent, coronal proxy for magnetic expansion into the solar wind, a quantity often used to parameterize and predict the solar wind speed at Earth. We introduce a new method for explicitly calculating expansion factorsmore » from CoMP coronal linear-polarization observations, which does not require photospheric extrapolations. We conclude that linearly polarized light is a powerful new diagnostic of critical coronal magnetic topologies and the expanding magnetic flux tubes that channel the solar wind.« less

Magnetic Nulls and Super-Radial Expansion in the Solar Corona

NASA Technical Reports Server (NTRS)

Gibson, Sarah E.; Dalmasse, Kevin; Rachmeler, Laurel A.; De Rosa, Marc L.; Tomczyk, Steven; De Toma, Giuliana; Burkepile, Joan; Galloy, Michael

2017-01-01

Magnetic fields in the Sun's outer atmosphere, the corona, control both solar-wind acceleration and the dynamics of solar eruptions. We present the first clear observational evidence of coronal magnetic nulls in off-limb linearly polarized observations of pseudostreamers, taken by the Coronal Multichannel Polarimeter (CoMP) telescope. These nulls represent regions where magnetic reconnection is likely to act as a catalyst for solar activity.CoMP linear-polarization observations also provide an independent, coronal proxy for magnetic expansion into the solar wind, a quantity often used to parameterize and predict the solar wind speed at Earth. We introduce a new method for explicitly calculating expansion factors from CoMP coronal linear-polarization observations, which does not require photospheric extrapolations. We conclude that linearly polarized light is a powerful new diagnostic of critical coronal magnetic topologies and the expanding magnetic flux tubes that channel the solar wind.

Physics of crypto-nonlocality

NASA Astrophysics Data System (ADS)

Navascués, Miguel

2014-02-01

In 2003, Leggett introduced his model of crypto-nonlocality based on considerations on the reality of photon polarization [A. J. Leggett, Found. Phys. 33, 1469 (2003), 10.1023/A:1026096313729]. In this paper, we prove that, contrary to hints in subsequent literature, crypto-nonlocality does not follow naturally from the postulate that polarization is a realistic variable. More explicitly, consider physical theories where (a) faster-than-light communication is impossible, (b) all physical photon states have a definite polarization, and (c) given two separate photons, if we measure one of them and post-select on the result, the measurement statistics of the remaining system correspond to a photon state. We show that the outcomes of any two-photon polarization experiment in these theories must follow the statistics generated by measuring a separable two-qubit quantum state. Consequently, in such experiments any instance of entanglement detection—and not necessarily a Leggett inequality violation—can be regarded as a refutation of this class of theories.

Inclusion of exact exchange in the noniterative partial-differential-equation method of electron-molecule scattering - Application to e-N2

NASA Technical Reports Server (NTRS)

Weatherford, C. A.; Onda, K.; Temkin, A.

1985-01-01

The noniterative partial-differential-equation (PDE) approach to electron-molecule scattering of Onda and Temkin (1983) is modified to account for the effects of exchange explicitly. The exchange equation is reduced to a set of inhomogeneous equations containing no integral terms and solved noniteratively in a difference form; a method for propagating the solution to large values of r is described; the changes in the polarization potential of the original PDE method required by the inclusion of exact static exchange are indicated; and the results of computations for e-N2 scattering in the fixed-nuclei approximation are presented in tables and graphs and compared with previous calculations and experimental data. Better agreement is obtained using the modified PDE method.

Hamiltonian theory of gaps, masses, and polarization in quantum Hall states

NASA Astrophysics Data System (ADS)

Shankar, R.

2001-02-01

In two short papers I had described an extension, to all length scales, of the Hamiltonian theory of composite fermions (CF) that Murthy and I developed for the infrared, and applied it to compute finite-temperature quantities for quantum Hall fractions. I furnish details of the extended theory and apply it to Jain fractions ν=p/(2ps+1). The explicit operator description in terms of the CF allows one to answer quantitative and qualitative issues, some of which cannot even be posed otherwise. I compute activation gaps for several potentials, exhibit their particle-hole symmetry, the profiles of charge density in states with a quasiparticle or hole (all in closed form), and compare to results from trial wave functions and exact diagonalization. The Hartree-Fock approximation is used, since much of the nonperturbative physics is built-in at tree level. I compare the gaps to experiment, and comment on the rough equality of normalized masses near half- and quarter-filling. I compute the critical fields at which the Hall system will jump from one quantized value of polarization to another, and the polarization and relaxation rates for half-filling as a function of temperature and propose a Korringa-like law. After providing some plausibility arguments, I explore the possibility of describing several magnetic phenomena in dirty systems with an effective potential, by extracting a free parameter describing the potential from one data point and then using it to predict all the others from that sample. This works to the accuracy typical of this theory (10-20 %). I explain why the CF behaves like a free particle in some magnetic experiments when it is not, what exactly the CF is made of, what one means by its dipole moment, and how the comparison of theory to experiment must be modified to fit the peculiarities of the quantized Hall problem.

Polar codes for achieving the classical capacity of a quantum channel

NASA Astrophysics Data System (ADS)

Guha, Saikat; Wilde, Mark

2012-02-01

We construct the first near-explicit, linear, polar codes that achieve the capacity for classical communication over quantum channels. The codes exploit the channel polarization phenomenon observed by Arikan for classical channels. Channel polarization is an effect in which one can synthesize a set of channels, by ``channel combining'' and ``channel splitting,'' in which a fraction of the synthesized channels is perfect for data transmission while the other fraction is completely useless for data transmission, with the good fraction equal to the capacity of the channel. Our main technical contributions are threefold. First, we demonstrate that the channel polarization effect occurs for channels with classical inputs and quantum outputs. We then construct linear polar codes based on this effect, and the encoding complexity is O(N log N), where N is the blocklength of the code. We also demonstrate that a quantum successive cancellation decoder works well, i.e., the word error rate decays exponentially with the blocklength of the code. For a quantum channel with binary pure-state outputs, such as a binary-phase-shift-keyed coherent-state optical communication alphabet, the symmetric Holevo information rate is in fact the ultimate channel capacity, which is achieved by our polar code.

Collision-induced stimulated photon echoes in ‘strong’ magnetic field

NASA Astrophysics Data System (ADS)

Reshetov, V. A.

2018-05-01

Collision-induced stimulated photon echoes formed in a gaseous medium on the transition with the angular momentum change Ja=0 → Jb=1 under the action of ‘strong’ longitudinal magnetic field, when the echo pulse becomes unpolarized, are considered with an account of elastic depolarizing collisions. In the case of narrow spectral line the explicit expressions for the echo polarization density matrix and the degree of polarization are obtained. In the case of broad spectral line the results of the numeric calculations reproduce qualitatively the curve obtained in the experiments with ytterbium vapor.

Direct folding simulation of a long helix in explicit water

NASA Astrophysics Data System (ADS)

Gao, Ya; Lu, Xiaoliang; Duan, Lili; Zhang, Dawei; Mei, Ye; Zhang, John Z. H.

2013-05-01

A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix.

Spectral amplitude code label switching system for IM, DQPSK and PDM-DQPSK with frequency swept coherent detection

NASA Astrophysics Data System (ADS)

Isaac, Aboagye Adjaye; Yongsheng, Cao; Fushen, Chen

2018-05-01

We present and compare the outcome of implicit and explicit labels using intensity modulation (IM), differential quadrature phase shift keying (DQPSK), and polarization division multiplexed (PDM-DQPSK). A payload bit rate of 1, 2, and 5 Gb/s is considered for IM implicit labels, while payloads of 40, 80, and 112 Gb/s are considered in DQPSK and PDM-DQPSK explicit labels by stimulating a 4-code 156-Mb/s SAC label. The generated label and payloads are observed by assessing the eye diagram, received optical power (ROP), and optical signal to noise ratio (OSNR).

Kinetics and dynamics of the C(3P) + H2O reaction on a full-dimensional accurate triplet state potential energy surface.

PubMed

Li, Jun; Xie, Changjian; Guo, Hua

2017-08-30

A full dimensional accurate potential energy surface (PES) for the C( 3 P) and H 2 O reaction is developed based on ∼34 000 data points calculated at the level of the explicitly correlated unrestricted coupled cluster method with single, double, and perturbative triple excitations with the augmented correlation-consistent polarized triple zeta basis set (CCSD(T)-F12a/AVTZ). The PES is invariant with respect to the permutation of the two hydrogen atoms and the total root mean square error (RMSE) of the fit is only 0.31 kcal mol -1 . The PES features two barriers in the entrance channel and several potential minima, as well as multiple product channels. The rate coefficients of this reaction calculated using a transition-state theory and quasi-classical trajectory (QCT) method are small near room temperature, consistent with experiments. The reaction dynamics is also investigated with QCT on the new PES, which found that the reactivity is constrained by the entrance barriers and the final product branching is not statistical.

Superintegrability on N-dimensional spaces of constant curvature from so( N + 1) and its contractions

NASA Astrophysics Data System (ADS)

Herranz, F. J.; Ballesteros, Á.

2008-05-01

The Lie—Poisson algebra so( N + 1) and some of its contractions are used to construct a family of superintegrable Hamiltonians on the N-dimensional spherical, Euclidean, hyperbolic, Minkowskian, and (anti-)de Sitter spaces. We firstly present a Hamiltonian which is a superposition of an arbitrary central potential with N arbitrary centrifugal terms. Such a system is quasi-maximally superintegrable since this is endowed with 2 N — 3 functionally independent constants of motion (plus the Hamiltonian). Secondly, we identify two maximally superintegrable Hamiltonians by choosing a specific central potential and finding at the same time the remaining integral. The former is the generalization of the Smorodinsky—Winternitz system to the above six spaces, while the latter is a generalization of the Kepler—Coulomb potential, for which the Laplace—Runge—Lenz N vector is also given. All the systems and constants of motion are explicitly expressed in a unified form in terms of ambient and polar coordinates as they are parametrized by two contraction parameters (curvature and signature of the metric).

Development of a Coherent Bistatic Vegetation Model for Signal of Opportunity Applications at VHF UHF-Bands

NASA Technical Reports Server (NTRS)

Kurum, Mehmet; Deshpande, Manohar; Joseph, Alicia T.; O'Neill, Peggy E.; Lang, Roger H.; Eroglu, Orhan

2017-01-01

A coherent bistatic vegetation scattering model, based on a Monte Carlo simulation, is being developed to simulate polarimetric bi-static reflectometry at VHF/UHF-bands (240-270 MHz). The model is aimed to assess the value of geostationary satellite signals of opportunity to enable estimation of the Earth's biomass and root-zone soil moisture. An expression for bistatic scattering from a vegetation canopy is derived for the practical case of a ground-based/low altitude platforms with passive receivers overlooking vegetation. Using analytical wave theory in conjunction with distorted Born approximation (DBA), the transmit and receive antennas effects (i.e., polarization, orientation, height, etc.) are explicitly accounted for. Both the coherency nature of the model (joint phase and amplitude information) and the explicit account of system parameters (antenna, altitude, polarization, etc) enable one to perform various beamforming techniques to evaluate realistic deployment configurations. In this paper, several test scenarios will be presented and the results will be evaluated for feasibility for future biomass and root-zone soil moisture application using geostationary communication satellite signals of opportunity at low frequencies.

Predicting Nonspecific Ion Binding Using DelPhi

PubMed Central

Petukh, Marharyta; Zhenirovskyy, Maxim; Li, Chuan; Li, Lin; Wang, Lin; Alexov, Emil

2012-01-01

Ions are an important component of the cell and affect the corresponding biological macromolecules either via direct binding or as a screening ion cloud. Although some ion binding is highly specific and frequently associated with the function of the macromolecule, other ions bind to the protein surface nonspecifically, presumably because the electrostatic attraction is strong enough to immobilize them. Here, we test such a scenario and demonstrate that experimentally identified surface-bound ions are located at a potential that facilitates binding, which indicates that the major driving force is the electrostatics. Without taking into consideration geometrical factors and structural fluctuations, we show that ions tend to be bound onto the protein surface at positions with strong potential but with polarity opposite to that of the ion. This observation is used to develop a method that uses a DelPhi-calculated potential map in conjunction with an in-house-developed clustering algorithm to predict nonspecific ion-binding sites. Although this approach distinguishes only the polarity of the ions, and not their chemical nature, it can predict nonspecific binding of positively or negatively charged ions with acceptable accuracy. One can use the predictions in the Poisson-Boltzmann approach by placing explicit ions in the predicted positions, which in turn will reduce the magnitude of the local potential and extend the limits of the Poisson-Boltzmann equation. In addition, one can use this approach to place the desired number of ions before conducting molecular-dynamics simulations to neutralize the net charge of the protein, because it was shown to perform better than standard screened Coulomb canned routines, or to predict ion-binding sites in proteins. This latter is especially true for proteins that are involved in ion transport, because such ions are loosely bound and very difficult to detect experimentally. PMID:22735539

Late positive potential to explicit sexual images associated with the number of sexual intercourse partners

PubMed Central

Steele, Vaughn R.; Staley, Cameron; Sabatinelli, Dean

2015-01-01

Risky sexual behaviors typically occur when a person is sexually motivated by potent, sexual reward cues. Yet, individual differences in sensitivity to sexual cues have not been examined with respect to sexual risk behaviors. A greater responsiveness to sexual cues might provide greater motivation for a person to act sexually; a lower responsiveness to sexual cues might lead a person to seek more intense, novel, possibly risky, sexual acts. In this study, event-related potentials were recorded in 64 men and women while they viewed a series of emotional, including explicit sexual, photographs. The motivational salience of the sexual cues was varied by including more and less explicit sexual images. Indeed, the more explicit sexual stimuli resulted in enhanced late positive potentials (LPP) relative to the less explicit sexual images. Participants with fewer sexual intercourse partners in the last year had reduced LPP amplitude to the less explicit sexual images than the more explicit sexual images, whereas participants with more partners responded similarly to the more and less explicit sexual images. This pattern of results is consistent with a greater responsivity model. Those who engage in more sexual behaviors consistent with risk are also more responsive to less explicit sexual cues. PMID:24526189

Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model.

PubMed

Das, Debananda; Koh, Yasuhiro; Tojo, Yasushi; Ghosh, Arun K; Mitsuya, Hiroaki

2009-12-01

Reliable and robust prediction of the binding affinity for drug molecules continues to be a daunting challenge. We simulated the binding interactions and free energy of binding of nine protease inhibitors (PIs) with wild-type and various mutant proteases by performing GBSA simulations in which each PI's partial charge was determined by quantum mechanics (QM) and the partial charge accounts for the polarization induced by the protease environment. We employed a hybrid solvation model that retains selected explicit water molecules in the protein with surface-generalized Born (SGB) implicit solvent. We examined the correlation of the free energy with the antiviral potency of PIs with regard to amino acid substitutions in protease. The GBSA free energy thus simulated showed strong correlations (r > 0.75) with antiviral IC(50) values of PIs when amino acid substitutions were present in the protease active site. We also simulated the binding free energy of PIs with P2-bis-tetrahydrofuranylurethane (bis-THF) or related cores, utilizing a bis-THF-containing protease crystal structure as a template. The free energy showed a strong correlation (r = 0.93) with experimentally determined anti-HIV-1 potency. The present data suggest that the presence of selected explicit water in protein and protein polarization-induced quantum charges for the inhibitor, compared to lack of explicit water and a static force-field-based charge model, can serve as an improved lead optimization tool and warrants further exploration.

Collisional rates based on the first potential energy surface of the NeH+ -He system

NASA Astrophysics Data System (ADS)

Bop, Cheikh T.; Hammami, K.; Faye, N. A. B.

2017-09-01

The potential energy surface is computed at the explicitly correlated coupled cluster with simple, second and perturbative triple excitation method (CCSD(T)-F12) in connection with the augmented-correlation consistent-polarized valence triple zeta (aug-cc-pVTZ) Gaussian basis set for the NeH+ -He system. The calculations were performed by first taking into account the vibration of the molecule and then averaging the so-obtained three-dimensional potential. From this average interaction potential, cross-sections among the 11 first rotational levels of NeH+ induced by collision with He are calculated for energies up to 4000 cm-1 using the quantum mechanical close coupling (CC) approach. Collisional rate coefficients are obtained by thermally averaging these cross-sections at low temperature (T ≤ 300 K). The propensity rules of the rotational transitions obtained in this paper are discussed and compared with those of HeH+ and ArH+ in collision with electron. This work may be helpful for the eventual investigations, both theoretical and experimental, focused to detect the key cationic noble gas hydride NeH+ in the interstellar and circumstellar media as well as in laboratory experiments.

A multiscale model for charge inversion in electric double layers

NASA Astrophysics Data System (ADS)

Mashayak, S. Y.; Aluru, N. R.

2018-06-01

Charge inversion is a widely observed phenomenon. It is a result of the rich statistical mechanics of the molecular interactions between ions, solvent, and charged surfaces near electric double layers (EDLs). Electrostatic correlations between ions and hydration interactions between ions and water molecules play a dominant role in determining the distribution of ions in EDLs. Due to highly polar nature of water, near a surface, an inhomogeneous and anisotropic arrangement of water molecules gives rise to pronounced variations in the electrostatic and hydration energies of ions. Classical continuum theories fail to accurately describe electrostatic correlations and molecular effects of water in EDLs. In this work, we present an empirical potential based quasi-continuum theory (EQT) to accurately predict the molecular-level properties of aqueous electrolytes. In EQT, we employ rigorous statistical mechanics tools to incorporate interatomic interactions, long-range electrostatics, correlations, and orientation polarization effects at a continuum-level. Explicit consideration of atomic interactions of water molecules is both theoretically and numerically challenging. We develop a systematic coarse-graining approach to coarse-grain interactions of water molecules and electrolyte ions from a high-resolution atomistic scale to the continuum scale. To demonstrate the ability of EQT to incorporate the water orientation polarization, ion hydration, and electrostatic correlations effects, we simulate confined KCl aqueous electrolyte and show that EQT can accurately predict the distribution of ions in a thin EDL and also predict the complex phenomenon of charge inversion.

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

Dielectric constant and low-frequency infrared spectra for liquid water and ice Ih within the E3B model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, L.; Ni, Y.; Drews, S. E. P.

2014-08-28

Two intrinsic difficulties in modeling condensed-phase water with conventional rigid non-polarizable water models are: reproducing the static dielectric constants for liquid water and ice Ih, and generating the peak at about 200 cm{sup −1} in the low-frequency infrared spectrum for liquid water. The primary physical reason for these failures is believed to be the missing polarization effect in these models, and consequently various sophisticated polarizable water models have been developed. However, in this work we pursue a different strategy and propose a simple empirical scheme to include the polarization effect only on the dipole surface (without modifying a model's intermolecularmore » interaction potential). We implement this strategy for our explicit three-body (E3B) model. Our calculated static dielectric constants and low-frequency infrared spectra are in good agreement with experiment for both liquid water and ice Ih over wide temperature ranges, albeit with one fitting parameter for each phase. The success of our modeling also suggests that thermal fluctuations about local minima and the energy differences between different proton-disordered configurations play minor roles in the static dielectric constant of ice Ih. Our analysis shows that the polarization effect is important in resolving the two difficulties mentioned above and sheds some light on the origin of several features in the low-frequency infrared spectra for liquid water and ice Ih.« less

Molecular modelling of protein-protein/protein-solvent interactions

NASA Astrophysics Data System (ADS)

Luchko, Tyler

The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule destabilization. No conformational change was observed but a nucleotide dependent 'softening' of the interaction was found instead, suggesting that an entropic force in a microtubule configuration could be the mechanism of microtubule collapse. Finally, to overcome much of the computational costs associated with explicit soIvent calculations, a new combination of molecular dynamics with the 3D-reference interaction site model (3D-RISM) of solvation was integrated into the Amber molecular dynamics package. Our implementation of 3D-RISM shows excellent agreement with explicit solvent free energy calculations. Several optimisation techniques, including a new multiple time step method, provide a nearly 100 fold performance increase, giving similar computational performance to explicit solvent.

Monochromatic Measurements of the JPSS-1 VIIRS Polarization Sensitivity

NASA Technical Reports Server (NTRS)

McIntire, Jeff; Moyer, David; Brown, Steven W.; Lykke, Keith R.; Waluschka, Eugene; Oudrari, Hassan; Xiong, Xiaoxiong

2016-01-01

Polarization sensitivity is a critical property that must be characterized for spaceborne remote sensing instruments designed to measure reflected solar radiation. Broadband testing of the first Joint Polar-orbiting Satellite System (JPSS-1) Visible Infrared Imaging Radiometer Suite (VIIRS) showed unexpectedly large polarization sensitivities for the bluest bands on VIIRS (centered between 400 and 600 nm). Subsequent ray trace modeling indicated that large diattenuation on the edges of the bandpass for these spectral bands was the driver behind these large sensitivities. Additional testing using the National Institute of Standards and Technologies Traveling Spectral Irradiance and Radiance Responsivity Calibrations Using Uniform Sources was added to the test program to verify and enhance the model. The testing was limited in scope to two spectral bands at two scan angles; nonetheless, this additional testing provided valuable insight into the polarization sensitivity. Analysis has shown that the derived diattenuation agreed with the broadband measurements to within an absolute difference of about0.4 and that the ray trace model reproduced the general features of the measured data. Additionally, by deriving the spectral responsivity, the linear diattenuation is shown to be explicitly dependent on the changes in bandwidth with polarization state.

Titan Polar Landscape Evolution

NASA Technical Reports Server (NTRS)

Moore, Jeffrey M.

2016-01-01

With the ongoing Cassini-era observations and studies of Titan it is clear that the intensity and distribution of surface processes (particularly fluvial erosion by methane and Aeolian transport) has changed through time. Currently however, alternate hypotheses substantially differ among specific scenarios with respect to the effects of atmospheric evolution, seasonal changes, and endogenic processes. We have studied the evolution of Titan's polar region through a combination of analysis of imaging, elevation data, and geomorphic mapping, spatially explicit simulations of landform evolution, and quantitative comparison of the simulated landscapes with corresponding Titan morphology. We have quantitatively evaluated alternate scenarios for the landform evolution of Titan's polar terrain. The investigations have been guided by recent geomorphic mapping and topographic characterization of the polar regions that are used to frame hypotheses of process interactions, which have been evaluated using simulation modeling. Topographic information about Titan's polar region is be based on SAR-Topography and altimetry archived on PDS, SAR-based stereo radar-grammetry, radar-sounding lake depth measurements, and superposition relationships between geomorphologic map units, which we will use to create a generalized topographic map.

Dependence of spin dephasing on initial spin polarization in a high-mobility two-dimensional electron system

NASA Astrophysics Data System (ADS)

Stich, D.; Zhou, J.; Korn, T.; Schulz, R.; Schuh, D.; Wegscheider, W.; Wu, M. W.; Schüller, C.

2007-11-01

We have studied the spin dynamics of a high-mobility two-dimensional electron system in a GaAs/Al0.3Ga0.7As single quantum well by time-resolved Faraday rotation and time-resolved Kerr rotation in dependence on the initial degree of spin polarization, P , of the electrons. By increasing the initial spin polarization from the low- P regime to a significant P of several percent, we find that the spin dephasing time, T2* , increases from about 20to200ps . Moreover, T2* increases with temperature at small spin polarization but decreases with temperature at large spin polarization. All these features are in good agreement with theoretical predictions by Weng and Wu [Phys. Rev. B 68, 075312 (2003)]. Measurements as a function of spin polarization at fixed electron density are performed to further confirm the theory. A fully microscopic calculation is performed by setting up and numerically solving the kinetic spin Bloch equations, including the D’yakonov-Perel’ and the Bir-Aronov-Pikus mechanisms, with all the scattering explicitly included. We reproduce all principal features of the experiments, i.e., a dramatic decrease of spin dephasing with increasing P and the temperature dependences at different spin polarizations.

Influence of concentration polarization on DNA translocation through a nanopore.

PubMed

Zhai, Shengjie; Zhao, Hui

2016-05-01

Concentration polarization can be induced by the unique ion-perm selectivity of small nanopores, leading to a salt concentration gradient across nanopores. This concentration gradient can create diffusio-osmosis and induce an electric field, affecting ionic currents on DNA that translocates through a nanopore. Here this influence is theoretically investigated by solving the continuum Poisson-Nernst-Planck model for different salt concentrations, DNA surface charge densities, and pore properties. By implementing the perturbation method, we can explicitly compute the contribution of concentration polarization to the ionic current. The induced electric field by concentration polarization is opposite to the imposed electric field and decreases the migration current, and the induced diffusio-osmosis can decrease the convection current as well. Our studies suggest that the importance of the concentration polarization can be determined by the parameter λ/G where λ is the double-layer thickness and G is the gap size. When λ/G is larger than a critical value, the influence of concentration polarization becomes more prominent. This conclusion is supported by the studies on the dependence of the ionic current on salt concentration and pore properties, showing that the difference between two models with and without accounting for concentration polarization is larger for low salts and small pores, which correspond to larger λ/G.

The disturbing function for polar Centaurs and transneptunian objects

NASA Astrophysics Data System (ADS)

Namouni, F.; Morais, M. H. M.

2017-10-01

The classical disturbing function of the three-body problem is based on an expansion of the gravitational interaction in the vicinity of nearly coplanar orbits. Consequently, it is not suitable for the identification and study of resonances of the Centaurs and transneptunian objects on nearly polar orbits with the Solar system planets. Here, we provide a series expansion algorithm of the gravitational interaction in the vicinity of polar orbits and produce explicitly the disturbing function to fourth order in eccentricity and inclination cosine. The properties of the polar series differ significantly from those of the classical disturbing function: the polar series can model any resonance, as the expansion order is not related to the resonance order. The powers of eccentricity and inclination of the force amplitude of a p:q resonance do not depend on the value of the resonance order |p - q| but only on its parity. Thus, all even resonance order eccentricity amplitudes are ∝e2 and odd ones ∝e to lowest order in eccentricity e. With the new findings on the structure of the polar disturbing function and the possible resonant critical arguments, we illustrate the dynamics of the polar resonances 1:3, 3:1, 2:9 and 7:9 where transneptunian object 471325 could currently be locked.

A fully polarimetric scattering model for a coniferous forest

NASA Technical Reports Server (NTRS)

Karam, M. A.; Fung, A. K.; Lopes, A.; Mougin, E.

1991-01-01

For an elliptically polarized plane wave exciting a coniferous forested canopy a fully polarimetric scattering model has been developed to account for the size and orientation distributions of each forest constituent. A canopy is divided into three layers over a rough interface. The upper two layers represent the crown with its constituents (leaves, stems, and branches). The lower layer stands for the trunks and the rough interface is the canopy-ground interface. For a plane wave exciting the canopy, the explicit expressions for the bistatic scattering coefficient associated with each scattering mechanism are given. For an elliptically polarized incidence wave, the present model can be recast in a form suitable for polarimetric wave synthesis. The model validation is justified by comparing the measured and the calculated values of the backscattering coefficients for a linearly polarized incident wave. The comparison is made over a wide range of frequencies and incident angles. Numerical simulations are conducted to calculate the radar polarization signature of the canopy for different incident frequencies and angles.

Role of polarizer-tilting-angle in zero-field spin-transfer nano-oscillators with perpendicular anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gonzalez-Fuentes, C.; Gallardo, R. A., E-mail: rodolfo.gallardo@usm.cl; Landeros, P.

2015-10-05

An analytical model for studying the stability of a single domain ferromagnetic layer under the influence of a spin-polarized current is presented. The theory is applied to bias-field-free nano-oscillators with perpendicular anisotropy, which allows to obtain a polarizer-angle vs. current phase diagram that describes the stability of magnetic states. Explicit formulae for the critical current densities unveil the influence of the relative orientation between free and polarizer layers, allowing the emergence of precessional steady-states, and also the possibility to reduce the magnitude of the threshold current density to produce microwave oscillations. It is shown that oscillating steady-states arise in amore » broad angular region, and the dependence of their boundaries is fully specified by the model. The reliability of the analytical results has been corroborated by comparison to numerical calculations. Such structures are currently under intense research because of remarkable properties offering new prospects for microwave applications in communication technologies.« less

Photoionization of sodium atoms and electron scattering from ionized sodium

NASA Technical Reports Server (NTRS)

Dasgupta, A.; Bhatia, A. K.

1985-01-01

The polarized-orbital method of Temkin (1957) is applied using polarized orbitals determined from Sternheimer's equation to compute the photoionization cross sections of Na atoms from threshold to about 60 eV. The approximations involved in the analysis are explained in detail; the explicit forms of the integrals and matrix expressions are given in appendices; and the results are presented in tables and graphs. Good agreement is found with the results of Chang and Kelly (1975), and the possibility that small amounts of molecular vapor in Na-photoionization experiments are responsible for the discrepancies between calculated and measured cross sections is considered.

Formulation of an explicit-multiple-time-step time integration method for use in a global primitive equation grid model

NASA Technical Reports Server (NTRS)

Chao, W. C.

1982-01-01

With appropriate modifications, a recently proposed explicit-multiple-time-step scheme (EMTSS) is incorporated into the UCLA model. In this scheme, the linearized terms in the governing equations that generate the gravity waves are split into different vertical modes. Each mode is integrated with an optimal time step, and at periodic intervals these modes are recombined. The other terms are integrated with a time step dictated by the CFL condition for low-frequency waves. This large time step requires a special modification of the advective terms in the polar region to maintain stability. Test runs for 72 h show that EMTSS is a stable, efficient and accurate scheme.

Active motion on curved surfaces

NASA Astrophysics Data System (ADS)

Castro-Villarreal, Pavel; Sevilla, Francisco J.

2018-05-01

A theoretical analysis of active motion on curved surfaces is presented in terms of a generalization of the telegrapher equation. Such a generalized equation is explicitly derived as the polar approximation of the hierarchy of equations obtained from the corresponding Fokker-Planck equation of active particles diffusing on curved surfaces. The general solution to the generalized telegrapher equation is given for a pulse with vanishing current as initial data. Expressions for the probability density and the mean squared geodesic displacement are given in the limit of weak curvature. As an explicit example of the formulated theory, the case of active motion on the sphere is presented, where oscillations observed in the mean squared geodesic displacement are explained.

The spin-temperature theory of dynamic nuclear polarization and nuclear spin-lattice relaxation

NASA Technical Reports Server (NTRS)

Byvik, C. E.; Wollan, D. S.

1974-01-01

A detailed derivation of the equations governing dynamic nuclear polarization (DNP) and nuclear spin lattice relaxation by use of the spin temperature theory has been carried to second order in a perturbation expansion of the density matrix. Nuclear spin diffusion in the rapid diffusion limit and the effects of the coupling of the electron dipole-dipole reservoir (EDDR) with the nuclear spins are incorporated. The complete expression for the dynamic nuclear polarization has been derived and then examined in detail for the limit of well resolved solid effect transitions. Exactly at the solid effect transition peaks, the conventional solid-effect DNP results are obtained, but with EDDR effects on the nuclear relaxation and DNP leakage factor included. Explicit EDDR contributions to DNP are discussed, and a new DNP effect is predicted.

Dual-Processes in Learning and Judgment: Evidence from the Multiple Cue Probability Learning Paradigm

ERIC Educational Resources Information Center

Rolison, Jonathan J.; Evans, Jonathan St. B. T.; Dennis, Ian; Walsh, Clare R.

2012-01-01

Multiple cue probability learning (MCPL) involves learning to predict a criterion based on a set of novel cues when feedback is provided in response to each judgment made. But to what extent does MCPL require controlled attention and explicit hypothesis testing? The results of two experiments show that this depends on cue polarity. Learning about…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brizard, Alain J.; Tronci, Cesare

The variational formulations of guiding-center Vlasov-Maxwell theory based on Lagrange, Euler, and Euler-Poincaré variational principles are presented. Each variational principle yields a different approach to deriving guiding-center polarization and magnetization effects into the guiding-center Maxwell equations. The conservation laws of energy, momentum, and angular momentum are also derived by Noether method, where the guiding-center stress tensor is now shown to be explicitly symmetric.

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations.

PubMed

Kortkhonjia, Ekaterine; Brandman, Relly; Zhou, Joe Zhongxiang; Voelz, Vincent A; Chorny, Ilya; Kabakoff, Bruce; Patapoff, Thomas W; Dill, Ken A; Swartz, Trevor E

2013-01-01

The solution dynamics of antibodies are critical to antibody function. We explore the internal solution dynamics of antibody molecules through the combination of time-resolved fluorescence anisotropy experiments on IgG1 with more than two microseconds of all-atom molecular dynamics (MD) simulations in explicit water, an order of magnitude more than in previous simulations. We analyze the correlated motions with a mutual information entropy quantity, and examine state transition rates in a Markov-state model, to give coarse-grained descriptors of the motions. Our MD simulations show that while there are many strongly correlated motions, antibodies are highly flexible, with F(ab) and F(c) domains constantly forming and breaking contacts, both polar and non-polar. We find that salt bridges break and reform, and not always with the same partners. While the MD simulations in explicit water give the right time scales for the motions, the simulated motions are about 3-fold faster than the experiments. Overall, the picture that emerges is that antibodies do not simply fluctuate around a single state of atomic contacts. Rather, in these large molecules, different atoms come in contact during different motions.

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water.

PubMed

Tamamis, Phanourios; Skourtis, Spiros S; Morikis, Dimitrios; Lambris, John D; Archontis, Georgios

2007-09-01

The cyclic 13-residue peptide compstatin is a potential therapeutic agent against the unregulated activation of the complement system. A thorough knowledge of its structural and dynamical properties in solution may assist the design of improved complement inhibitors. NMR studies have suggested that the 5-8 segment of free compstatin folds into a critical for activity 5-8 beta turn and the rest of the peptide is mainly disordered. Earlier computational studies of compstatin analogues with a polar-hydrogen/generalized-Born approximation reproduced the 5-8 turn, but also indicated the formation of beta-hairpin or alpha-helical elements and the existence of interactions between certain charged or aromatic sidechains. However, these features are absent or partly present in the NMR spectra, due to extensive conformational averaging. In order to check the compstatin properties with a more rigorous model of the intra- and intermolecular interactions, we conduct here 98-ns all-atom/explicit-water simulations of three compstatin analogues with variable activity; a native analogue, the more active mutant V4W/H9A and the inactive mutant Q5G. The 5-8 beta-turn population is in good accord with NMR. For the systems studied here, the simulations suggest that the 5-8 turn population does not correlate strictly with activity, in agreement with earlier mutational studies. Furthermore, they show structural differences among the analogues outside the 5-8 region. The possible role of these differences in activity is discussed. The probability of beta-hairpin or alpha-helix elements is much smaller with respect to the polar-hydrogen/GB simulations, and the persistent Trp4-Trp7 or Asp6-Arg11 sidechain interactions of the earlier GB studies are not reproduced. The present simulations extend the NMR data and improve our understanding of the properties of compstatin and related analogues.

Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red

NASA Astrophysics Data System (ADS)

Zuehlsdorff, T. J.; Haynes, P. D.; Payne, M. C.; Hine, N. D. M.

2017-03-01

The solvatochromic shift, as well as the change in colour of the simple organic dye nile red, is studied in two polar and two non-polar solvents in the context of large-scale time-dependent density-functional theory (TDDFT) calculations treating large parts of the solvent environment from first principles. We show that an explicit solvent representation is vital to resolve absorption peak shifts between nile red in n-hexane and toluene, as well as acetone and ethanol. The origin of the failure of implicit solvent models for these solvents is identified as being due to the strong solute-solvent interactions in form of π-stacking and hydrogen bonding in the case of toluene and ethanol. We furthermore demonstrate that the failures of the computationally inexpensive Perdew-Burke-Ernzerhof (PBE) functional in describing some features of the excited state potential energy surface of the S1 state of nile red can be corrected for in a straightforward fashion, relying only on a small number of calculations making use of more sophisticated range-separated hybrid functionals. The resulting solvatochromic shifts and predicted colours are in excellent agreement with experiment, showing the computational approach outlined in this work to yield very robust predictions of optical properties of dyes in solution.

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

PubMed Central

Wagoner, Jason A.; Baker, Nathan A.

2006-01-01

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks–Chandler–Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces. PMID:16709675

Circularly polarized few-cycle optical rogue waves: rotating reduced Maxwell-Bloch equations.

PubMed

Xu, Shuwei; Porsezian, K; He, Jingsong; Cheng, Yi

2013-12-01

The rotating reduced Maxwell-Bloch (RMB) equations, which describe the propagation of few-cycle optical pulses in a transparent media with two isotropic polarized electronic field components, are derived from a system of complete Maxwell-Bloch equations without using the slowly varying envelope approximations. Two hierarchies of the obtained rational solutions, including rogue waves, which are also called few-cycle optical rogue waves, of the rotating RMB equations are constructed explicitly through degenerate Darboux transformation. In addition to the above, the dynamical evolution of the first-, second-, and third-order few-cycle optical rogue waves are constructed with different patterns. For an electric field E in the three lower-order rogue waves, we find that rogue waves correspond to localized large amplitude oscillations of the polarized electric fields. Further a complementary relationship of two electric field components of rogue waves is discussed in terms of analytical formulas as well as numerical figures.

Division B Commission 25: Astronomical Photometry and Polarimetry

NASA Astrophysics Data System (ADS)

Walker, Alistair; Adelman, Saul; Milone, Eugene; Anthony-Twarog, Barbara; Bastien, Pierre; Chen, Wen Ping; Howell, Steve; Knude, Jens; Kurtz, Donald; Magalhães, Antonio Mario; Menzies, John; Smith, Allyn; Volk, Kevin

2016-04-01

Commission 25 (C25) deals with the techniques and issues involved with the measurement of optical and infrared radiation intensities and polarization from astronomical sources. As such, in recent years attention has focused on photometric standard stars, atmospheric extinction, photometric passbands, transformation between systems, nomenclature, and observing and reduction techniques. At the start of the trimester C25 changed its name from Stellar Photometry and Polarization to Astronomical Photometry and Polarization so as to explicitly include in its mandate particular issues arising from the measurement of resolved sources, given the importance of photometric redshifts of distant galaxies for many of the large photometric surveys now underway. We begin by summarizing commission activities over the 2012-2014 period, follow with a report on Polarimetry, continue with Photometry topics that have been of interest to C25 members, and conclude with a Vision for the Future.

Polarization operator of a photon in a magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katkov, V. M., E-mail: V.M.Katkov@inp.nsk.su

2016-08-15

The polarization operator of a photon in a static uniform magnetic field has been studied at photon energies both above and below the threshold of electron–positron pair production by a photon. In the first order of the fine-structure constant α, expressions for the refractive index of a photon with a certain polarization in both low and high fields as compared to the critical field H{sub 0} = 4.41 × 10{sup 13} G have been obtained. Both the purely quantum range of photon energies, where the particles of a pair are produced at the lowest Landau levels, and the region ofmore » applicability of the semiclassical approximation in the case of the population of high energy levels have been considered. A general spectral integral formula has been obtained with divergent threshold terms separated in an explicit form.« less

A Combined FEM/MoM/GTD Technique To Analyze Elliptically Polarized Cavity-Backed Antennas With Finite Ground Plane

NASA Technical Reports Server (NTRS)

Reddy, C. J.; Deshpande, M. D.; Fralick, D. T.; Cockrell, C. R.; Beck, F. B.

1996-01-01

Radiation pattern prediction analysis of elliptically polarized cavity-backed aperture antennas in a finite ground plane is performed using a combined Finite Element Method/Method of Moments/Geometrical Theory of Diffraction (FEM/MoM/GTD) technique. The magnetic current on the cavity-backed aperture in an infinite ground plane is calculated using the combined FEM/MoM analysis. GTD, including the slope diffraction contribution, is used to calculate the diffracted fields caused by both soft and hard polarizations at the edges of the finite ground plane. Explicit expressions for regular diffraction coefficients and slope diffraction coefficients are presented. The slope of the incident magnetic field at the diffraction points is derived and analytical expressions are presented. Numerical results for the radiation patterns of a cavity-backed circular spiral microstrip patch antenna excited by a coaxial probe in a finite rectangular ground plane are computed and compared with experimental results.

Coronal emission-line polarization from the statistical equilibrium of magnetic sublevels. II. Fe XIV 5303 A

DOE Office of Scientific and Technical Information (OSTI.GOV)

House, L.L.; Querfeld, C.W.; Rees, D.E.

1982-04-15

Coronal magnetic fields influence in the intensity and linear polarization of light scattered by coronal Fe XIV ions. To interpret polarization measurements of Fe XIV 5303 A coronal emission requires a detailed understanding of the dependence of the emitted Stokes vector on coronal magnetic field direction, electron density, and temperature and on height of origin. The required dependence is included in the solutions of statistical equilibrium for the ion which are solved explicitly for 34 magnetic sublevels in both the ground and four excited terms. The full solutions are reduced to equivalent simple analytic forms which clearly show the requiredmore » dependence on coronal conditions. The analytic forms of the reduced solutions are suitable for routine analysis of 5303 green line polarimetric data obtained at Pic du Midi and from the Solar Maximum Mission Coronagraph/Polarimeter.« less

Prediction of global vapor-liquid equilibria for mixtures containing polar and associating components with improved renormalization group theory.

PubMed

Mi, Jianguo; Tang, Yiping; Zhong, Chongli; Li, Yi-Gui

2005-11-03

Our recently improved renormalization group (RG) theory is further reformulated within the context of density functional theory. To improve the theory for polar and associating fluids, an explicit and complete expression of the theory is derived in which the density fluctuation is expanded up to the third-order term instead of the original second-order term. A new predictive equation of state based on the first-order mean spherical approximation statistical associating fluid theory (FMSA-SAFT) and the newly improved RG theory is proposed for systems containing polar and associating fluids. The calculated results for both pure fluids and mixtures are in good agreement with experimental data both inside and outside the critical region. This work demonstrates that the RG theory incorporated with the solution of FMSA is a promising route for accurately describing the global phase behavior of complex fluids and mixtures.

Magnetic Interactions at the Nanoscale in Trilayer Titanates

NASA Astrophysics Data System (ADS)

Cao, Yanwei; Yang, Zhenzhong; Kareev, M.; Liu, Xiaoran; Meyers, D.; Middey, S.; Choudhury, D.; Shafer, P.; Guo, Jiandong; Freeland, J. W.; Arenholz, E.; Gu, Lin; Chakhalian, J.

2016-02-01

We report on the phase diagram of competing magnetic interactions at the nanoscale in engineered ultrathin trilayer heterostructures of LaTiO3 /SrTiO3/YTiO3 , in which the interfacial inversion symmetry is explicitly broken. Combined atomic layer resolved scanning transmission electron microscopy with electron energy loss spectroscopy and electrical transport have confirmed the formation of a spatially separated two-dimensional electron liquid and high density two-dimensional localized magnetic moments at the LaTiO3 /SrTiO3 and SrTiO3 /YTiO3 interfaces, respectively. Resonant soft x-ray linear dichroism spectroscopy has demonstrated the presence of orbital polarization of the conductive LaTiO3 /SrTiO3 and localized SrTiO3 /YTiO3 electrons. Our results provide a route with prospects for exploring new magnetic interfaces, designing a tunable two-dimensional d -electron Kondo lattice, and potential spin Hall applications.

Gauge-free gyrokinetic theory

NASA Astrophysics Data System (ADS)

Burby, Joshua; Brizard, Alain

2017-10-01

Test-particle gyrocenter equations of motion play an essential role in the diagnosis of turbulent strongly-magnetized plasmas, and are playing an increasingly-important role in the formulation of kinetic-gyrokinetic hybrid models. Previous gyrocenter models required the knowledge of the perturbed electromagnetic potentials, which are not directly observable quantities (since they are gauge-dependent). A new gauge-free formulation of gyrocenter motion is presented, which enables gyrocenter trajectories to be determined using only measured values of the directly-observable electromagnetic field. Our gauge-free gyrokinetic theory is general enough to allow for gyroradius-scale fluctuations in both the electric and magnetic field. In addition, we provide gauge-free expressions for the charge and current densities produced by a distribution of gyrocenters, which explicitly include guiding-center and gyrocenter polarization and magnetization effects. This research was supported by the U.S. DOE Contract Nos. DE-SC0014032 (AB) and DE-AC05-06OR23100 (JB).

Beyond Point Charges: Dynamic Polarization from Neural Net Predicted Multipole Moments.

PubMed

Darley, Michael G; Handley, Chris M; Popelier, Paul L A

2008-09-09

Intramolecular polarization is the change to the electron density of a given atom upon variation in the positions of the neighboring atoms. We express the electron density in terms of multipole moments. Using glycine and N-methylacetamide (NMA) as pilot systems, we show that neural networks can capture the change in electron density due to polarization. After training, modestly sized neural networks successfully predict the atomic multipole moments from the nuclear positions of all atoms in the molecule. Accurate electrostatic energies between two atoms can be then obtained via a multipole expansion, inclusive of polarization effects. As a result polarization is successfully modeled at short-range and without an explicit polarizability tensor. This approach puts charge transfer and multipolar polarization on a common footing. The polarization procedure is formulated within the context of quantum chemical topology (QCT). Nonbonded atom-atom interactions in glycine cover an energy range of 948 kJ mol(-1), with an average energy difference between true and predicted energy of 0.2 kJ mol(-1), the largest difference being just under 1 kJ mol(-1). Very similar energy differences are found for NMA, which spans a range of 281 kJ mol(-1). The current proof-of-concept enables the construction of a new protein force field that incorporates electron density fragments that dynamically respond to their fluctuating environment.

A new cue to figure-ground coding: top-bottom polarity.

PubMed

Hulleman, Johan; Humphreys, Glyn W

2004-11-01

We present evidence for a new figure-ground cue: top-bottom polarity. In an explicit reporting task, participants were more likely to interpret stimuli with a wide base and a narrow top as a figure. A similar advantage for wide-based stimuli also occurred in a visual short-term memory task, where the stimuli had ambiguous figure-ground relations. Further support comes from a figural search task. Figural search is a discrimination task in which participants are set to search for a symmetric target in a display with ambiguous figure-ground organization. We show that figural search was easier when stimuli with a top-bottom polarity were placed in an orientation where they had a wide base and a narrow top, relative to when this orientation was inverted. This polarity effect was present when participants were set to use color to parse figure from ground, and it was magnified when the participants did not have any foreknowledge of the color of the symmetric target. Taken together the results suggest that top-bottom polarity influences figure-ground assignment, with wide base stimuli being preferred as a figure. In addition, the figural search task can serve as a useful procedure to examine figure-ground assignment.

Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine

PubMed Central

2017-01-01

The solvatochromic effects of six different solvents on the UV absorption spectrum of 2-thiocytosine have been studied by a combination of experimental and theoretical techniques. The steady-state absorption spectra show significant shifts of the absorption bands, where in more polar solvents the first absorption maximum shifts to higher transition energies and the second maximum to lower energies. The observed solvatochromic shifts have been rationalized using three popular solvatochromic scales and with high-level multireference quantum chemistry calculations including implicit and explicit solvent effects. It has been found that the dipole moments of the excited states account for some general shifts in the excitation energies, whereas the explicit solvent interactions explain the differences in the spectra recorded in the different solvents. PMID:28452483

Implicit versus explicit momentum relaxation time solution for semiconductor nanowires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marin, E. G., E-mail: egmarin@ugr.es; Ruiz, F. G., E-mail: franruiz@ugr.es; Godoy, A., E-mail: agodoy@ugr.es

2015-07-14

We discuss the necessity of the exact implicit Momentum Relaxation Time (MRT) solution of the Boltzmann transport equation in order to achieve reliable carrier mobility results in semiconductor nanowires. Firstly, the implicit solution for a 1D electron gas with a isotropic bandstructure is presented resulting in the formulation of a simple matrix system. Using this solution as a reference, the explicit approach is demonstrated to be inaccurate for the calculation of inelastic anisotropic mechanisms such as polar optical phonons, characteristic of III-V materials. Its validity for elastic and isotropic mechanisms is also evaluated. Finally, the implications of the MRT explicitmore » approach inaccuracies on the total mobility of Si and III-V NWs are studied.« less

The contribution of scalars to N = 4 SYM amplitudes II: Young tableaux, asymptotic factorisation and strong coupling

NASA Astrophysics Data System (ADS)

Bonini, Alfredo; Fioravanti, Davide; Piscaglia, Simone; Rossi, Marco

2018-06-01

We disentangle the contribution of scalars to the OPE series of null hexagonal Wilson loops/MHV gluon scattering amplitudes in multicolour N = 4 SYM. In specific, we develop a systematic computation of the SU (4) matrix part of the Wilson loop by means of Young tableaux (with several examples). Then, we use a peculiar factorisation property (when a group of rapidities becomes large) to deduce an explicit polar form. Furthermore, we emphasise the advantages of expanding the logarithm of the Wilson loop in terms of 'connected functions' as we apply this procedure to find an explicit strong coupling expansion (definitively proving that the leading order can prevail on the classical AdS5 string contribution).

Nonlinear optical susceptibility described with a spherical formalism applied to coherent anti-Stokes Raman scattering

NASA Astrophysics Data System (ADS)

Cleff, Carsten; Rigneault, Hervé; Brasselet, Sophie; Duboisset, Julien

2017-07-01

We describe coherent Raman scattering in a complete spherical formalism allowing a better understanding of the coherent Raman process with respect to its symmetry properties, which is especially helpful in polarized coherent Raman microscopy. We describe how to build the coherent Raman tensor from spontaneous Raman tensor for crystalline and disordered media. We introduce a distribution function for molecular bonds and show how this distribution function results in a new macroscopic symmetry which can be very different from the symmetry of vibrational modes. Finally, we explicitly show polarization configurations for coherent anti-Stokes Raman scattering to probe specific vibration symmetries in crystalline samples and lipid layers.

Plate motion and the secular shift of the mean pole

NASA Technical Reports Server (NTRS)

Liu, H.; Carpenter, L.; Agreen, R. W.

1973-01-01

The global plate motion indicates that changes in the products of inertia of the earth due to tectonic plate movement may provide a secular shift of the mean pole. A mathematical procedure for calculating this shift based on the plate theory is presented. Explicit expressions were obtained for the dependence of the secular polar shift on the dimensions and locations of the plate boundaries. Numerical results show that the secular motion of the mean pole is 0.0002 sec/year in the direction of 67 W. Hence, it is deduced that the influence of the plate motion on the secular polar shift may account for 10% of the observed value.

Two-dimensional shape classification using generalized Fourier representation and neural networks

NASA Astrophysics Data System (ADS)

Chodorowski, Artur; Gustavsson, Tomas; Mattsson, Ulf

2000-04-01

A shape-based classification method is developed based upon the Generalized Fourier Representation (GFR). GFR can be regarded as an extension of traditional polar Fourier descriptors, suitable for description of closed objects, both convex and concave, with or without holes. Explicit relations of GFR coefficients to regular moments, moment invariants and affine moment invariants are given in the paper. The dual linear relation between GFR coefficients and regular moments was used to compare shape features derive from GFR descriptors and Hu's moment invariants. the GFR was then applied to a clinical problem within oral medicine and used to represent the contours of the lesions in the oral cavity. The lesions studied were leukoplakia and different forms of lichenoid reactions. Shape features were extracted from GFR coefficients in order to classify potentially cancerous oral lesions. Alternative classifiers were investigated based on a multilayer perceptron with different architectures and extensions. The overall classification accuracy for recognition of potentially cancerous oral lesions when using neural network classifier was 85%, while the classification between leukoplakia and reticular lichenoid reactions gave 96% (5-fold cross-validated) recognition rate.

Theoretical study of charge and spin-resolved quantum transport in III-V semiconductor nanostructures

NASA Astrophysics Data System (ADS)

Botha, Andre Erasmus

2003-07-01

This thesis is a theoretical investigation into the spin-resolved transport properties of III-V semiconductor quantum wells. Based on a modified 8 x 8 k · p matrix Hamiltonian, a theory is developed to study the recombination rate in type-II semi metallic quantum wells. The non-parabolicity of the energy band structure and its anisotropy is included via the interband matrix elements and the addition of an anisotropic crystal field potential (parameterized by delta). The effects of externally applied electric and magnetic fields are incorporated into the theory. The electric field is incorporated using a WKB-type approximation. In order to study the anisotropy, the magnetic field is incorporated so that it can be applied at an arbitrary angle theta, with respect to the crystallographic direction c[001]. The case of oblique tunneling (k|| ≠ 0), is also considered. Several interesting results, from calculations of the transmission coefficient, recombination rate, and electron-spin polarization, are presented and discussed for both n-type and p-type single and double quantum wells made from clean InAs and GaSb. For example, in the case of a 150 A wide GaSb/InAs/GaSb quantum well, with B = 4 T, and theta = pi/8, the two maxima in the electron-spin polarization, from the ground and first excited resonant states, are found to be approximately 75%, and 35%, respectively. As theta is varied, a maximum polarization is achieved for a given magnetic field, and this maximum depends on the value of the anisotropy parameter, delta. By using a more sophisticated 14 x 14 band k · p formalism, which explicitly takes into account the coupling between higher bands ( Gc15-Gu 15,Gc1-G u15 , and Gc1-Gc15 ), a theory is developed for the total zero-field spin-splitting and resulting electron-spin polarization in symmetric and asymmetric type-II quantum wells. This theory includes the non-parabolicity, non sphericity, and anisotropy of the energy band structure. The anisotropy in the band structure is introduced via the addition of an anisotropic crystal potential. In the case of an asymmetric GaSb/InAs/GaSb quantum well, it is predicted that the two contributions to the total spin-splitting will be roughly of equal importance. It is also shown that the polarization maxima and minima, for a given resonance state, may not be equal in magnitude. If the resonant state lies close to the forbidden energy gap, the transmission peaks for spin-up and spin-down are skewed. This feature may have potential applications in the design of spintronic filtering and switching devices, in which it is desirable to filter unpolarized electrons (with respect to energy and spin) in order to produce highly polarized, adjustable low-energy beams.

Role of Multiple Soliton Interactions in the Generation of Rogue Waves: The Modified Korteweg-de Vries Framework.

PubMed

Slunyaev, A V; Pelinovsky, E N

2016-11-18

The role of multiple soliton and breather interactions in the formation of very high waves is disclosed within the framework of the integrable modified Korteweg-de Vries (MKdV) equation. Optimal conditions for the focusing of many solitons are formulated explicitly. Namely, trains of ordered solitons with alternate polarities evolve to huge strongly localized transient waves. The focused wave amplitude is exactly the sum of the focusing soliton heights; the maximum wave inherits the polarity of the fastest soliton in the train. The focusing of several solitary waves or/and breathers may naturally occur in a soliton gas and will lead to rogue-wave-type dynamics; hence, it represents a new nonlinear mechanism of rogue wave generation. The discovered scenario depends crucially on the soliton polarities (phases), and is not taken into account by existing kinetic theories. The performance of the soliton mechanism of rogue wave generation is shown for the example of the focusing MKdV equation, when solitons possess "frozen" phases (certain polarities), though the approach is efficient in some other integrable systems which admit soliton and breather solutions.

Role of Multiple Soliton Interactions in the Generation of Rogue Waves: The Modified Korteweg-de Vries Framework

NASA Astrophysics Data System (ADS)

Slunyaev, A. V.; Pelinovsky, E. N.

2016-11-01

The role of multiple soliton and breather interactions in the formation of very high waves is disclosed within the framework of the integrable modified Korteweg-de Vries (MKdV) equation. Optimal conditions for the focusing of many solitons are formulated explicitly. Namely, trains of ordered solitons with alternate polarities evolve to huge strongly localized transient waves. The focused wave amplitude is exactly the sum of the focusing soliton heights; the maximum wave inherits the polarity of the fastest soliton in the train. The focusing of several solitary waves or/and breathers may naturally occur in a soliton gas and will lead to rogue-wave-type dynamics; hence, it represents a new nonlinear mechanism of rogue wave generation. The discovered scenario depends crucially on the soliton polarities (phases), and is not taken into account by existing kinetic theories. The performance of the soliton mechanism of rogue wave generation is shown for the example of the focusing MKdV equation, when solitons possess "frozen" phases (certain polarities), though the approach is efficient in some other integrable systems which admit soliton and breather solutions.

Positive vs. Negative: The Impact of Question Polarity in Voting Advice Applications

PubMed Central

Krouwel, André; van de Pol, Jasper; de Vreese, Claes

2016-01-01

Online Voting Advice Applications (VAAs) are survey-like instruments that help citizens to shape their political preferences and compare them with those of political parties. Especially in multi-party democracies, their increasing popularity indicates that VAAs play an important role in opinion formation for citizens, as well as in the public debate prior to elections. Hence, the objectivity and transparency of VAAs are crucial. In the design of VAAs, many choices have to be made. Extant research in survey methodology shows that the seemingly arbitrary choice to word questions positively (e.g., ‘The city council should allow cars into the city centre’) or negatively (‘The city council should ban cars from the city centre’) systematically affects the answers. This asymmetry in answers is in line with work on negativity bias in other areas of linguistics and psychology. Building on these findings, this study investigated whether question polarity also affects the answers to VAA statements. In a field experiment (N = 31,112) during the Dutch municipal elections we analysed the effects of polarity for 16 out of 30 VAA statements with a large variety of linguistic contrasts. Analyses show a significant effect of question wording for questions containing a wide range of implicit negations (such as ‘forbid’ vs. ‘allow’), as well as for questions with explicit negations (e.g., ‘not’). These effects of question polarity are found especially for VAA users with lower levels of political sophistication. As these citizens are an important target group for Voting Advice Applications, this stresses the need for VAA builders to be sensitive to wording choices when designing VAAs. This study is the first to show such consistent wording effects not only for political attitude questions with implicit negations in VAAs, but also for political questions containing explicit negations. PMID:27723776

Non-hydrostatic general circulation model of the Venus atmosphere

NASA Astrophysics Data System (ADS)

Rodin, Alexander V.; Mingalev, Igor; Orlov, Konstantin; Ignatiev, Nikolay

We present the first non-hydrostatic global circulation model of the Venus atmosphere based on the complete set of gas dynamics equations. The model employs a spatially uniform triangular mesh that allows to avoid artificial damping of the dynamical processes in the polar regions, with altitude as a vertical coordinate. Energy conversion from the solar flux into atmospheric motion is described via explicitly specified heating and cooling rates or, alternatively, with help of the radiation block based on comprehensive treatment of the Venus atmosphere spectroscopy, including line mixing effects in CO2 far wing absorption. Momentum equations are integrated using the semi-Lagrangian explicit scheme that provides high accuracy of mass and energy conservation. Due to high vertical grid resolution required by gas dynamics calculations, the model is integrated on the short time step less than one second. The model reliably repro-duces zonal superrotation, smoothly extending far below the cloud layer, tidal patterns at the cloud level and above, and non-rotating, sun-synchronous global convective cell in the upper atmosphere. One of the most interesting features of the model is the development of the polar vortices resembling those observed by Venus Express' VIRTIS instrument. Initial analysis of the simulation results confirms the hypothesis that it is thermal tides that provides main driver for the superrotation.

Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

PubMed Central

Edwards, Ceiridwen J.; Suchard, Marc A.; Lemey, Philippe; Welch, John J.; Barnes, Ian; Fulton, Tara L.; Barnett, Ross; O’Connell, Tamsin C.; Coxon, Peter; Monaghan, Nigel; Valdiosera, Cristina E.; Lorenzen, Eline D.; Willerslev, Eske; Baryshnikov, Gennady F.; Rambaut, Andrew; Thomas, Mark G.; Bradley, Daniel G.; Shapiro, Beth

2015-01-01

Summary Background Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change. Results We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene. Conclusions The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration. PMID:21737280

Ancient hybridization and an Irish origin for the modern polar bear matriline.

PubMed

Edwards, Ceiridwen J; Suchard, Marc A; Lemey, Philippe; Welch, John J; Barnes, Ian; Fulton, Tara L; Barnett, Ross; O'Connell, Tamsin C; Coxon, Peter; Monaghan, Nigel; Valdiosera, Cristina E; Lorenzen, Eline D; Willerslev, Eske; Baryshnikov, Gennady F; Rambaut, Andrew; Thomas, Mark G; Bradley, Daniel G; Shapiro, Beth

2011-08-09

Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change. We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene. The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration. Copyright © 2011 Elsevier Ltd. All rights reserved.

Junocam: Juno's Outreach Camera

NASA Astrophysics Data System (ADS)

Hansen, C. J.; Caplinger, M. A.; Ingersoll, A.; Ravine, M. A.; Jensen, E.; Bolton, S.; Orton, G.

2017-11-01

Junocam is a wide-angle camera designed to capture the unique polar perspective of Jupiter offered by Juno's polar orbit. Junocam's four-color images include the best spatial resolution ever acquired of Jupiter's cloudtops. Junocam will look for convective clouds and lightning in thunderstorms and derive the heights of the clouds. Junocam will support Juno's radiometer experiment by identifying any unusual atmospheric conditions such as hotspots. Junocam is on the spacecraft explicitly to reach out to the public and share the excitement of space exploration. The public is an essential part of our virtual team: amateur astronomers will supply ground-based images for use in planning, the public will weigh in on which images to acquire, and the amateur image processing community will help process the data.

Product operator descriptions of INEPT and RINEPT NMR spectroscopies for ISn (I=1/2, S=3/2) spin systems.

PubMed

Tokatli, Ahmet; Gençten, Azmi; Sahin, Mükerrem; Tezel, Ozden; Bahçeli, Semiha

2004-07-01

The product operator descriptions of INEPT and reverse INEPT (RINEPT) NMR experiments are introduced for weakly coupled ISn (I=1/2, S=3/2 with n=1,2,3) spin systems. Explicit expressions for polarization transfer from spin-3/2 quadrupolar nuclei to spin-1/2 nuclei (and reversed polarization transfer) are given in detail by using the evolutions of product operators under the spin-spin coupling Hamiltonian. The results calculated for the intensities and positions of the observable signals are simulated in the molecules containing the 119Sn (I=1/2) and 35Cl (S=3/2) nuclei at the coupling constant of J(Sn-Cl)=375 Hz by using the Maple programme on computer.

Product operator descriptions of INEPT and RINEPT NMR spectroscopies for ISn ( I=1/2, S=3/2) spin systems

NASA Astrophysics Data System (ADS)

Tokatlı, Ahmet; Gençten, Azmi; Şahin, Mükerrem; Tezel, Özden; Bahçeli, Semiha

2004-07-01

The product operator descriptions of INEPT and reverse INEPT (RINEPT) NMR experiments are introduced for weakly coupled ISn ( I=1/2, S=3/2 with n=1,2,3) spin systems. Explicit expressions for polarization transfer from spin-3/2 quadrupolar nuclei to spin-1/2 nuclei (and reversed polarization transfer) are given in detail by using the evolutions of product operators under the spin-spin coupling Hamiltonian. The results calculated for the intensities and positions of the observable signals are simulated in the molecules containning the 119Sn ( I=1/2) and 35Cl ( S=3/2) nuclei at the coupling constant of JSn-Cl=375 Hz by using the Maple programme on computer.

Optimized Unlike-Pair Interactions for Water-Carbon Dioxide Mixtures described by the SPC/E and EPM2 Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlcek, Lukas; Chialvo, Ariel A; Cole, David

The unlike- pair interaction parameters for the SPC/E- EPM2 models have been optimized to reproduce the mutual solubility of water and carbon dioxide at the conditions of liquid- supercritical fluid phase equilibria. An efficient global optimization of the parameters is achieved through an implementation of the coupling parameter approach, adapted to phase equilibria calculations in the Gibbs ensemble, that explicitly corrects for the over- polarization of the SPC/E water molecule in the non- polar CO2 environments. The resulting H2O- CO2 force field reproduces accurately the available experimental solubilities at the two fluid phases in equilibria as well as the correspondingmore » species tracer diffusion coefficients.« less

Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

NASA Astrophysics Data System (ADS)

Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

2017-09-01

We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

Vacuum polarization of the electromagnetic field near a rotating black hole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frolov, V.P.; Zel'nikov, A.I.

1985-12-15

The electromagnetic field contribution to the vacuum polarization near a rotating black hole is considered. It is shown that the problem of calculating the renormalized average value of the stress-energy tensor /sup ren/ for the Hartle-Hawking vacuum state at the pole of the event horizon can be reduced to the problem of electro- and magnetostatics in the Kerr spacetime. An explicit expression for /sup ren/ at the pole of the event horizon is obtained and its properties are discussed. It is shown that in the case of a nonrotating black hole the Page-Brown approximation for the electromagnetic stress-energy tensor givesmore » a result which coincides at the event horizon with the exact value of /sup ren/. .AE« less

Low-Energy Electron Effects on the Polar Wind Observed by the POLAR Spacecraft

NASA Technical Reports Server (NTRS)

Horwitz, J. L.; Su, Y.-J.; Dors, E. E.; Moore, Thomas E.; Giles, Barbara L.; Chandler, Michael O.; Craven, Paul D.; Chang, S.-W.; Scudder, J.

1998-01-01

Large ion outflow velocity variation at POLAR apogee have been observed. The observed H+ flow velocities were in the range of 23-110 km/s and 0+ flow velocities were in the range of 5-25 km/s. These velocity ranges lie between those predicted by simulations of the photoelectron-driven polar wind and "baseline" polar wind. The electric current contributions of the photoelectrons and polar rain are expected to control the size and altitude of an electric potential drop which accelerates the polar wind at relatively high altitudes. In this presentation, we compare polar wind characteristics observed near 5000 km and 8 RE altitudes by the Thermal Ion Dynamics Experiment (TIDE) with measurements of low-energy electrons sampled by HYDRA, both from the POLAR spacecraft, to examine possible effects of the polar rain and photoelectrons on the polar wind. Both correlations and anti-correlations are found between the polar wind velocities and the polar rain fluxes at POLAR apogee during different polar cap crossings. Also, the low-altitude upward/downward photoelectron spectra are used to estimates the potential drops above the spacecraft. We interpret these observations in terms of the effects that both photoelectrons and polar rain may have on the electric potential and polar wind acceleration along polar cap magnetic field lines.

Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation

PubMed Central

Ramirez, Samuel A.; Elston, Timothy C.

2018-01-01

Polarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and many other cell types, the Rho GTPase Cdc42 is the key molecular player in polarity establishment. During yeast polarization, multiple patches of Cdc42 initially form, then resolve into a single front. Because polarization relies on strong positive feedback, it is likely that the amplification of molecular-level fluctuations underlies the generation of multiple nascent patches. In the absence of spatial cues, these fluctuations may be key to driving polarization. Here we used particle-based simulations to investigate the role of stochastic effects in a Turing-type model of yeast polarity establishment. In the model, reactions take place either between two molecules on the membrane, or between a cytosolic and a membrane-bound molecule. Thus, we developed a computational platform that explicitly simulates molecules at and near the cell membrane, and implicitly handles molecules away from the membrane. To evaluate stochastic effects, we compared particle simulations to deterministic reaction-diffusion equation simulations. Defining macroscopic rate constants that are consistent with the microscopic parameters for this system is challenging, because diffusion occurs in two dimensions and particles exchange between the membrane and cytoplasm. We address this problem by empirically estimating macroscopic rate constants from appropriately designed particle-based simulations. Ultimately, we find that stochastic fluctuations speed polarity establishment and permit polarization in parameter regions predicted to be Turing stable. These effects can operate at Cdc42 abundances expected of yeast cells, and promote polarization on timescales consistent with experimental results. To our knowledge, our work represents the first particle-based simulations of a model for yeast polarization that is based on a Turing mechanism. PMID:29529021

Flocking and Turning: a New Model for Self-organized Collective Motion

NASA Astrophysics Data System (ADS)

Cavagna, Andrea; Del Castello, Lorenzo; Giardina, Irene; Grigera, Tomas; Jelic, Asja; Melillo, Stefania; Mora, Thierry; Parisi, Leonardo; Silvestri, Edmondo; Viale, Massimiliano; Walczak, Aleksandra M.

2015-02-01

Birds in a flock move in a correlated way, resulting in large polarization of velocities. A good understanding of this collective behavior exists for linear motion of the flock. Yet observing actual birds, the center of mass of the group often turns giving rise to more complicated dynamics, still keeping strong polarization of the flock. Here we propose novel dynamical equations for the collective motion of polarized animal groups that account for correlated turning including solely social forces. We exploit rotational symmetries and conservation laws of the problem to formulate a theory in terms of generalized coordinates of motion for the velocity directions akin to a Hamiltonian formulation for rotations. We explicitly derive the correspondence between this formulation and the dynamics of the individual velocities, thus obtaining a new model of collective motion. In the appropriate overdamped limit we recover the well-known Vicsek model, which dissipates rotational information and does not allow for polarized turns. Although the new model has its most vivid success in describing turning groups, its dynamics is intrinsically different from previous ones in a wide dynamical regime, while reducing to the hydrodynamic description of Toner and Tu at very large length-scales. The derived framework is therefore general and it may describe the collective motion of any strongly polarized active matter system.

Second-harmonic generation in shear wave beams with different polarizations

NASA Astrophysics Data System (ADS)

Spratt, Kyle S.; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F.

2015-10-01

A coupled pair of nonlinear parabolic equations was derived by Zabolotskaya [1] that model the transverse components of the particle motion in a collimated shear wave beam propagating in an isotropic elastic solid. Like the KZK equation, the parabolic equation for shear wave beams accounts consistently for the leading order effects of diffraction, viscosity and nonlinearity. The nonlinearity includes a cubic nonlinear term that is equivalent to that present in plane shear waves, as well as a quadratic nonlinear term that is unique to diffracting beams. The work by Wochner et al. [2] considered shear wave beams with translational polarizations (linear, circular and elliptical), wherein second-order nonlinear effects vanish and the leading order nonlinear effect is third-harmonic generation by the cubic nonlinearity. The purpose of the current work is to investigate the quadratic nonlinear term present in the parabolic equation for shear wave beams by considering second-harmonic generation in Gaussian beams as a second-order nonlinear effect using standard perturbation theory. In order for second-order nonlinear effects to be present, a broader class of source polarizations must be considered that includes not only the familiar translational polarizations, but also polarizations accounting for stretching, shearing and rotation of the source plane. It is found that the polarization of the second harmonic generated by the quadratic nonlinearity is not necessarily the same as the polarization of the source-frequency beam, and we are able to derive a general analytic solution for second-harmonic generation from a Gaussian source condition that gives explicitly the relationship between the polarization of the source-frequency beam and the polarization of the second harmonic.

Solvent Reaction Field Potential inside an Uncharged Globular Protein: A Bridge between Implicit and Explicit Solvent Models?

PubMed Central

Baker, Nathan A.; McCammon, J. Andrew

2008-01-01

The solvent reaction field potential of an uncharged protein immersed in Simple Point Charge/Extended (SPC/E) explicit solvent was computed over a series of molecular dynamics trajectories, intotal 1560 ns of simulation time. A finite, positive potential of 13 to 24 kbTec−1 (where T = 300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 Å from the solute surface, on average 0.008 ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit-solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99. PMID:17949217

Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

NASA Astrophysics Data System (ADS)

Cerutti, David S.; Baker, Nathan A.; McCammon, J. Andrew

2007-10-01

The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560ns of simulation time. A finite, positive potential of 13-24 kbTec-1 (where T =300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0Å from the solute surface, on average 0.008ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99.

Second-order Boltzmann equation: gauge dependence and gauge invariance

NASA Astrophysics Data System (ADS)

Naruko, Atsushi; Pitrou, Cyril; Koyama, Kazuya; Sasaki, Misao

2013-08-01

In the context of cosmological perturbation theory, we derive the second-order Boltzmann equation describing the evolution of the distribution function of radiation without a specific gauge choice. The essential steps in deriving the Boltzmann equation are revisited and extended given this more general framework: (i) the polarization of light is incorporated in this formalism by using a tensor-valued distribution function; (ii) the importance of a choice of the tetrad field to define the local inertial frame in the description of the distribution function is emphasized; (iii) we perform a separation between temperature and spectral distortion, both for the intensity and polarization for the first time; (iv) the gauge dependence of all perturbed quantities that enter the Boltzmann equation is derived, and this enables us to check the correctness of the perturbed Boltzmann equation by explicitly showing its gauge-invariance for both intensity and polarization. We finally discuss several implications of the gauge dependence for the observed temperature.

Image method for induced surface charge from many-body system of dielectric spheres

NASA Astrophysics Data System (ADS)

Qin, Jian; de Pablo, Juan J.; Freed, Karl F.

2016-09-01

Charged dielectric spheres embedded in a dielectric medium provide the simplest model for many-body systems of polarizable ions and charged colloidal particles. We provide a multiple scattering formulation for the total electrostatic energy for such systems and demonstrate that the polarization energy can be rapidly evaluated by an image method that generalizes the image methods for conducting spheres. Individual contributions to the total electrostatic energy are ordered according to the number of polarized surfaces involved, and each additional surface polarization reduces the energy by a factor of (a/R)3ɛ, where a is the sphere radius, R the average inter-sphere separation, and ɛ the relevant dielectric mismatch at the interface. Explicit expressions are provided for both the energy and the forces acting on individual spheres, which can be readily implemented in Monte Carlo and molecular dynamics simulations of polarizable charged spheres, thereby avoiding costly computational techniques that introduce a surface charge distribution that requires numerical solution.

Rogue-pair and dark-bright-rogue waves of the coupled nonlinear Schrödinger equations from inhomogeneous femtosecond optical fibers.

PubMed

Yomba, Emmanuel; Zakeri, Gholam-Ali

2016-08-01

The coupled inhomogeneous Schrödinger equations with a wide range of applications describing a field of pluses with the right and the left polarizations that take into account cross-phase modulations, stimulated Ramani scattering, and absorption effects are investigated. A combination of several different approaches is used in a novel way to obtain the explicit expressions for the rogue-pair and dark-bright-rogue waves. We study the dynamics of these structurally stable rogues and analyze the effects of a parameter that controls the region of stability that intrinsically connects the cross-phase modulation and other Kerr nonlinearity factors. The effects of the right and left polarizations on the shape of the rogue-pair and other solitary rogue waves are graphically analyzed. These rogue-pair waves are studied on periodic and non-periodic settings. We observe that rogue-pair wave from the right and left polarizations has a similar structure while the dark-bright-rogue waves have quite different intensity profiles.

IImage method for induced surface charge from many-body system of dielectric spheres

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, Jian; de Pablo, Juan J.; Freed, Karl F.

2016-09-28

Charged dielectric spheres embedded in a dielectric medium provide the simplest model for many-body systems of polarizable ions and charged colloidal particles. We provide a multiple scattering formulation for the total electrostatic energy for such systems and demonstrate that the polarization energy can be rapidly evaluated by an image method that generalizes the image methods for conducting spheres. Individual contributions to the total electrostatic energy are ordered according to the number of polarized surfaces involved, and each additional surface polarization reduces the energy by a factor of (a/R)(3) epsilon, where a is the sphere radius, R the average inter-sphere separation,more » and. the relevant dielectric mismatch at the interface. Explicit expressions are provided for both the energy and the forces acting on individual spheres, which can be readily implemented in Monte Carlo and molecular dynamics simulations of polarizable charged spheres, thereby avoiding costly computational techniques that introduce a surface charge distribution that requires numerical solution.« less

Vacuum polarization effects on flat branes due to a global monopole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bezerra de Mello, E.R.

2006-05-15

In this paper we analyze the vacuum polarization effects associated with a massless scalar field in the higher-dimensional spacetime. Specifically we calculate the renormalized vacuum expectation value of the square of the field, <{phi}{sup 2}(x)>{sub Ren}, induced by a global monopole in the 'braneworld' scenario. In this context the global monopole lives in a n=3-dimensional submanifold of the higher-dimensional (bulk) spacetime, and our universe is represented by a transverse flat (p-1)-dimensional brane. In order to develop this analysis we calculate the general Green function admitting that the scalar field propagates in the bulk. Also a general curvature coupling parameter betweenmore » the field and the geometry is assumed. We explicitly show that the vacuum polarization effects depend crucially on the values attributed to p. We also investigate the general structure of the renormalized vacuum expectation value of the energy-momentum tensor, {sub Ren}, for p=3.« less

QM/MM investigation of the concentration effects on the second-order nonlinear optical responses of solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hidalgo Cardenuto, Marcelo, E-mail: marcelo.hidalgo@unamur.be, E-mail: benoit.champagne@unamur.be; Instituto de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP; Champagne, Benoît, E-mail: marcelo.hidalgo@unamur.be, E-mail: benoit.champagne@unamur.be

2014-12-21

A multiscale approach combining quantum mechanics (QM) and molecular mechanics methods has been employed to investigate the effects of solute-solute interactions and therefore of concentration on the first hyperpolarizability of solutions of nitrobenzene in benzene. First, spatial distributions of solute and solvent molecules are generated using Monte Carlo simulations where the intermolecular interactions are described using the Lennard-Jones potentials and Coulomb terms. Then, a reduced number of statistically-uncorrelated configurations are sampled and submitted to time-dependent Hartree-Fock calculations of the first hyperpolarizability. When only one molecule is described quantum-mechanically and is embedded in the electrostatic polarization field of the solution describedmore » by point charges, β{sub HRS} and β{sub //} as well as the depolarization ratio increase in parallel with the concentration in nitrobenzene. This effect is attributed to the increase of the polarization field associated with the presence of polar nitrobenzene molecules in the surrounding. Then, the first solvation shell is considered explicitly in the QM calculation to address solute-solute interactions effects. When the number of nitrobenzenes in the first solvation shell increases, β{sub HRS} and β{sub //} normalized to the number of nitrobenzene molecules decrease and this decrease attains roughly 50% when there are 3 nitrobenzene molecules in the first solvation shell. These drastic reductions of the first hyperpolarizability result from (partial) centro-symmetric arrangements between the nitrobenzene molecules, as supported by the relationship between β and the angle between the nitrobenzene charge transfer axes. Moreover, these β decreases originate mostly from the reduction of the dipolar β component, whereas the octupolar one is rather constant as a function of the nitrobenzene concentration.« less

Capabilities and limitations of dispersive liquid-liquid microextraction with solidification of floating organic drop for the extraction of organic pollutants from water samples.

PubMed

Vera-Avila, Luz E; Rojo-Portillo, Tania; Covarrubias-Herrera, Rosario; Peña-Alvarez, Araceli

2013-12-17

Dispersive liquid-liquid microextraction with solidification of floating organic drop (DLLME-SFO) is one of the most interesting sample preparation techniques developed in recent years. Although several applications have been reported, the potentiality and limitations of this simple and rapid extraction technique have not been made sufficiently explicit. In this work, the extraction efficiency of DLLME-SFO for pollutants from different chemical families was determined. Studied compounds include: 10 polycyclic aromatic hydrocarbons, 5 pesticides (chlorophenoxy herbicides and DDT), 8 phenols and 6 sulfonamides, thus, covering a large range of polarity and hydrophobicity (LogKow 0-7, overall). After optimization of extraction conditions using 1-dodecanol as extractant, the procedure was applied for extraction of each family from 10-mL spiked water samples, only adjusting sample pH as required. Absolute recoveries for pollutants with LogKow 3-7 were >70% and recovery values within this group (18 compounds) were independent of structure or hydrophobicity; the precision of recovery was very acceptable (RSD<12%) and linear behavior was observed in the studied concentration range (r(2)>0.995). Extraction recoveries for pollutants with LogKow 1.46-2.8 were in the range 13-62%, directly depending on individual LogKow values; however, good linearity (r(2)>0.993) and precision (RSD<6.5%) were also demonstrated for these polar solutes, despite recovery level. DLLME-SFO with 1-dodecanol completely failed for extraction of compounds with LogKow≤1 (sulfa drugs), other more polar extraction solvents (ionic liquids) should be explored for highly hydrophilic pollutants. Copyright © 2013 Elsevier B.V. All rights reserved.

Polarization effects in low-energy electron-CH4 elastic collisions in an exact exchange treatment

NASA Astrophysics Data System (ADS)

Jain, Ashok; Weatherford, C. A.; Thompson, D. G.; McNaughten, P.

1989-12-01

We have investigated the polarization effects in very-low-energy (below 1 eV) electron- CH4 collisions in an exact-exchange treatment. The two models of the parameter-free polarization potential are employed; one, the VpolJT potential, introduced by Jain and Thompson [J. Phys. B 15, L631 (1982)], is based on an approximate polarized-orbital method, and two, the correlation-polarization potential VpolCP, first proposed by O'Connel and Lane [Phys. Rev. A 27, 1893 (1983)], is given as a simple analytic form in terms of the charge density of the target. In this rather very low-energy region, the polarization effects play a decisive role, particularly in creating structure in the differential cross section (DCS) and producing the Ramsauer-Townsend minimum in the total cross section. Our DCS at 0.2, 0.4, and 0.6 eV are compared with recent measurements. We found that a local parameter-free approximation for the polarization potential is quite successful if it is determined under the polarized-orbital-type technique rather than based on the correlation-polarization approach.

Revisiting the `forbidden' region: AGN radiative feedback with radiation trapping

NASA Astrophysics Data System (ADS)

Ishibashi, W.; Fabian, A. C.; Ricci, C.; Celotti, A.

2018-06-01

Active galactic nucleus (AGN) feedback, driven by radiation pressure on dust, is an important mechanism for efficiently coupling the accreting black hole to the surrounding environment. Recent observations confirm that X-ray selected AGN samples respect the effective Eddington limit for dusty gas in the plane defined by the observed column density versus the Eddington ratio, the so-called NH - λ plane. A `forbidden' region occurs in this plane, where obscuring clouds cannot be long-lived, due to the action of radiation pressure on dust. Here we compute the effective Eddington limit by explicitly taking into account the trapping of reprocessed radiation (which has been neglected in previous works), and investigate its impact on the NH - λ plane. We show that the inclusion of radiation trapping leads to an enhanced forbidden region, such that even Compton-thick material can potentially be disrupted by sub-Eddington luminosities. We compare our model results to the most complete sample of local AGNs with measured X-ray properties, and find good agreement. Considering the anisotropic emission from the accretion disc, we also expect the development of dusty outflows along the polar axis, which may naturally account for the polar dust emission recently detected in several AGNs from mid-infrared observations. Radiative feedback thus appears to be the key mechanism regulating the obscuration properties of AGNs, and we discuss its physical implications in the context of co-evolution scenarios.

Time Domain Radar Laboratory Operating System Development and Transient EM Analysis.

DTIC Science & Technology

1981-09-01

polarization of the return, arg used. Other similar methods use amplitude and phase differences or special properties of Rayleigh region scattering. All these...3ptias Inverse Scattering ... 19 2. "!xact" Inverse Scattering !Nethod .. 20 3. Other Methods ................... 21 C. REVIEW OF TDRL PROGRESS AT SPS...explicit independant variable in.most methods . In the past, frequency domain analysis has been the primary means of analyzing aan-monochromatic EM

Propagation of Polarization Modulated Beams Through a Turbulent Atmosphere

DTIC Science & Technology

2014-11-24

Clifford Algebra to Geometric Calculus , Reidel, 1984. Hirschfelder, J.O., Curtiss, C.F. & Bird, R.B., Molecular Theory of Gases and Liquids, Wiley, 1954...are made explicit in a Poincaré sphere and geometric (Clifford) algebra representation. Section 5.0 of this report provides the evidence supporting...MEDIA 4.0 LABORATORY TEST CONFIGURATIONS 5.0 TEST RESULTS 5.1 DATA ANALYSIS METHODS 5.2 DATA ANALYSIS 6.0 GEOMETRIC ALGEBRA 6.1 INTRODUCTION

Polar Rain Gradients and Field-Aligned Polar Cap Potentials

NASA Technical Reports Server (NTRS)

Fairfield, D. H.; Wing, S.; Newell, P. T.; Ruohoniemi, J. M.; Gosling, J. T.; Skoug, R. M.

2008-01-01

ACE SWEPAM measurements of solar wind field-aligned electrons have been compared with simultaneous measurements of polar rain electrons precipitating over the polar cap and detected by DMSP spacecraft. Such comparisons allow investigation of cross-polar-cap gradients in the intensity of otherwise-steady polar rain. The generally good agreement of the distribution functions, f, from the two data sources confirms that direct entry of solar electrons along open field lines is indeed the cause of polar rain. The agreement between the data sets is typically best on the side of the polar cap with most intense polar rain but the DMSP f's in less intense regions can be brought into agreement with ACE measurements by shifting all energies by a fixed amounts that range from tens to several hundred eV. In most cases these shifts are positive which implies that field-aligned potentials of these amounts exist on polar cap field lines which tend to retard the entry of electrons and produce the observed gradients. These retarding potentials undoubtedly appear in order to prevent the entry of low-energy electrons and maintain charge quasi-neutrality that would otherwise be violated since most tailward flowing magnetosheath ions are unable to follow polar rain electrons down to the polar cap. In more limited regions near the boundary of the polar cap there is sometimes evidence for field-aligned potentials of the opposite sign that accelerate polar rain electrons. A solar electron burst is also studied and it is concluded that electrons from such bursts can enter the magnetotail and precipitate in the same manner as polar rain.

Polarity effects and apparent ion recombination in microionization chambers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Jessica R., E-mail: miller@humonc.wisc.edu; Hooten, Brian D.; Micka, John A.

Purpose: Microchambers demonstrate anomalous voltage-dependent polarity effects. Existing polarity and ion recombination correction factors do not account for these effects. As a result, many commercial microchamber models do not meet the specification of a reference-class ionization chamber as defined by the American Association of Physicists in Medicine. The purpose of this investigation is to determine the cause of these voltage-dependent polarity effects. Methods: A series of microchamber prototypes were produced to isolate the source of the voltage-dependent polarity effects. Parameters including ionization-chamber collecting-volume size, stem and cable irradiation, chamber assembly, contaminants, high-Z materials, and individual chamber components were investigated. Measurementsmore » were performed with electrodes coated with graphite to isolate electrode conductivity. Chamber response was measured as the potential bias of the guard electrode was altered with respect to the collecting electrode, through the integration of additional power supplies. Ionization chamber models were also simulated using COMSOL Multiphysics software to investigate the effect of a potential difference between electrodes on electric field lines and collecting volume definition. Results: Investigations with microchamber prototypes demonstrated that the significant source of the voltage-dependent polarity effects was a potential difference between the guard and collecting electrodes of the chambers. The voltage-dependent polarity effects for each prototype were primarily isolated to either the guard or collecting electrode. Polarity effects were reduced by coating the isolated electrode with a conductive layer of graphite. Polarity effects were increased by introducing a potential difference between the electrodes. COMSOL simulations further demonstrated that for a given potential difference between electrodes, the collecting volume of the chamber changed as the applied voltage was altered, producing voltage-dependent polarity effects in the chamber response. Ionization chamber measurements and COMSOL simulations demonstrated an inverse relationship between the chamber collecting volume size and the severity of voltage-dependent polarity effects on chamber response. The effect of a given potential difference on chamber polarity effects was roughly ten times greater for microchambers as compared to Farmer-type chambers. Stem and cable irradiations, chamber assembly, contaminants, and high-Z materials were not found to be a significant source of the voltage-dependent polarity effects. Conclusions: A potential difference between the guard and collecting electrodes was found to be the primary source of the voltage-dependent polarity effects demonstrated by microchambers. For a given potential difference between electrodes, the relative change in the collecting volume is smaller for larger-volume chambers, illustrating why these polarity effects are not seen in larger-volume chambers with similar guard and collecting electrode designs. Thus, for small-volume chambers, it is necessary to reduce the potential difference between the guard and collecting electrodes in order to reduce polarity effects for reference dosimetry measurements.« less

Giant photovoltaic effects driven by residual polar field within unit-cell-scale LaAlO3 films on SrTiO3

PubMed Central

Liang, Haixing; Cheng, Long; Zhai, Xiaofang; Pan, Nan; Guo, Hongli; Zhao, Jin; Zhang, Hui; Li, Lin; Zhang, Xiaoqiang; Wang, Xiaoping; Zeng, Changgan; Zhang, Zhenyu; Hou, J. G.

2013-01-01

For polar/nonpolar heterostructures, Maxwell's theory dictates that the electric potential in the polar components will increase divergently with the film thickness. For LaAlO3/SrTiO3, a conceptually intriguing route, termed charge reconstruction, has been proposed to avert such “polar catastrophe”. The existence of a polar potential in LaAlO3 is a prerequisite for the validity of the charge reconstruction picture, yet to date, its direct measurement remains a major challenge. Here we establish unambiguously the existence of the residual polar potential in ultrathin LaAlO3 films on SrTiO3, using a novel photovoltaic device design as an effective probe. The measured lower bound of the residual polar potential is 1.0 V. Such a direct observation of the giant residual polar potential within the unit-cell-scale LaAlO3 films amounts to a definitive experimental evidence for the charge reconstruction picture, and also points to new technological significance of oxide heterostructures in photovoltaic and sensing devices with atomic-scale control. PMID:23756918

Understanding biogeobatteries: Where geophysics meets microbiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Revil, A.; Mendonca, C.A.; Atekwana, E.A.

2009-08-15

Although recent research suggests that contaminant plumes behave as geobatteries that produce an electrical current in the ground, no associated model exists that honors both geophysical and biogeochemical constraints. Here, we develop such a model to explain the two main electrochemical contributions to self-potential signals in contaminated areas. Both contributions are associated with the gradient of the activity of two types of charge carriers, ions and electrons. In the case of electrons, bacteria act as catalysts for reducing the activation energy needed to exchange the electrons between electron donor and electron acceptor. Possible mechanisms that facilitate electron migration include ironmore » oxides, clays, and conductive biological materials, such as bacterial conductive pili or other conductive extracellular polymeric substances. Because we explicitly consider the role of biotic processes in the geobattery model, we coined the term 'biogeobattery'. After theoretical development of the biogeobattery model, we compare model predictions with self-potential responses associated with laboratory and field-scale conducted in contaminated environments. We demonstrate that the amplitude and polarity of large (>100 mV) self-potential signatures requires the presence of an electronic conductor to serve as a bridge between electron donors and acceptors. Small self-potential anomalies imply that electron donors and electron acceptors are not directly interconnected, but instead result simply from the gradient of the activity of the ionic species that are present in the system.« less

Functional differences between statistical learning with and without explicit training

PubMed Central

Reber, Paul J.; Paller, Ken A.

2015-01-01

Humans are capable of rapidly extracting regularities from environmental input, a process known as statistical learning. This type of learning typically occurs automatically, through passive exposure to environmental input. The presumed function of statistical learning is to optimize processing, allowing the brain to more accurately predict and prepare for incoming input. In this study, we ask whether the function of statistical learning may be enhanced through supplementary explicit training, in which underlying regularities are explicitly taught rather than simply abstracted through exposure. Learners were randomly assigned either to an explicit group or an implicit group. All learners were exposed to a continuous stream of repeating nonsense words. Prior to this implicit training, learners in the explicit group received supplementary explicit training on the nonsense words. Statistical learning was assessed through a speeded reaction-time (RT) task, which measured the extent to which learners used acquired statistical knowledge to optimize online processing. Both RTs and brain potentials revealed significant differences in online processing as a function of training condition. RTs showed a crossover interaction; responses in the explicit group were faster to predictable targets and marginally slower to less predictable targets relative to responses in the implicit group. P300 potentials to predictable targets were larger in the explicit group than in the implicit group, suggesting greater recruitment of controlled, effortful processes. Taken together, these results suggest that information abstracted through passive exposure during statistical learning may be processed more automatically and with less effort than information that is acquired explicitly. PMID:26472644

Quantitative analysis of domain texture in polycrystalline barium titanate by polarized Raman microprobe spectroscopy

NASA Astrophysics Data System (ADS)

Sakashita, Tatsuo; Chazono, Hirokazu; Pezzotti, Giuseppe

2007-12-01

A quantitative determination of domain distribution in polycrystalline barium titanate (BaTiO3, henceforth BT) ceramics has been pursued with the aid of a microprobe polarized Raman spectrometer. The crystallographic texture and domain orientation distribution of BT ceramics, which switched upon applying stress according to ferroelasticity principles, were determined from the relative intensity of selected phonon modes, taking into consideration a theoretical analysis of the angular dependence of phonon mode intensity for the tetragonal BT phase. Furthermore, the angular dependence of Raman intensity measured in polycrystalline BT depended on the statistical distribution of domain angles in the laser microprobe, which was explicitly taken into account in this work for obtaining a quantitative analysis of domain orientation for in-plane textured BT polycrystalline materials.

Polar Rain Gradients and Field-Aligned Polar Cap Potentials

NASA Technical Reports Server (NTRS)

Fairfield, D. H.; Wing, S.; Newell, P. T.; Ruohoniemi, J. M.; Gosling, J. T.; Skoug, R. M.

2008-01-01

ACE SWEPAM measurements of solar wind field-aligned electrons have been compared with simultaneous measurements of polar rain electrons precipitating over the polar cap and detected by DMSP spacecraft. Such comparisons allow investigation of cross-polarcap gradients in the intensity of otherwise-steady polar rain. The generally good agreement of the distribution functions, f, from the two data sources confirms that direct entry of solar electrons along open field lines is indeed the cause of polar rain. The agreement between the data sets is typically best on the side of the polar cap with most intense polar rain but the DMSP f's in less intense regions can be brought into agreement with ACE measurements by shifting all energies by a fixed amounts that range from tens to several hundred eV. In most cases these shifts are positive which implies that field-aligned potentials of these amounts exist on polar cap field lines which tend to retard the entry of electrons and produce the observed gradients. These retarding potentials undoubtedly appear in order to prevent the entry of low-energy electrons and maintain charge quasi-neutrality that would otherwise be violated since most tailward flowing magnetosheath ions are unable to follow polar rain electrons down to the polar cap. In more limited regions near the boundary of the polar cap there is sometimes evidence for field-aligned potentials of the opposite sign that accelerate polar rain electrons. A solar electron burst is also studied and it is concluded that electrons from such bursts can enter the magnetotail and precipitate in the same manner as polar rain.

Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.

PubMed

Chen, Duan; Chen, Zhan; Wei, Guo-Wei

2012-01-01

Proton transport plays an important role in biological energy transduction and sensory systems. Therefore, it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic, and quantum descriptions, assisted with the evolution, formation, and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free-energy functional to put proton kinetic and potential energies, the free energy of all other ions, and the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation, and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet-to-Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The gramicidin A channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model. Copyright © 2011 John Wiley & Sons, Ltd.

Magnetic Interactions at the Nanoscale in Trilayer Titanates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Yanwei; Yang, Zhenzhong; Kareev, M.

2016-02-17

We report on the phase diagram of competing magnetic interactions at the nanoscale in engineered ultrathin trilayer heterostructures of LaTiO3/SrTiO3/YTiO3, in which the interfacial inversion symmetry is explicitly broken. Combined atomic layer resolved scanning transmission electron microscopy with electron energy loss spectroscopy and electrical transport have confirmed the formation of a spatially separated two-dimensional electron liquid and high density two-dimensional localized magnetic moments at the LaTiO3/SrTiO3 and SrTiO3/YTiO3 interfaces, respectively. Resonant soft x-ray linear dichroism spectroscopy has demonstrated the presence of orbital polarization of the conductive LaTiO3/SrTiO3 and localized SrTiO3/YTiO3 electrons. Our results provide a route with prospects for exploringmore » new magnetic interfaces, designing a tunable two-dimensional d-electron Kondo lattice, and potential spin Hall applications.« less

Comparison of polar cap potential drops estimated from solar wind and ground magnetometer data - CDAW 6

NASA Technical Reports Server (NTRS)

Reiff, P. H.; Spiro, R. W.; Wolf, R. A.; Kamide, Y.; King, J. H.

1985-01-01

It is pointed out that the maximum electrostatic potential difference across the polar cap, Phi, is a fundamental measure of the coupling between the solar wind and the earth's magnetosphere/ionosphere sytem. During the Coordinated Data Analysis Workshop (CDAW) 6 intervals, no suitably instrumented spacecraft was in an appropriate orbit to determine the polar-cap potential drop directly. However, two recently developed independent techniques make it possible to estimate the polar-cap potential drop for times when direct spacecraft data are not available. The present investigation is concerned with a comparison of cross-polar-cap potential drop estimates calculated for the two CDAW 6 intervals on the basis of these two techniques. In the case of one interval, the agreement between the potential drops and Joule heating rates is relatively good. In the second interval, however, the agreement is not very good. Explanations for this discrepancy are discussed.

Explicitly Linking Pedagogy and Facilities to Campus Sustainability: Lessons from Carleton College and the University of Minnesota

ERIC Educational Resources Information Center

Savanick, Suzanne; Strong, Richard; Manning, Christie

2008-01-01

Campus sustainability projects provide an opportunity to explicitly link campus operations and academics. College and university buildings and grounds offer the potential for numerous hands-on sustainability projects. Few schools explicitly link sustainability projects with academics as often the academic side of an institution is separate from…

An exact solution to the relativistic equation of motion of a charged particle driven by a linearly polarized electromagnetic wave

NASA Technical Reports Server (NTRS)

Shebalin, John V.

1988-01-01

An exact analytic solution is found for a basic electromagnetic wave-charged particle interaction by solving the nonlinear equations of motion. The particle position, velocity, and corresponding time are found to be explicit functions of the total phase of the wave. Particle position and velocity are thus implicit functions of time. Applications include describing the motion of a free electron driven by an intense laser beam..

Cis-to- Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics.

PubMed

Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark

2018-04-10

Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of reaction rates and an improved understanding of activated states.

The Feasibility of Formation and Kinetics of NMR Signal Amplification by Reversible Exchange (SABRE) at High Magnetic Field (9.4 T)

PubMed Central

2015-01-01

1H NMR signal amplification by reversible exchange (SABRE) was observed for pyridine and pyridine-d5 at 9.4 T, a field that is orders of magnitude higher than what is typically utilized to achieve the conventional low-field SABRE effect. In addition to emissive peaks for the hydrogen spins at the ortho positions of the pyridine substrate (both free and bound to the metal center), absorptive signals are observed from hyperpolarized orthohydrogen and Ir-complex dihydride. Real-time kinetics studies show that the polarization build-up rates for these three species are in close agreement with their respective 1H T1 relaxation rates at 9.4 T. The results suggest that the mechanism of the substrate polarization involves cross-relaxation with hyperpolarized species in a manner similar to the spin-polarization induced nuclear Overhauser effect. Experiments utilizing pyridine-d5 as the substrate exhibited larger enhancements as well as partial H/D exchange for the hydrogen atom in the ortho position of pyridine and concomitant formation of HD molecules. While the mechanism of polarization enhancement does not explicitly require chemical exchange of hydrogen atoms of parahydrogen and the substrate, the partial chemical modification of the substrate via hydrogen exchange means that SABRE under these conditions cannot rigorously be referred to as a non-hydrogenative parahydrogen induced polarization process. PMID:24528143

The feasibility of formation and kinetics of NMR signal amplification by reversible exchange (SABRE) at high magnetic field (9.4 T).

PubMed

Barskiy, Danila A; Kovtunov, Kirill V; Koptyug, Igor V; He, Ping; Groome, Kirsten A; Best, Quinn A; Shi, Fan; Goodson, Boyd M; Shchepin, Roman V; Coffey, Aaron M; Waddell, Kevin W; Chekmenev, Eduard Y

2014-03-05

(1)H NMR signal amplification by reversible exchange (SABRE) was observed for pyridine and pyridine-d5 at 9.4 T, a field that is orders of magnitude higher than what is typically utilized to achieve the conventional low-field SABRE effect. In addition to emissive peaks for the hydrogen spins at the ortho positions of the pyridine substrate (both free and bound to the metal center), absorptive signals are observed from hyperpolarized orthohydrogen and Ir-complex dihydride. Real-time kinetics studies show that the polarization build-up rates for these three species are in close agreement with their respective (1)H T1 relaxation rates at 9.4 T. The results suggest that the mechanism of the substrate polarization involves cross-relaxation with hyperpolarized species in a manner similar to the spin-polarization induced nuclear Overhauser effect. Experiments utilizing pyridine-d5 as the substrate exhibited larger enhancements as well as partial H/D exchange for the hydrogen atom in the ortho position of pyridine and concomitant formation of HD molecules. While the mechanism of polarization enhancement does not explicitly require chemical exchange of hydrogen atoms of parahydrogen and the substrate, the partial chemical modification of the substrate via hydrogen exchange means that SABRE under these conditions cannot rigorously be referred to as a non-hydrogenative parahydrogen induced polarization process.

The ellipsoidal universe in the Planck satellite era

NASA Astrophysics Data System (ADS)

Cea, Paolo

2014-06-01

Recent Planck data confirm that the cosmic microwave background displays the quadrupole power suppression together with large-scale anomalies. Progressing from previous results, that focused on the quadrupole anomaly, we strengthen the proposal that the slightly anisotropic ellipsoidal universe may account for these anomalies. We solved at large scales the Boltzmann equation for the photon distribution functions by taking into account both the effects of the inflation produced primordial scalar perturbations and the anisotropy of the geometry in the ellipsoidal universe. We showed that the low quadrupole temperature correlations allowed us to fix the eccentricity at decoupling, edec = (0.86 ± 0.14) 10-2, and to constraint the direction of the symmetry axis. We found that the anisotropy of the geometry of the universe contributes only to the large-scale temperature anisotropies without affecting the higher multipoles of the angular power spectrum. Moreover, we showed that the ellipsoidal geometry of the universe induces sizeable polarization signal at large scales without invoking the reionization scenario. We explicitly evaluated the quadrupole TE and EE correlations. We found an average large-scale polarization ΔTpol = (1.20 ± 0.38) μK. We point out that great care is needed in the experimental determination of the large-scale polarization correlations since the average temperature polarization could be misinterpreted as foreground emission leading, thereby, to a considerable underestimate of the cosmic microwave background polarization signal.

Potential Sources of Polarized Light from a Plant Canopy

NASA Technical Reports Server (NTRS)

Vanderbilt, Vern; Daughtry, Craig; Dahlgren, Robert

2016-01-01

Field measurements have demonstrated that sunlight polarized during a first surface reflection by shiny leaves dominates the optical polarization of the light reflected by shiny-leafed plant canopies having approximately spherical leaf angle probability density functions ("Leaf Angle Distributions" - LAD). Yet for other canopies - specifically those without shiny leaves and/or spherical LADs - potential sources of optically polarized light may not always be obvious. Here we identify possible sources of polarized light within those other canopies and speculate on the ecologically important information polarization measurements of those sources might contain.

Implicit and Explicit Measures of Sensitivity to Violations in Second Language Grammar: An Event-Related Potential Investigation

ERIC Educational Resources Information Center

Tokowicz, Natasha; MacWhinney, Brian

2005-01-01

We used event-related brain potentials (ERPs) to investigate the contributions of explicit and implicit processes during second language (L2) sentence comprehension. We used a L2 grammaticality judgment task (GJT) to test 20 native English speakers enrolled in the first four semesters of Spanish while recording both accuracy and ERP data. Because…

Belief propagation decoding of quantum channels by passing quantum messages

NASA Astrophysics Data System (ADS)

Renes, Joseph M.

2017-07-01

The belief propagation (BP) algorithm is a powerful tool in a wide range of disciplines from statistical physics to machine learning to computational biology, and is ubiquitous in decoding classical error-correcting codes. The algorithm works by passing messages between nodes of the factor graph associated with the code and enables efficient decoding of the channel, in some cases even up to the Shannon capacity. Here we construct the first BP algorithm which passes quantum messages on the factor graph and is capable of decoding the classical-quantum channel with pure state outputs. This gives explicit decoding circuits whose number of gates is quadratic in the code length. We also show that this decoder can be modified to work with polar codes for the pure state channel and as part of a decoder for transmitting quantum information over the amplitude damping channel. These represent the first explicit capacity-achieving decoders for non-Pauli channels.

Explicit and spontaneous retrieval of emotional scenes: electrophysiological correlates.

PubMed

Weymar, Mathias; Bradley, Margaret M; El-Hinnawi, Nasryn; Lang, Peter J

2013-10-01

When event-related potentials (ERP) are measured during a recognition task, items that have previously been presented typically elicit a larger late (400-800 ms) positive potential than new items. Recent data, however, suggest that emotional, but not neutral, pictures show ERP evidence of spontaneous retrieval when presented in a free-viewing task (Ferrari, Bradley, Codispoti, Karlsson, & Lang, 2012). In two experiments, we further investigated the brain dynamics of implicit and explicit retrieval. In Experiment 1, brain potentials were measured during a semantic categorization task, which did not explicitly probe episodic memory, but which, like a recognition task, required an active decision and a button press, and were compared to those elicited during recognition and free viewing. Explicit recognition prompted a late enhanced positivity for previously presented, compared with new, pictures regardless of hedonic content. In contrast, only emotional pictures showed an old-new difference when the task did not explicitly probe episodic memory, either when making an active categorization decision regarding picture content, or when simply viewing pictures. In Experiment 2, however, neutral pictures did prompt a significant old-new ERP difference during subsequent free viewing when emotionally arousing pictures were not included in the encoding set. These data suggest that spontaneous retrieval is heightened for salient cues, perhaps reflecting heightened attention and elaborative processing at encoding.

Explicit and spontaneous retrieval of emotional scenes: Electrophysiological correlates

PubMed Central

Weymar, Mathias; Bradley, Margaret M.; El-Hinnawi, Nasryn; Lang, Peter J.

2014-01-01

When event-related potentials are measured during a recognition task, items that have previously been presented typically elicit a larger late (400–800 ms) positive potential than new items. Recent data, however, suggest that emotional, but not neutral, pictures show ERP evidence of spontaneous retrieval when presented in a free-viewing task (Ferrari, Bradley, Codispoti & Lang, 2012). In two experiments, we further investigated the brain dynamics of implicit and explicit retrieval. In Experiment 1, brain potentials were measured during a semantic categorization task, which did not explicitly probe episodic memory, but which, like a recognition task, required an active decision and a button press, and were compared to those elicited during recognition and free viewing. Explicit recognition prompted a late enhanced positivity for previously presented, compared to new, pictures regardless of hedonic content. In contrast, only emotional pictures showed an old-new difference when the task did not explicitly probe episodic memory, either when either making an active categorization decision regarding picture content, or when simply viewing pictures. In Experiment 2, however, neutral pictures did prompt a significant old-new ERP difference during subsequent free viewing when emotionally arousing pictures were not included in the encoding set. These data suggest that spontaneous retrieval is heightened for salient cues, perhaps reflecting heightened attention and elaborative processing at encoding. PMID:23795588

Polar clouds and radiation in satellite observations, reanalyses, and climate models

NASA Astrophysics Data System (ADS)

Lenaerts, Jan T. M.; Van Tricht, Kristof; Lhermitte, Stef; L'Ecuyer, Tristan S.

2017-04-01

Clouds play a pivotal role in the surface energy budget of the polar regions. Here we use two largely independent data sets of cloud and surface downwelling radiation observations derived by satellite remote sensing (2007-2010) to evaluate simulated clouds and radiation over both polar ice sheets and oceans in state-of-the-art atmospheric reanalyses (ERA-Interim and Modern Era Retrospective-Analysis for Research and Applications-2) and the Coupled Model Intercomparison Project Phase 5 (CMIP5) climate model ensemble. First, we show that, compared to Clouds and the Earth's Radiant Energy System-Energy Balanced and Filled, CloudSat-CALIPSO better represents cloud liquid and ice water path over high latitudes, owing to its recent explicit determination of cloud phase that will be part of its new R05 release. The reanalyses and climate models disagree widely on the amount of cloud liquid and ice in the polar regions. Compared to the observations, we find significant but inconsistent biases in the model simulations of cloud liquid and ice water, as well as in the downwelling radiation components. The CMIP5 models display a wide range of cloud characteristics of the polar regions, especially with regard to cloud liquid water, limiting the representativeness of the multimodel mean. A few CMIP5 models (CNRM, GISS, GFDL, and IPSL_CM5b) clearly outperform the others, which enhances credibility in their projected future cloud and radiation changes over high latitudes. Given the rapid changes in polar regions and global feedbacks involved, future climate model developments should target improved representation of polar clouds. To that end, remote sensing observations are crucial, in spite of large remaining observational uncertainties, which is evidenced by the substantial differences between the two data sets.

Increasing nest predation will be insufficient to maintain polar bear body condition in the face of sea ice loss.

PubMed

Dey, Cody J; Richardson, Evan; McGeachy, David; Iverson, Samuel A; Gilchrist, Hugh G; Semeniuk, Christina A D

2017-05-01

Climate change can influence interspecific interactions by differentially affecting species-specific phenology. In seasonal ice environments, there is evidence that polar bear predation of Arctic bird eggs is increasing because of earlier sea ice breakup, which forces polar bears into nearshore terrestrial environments where Arctic birds are nesting. Because polar bears can consume a large number of nests before becoming satiated, and because they can swim between island colonies, they could have dramatic influences on seabird and sea duck reproductive success. However, it is unclear whether nest foraging can provide an energetic benefit to polar bear populations, especially given the capacity of bird populations to redistribute in response to increasing predation pressure. In this study, we develop a spatially explicit agent-based model of the predator-prey relationship between polar bears and common eiders, a common and culturally important bird species for northern peoples. Our model is composed of two types of agents (polar bear agents and common eider hen agents) whose movements and decision heuristics are based on species-specific bioenergetic and behavioral ecological principles, and are influenced by historical and extrapolated sea ice conditions. Our model reproduces empirical findings that polar bear predation of bird nests is increasing and predicts an accelerating relationship between advancing ice breakup dates and the number of nests depredated. Despite increases in nest predation, our model predicts that polar bear body condition during the ice-free period will continue to decline. Finally, our model predicts that common eider nests will become more dispersed and will move closer to the mainland in response to increasing predation, possibly increasing their exposure to land-based predators and influencing the livelihood of local people that collect eider eggs and down. These results show that predator-prey interactions can have nonlinear responses to changes in climate and provides important predictions of ecological change in Arctic ecosystems. © 2016 John Wiley & Sons Ltd.

Electron correlation by polarization of interacting densities

NASA Astrophysics Data System (ADS)

Whitten, Jerry L.

2017-02-01

Coulomb interactions that occur in electronic structure calculations are correlated by allowing basis function components of the interacting densities to polarize dynamically, thereby reducing the magnitude of the interaction. Exchange integrals of molecular orbitals are not correlated. The modified Coulomb interactions are used in single-determinant or configuration interaction calculations. The objective is to account for dynamical correlation effects without explicitly introducing higher spherical harmonic functions into the molecular orbital basis. Molecular orbital densities are decomposed into a distribution of spherical components that conserve the charge and each of the interacting components is considered as a two-electron wavefunction embedded in the system acted on by an average field Hamiltonian plus r12-1. A method of avoiding redundancy is described. Applications to atoms, negative ions, and molecules representing different types of bonding and spin states are discussed.

Evolution of the Antarctic polar vortex in spring: Response of a GCM to a prescribed Antarctic ozone hole

NASA Technical Reports Server (NTRS)

Boville, B. A.; Kiehl, J. T.; Briegleb, B. P.

1988-01-01

The possible effect of the Antartic ozone hole on the evolution of the polar vortex during late winter and spring using a general circulation model (GCM) is examined. The GCM is a version of the NCAR Community Climate Model whose domain extends from the surface to the mesosphere and is similar to that described on Boville and Randel (1986). Ozone is not a predicted variable in the model. A zonally averaged ozone distribution is specified as a function of latitude, pressure and month for the radiation parameterization. Rather that explicitly address reasons for the formation of the ozone hole, researchers postulate its existence and ask what effect it has on the subsequent evolution of the vortex. The evolution of the model when an ozone hole is imposed is then discussed.

Antisymmetric Spin-Orbit Coupling in a d-p Model on a Zigzag Chain

DOE PAGES

Sugita, Yusuke; Hayami, Satoru; Motome, Yukitoshi

2015-12-29

In this paper, we theoretically investigate how an antisymmetric spin-orbit coupling emerges in electrons moving on lattice structures which are centrosymmetric but break the spatial inversion symme- try at atomic positions. We construct an effective d-p model on the simplest lattice structure, a zigzag chain of edge-sharing octahedra, with taking into account the crystalline electric field, the spin-orbit coupling, and on-site and inter-site d-p hybridizations. We show that an effective antisymmetric spin-orbit coupling arises in the sublattice-dependent form, which results in a hidden spin polarization in the band structure. Finally, we explicitly derive the effective antisymmetric spin-orbit coupling for dmore » electrons, which not only explains the hidden spin polarization but also indicates how to enhance it.« less

Antisymmetric Spin-Orbit Coupling in a d-p Model on a Zigzag Chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugita, Yusuke; Hayami, Satoru; Motome, Yukitoshi

In this paper, we theoretically investigate how an antisymmetric spin-orbit coupling emerges in electrons moving on lattice structures which are centrosymmetric but break the spatial inversion symme- try at atomic positions. We construct an effective d-p model on the simplest lattice structure, a zigzag chain of edge-sharing octahedra, with taking into account the crystalline electric field, the spin-orbit coupling, and on-site and inter-site d-p hybridizations. We show that an effective antisymmetric spin-orbit coupling arises in the sublattice-dependent form, which results in a hidden spin polarization in the band structure. Finally, we explicitly derive the effective antisymmetric spin-orbit coupling for dmore » electrons, which not only explains the hidden spin polarization but also indicates how to enhance it.« less

Paleointensity Behavior and Intervals Between Geomagnetic Reversals in the Last 167 Ma

NASA Astrophysics Data System (ADS)

Kurazhkovskii, A. Yu.; Kurazhkovskaya, N. A.; Klain, B. I.

2018-01-01

The results of comparative analysis of the behavior of paleointensity and polarity (intervals between reversals) of the geomagnetic field for the last 167 Ma are presented. Similarities and differences in the behavior of these characteristics of the geomagnetic field are discussed. It is shown that bursts of paleointensity and long intervals between reversals occurred at high mean values of paleointensity in the Cretaceous and Paleogene. However, there are differences between the paleointensity behavior and the reversal regime: (1) the characteristic times of paleointensity variations are less than the characteristic times of the frequency of geomagnetic reversals, (2) the achievement of maximum values of paleointensity at the Cretaceous-Paleogene boundary and the termination of paleointensity bursts after the boundary of 45-40 Ma are not marked by explicit features in the geomagnetic polarity behavior.

Comment on ``Nonlinear gyrokinetic theory with polarization drift'' [Phys. Plasmas 17, 082304 (2010)

NASA Astrophysics Data System (ADS)

Leerink, S.; Parra, F. I.; Heikkinen, J. A.

2010-12-01

In this comment, we show that by using the discrete particle distribution function the changes of the phase-space volume of gyrocenter coordinates due to the fluctuating E ×B velocity do not explicitly appear in the Poisson equation and the [Sosenko et al., Phys. Scr. 64, 264 (2001)] result is recovered. It is demonstrated that there is no contradiction between the work presented by Sosenko et al. and the work presented by [Wang et al., Phys. Plasmas 17, 082304 (2010)].

Implications of a quadratic stream definition in radiative transfer theory.

NASA Technical Reports Server (NTRS)

Whitney, C.

1972-01-01

An explicit definition of the radiation-stream concept is stated and applied to approximate the integro-differential equation of radiative transfer with a set of twelve coupled differential equations. Computational efficiency is enhanced by distributing the corresponding streams in three-dimensional space in a totally symmetric way. Polarization is then incorporated in this model. A computer program based on the model is briefly compared with a Monte Carlo program for simulation of horizon scans of the earth's atmosphere. It is found to be considerably faster.

Coherent perfect rotation

NASA Astrophysics Data System (ADS)

Crescimanno, Michael; Dawson, Nathan J.; Andrews, James H.

2012-09-01

Two classes of conservative, linear, optical rotary effects (optical activity and Faraday rotation) are distinguished by their behavior under time reversal. Faraday rotation, but not optical activity, is capable of coherent perfect rotation, by which we mean the complete transfer of counterpropagating coherent light fields into their orthogonal polarization. Unlike coherent perfect absorption, however, this process is explicitly energy conserving and reversible. Our study highlights the necessity of time-reversal-odd processes (not just absorption) and coherence in perfect mode conversion and thus informs the optimization of active multiport optical devices.

Proceedings of a Workshop on Polar Stratospheric Clouds: Their Role in Atmospheric Processes

NASA Technical Reports Server (NTRS)

Hamill, P. (Editor); Mcmaster, L. R. (Editor)

1984-01-01

The potential role of polar stratospheric clouds in atmospheric processes was assessed. The observations of polar stratospheric clouds with the Nimbus 7 SAM II satellite experiment were reviewed and a preliminary analysis of their formation, impact on other remote sensing experiments, and potential impact on climate were presented. The potential effect of polar stratospheric clouds on climate, radiation balance, atmospheric dynamics, stratospheric chemistry and water vapor budget, and cloud microphysics was assessed. Conclusions and recommendations, a synopsis of materials and complementary material to support those conclusions and recommendations are presented.

A family of approximate solutions and explicit error estimates for the nonlinear stationary Navier-Stokes problem

NASA Technical Reports Server (NTRS)

Gabrielsen, R. E.; Karel, S.

1975-01-01

An algorithm for solving the nonlinear stationary Navier-Stokes problem is developed. Explicit error estimates are given. This mathematical technique is potentially adaptable to the separation problem.

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

PubMed Central

2016-01-01

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

Photoelectron Effects on the Self-Consistent Potential in the Collisionless Polar Wind

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Liemohn, M. W.; Moore, T. E.

1997-01-01

The presence of unthermalized photoelectrons in the sunlit polar cap leads to an enhanced ambipolar potential drop and enhanced upward ion acceleration. Observations in the topside ionosphere have led to the conclusion that large-scale electrostatic potential drops exist above the spacecraft along polar magnetic field lines connected to regions of photoelectron production. A kinetic approach is used for the O(+), H(+), and photoelectron (p) distributions, while a fluid approach is used to describe the thermal electrons (e) and self-consistent electric field (E(sub II)) electrons are allowed to carry a flux that compensates for photoelectron escape, a critical assumption. Collisional processes are excluded, leading to easier escape of polar wind particles and therefore to the formation of the largest potential drop consistent with this general approach. We compute the steady state electric field enhancement and net potential drop expected in the polar wind due to the presence of photoelectrons as a function of the fractional photoelectron content and the thermal plasma characteristics. For a set of low-altitude boundary conditions typical of the polar wind ionosphere, including 0.1% photoelectron content, we found a potential drop from 500 km to 5 R(sub E) of 6.5 V and a maximum thermal electron temperature of 8800 K. The reasonable agreement of our results with the observed polar wind suggests that the assumptions of this approach are valid.

Remote Monitoring of the Polarized Target's Control for E1039

NASA Astrophysics Data System (ADS)

Fox, David; SeaQuest Collaboration

2017-09-01

The 1039 experiment at FNAL will further our understanding of spin structure by measuring the contribution that sea quarks orbital angular momentum provide to overall nucleon spin. It is accepted that the valence-quarks of nucleons only provide 30% of the total nucleon spin. To study the nucleon's sea quark contribution, E1039 will use the Drell-Yan process by colliding 120 GeV un-polarized beam protons with polarized ammonia targets of hydrogen and deuterium. The asymmetric spin distributions of resulting dimuons will be measured. These asymmetries are sensitive, among other effects, to the orbital angular momentum contribution of the sea quarks. The polarized target requires a multi-stage vacuum pump located near the target. Since access to its present controls will not be possible during running, remote control and monitoring upgrades were required. A secondary control panel was purchased and tested. Information from the programmable logic controller (PLC) must be fed into our data stream to enable remote monitoring and to signal possible alarm conditions. This solution and the program created using explicit TCP/IP messaging to extract data tags from the PLC and log it within our databases will be presented. Supported by U.S. D.O.E. Medium Energy Nuclear Physics under Grant DE-FG02-03ER41243.

Corrosion evaluation of heat recovery steam generator superheater tube in two methods of testing: Tafel polarization and electrochemical impedance spectroscopy (EIS)

NASA Astrophysics Data System (ADS)

Santoso, Rio Pudjidarma; Riastuti, Rini

2018-05-01

The purpose of this research is to evaluate the corrosion process which occurs on the water side of Heat Recovery Steam Generator (HRSG) superheater tube. The tube was 13CrMo44 and divided into 3 types of specimen: new tube, used tube (with oxide layer on surface), cleaned-used tube (without oxide layer on surface). The evaluation of corrosion parameters wasperformed using deaerated ultra-high purity water (boiler feed water) in two methods of testing: Tafel polarization and Electrochemical Impedance Spectroscopy (EIS). Tafel polarization was excellent as its capability to show the value of corrosion current and the corrosion rate explicitly, on the other hand, EIS was excellent as its capability to explain for corrosion mechanism on metal interface in detail. Both methods showed that the increase of electrolyte temperature from 25°C to 55°C would increase the corrosion rate with the mechanism of decreasing polarization resistance due to thinning out the passive film thickness and enlarge the area of reduction reaction of cathode. Magnetite oxide scale which is laid on the surface of used tube specimen shows protective nature to reduce the corrosion rate, and clear up this oxide would increase the corrosion rate back as new tube.

Test of a flexible spacecraft dynamics simulator

NASA Technical Reports Server (NTRS)

Dichmann, Donald; Sedlak, Joseph

1998-01-01

There are a number of approaches one can take to modeling the dynamics of a flexible body. While one can attempt to capture the full dynamical behavior subject to disturbances from actuators and environmental torques, such a detailed description often is unnecessary. Simplification is possible either by limiting the amplitude of motion to permit linearization of the dynamics equations or by restricting the types of allowed motion. In this work, we study the nonlinear dynamics of bending deformations of wire booms on spinning spacecraft. The theory allows for large amplitude excursions from equilibrium while enforcing constraints on the dynamics to prohibit those modes that are physically less relevant or are expected to damp out fast. These constraints explicitly remove the acoustic modes (i.e., longitudinal sound waves and shear waves) while allowing for arbitrary bending and twisting, motions which typically are of lower frequency. As a test case, a spin axis reorientation maneuver by the Polar Plasma Laboratory (POLAR) spacecraft has been simulated. POLAR was chosen as a representative spacecraft because it has flexible wire antennas that extend to a length of 65 meters. Bending deformations in these antennas could be quite large and have a significant effect on the attitude dynamics of the spacecraft body. Summary results from the simulation are presented along, with a comparison with POLAR flight data.

Prompt charmonia production and polarization at the LHC in the NRQCD with kT-factorization. III. J /ψ meson

NASA Astrophysics Data System (ADS)

Baranov, S. P.; Lipatov, A. V.

2017-08-01

In the framework of the kT-factorization approach, the production and polarization of prompt J /ψ mesons at the LHC energies is studied. Our consideration is based on the nonrelativistic QCD formalism for bound states and off-shell amplitudes for hard partonic subprocesses. Both the direct production mechanism and feed-down contributions from χc and ψ (2 S ) decays are taken into account. The transverse momentum dependent (or unintegrated) gluon densities in a proton were derived from Ciafaloni-Catani-Fiorani-Marchesini evolution equation or, alternatively, were chosen in accordance with Kimber-Martin-Ryskin prescription. The nonperturbative color-octet matrix elements were first deduced from the fits to the latest CMS data on J /ψ transverse momentum distributions and then applied to describe the ATLAS and LHCb data on J /ψ production and polarization at √{s }=7 , 8 and 13 TeV. We perform an estimation of polarization parameters λθ, λϕ, and λθ ϕ which determine J /ψ spin density matrix and demonstrate that treating the soft gluon emission as a series of explicit color-electric dipole transitions within NRQCD leads to unpolarized J /ψ production at high transverse momenta, that is in qualitative agreement with the LHC data.

Calculations of the Electric Fields in Liquid Solutions

PubMed Central

Fried, Stephen D.; Wang, Lee-Ping; Boxer, Steven G.; Ren, Pengyu; Pande, Vijay S.

2014-01-01

The electric field created by a condensed phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe non-polar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate some results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins. PMID:24304155

Explicit robust schemes for implementation of general principal value-based constitutive models

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Saleeb, A. F.; Tan, H. Q.; Zhang, Y.

1993-01-01

The issue of developing effective and robust schemes to implement general hyperelastic constitutive models is addressed. To this end, special purpose functions are used to symbolically derive, evaluate, and automatically generate the associated FORTRAN code for the explicit forms of the corresponding stress function and material tangent stiffness tensors. These explicit forms are valid for the entire deformation range. The analytical form of these explicit expressions is given here for the case in which the strain-energy potential is taken as a nonseparable polynomial function of the principle stretches.

The Airborne Measurements of Methane Fluxes (AIRMETH) Arctic Campaign (Invited)

NASA Astrophysics Data System (ADS)

Serafimovich, A.; Metzger, S.; Hartmann, J.; Kohnert, K.; Sachs, T.

2013-12-01

One of the most pressing questions with regard to climate feedback processes in a warming Arctic is the regional-scale methane release from Arctic permafrost areas. The Airborne Measurements of Methane Fluxes (AIRMETH) campaign is designed to quantitatively and spatially explicitly address this question. Ground-based eddy covariance (EC) measurements provide continuous in-situ observations of the surface-atmosphere exchange of methane. However, these observations are rare in the Arctic permafrost zone and site selection is bound by logistical constraints among others. Consequently, these observations cover only small areas that are not necessarily representative of the region of interest. Airborne measurements can overcome this limitation by covering distances of hundreds of kilometers over time periods of a few hours. Here, we present the potential of environmental response functions (ERFs) for quantitatively linking methane flux observations in the atmospheric surface layer to meteorological and biophysical drivers in the flux footprints. For this purpose thousands of kilometers of AIRMETH data across the Alaskan North Slope are utilized, with the aim to extrapolate the airborne EC methane flux observations to the entire North Slope. The data were collected aboard the research aircraft POLAR 5, using its turbulence nose boom and fast response methane and meteorological sensors. After thorough data pre-processing, Reynolds averaging is used to derive spatially integrated fluxes. To increase spatial resolution and to derive ERFs, we then use wavelet transforms of the original high-frequency data. This enables much improved spatial discretization of the flux observations, and the quantification of continuous and biophysically relevant land cover properties in the flux footprint of each observation. A machine learning technique is then employed to extract and quantify the functional relationships between the methane flux observations and the meteorological and biophysical drivers in the flux footprints. Lastly, the resulting ERFs are used to extrapolate the methane release over spatio-temporally explicit grids of the Alaskan North Slope. Metzger et al. (2013) have demonstrated the efficacy of this technique for regionalizing airborne EC heat flux observations to within an accuracy of ≤18% and a precision of ≤5%. Here, we show for the first time results from applying the ERF procedure to airborne methane EC measurements, and report its potential for spatio-temporally explicit inventories of the regional-scale methane exchange. References: Metzger, S., Junkermann, W., Mauder, M., Butterbach-Bahl, K., Trancón y Widemann, B., Neidl, F., Schäfer, K., Wieneke, S., Zheng, X. H., Schmid, H. P., and Foken, T.: Spatially explicit regionalization of airborne flux measurements using environmental response functions, Biogeosciences, 10, 2193-2217, doi:10.5194/bg-10-2193-2013, 2013.

An Electrophysiological Signature of Unconscious Recognition Memory

PubMed Central

Voss, Joel L.; Paller, Ken A.

2009-01-01

Contradicting the common assumption that accurate recognition reflects explicit-memory processing, we describe evidence for recognition lacking two hallmark explicit-memory features: awareness of memory retrieval and facilitation by attentive encoding. Kaleidoscope images were encoded in conjunction with an attentional diversion and subsequently recognized more accurately than those encoded without diversion. Confidence in recognition was superior following attentive encoding, though recognition was remarkably accurate when people claimed to be unaware of memory retrieval. This “implicit recognition” was associated with frontal-occipital negative brain potentials at 200-400 ms post-stimulus-onset, which were spatially and temporally distinct from positive brain potentials corresponding to explicit recollection and familiarity. This dissociation between behavioral and electrophysiological characteristics of “implicit recognition” versus explicit recognition indicates that a neurocognitive mechanism with properties similar to those that produce implicit memory can be operative in standard recognition tests. People can accurately discriminate repeat stimuli from new stimuli without necessarily knowing it. PMID:19198606

Anomalous surface potential behavior observed in InN by photoassisted Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Sun, Xiaoxiao; Wei, Jiandong; Wang, Xinqiang; Wang, Ping; Li, Shunfeng; Waag, Andreas; Li, Mo; Zhang, Jian; Ge, Weikun; Shen, Bo

2017-05-01

Lattice-polarity dependence of InN surface photovoltage has been identified by an anomalous surface potential behavior observed via photoassisted Kelvin probe force microscopy. Upon above bandgap light illumination in the ambient atmosphere, the surface photovoltage of the In-polar InN shows a pronounced decrease, while that of the N-polar one keeps almost constant. Those different behaviors between N-polar and In-polar surfaces are attributed to a polarity-related surface reactivity, which is found not to be influenced by Mg-doping. These findings provide a simple and non-destructive approach to determine the lattice polarity and allow us to suggest that the In-polar InN, especially that with buried p-type conduction, should be chosen for sensing application.

In situ measurements of dissolved oxygen, pH and redox potential of biocathode microenvironments using microelectrodes.

PubMed

Wang, Zejie; Deng, Huan; Chen, Lihui; Xiao, Yong; Zhao, Feng

2013-03-01

Biofilms are the core component of bioelectrochemical systems (BESs). To understand the polarization effects on biocathode performance of BES, dissolved oxygen concentrations, pHs and oxidation-reduction potentials of biofilm microenvironments were determined in situ. The results showed that lower polarization potentials resulted in the generation of larger currents and higher pH values, as well as the consumption of more oxygen. Oxidation-reduction potentials of biofilms were mainly affected by polarization potentials of the electrode rather than the concentration of dissolved oxygen or pH value, and its changes in the potentials corresponded to the electric field distribution of the electrode surface. The results demonstrated that a sufficient supply of dissolved oxygen and pH control of the biocathode are necessary to obtain optimal performance of BESs; a lower polarization potential endowed microorganisms with a higher electrochemical activity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Potential energy surface and rate coefficients of protonated cyanogen (HNCCN+) induced by collision with helium (He) at low temperature

NASA Astrophysics Data System (ADS)

Bop, Cheikh T.; Faye, N. AB; Hammami, K.

2018-05-01

Nitriles have been identified in space. Accurately modeling their abundance requires calculations of collisional rate coefficients. These data are obtained by first computing potential energy surfaces (PES) and cross-sections using high accurate quantum methods. In this paper, we report the first interaction potential of the HNCCN+-He collisional system along with downward rate coefficients among the 11 lowest rotational levels of HNCCN+. The PES was calculated using the explicitly correlated coupled cluster approach with simple, second and non-iterative triple excitation (CCSD(T)-F12) in conjunction with the augmented-correlation consistent-polarized valence triple zeta (aug-cc-pVTZ) Gaussian basis set. It presents two local minima of ˜283 and ˜136 cm-1, the deeper one is located at R = 9 a0 towards the H end (HeṡṡṡHNCCN+). Using the so-computed PES, we calculated rotational cross-sections of HNCCN+ induced by collision with He for energies ranging up to 500 cm-1 with the exact quantum mechanical close coupling (CC) method. Downward rate coefficients were then worked out by thermally averaging the cross-sections at low temperature (T ≤ 100 K). The discussion on propensity rules showed that the odd Δj transitions were favored. The results obtained in this work may be crucially needed to accurately model the abundance of cyanogen and its protonated form in space.

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

PubMed

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

Decreased response inhibition to sad faces during explicit and implicit tasks in females with depression: Evidence from an event-related potential study.

PubMed

Yu, Fengqiong; Zhou, Xiaoqing; Qing, Wu; Li, Dan; Li, Jing; Chen, Xingui; Ji, Gongjun; Dong, Yi; Luo, Yuejia; Zhu, Chunyan; Wang, Kai

2017-01-30

The present study aimed to investigate neural substrates of response inhibition to sad faces across explicit and implicit tasks in depressed female patients. Event-related potentials were obtained while participants performed modified explicit and implicit emotional go/no-go tasks. Compared to controls, depressed patients showed decreased discrimination accuracy and amplitudes of original and nogo-go difference waves at the P3 interval in response inhibition to sad faces during explicit and implicit tasks. P3 difference wave were positively correlated with discrimination accuracy and were independent of clinical assessment. The activation of right dorsal prefrontal cortex was larger for the implicit than for the explicit task in sad condition in health controls, but was similar for the two tasks in depressed patients. The present study indicated that selectively impairment in response inhibition to sad faces in depressed female patients occurred at the behavior inhibition stage across implicit and explicit tasks and may be a trait-like marker of depression. Longitudinal studies are required to determine whether decreased response inhibition to sad faces increases the risk for future depressive episodes so that appropriate treatment can be administered to patients. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Polarization-resolved optical response of plasmonic particle-on-film nanocavities

NASA Astrophysics Data System (ADS)

Zhang, Q.; Li, G.-C.; Lo, T. W.; Lei, D. Y.

2018-02-01

Placing a metal nanoparticle atop a metal film forms a plasmonic particle-on-film nanocavity. Such a nanocavity supports strong plasmonic coupling that results in rich hybridized plasmon modes, rendering the cavity a versatile platform for exploiting a wide range of plasmon-enhanced spectroscopy applications. In this paper, we fully address the polarization-resolved, orientation-dependent far-field optical responses of plasmonic monomer- and dimer-on-film nanocavities by numerical simulations and experiments. With polarization-resolved dark-field spectroscopy, the distinct plasmon resonances of these nanocavities are clearly determined from their scattering spectra. Moreover, the radiation patterns of respective plasmon modes, which are often mixed together in common dark-field imaging, can be unambiguously resolved with our proposed quasi-multispectral imaging method. Explicitly, the radiation pattern of the monomer-on-film nanocavity gradually transitions from a solid spot in the green imaging channel to a doughnut ring in the red channel when tuning the excitation polarization from parallel to perpendicular to the sample surface. This observation holds true for the plasmonic dimer-on-film nanocavity with the dimer axis aligned in the incidence plane; when the dimer axis is normal to the incidence plane, the pattern transitions from a solid spot to a doughnut ring both in the red channel. These studies not only demonstrate a flexible polarization control over the optical responses of plasmonic particle-on-film nanostructures but also enrich the optical tool kit for far-field imaging and spectroscopy characterization of various plasmonic nanostructures.

Regional Scaling of Airborne Eddy Covariance Flux Observation

NASA Astrophysics Data System (ADS)

Sachs, T.; Serafimovich, A.; Metzger, S.; Kohnert, K.; Hartmann, J.

2014-12-01

The earth's surface is tightly coupled to the global climate system by the vertical exchange of energy and matter. Thus, to better understand and potentially predict changes to our climate system, it is critical to quantify the surface-atmosphere exchange of heat, water vapor, and greenhouse gases on climate-relevant spatial and temporal scales. Currently, most flux observations consist of ground-based, continuous but local measurements. These provide a good basis for temporal integration, but may not be representative of the larger regional context. This is particularly true for the Arctic, where site selection is additionally bound by logistical constraints, among others. Airborne measurements can overcome this limitation by covering distances of hundreds of kilometers over time periods of a few hours. The Airborne Measurements of Methane Fluxes (AIRMETH) campaigns are designed to quantitatively and spatially explicitly address this issue: The research aircraft POLAR 5 is used to acquire thousands of kilometers of eddy-covariance flux data. During the AIRMETH-2012 and AIRMETH-2013 campaigns we measured the turbulent exchange of energy, methane, and (in 2013) carbon dioxide over the North Slope of Alaska, USA, and the Mackenzie Delta, Canada. Here, we present the potential of environmental response functions (ERFs) for quantitatively linking flux observations to meteorological and biophysical drivers in the flux footprints. We use wavelet transforms of the original high-frequency data to improve spatial discretization of the flux observations. This also enables the quantification of continuous and biophysically relevant land cover properties in the flux footprint of each observation. A machine learning technique is then employed to extract and quantify the functional relationships between flux observations and the meteorological and biophysical drivers. The resulting ERFs are used to extrapolate fluxes over spatio-temporally explicit grids of the study area. The presentation will focus on 2012 sensible and latent heat fluxes observed over the North Slope of Alaska and the scaling performance of the ERF approach.

Metasurface quantum-cascade laser with electrically switchable polarization

DOE PAGES

Xu, Luyao; Chen, Daguan; Curwen, Christopher A.; ...

2017-04-20

Dynamic control of a laser’s output polarization state is desirable for applications in polarization sensitive imaging, spectroscopy, and ellipsometry. Using external elements to control the polarization state is a common approach. Less common and more challenging is directly switching the polarization state of a laser, which, however, has the potential to provide high switching speeds, compactness, and power efficiency. Here, we demonstrate a new approach to achieve direct and electrically controlled polarization switching of a semiconductor laser. This is enabled by integrating a polarization-sensitive metasurface with a semiconductor gain medium to selectively amplify a cavity mode with the designed polarizationmore » state, therefore leading to an output in the designed polarization. Here, the demonstration is for a terahertz quantum-cascade laser, which exhibits electrically controlled switching between two linear polarizations separated by 80°, while maintaining an excellent beam with a narrow divergence of ~3°×3° and a single-mode operation fixed at ~3.4 THz, combined with a peak power as high as 93 mW at a temperature of 77 K. The polarization-sensitive metasurface is composed of two interleaved arrays of surface-emitting antennas, all of which are loaded with quantum-cascade gain materials. Each array is designed to resonantly interact with one specific polarization; when electrical bias is selectively applied to the gain material in one array, selective amplification of one polarization occurs. The amplifying metasurface is used along with an output coupler reflector to build a vertical-external-cavity surface-emitting laser whose output polarization state can be switched solely electrically. In conclusion, this work demonstrates the potential of exploiting amplifying polarization-sensitive metasurfaces to create lasers with desirable polarization states—a concept which is applicable beyond the terahertz and can potentially be applied to shorter wavelengths.« less

Metasurface quantum-cascade laser with electrically switchable polarization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Luyao; Chen, Daguan; Curwen, Christopher A.

Dynamic control of a laser’s output polarization state is desirable for applications in polarization sensitive imaging, spectroscopy, and ellipsometry. Using external elements to control the polarization state is a common approach. Less common and more challenging is directly switching the polarization state of a laser, which, however, has the potential to provide high switching speeds, compactness, and power efficiency. Here, we demonstrate a new approach to achieve direct and electrically controlled polarization switching of a semiconductor laser. This is enabled by integrating a polarization-sensitive metasurface with a semiconductor gain medium to selectively amplify a cavity mode with the designed polarizationmore » state, therefore leading to an output in the designed polarization. Here, the demonstration is for a terahertz quantum-cascade laser, which exhibits electrically controlled switching between two linear polarizations separated by 80°, while maintaining an excellent beam with a narrow divergence of ~3°×3° and a single-mode operation fixed at ~3.4 THz, combined with a peak power as high as 93 mW at a temperature of 77 K. The polarization-sensitive metasurface is composed of two interleaved arrays of surface-emitting antennas, all of which are loaded with quantum-cascade gain materials. Each array is designed to resonantly interact with one specific polarization; when electrical bias is selectively applied to the gain material in one array, selective amplification of one polarization occurs. The amplifying metasurface is used along with an output coupler reflector to build a vertical-external-cavity surface-emitting laser whose output polarization state can be switched solely electrically. In conclusion, this work demonstrates the potential of exploiting amplifying polarization-sensitive metasurfaces to create lasers with desirable polarization states—a concept which is applicable beyond the terahertz and can potentially be applied to shorter wavelengths.« less

Accuracy of RGD approximation for computing light scattering properties of diffusing and motile bacteria. [Rayleigh-Gans-Debye

NASA Technical Reports Server (NTRS)

Kottarchyk, M.; Chen, S.-H.; Asano, S.

1979-01-01

The study tests the accuracy of the Rayleigh-Gans-Debye (RGD) approximation against a rigorous scattering theory calculation for a simplified model of E. coli (about 1 micron in size) - a solid spheroid. A general procedure is formulated whereby the scattered field amplitude correlation function, for both polarized and depolarized contributions, can be computed for a collection of particles. An explicit formula is presented for the scattered intensity, both polarized and depolarized, for a collection of randomly diffusing or moving particles. Two specific cases for the intermediate scattering functions are considered: diffusing particles and freely moving particles with a Maxwellian speed distribution. The formalism is applied to microorganisms suspended in a liquid medium. Sensitivity studies revealed that for values of the relative index of refraction greater than 1.03, RGD could be in serious error in computing the intensity as well as correlation functions.

Molecular dynamics simulations of methane hydrate using polarizable force fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

2007-06-14

Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are foundmore » between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane onl« less

Self-interaction-corrected time-dependent density-functional-theory calculations of x-ray-absorption spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tu, Guangde; Rinkevicius, Zilvinas; Vahtras, Olav

We outline an approach within time-dependent density functional theory that predicts x-ray spectra on an absolute scale. The approach rests on a recent formulation of the resonant-convergent first-order polarization propagator [P. Norman et al., J. Chem. Phys. 123, 194103 (2005)] and corrects for the self-interaction energy of the core orbital. This polarization propagator approach makes it possible to directly calculate the x-ray absorption cross section at a particular frequency without explicitly addressing the excited-state spectrum. The self-interaction correction for the employed density functional accounts for an energy shift of the spectrum, and fully correlated absolute-scale x-ray spectra are thereby obtainedmore » based solely on optimization of the electronic ground state. The procedure is benchmarked against experimental spectra of a set of small organic molecules at the carbon, nitrogen, and oxygen K edges.« less

Double Parton Fragmentation Function and its Evolution in Quarkonium Production

NASA Astrophysics Data System (ADS)

Kang, Zhong-Bo

2014-01-01

We summarize the results of a recent study on a new perturbative QCD factorization formalism for the production of heavy quarkonia of large transverse momentum pT at collider energies. Such a new factorization formalism includes both the leading power (LP) and next-to-leading power (NLP) contributions to the cross section in the mQ2/p_T^2 expansion for heavy quark mass mQ. For the NLP contribution, the so-called double parton fragmentation functions are involved, whose evolution equations have been derived. We estimate fragmentation functions in the non-relativistic QCD formalism, and found that their contribution reproduce the bulk of the large enhancement found in explicit NLO calculations in the color singlet model. Heavy quarkonia produced from NLP channels prefer longitudinal polarization, in contrast to the single parton fragmentation function. This might shed some light on the heavy quarkonium polarization puzzle.

Locv Calculations for Polarized Liquid 3He with the Spin-Dependent Correlation

NASA Astrophysics Data System (ADS)

Bordbar, G. H.; Karimi, M. J.

We have used the lowest order constrained variational (LOCV) method to calculate some ground-state properties of polarized liquid 3 He at zero temperature with the spin-dependent correlation function employing the Lennard-Jones and Aziz pair potentials. We have seen that the total energy of polarized liquid 3He increases with increasing polarization. For all polarizations, it is shown that the total energy in the spin-dependent case is lower than the spin-independent case. We have seen that the difference between the energies of spin-dependent and spin-independent cases decreases by increasing the polarization. We have shown that the main contribution of the potential energy comes from the spin-triplet state.

Measuring Explicit Word Learning of Preschool Children: A Development Study.

PubMed

Kelley, Elizabeth Spencer

2017-08-15

The purpose of this article is to present preliminary results related to the development of a new measure of explicit word learning. The measure incorporated elements of explicit vocabulary instruction and dynamic assessment and was designed to be sensitive to differences in word learning skill and to be feasible for use in clinical settings. The explicit word learning measure included brief teaching trials and repeated fine-grained measurement of semantic knowledge and production of 3 novel words (2 verbs and 1 adjective). Preschool children (N = 23) completed the measure of explicit word learning; standardized, norm-referenced measures of expressive and receptive vocabulary; and an incidental word learning task. The measure of explicit word learning provided meaningful information about word learning. Performance on the explicit measure was related to existing vocabulary knowledge and incidental word learning. Findings from this development study indicate that further examination of the measure of explicit word learning is warranted. The measure may have the potential to identify children who are poor word learners. https://doi.org/10.23641/asha.5170738.

Primordial features and Planck polarization

NASA Astrophysics Data System (ADS)

Hazra, Dhiraj Kumar; Shafieloo, Arman; Smoot, George F.; Starobinsky, Alexei A.

2016-09-01

With the Planck 2015 Cosmic Microwave Background (CMB) temperature and polarization data, we search for possible features in the primordial power spectrum (PPS). We revisit the Wiggly Whipped Inflation (WWI) framework and demonstrate how generation of some particular primordial features can improve the fit to Planck data. WWI potential allows the scalar field to transit from a steeper potential to a nearly flat potential through a discontinuity either in potential or in its derivatives. WWI offers the inflaton potential parametrizations that generate a wide variety of features in the primordial power spectra incorporating most of the localized and non-local inflationary features that are obtained upon reconstruction from temperature and polarization angular power spectrum. At the same time, in a single framework it allows us to have a background parameter estimation with a nearly free-form primordial spectrum. Using Planck 2015 data, we constrain the primordial features in the context of Wiggly Whipped Inflation and present the features that are supported both by temperature and polarization. WWI model provides more than 13 improvement in χ2 fit to the data with respect to the best fit power law model considering combined temperature and polarization data from Planck and B-mode polarization data from BICEP and Planck dust map. We use 2-4 extra parameters in the WWI model compared to the featureless strict slow roll inflaton potential. We find that the differences between the temperature and polarization data in constraining background cosmological parameters such as baryon density, cold dark matter density are reduced to a good extent if we use primordial power spectra from WWI. We also discuss the extent of bispectra obtained from the best potentials in arbitrary triangular configurations using the BI-spectra and Non-Gaussianity Operator (BINGO).

Primordial features and Planck polarization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazra, Dhiraj Kumar; Smoot, George F.; Shafieloo, Arman

2016-09-01

With the Planck 2015 Cosmic Microwave Background (CMB) temperature and polarization data, we search for possible features in the primordial power spectrum (PPS). We revisit the Wiggly Whipped Inflation (WWI) framework and demonstrate how generation of some particular primordial features can improve the fit to Planck data. WWI potential allows the scalar field to transit from a steeper potential to a nearly flat potential through a discontinuity either in potential or in its derivatives. WWI offers the inflaton potential parametrizations that generate a wide variety of features in the primordial power spectra incorporating most of the localized and non-local inflationarymore » features that are obtained upon reconstruction from temperature and polarization angular power spectrum. At the same time, in a single framework it allows us to have a background parameter estimation with a nearly free-form primordial spectrum. Using Planck 2015 data, we constrain the primordial features in the context of Wiggly Whipped Inflation and present the features that are supported both by temperature and polarization. WWI model provides more than 13 improvement in χ{sup 2} fit to the data with respect to the best fit power law model considering combined temperature and polarization data from Planck and B-mode polarization data from BICEP and Planck dust map. We use 2-4 extra parameters in the WWI model compared to the featureless strict slow roll inflaton potential. We find that the differences between the temperature and polarization data in constraining background cosmological parameters such as baryon density, cold dark matter density are reduced to a good extent if we use primordial power spectra from WWI. We also discuss the extent of bispectra obtained from the best potentials in arbitrary triangular configurations using the BI-spectra and Non-Gaussianity Operator (BINGO).« less

Wave-function-based approach to quasiparticle bands: Insight into the electronic structure of c-ZnS

NASA Astrophysics Data System (ADS)

Stoyanova, A.; Hozoi, L.; Fulde, P.; Stoll, H.

2011-05-01

Ab initio wave-function-based methods are employed for the study of quasiparticle energy bands of zinc-blende ZnS, with focus on the Zn 3d “semicore” states. The relative energies of these states with respect to the top of the S 3p valence bands appear to be poorly described as compared to experimental values not only within the local density approximation (LDA), but also when many-body corrections within the GW approximation are applied to the LDA or LDA + U mean-field solutions [T. Miyake, P. Zhang, M. L. Cohen, and S. G. Louie, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.74.245213 74, 245213 (2006)]. In the present study, we show that for the accurate description of the Zn 3d states a correlation treatment based on wave-function methods is needed. Our study rests on a local Hamiltonian approach which rigorously describes the short-range polarization and charge redistribution effects around an extra hole or electron placed into the valence respective conduction bands of semiconductors and insulators. The method also facilitates the computation of electron correlation effects beyond relaxation and polarization. The electron correlation treatment is performed on finite clusters cut off the infinite system. The formalism makes use of localized Wannier functions and embedding potentials derived explicitly from prior periodic Hartree-Fock calculations. The on-site and nearest-neighbor charge relaxation lead to corrections of several eV to the Hartree-Fock band energies and gap. Corrections due to long-range polarization are of the order of 1.0 eV. The dispersion of the Hartree-Fock bands is only slightly affected by electron correlations. We find the Zn 3d “semicore” states to lie ~9.0 eV below the top of the S 3p valence bands, in very good agreement with values from valence-band x-ray photoemission.

Reduction of the field-aligned potential drop in the polar cap during large geomagnetic storms

NASA Astrophysics Data System (ADS)

Kitamura, N.; Seki, K.; Nishimura, Y.; Hori, T.; Terada, N.; Ono, T.; Strangeway, R. J.

2013-12-01

We have studied photoelectron flows and the inferred field-aligned potential drop in the polar cap during 5 large geomagnetic storms that occurred in the periods when the photoelectron observations in the polar cap were available near the apogee of the FAST satellite (~4000 km) at solar maximum, and the footprint of the satellite paths in the polar cap was under sunlit conditions most of the time. In contrast to the ~20 V potential drop during geomagnetically quiet periods at solar maximum identified by Kitamura et al. [JGR, 2012], the field-aligned potential drop frequently became smaller than ~5 V during the main and early recovery phases of the large geomagnetic storms. Because the potential acts to inhibit photoelectron escape, this result indicates that the corresponding acceleration of ions by the field-aligned potential drop in the polar cap and the lobe region is smaller during the main and early recovery phases of large geomagnetic storms compared to during geomagnetically quiet periods. Under small field-aligned current conditions, the number flux of outflowing ions should be nearly equal to the net escaping electron number flux. Since ions with large flux originating from the cusp/cleft ionosphere convect into the polar cap during geomagnetic storms [e.g., Kitamura et al., JGR, 2010], the net escaping electron number flux should increase to balance the enhanced ion outflows. The magnitude of the field-aligned potential drop would be reduced to let a larger fraction of photoelectrons escape.

Age and Social Support Seeking: Understanding the Role of Perceived Social Costs to Others.

PubMed

Jiang, Li; Drolet, Aimee; Kim, Heejung S

2018-07-01

We examined age differences in the use of different types of social support and the reasons for these differences. We found that older adults (age 60+) seek explicit social support less compared with young adults (age 18-25), but there is no difference in implicit social support seeking. Concerns about the potential social costs of seeking explicit support mediate the age differences in explicit social support seeking. Whereas young adults view this strategy as conferring more benefits than costs, older adults have a more balanced view of the costs and benefits of explicit social support seeking. Older and young adults do not differ in perceptions of the relative costs versus benefits of implicit social support seeking. Finally, we found older adults benefit more from implicit (vs. explicit) social support emotionally than young adults, which further explains why age groups differ in their use of explicit versus implicit social support.

Moderators of Implicit-Explicit Exercise Cognition Concordance.

PubMed

Berry, Tanya R; Rodgers, Wendy M; Markland, David; Hall, Craig R

2016-12-01

Investigating implicit-explicit concordance can aid in understanding underlying mechanisms and possible intervention effects. This research examined the concordance between implicit associations of exercise with health or appearance and related explicit motives. Variables considered as possible moderators were behavioral regulations, explicit attitudes, and social desirability. Participants (N = 454) completed measures of implicit associations of exercise with health and appearance and questionnaire measures of health and appearance motives, attitudes, social desirability, and behavioral regulations. Attitudes significantly moderated the relationship between implicit associations of exercise with health and health motives. Identified regulations significantly moderated implicit-explicit concordance with respect to associations with appearance. These results suggest that implicit and explicit exercise-related cognitions are not necessarily independent and their relationship to each other may be moderated by attitudes or some forms of behavioral regulation. Future research that takes a dual-processing approach to exercise behavior should consider potential theoretical moderators of concordance.

Spin Polarization and Color Superconductivity in the Nambu-Jona-Lasinio Model

NASA Astrophysics Data System (ADS)

Matsuoka, Hiroaki; Tsue, Yasuhiko; da Providência, João; Providência, Constança; Yamamura, Masatoshi

In this research we study a possibility that spins of quarks may polarize at large quark chemical potential. In order to discuss this possibility, we introduce a tensor-type interaction into the Nambu-Jona-Lasinio model. Here we pay attention to the relationship between chiral condensate, spin polarization and color superconductivity. It is shown that, at large quark chemical potential and low temperature, the coexisting phase where both the spin-polarized condensate and color superconducting gap exist together may be realized.

Nearly scale invariant spectrum of gravitational radiation from global phase transitions.

PubMed

Jones-Smith, Katherine; Krauss, Lawrence M; Mathur, Harsh

2008-04-04

Using a large N sigma model approximation we explicitly calculate the power spectrum of gravitational waves arising from a global phase transition in the early Universe and we confirm that it is scale invariant, implying an observation of such a spectrum may not be a unique feature of inflation. Moreover, the predicted amplitude can be over 3 orders of magnitude larger than the naive dimensional estimate, implying that even a transition that occurs after inflation may dominate in cosmic microwave background polarization or other gravity wave signals.

Decoherence of spin states induced by Rashba coupling for an electron confined to a semiconductor quantum dot in the presence of a magnetic field

NASA Astrophysics Data System (ADS)

Poszwa, A.

2018-05-01

We investigate quantum decoherence of spin states caused by Rashba spin-orbit (SO) coupling for an electron confined to a planar quantum dot (QD) in the presence of a magnetic field (B). The Schrödinger equation has been solved in a frame of second-order perturbation theory. The relationship between the von Neumann (vN) entropy and the spin polarization is obtained. The relation is explicitly demonstrated for the InSb semiconductor QD.

Molecular dynamics in drug design: new generations of compstatin analogs.

PubMed

Tamamis, Phanourios; López de Victoria, Aliana; Gorham, Ronald D; Bellows-Peterson, Meghan L; Pierou, Panayiota; Floudas, Christodoulos A; Morikis, Dimitrios; Archontis, Georgios

2012-05-01

We report the computational and rational design of new generations of potential peptide-based inhibitors of the complement protein C3 from the compstatin family. The binding efficacy of the peptides is tested by extensive molecular dynamics-based structural and physicochemical analysis, using 32 atomic detail trajectories in explicit water for 22 peptides bound to human, rat or mouse target protein C3, with a total of 257 ns. The criteria for the new design are: (i) optimization for C3 affinity and for the balance between hydrophobicity and polarity to improve solubility compared to known compstatin analogs; and (ii) development of dual specificity, human-rat/mouse C3 inhibitors, which could be used in animal disease models. Three of the new analogs are analyzed in more detail as they possess strong and novel binding characteristics and are promising candidates for further optimization. This work paves the way for the development of an improved therapeutic for age-related macular degeneration, and other complement system-mediated diseases, compared to known compstatin variants. © 2012 John Wiley & Sons A/S.

Strain-engineering stabilization of BaTi O3 -based polar metals

NASA Astrophysics Data System (ADS)

Ma, Chao; Jin, Kui-juan; Ge, Chen; Yang, Guo-zhen

2018-03-01

Polar metals, which possess ferroelectriclike polar structure and conductivity simultaneously, have attracted wide interest since the first solid example, LiOs O3 (below 140 K), was discovered. However, the lack of room-temperature polar metals hinders further research and applications. Thus abundant properties of polar metals are unexplored. Here, with first-principles calculations, we report that the polar metal phase can be stabilized in the strain-engineered BaTi O3 with electron doping. The mechanism relates to the competition between the shifting of the t2 g energy levels and the narrowing of their bandwidth. Surprisingly, it is predicted that the ferroelectric-to-paraelectric transition temperature can be increased by electron doping when the strain is large enough, which holds potential for room-temperature polar metals. Our results indicate that strain engineering is a promising way to achieve BaTi O3 -based polar metals, and they should have practical significance for obtaining easily accessible, ecofriendly, and potential room-temperature polar metals.

Ion-mediated interactions in suspensions of oppositely charged nanoparticles

NASA Astrophysics Data System (ADS)

Dahirel, Vincent; Hansen, Jean Pierre

2009-08-01

The structure of oppositely charged spherical nanoparticles (polyions), dispersed in ionic solutions with continuous solvent (primitive model), is investigated by Monte Carlo (MC) simulations, within explicit and implicit microion representations, over a range of polyion valences and densities, and microion concentrations. Systems with explicit microions are explored by semigrand canonical MC simulations, and allow density-dependent effective polyion pair potentials vαβeff(r ) to be extracted from measured partial pair distribution functions. Implicit microion MC simulations are based on pair potentials of mean force vαβ(2)(r ) computed by explicit microion simulations of two charged polyions, in the low density limit. In the vicinity of the liquid-gas separation expected for oppositely charged polyions, the implicit microion representation leads to an instability against density fluctuations for polyion valences |Z| significantly below those at which the instability sets in within the exact explicit microion representation. Far from this instability region, the vαβ(2)(r ) are found to be fairly close to but consistently more repulsive than the effective pair potentials vαβeff(r ). This is corroborated by additional calculations of three-body forces between polyion triplets, which are repulsive when one polyion is of opposite charge to the other two. The explicit microion MC data were exploited to determine the ratio of salt concentrations c and co within the dispersion and the reservoir (Donnan effect). c /co is found to first increase before finally decreasing as a function of the polyion packing fraction.

Complex polarization propagator approach in the restricted open-shell, self-consistent field approximation: the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine.

PubMed

Linares, Mathieu; Stafström, Sven; Rinkevicius, Zilvinas; Ågren, Hans; Norman, Patrick

2011-05-12

A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order polarization propagator approach that makes it possible to directly calculate the X-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted X-ray spectra relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects. The method is applied to the calculation of the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine. Comparison is made between the spectra of the radicals and those of the corresponding cations and anions to assess the effect of the increase of electron charge in the frontier orbital. The method offers the possibility for unique assignment of symmetry-independent atoms. The overall excellent spectral agreement motivates the application of the method as a routine precise tool for analyzing X-ray absorption of large systems of technological interest.

Active Polar Two-Fluid Macroscopic Dynamics

NASA Astrophysics Data System (ADS)

Pleiner, Harald; Svensek, Daniel; Brand, Helmut R.

2014-03-01

We study the dynamics of systems with a polar dynamic preferred direction. Examples include the pattern-forming growth of bacteria (in a solvent, shoals of fish (moving in water currents), flocks of birds and migrating insects (flying in windy air). Because the preferred direction only exists dynamically, but not statically, the macroscopic variable of choice is the macroscopic velocity associated with the motion of the active units. We derive the macroscopic equations for such a system and discuss novel static, reversible and irreversible cross-couplings connected to this second velocity. We find a normal mode structure quite different compared to the static descriptions, as well as linear couplings between (active) flow and e.g. densities and concentrations due to the genuine two-fluid transport derivatives. On the other hand, we get, quite similar to the static case, a direct linear relation between the stress tensor and the structure tensor. This prominent ``active'' term is responsible for many active effects, meaning that our approach can describe those effects as well. In addition, we also deal with explicitly chiral systems, which are important for many active systems. In particular, we find an active flow-induced heat current specific for the dynamic chiral polar order.

Ground roll attenuation using polarization analysis in the t-f-k domain

NASA Astrophysics Data System (ADS)

Wang, C.; Wang, Y.

2017-07-01

S waves travel slower than P waves and have a lower dominant frequency. Therefore, applying common techniques such as time-frequency filtering and f-k filtering to separate S waves from ground roll is difficult because ground roll is also characterized by slow velocity and low frequency. In this study, we present a method for attenuating ground roll using a polarization filtering method based on the t-f-k transform. We describe the particle motion of the waves by complex vector signals. Each pair of frequency components, whose frequencies have the same absolute value but different signs, of the complex signal indicate an elliptical or linear motion. The polarization parameters of the elliptical or linear motion are explicitly related to the two Fourier coefficients. We then extend these concepts to the t-f-k domain and propose a polarization filtering method for ground roll attenuation based on the t-f-k transform. The proposed approach can define automatically the time-varying reject zones on the f-k panel at different times as a function of the reciprocal ellipticity. Four attributes, time, frequency, apparent velocity and polarization are used to identify and extract the ground roll simultaneously. Thus, the ground roll and body waves can be separated as long as they are dissimilar in one of these attributes. We compare our method with commonly used filtering techniques by applying the methods to synthetic and real seismic data. The results indicate that our method can attenuate ground roll while preserving body waves more effectively than the other methods.

Mars' Annular Polar Vortices and their Response to Atmospheric Dust Opacity

NASA Astrophysics Data System (ADS)

Guzewich, S.; Waugh, D.; Toigo, A. D.

2016-12-01

The potential vorticity structure of the martian polar vortices is distinct from Earth's stratospheric or tropospheric vortices. Rather than exhibiting monotonically increasing potential vorticity toward the geographic pole, as on Earth, the martian fall and winter polar vortices are annular with the potential vorticity maximum situated off the pole and a local minimum in potential vorticity at the pole. Using the MarsWRF general circulation model (GCM), we perform a series of simulations to examine the source of this annular structure. We find that latent heat exchange from the formation of CO2 ice aerosols within the vortex, in a region very near the geographic pole, destroys potential vorticity and creates the annular structure. Furthermore, we describe Mars Climate Sounder and Thermal Emission Spectrometer observations of "transient vortex warming" events, where the air inside the northern hemisphere winter polar vortex is briefly warmed. During the Mars Year 28 (2007) global dust storm, the temperature inside the vortex increased by 70 K and dust directly entered the vortex. Using additional GCM simulations, we diagnose the dynamical changes associated with these transient vortex warming events and find that poleward expansion of the descending branch of the meridional overturning circulation during periods of increased dust opacity disrupts the northern hemisphere winter polar vortex. These increased temperatures also suppress CO2 condensation at the pole, creating a more Earth-like polar vortex where potential vorticity is maximized near the geographic pole.

Expect the unexpected: A look at teacher-researcher partnerships over the long-term

NASA Astrophysics Data System (ADS)

Warburton, J.; Bartholow, S.; Larson, A.

2016-02-01

For over ten years, the Arctic Research Consortium of the United States (ARCUS) has developed and implemented PolarTREC-Teachers and Researchers Exploring and Collaborating (PolarTREC). This unique program has brought K-12 educators and polar researchers together through an innovative teacher research experience model. Utilizing field-based experiences in the polar regions, PolarTREC provide teachers the content knowledge, pedagogical tools, confidence, understanding of science in the broader society, and experiences with scientific inquiry they need to promote authentic scientific research in their classroom. PolarTREC has the potential to transform the nature of STEM education. In this presentation, we will share how the PolarTREC model has led to teachers and researchers developing positive, professional relationships with the potential to grow into long-term partnerships. And, how these partnerships have led to both unexpected and amazing outcomes.

Accurate forced-choice recognition without awareness of memory retrieval.

PubMed

Voss, Joel L; Baym, Carol L; Paller, Ken A

2008-06-01

Recognition confidence and the explicit awareness of memory retrieval commonly accompany accurate responding in recognition tests. Memory performance in recognition tests is widely assumed to measure explicit memory, but the generality of this assumption is questionable. Indeed, whether recognition in nonhumans is always supported by explicit memory is highly controversial. Here we identified circumstances wherein highly accurate recognition was unaccompanied by hallmark features of explicit memory. When memory for kaleidoscopes was tested using a two-alternative forced-choice recognition test with similar foils, recognition was enhanced by an attentional manipulation at encoding known to degrade explicit memory. Moreover, explicit recognition was most accurate when the awareness of retrieval was absent. These dissociations between accuracy and phenomenological features of explicit memory are consistent with the notion that correct responding resulted from experience-dependent enhancements of perceptual fluency with specific stimuli--the putative mechanism for perceptual priming effects in implicit memory tests. This mechanism may contribute to recognition performance in a variety of frequently-employed testing circumstances. Our results thus argue for a novel view of recognition, in that analyses of its neurocognitive foundations must take into account the potential for both (1) recognition mechanisms allied with implicit memory and (2) recognition mechanisms allied with explicit memory.

Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

PubMed

Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

2013-08-15

Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

An alternative to the TEM (Transformed Eulerian Mean) equations

NASA Astrophysics Data System (ADS)

Gaßmann, Almut

2013-04-01

The TEM equations constitute a powerful means to get access to the residual circulation. However, due to their foundation on the wave perspective, they deliver only a zonally averaged picture without access to the three-dimensional structure or the local origins of the residual circulation. Therefore it is worth to investigate whether there are alternatives. The pathway followed here is to perform a transformation of the momentum and the potential temperature equation before taking the zonal mean. This is done by removing the steady state ideal wind solution vid = ?×?B-(?±P) from the equations (? - potential temperature, B - Bernoulli function, P - Ertel's potential vorticity EPV, ?± - density). The advantage of that approach is that the total EPV-flux does no longer contain an explicitly visible 'do-nothing-flux'. This flux, ?? ×?B, does only vanish when averaging on isentropic surfaces, but not on other isosurfaces. Here we find the reason why the conventional zonal mean on isentropes delivers a direct overturning cell on each hemisphere, whereas on other isosurfaces we obtain the typical three-cell structure with Headley, Ferrel, and polar cells. It will be demonstrated and made visible through idealized climate experiments with the ICON-IAP model that the zonal averages of the nonideal wind components vnid = v - vid and wnid = w - wid constitute similar direct overturning cells on non-isentropic surfaces as obtained with the TEM-generated v* and w*. It is also interesting to inspect fields of local nonideal wind components, the very origin of the residual circulation.

Why do morphological phylogenies vary in quality? An investigation based on the comparative history of lizard clades.

PubMed

Arnold, E N

1990-05-22

Phylogenies based on morphology vary considerably in their quality: some are robust and explicit with little conflict in the data set, whereas others are far more tenuous, with much conflict and many possible alternatives. The main primary reasons for untrue or inexplicit morphological phylogenies are: not enough characters developed between branching points, uncertain character polarity, poorly differentiated character states, homoplasy caused by parallelism or reversal, and extinction, which may remove species entirely from consideration and can make originally conflicting data sets misleadingly compatible, increasing congruence at the expense of truth. Extinction differs from other confounding factors in not being apparent either in the data set or in subsequent analysis. One possibility is that variation in the quality of morphological phylogenies has resulted from exposure to different ecological situations. To investigate this, it is necessary to compare the histories of the clades concerned. In the case of explicit morphological phylogenies, ecological and behavioural data can be integrated with them and it may then be possible to decide whether morphological characters are likely to have been elicited by the environments through which the clade has passed. The credibility of such results depends not only on the phylogeny being robust but also on its detailed topology: a pectinate phylogeny will often allow more certain and more explicit statements to be made about historical events. In the case of poor phylogenies, it is not possible to produce detailed histories, but they can be compared with robust phylogenies in the range of ecological situations occupied, and whether they occupy novel situations in comparison with their outgroups. LeQuesne testing can give information about niche homoplasy, and it may also be possible to see if morphological features are functionally associated with ecological parameters, even if the direction of change is unknown. Examination of the robust and explicit phylogeny of the semaphore geckoes (Pristurus) suggests that its quality does stem from a variety of environmental factors. The group has progressed along an ecological continuum, passing through a series of increasingly severe niches that appear to have elicited many morphological changes. The fact that niches are progressively filled reduces the likelihood of species reinvading a previous one with related character reversal. Because the niches of advanced Pristurus are virtually unique within the Gekkonidae the morphological changes produced are also very rare and therefore easy to polarize. Ecological changes on the main stem of the phylogeny are abrupt and associated character states consequently well differentiated.(ABSTRACT TRUNCATED AT 400 WORDS)

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

NASA Astrophysics Data System (ADS)

Bereau, Tristan; DiStasio, Robert A.; Tkatchenko, Alexandre; von Lilienfeld, O. Anatole

2018-06-01

Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning (ML), coined IPML, which is transferable across small neutral organic and biologically relevant molecules. ML models provide on-the-fly predictions for environment-dependent local atomic properties: electrostatic multipole coefficients (significant error reduction compared to previously reported), the population and decay rate of valence atomic densities, and polarizabilities across conformations and chemical compositions of H, C, N, and O atoms. These parameters enable accurate calculations of intermolecular contributions—electrostatics, charge penetration, repulsion, induction/polarization, and many-body dispersion. Unlike other potentials, this model is transferable in its ability to handle new molecules and conformations without explicit prior parametrization: All local atomic properties are predicted from ML, leaving only eight global parameters—optimized once and for all across compounds. We validate IPML on various gas-phase dimers at and away from equilibrium separation, where we obtain mean absolute errors between 0.4 and 0.7 kcal/mol for several chemically and conformationally diverse datasets representative of non-covalent interactions in biologically relevant molecules. We further focus on hydrogen-bonded complexes—essential but challenging due to their directional nature—where datasets of DNA base pairs and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and as a first look, we consider IPML for denser systems: water clusters, supramolecular host-guest complexes, and the benzene crystal.

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

Extension of the KLI approximation toward the exact optimized effective potential.

PubMed

Iafrate, G J; Krieger, J B

2013-03-07

The integral equation for the optimized effective potential (OEP) is utilized in a compact form from which an accurate OEP solution for the spin-unrestricted exchange-correlation potential, Vxcσ, is obtained for any assumed orbital-dependent exchange-correlation energy functional. The method extends beyond the Krieger-Li-Iafrate (KLI) approximation toward the exact OEP result. The compact nature of the OEP equation arises by replacing the integrals involving the Green's function terms in the traditional OEP equation by an equivalent first-order perturbation theory wavefunction often referred to as the "orbital shift" function. Significant progress is then obtained by solving the equation for the first order perturbation theory wavefunction by use of Dalgarno functions which are determined from well known methods of partial differential equations. The use of Dalgarno functions circumvents the need to explicitly address the Green's functions and the associated problems with "sum over states" numerics; as well, the Dalgarno functions provide ease in dealing with inherent singularities arising from the origin and the zeros of the occupied orbital wavefunctions. The Dalgarno approach for finding a solution to the OEP equation is described herein, and a detailed illustrative example is presented for the special case of a spherically symmetric exchange-correlation potential. For the case of spherical symmetry, the relevant Dalgarno function is derived by direct integration of the appropriate radial equation while utilizing a user friendly method which explicitly treats the singular behavior at the origin and at the nodal singularities arising from the zeros of the occupied states. The derived Dalgarno function is shown to be an explicit integral functional of the exact OEP Vxcσ, thus allowing for the reduction of the OEP equation to a self-consistent integral equation for the exact exchange-correlation potential; the exact solution to this integral equation can be determined by iteration with the natural zeroth order correction given by the KLI exchange-correlation potential. Explicit analytic results are provided to illustrate the first order iterative correction beyond the KLI approximation. The derived correction term to the KLI potential explicitly involves spatially weighted products of occupied orbital densities in any assumed orbital-dependent exchange-correlation energy functional; as well, the correction term is obtained with no adjustable parameters. Moreover, if the equation for the exact optimized effective potential is further iterated, one can obtain the OEP as accurately as desired.

Extension of the KLI approximation toward the exact optimized effective potential

NASA Astrophysics Data System (ADS)

Iafrate, G. J.; Krieger, J. B.

2013-03-01

The integral equation for the optimized effective potential (OEP) is utilized in a compact form from which an accurate OEP solution for the spin-unrestricted exchange-correlation potential, Vxcσ, is obtained for any assumed orbital-dependent exchange-correlation energy functional. The method extends beyond the Krieger-Li-Iafrate (KLI) approximation toward the exact OEP result. The compact nature of the OEP equation arises by replacing the integrals involving the Green's function terms in the traditional OEP equation by an equivalent first-order perturbation theory wavefunction often referred to as the "orbital shift" function. Significant progress is then obtained by solving the equation for the first order perturbation theory wavefunction by use of Dalgarno functions which are determined from well known methods of partial differential equations. The use of Dalgarno functions circumvents the need to explicitly address the Green's functions and the associated problems with "sum over states" numerics; as well, the Dalgarno functions provide ease in dealing with inherent singularities arising from the origin and the zeros of the occupied orbital wavefunctions. The Dalgarno approach for finding a solution to the OEP equation is described herein, and a detailed illustrative example is presented for the special case of a spherically symmetric exchange-correlation potential. For the case of spherical symmetry, the relevant Dalgarno function is derived by direct integration of the appropriate radial equation while utilizing a user friendly method which explicitly treats the singular behavior at the origin and at the nodal singularities arising from the zeros of the occupied states. The derived Dalgarno function is shown to be an explicit integral functional of the exact OEP Vxcσ, thus allowing for the reduction of the OEP equation to a self-consistent integral equation for the exact exchange-correlation potential; the exact solution to this integral equation can be determined by iteration with the natural zeroth order correction given by the KLI exchange-correlation potential. Explicit analytic results are provided to illustrate the first order iterative correction beyond the KLI approximation. The derived correction term to the KLI potential explicitly involves spatially weighted products of occupied orbital densities in any assumed orbital-dependent exchange-correlation energy functional; as well, the correction term is obtained with no adjustable parameters. Moreover, if the equation for the exact optimized effective potential is further iterated, one can obtain the OEP as accurately as desired.

Data Assimilation of Photosynthetic Light-use Efficiency using Multi-angular Satellite Data: II Model Implementation and Validation

NASA Technical Reports Server (NTRS)

Hilker, Thomas; Hall, Forest G.; Tucker, J.; Coops, Nicholas C.; Black, T. Andrew; Nichol, Caroline J.; Sellers, Piers J.; Barr, Alan; Hollinger, David Y.; Munger, J. W.

2012-01-01

Spatially explicit and temporally continuous estimates of photosynthesis will be of great importance for increasing our understanding of and ultimately closing the terrestrial carbon cycle. Current capabilities to model photosynthesis, however, are limited by accurate enough representations of the complexity of the underlying biochemical processes and the numerous environmental constraints imposed upon plant primary production. A potentially powerful alternative to model photosynthesis through these indirect observations is the use of multi-angular satellite data to infer light-use efficiency (e) directly from spectral reflectance properties in connection with canopy shadow fractions. Hall et al. (this issue) introduced a new approach for predicting gross ecosystem production that would allow the use of such observations in a data assimilation mode to obtain spatially explicit variations in e from infrequent polar-orbiting satellite observations, while meteorological data are used to account for the more dynamic responses of e to variations in environmental conditions caused by changes in weather and illumination. In this second part of the study we implement and validate the approach of Hall et al. (this issue) across an ecologically diverse array of eight flux-tower sites in North America using data acquired from the Compact High Resolution Imaging Spectroradiometer (CHRIS) and eddy-flux observations. Our results show significantly enhanced estimates of e and therefore cumulative gross ecosystem production (GEP) over the course of one year at all examined sites. We also demonstrate that e is greatly heterogeneous even across small study areas. Data assimilation and direct inference of GEP from space using a new, proposed sensor could therefore be a significant step towards closing the terrestrial carbon cycle.

Solvent effect in implicit/explicit model on FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra, linear, second- and third-nonlinear optical parameters of 2-(trifluoromethyl)benzoic acid: Experimental and computational study

NASA Astrophysics Data System (ADS)

Avcı, Davut; Altürk, Sümeyye; Tamer, Ömer; Kuşbazoğlu, Mustafa; Atalay, Yusuf

2017-09-01

FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra for 2-(trifluoromethyl)benzoic acid (2-TFMBA) were recorded. DFT//B3LYP/6-31++G(d,p) calculations were used to determine the optimized molecular geometry, vibrational frequencies, 1H, 13C and 19F GIAO-NMR chemical shifts of 2-TFMBA. The detailed assignments of vibrational frequencies were carried out on the basis of potential energy distribution (PED) by using VEDA program. TD-DFT/B3LYP/6-31++G(d,p) calculations with the PCM (polarizable continuum model) in ethanol and DMSO solvents based on implicit/explicit model and gas phase in the excited state were employed to investigate UV-vis absorption and fluorescence emission wavelengths. The UV-vis and emission spectra were given in ethanol and DMSO solvents, and the major contributions to the electronic transitions were obtained. In addition, the NLO parameters (β, γ and χ(3)) and frontier molecular orbital energies of 2-TFMBA were calculated by using B3LYP/6-31++G(d,p) level. The NLO parameters of 2-TFMBA were compared with that of para-Nitroaniline (pNA) and urea which are the typical NLO materials. The refractive index (n) is calculated by using the Lorentz-Lorenz equation to observe polarization behavior of 2-TFMBA in DMSO and ethanol solvents. In order to investigate intramolecular and hydrogen bonding interactions, NBO calculations were also performed by the same level. To sum up, considering the well-known biological role, photochemical properties of 2-TFMBA were discussed.

Predictive Validity of Explicit and Implicit Threat Overestimation in Contamination Fear

PubMed Central

Green, Jennifer S.; Teachman, Bethany A.

2012-01-01

We examined the predictive validity of explicit and implicit measures of threat overestimation in relation to contamination-fear outcomes using structural equation modeling. Undergraduate students high in contamination fear (N = 56) completed explicit measures of contamination threat likelihood and severity, as well as looming vulnerability cognitions, in addition to an implicit measure of danger associations with potential contaminants. Participants also completed measures of contamination-fear symptoms, as well as subjective distress and avoidance during a behavioral avoidance task, and state looming vulnerability cognitions during an exposure task. The latent explicit (but not implicit) threat overestimation variable was a significant and unique predictor of contamination fear symptoms and self-reported affective and cognitive facets of contamination fear. On the contrary, the implicit (but not explicit) latent measure predicted behavioral avoidance (at the level of a trend). Results are discussed in terms of differential predictive validity of implicit versus explicit markers of threat processing and multiple fear response systems. PMID:24073390

The generation of piezoelectricity and flexoelectricity in graphene by breaking the materials symmetries.

PubMed

Javvaji, Brahmanandam; He, Bo; Zhuang, Xiaoying

2018-06-01

Graphene is a non-piezoelectric material. Engineering the piezoelectricity in graphene is possible with the help of impurities, defects and structural modifications. This study reports the mechanism of strain induced polarization and the estimation of piezoelectric and flexoelectric coefficients for graphene system. The combination of charge-dipole potential and the strong many-body potential is employed for describing the inter-atomic interactions. The breaking of symmetry in graphene material is utilized to generate the polarization. Pristine graphene, graphene with circular defect, graphene with triangular defect and trapezium-shaped graphene are considered. Molecular dynamics simulations are performed for straining the graphene atomic systems. The optimization of charge-dipole potential functions measure the polarization for these systems. Pristine and circular defect graphene systems show a constant polarization with strain. The polarization is varying with strain for a triangular defected and trapezium-shaped graphene system. The local atomic deformation produces a change in polarization with respect to the strain gradient. Estimated piezo and flexo coefficients motivate the usage of graphene in electro-mechanical devices.

The generation of piezoelectricity and flexoelectricity in graphene by breaking the materials symmetries

NASA Astrophysics Data System (ADS)

Javvaji, Brahmanandam; He, Bo; Zhuang, Xiaoying

2018-06-01

Graphene is a non-piezoelectric material. Engineering the piezoelectricity in graphene is possible with the help of impurities, defects and structural modifications. This study reports the mechanism of strain induced polarization and the estimation of piezoelectric and flexoelectric coefficients for graphene system. The combination of charge-dipole potential and the strong many-body potential is employed for describing the inter-atomic interactions. The breaking of symmetry in graphene material is utilized to generate the polarization. Pristine graphene, graphene with circular defect, graphene with triangular defect and trapezium-shaped graphene are considered. Molecular dynamics simulations are performed for straining the graphene atomic systems. The optimization of charge-dipole potential functions measure the polarization for these systems. Pristine and circular defect graphene systems show a constant polarization with strain. The polarization is varying with strain for a triangular defected and trapezium-shaped graphene system. The local atomic deformation produces a change in polarization with respect to the strain gradient. Estimated piezo and flexo coefficients motivate the usage of graphene in electro-mechanical devices.

Kinetic Behavior of Leucine and Other Amino Acids Modulating Cognitive Performance via mTOR Pathway

DTIC Science & Technology

2011-12-02

is a potential target for modulation with leucine (or other therapeutic agents), to maintain/enhance normal functioning under stress conditions. Such... functioning under stress conditions. Such an effect has potential for optimizing warfighter cognitive performance under high demand conditions. The... Isoleucine L1 Essential Neutral Non-polar Branched chain Lysine Basic Y+ Essential Basic Polar Proline L1? Neutral Non-polar Aromatic Asparagine Neutral

Potential Arctic sea ice refuge for sustaining a remnant polar bear population (Invited)

NASA Astrophysics Data System (ADS)

Durner, G. M.; Amstrup, S. C.; Douglas, D. C.; Gautier, D. L.

2010-12-01

Polar bears depend on sea ice as a platform from which they capture seals. Sea ice availability must be spatially and temporally adequate for birth and weaning of seal pups, and to maximize seal hunting opportunities for polar bears. Projected declines in the spatial and temporal extent of summer and autumn sea ice could potentially limit the ability of polar bears to build up body stores sufficient to maintain reproductive fitness. General circulation models, however, suggest that summer and autumn sea ice may persist in the shelf waters of the Canadian Archipelago and northern Greenland adjacent to the Arctic basin. While winter-formed ice is important, a primary mechanism for sea ice accumulation in this region is by mechanical thickening of the sea ice facilitated by convergent forces from the Beaufort Gyre and the Transpolar Drift Stream. Collectively these areas could provide a polar bear refugium when other regions have lost the sea ice necessary to support viable populations. The potential for a polar bear refugium, however, must include other resource considerations. Projected declines of sea ice in the Northwest Passage may expose polar bears to hazards related to increase shipping and other commerce. Increasing global demands and limited opportunities elsewhere make the Arctic an increasingly attractive area for petroleum exploration. The Canadian Archipelago coincides with the Sverdrup basin, where petroleum accumulations have already been discovered but as yet are undeveloped. The Lincoln Sea Basin offshore of northern Greenland has the geological possibility of significant petroleum accumulations, and northeastern Greenland is one of the most prospective areas in the Arctic for undiscovered oil. Activities associated with commerce and petroleum development could reduce the potential viability of the region as a polar bear refugium. Hence, if the goal is a sustainable (albeit reduced) polar bear population, important considerations include commerce, hydrocarbon extraction and polar bear habitat.

Relation Between Open Circuit Potential and Polarization Resistance with Rust and Corrosion Monitoring of Mild Steel

NASA Astrophysics Data System (ADS)

Choudhary, S.; Garg, A.; Mondal, K.

2016-07-01

The present work discusses continuous corrosion assessment from a unique correlation of open circuit potential (OCP) and linear polarization resistance with rust formation on mild steel after prolong exposure in 3.5% NaCl salt fog environment. The OCP measurement and linear polarization tests were carried out of the rusted samples only without the removal of rust. It also discusses the strong influence of the composition, fraction, and morphology of the rust layers with OCP and linear polarization resistance. The rust characterization was done after the measurement of OCP and linear polarization resistance of the rusted steel samples. Therefore, monitoring of both the OCP and linear polarization resistance of the rusted mild steels coupled with rust characterization could be used for easy and dynamic assessment of the nature of corrosion.

A new approach to the Schrödinger equation with rational potentials

NASA Astrophysics Data System (ADS)

Dong, Ming-de; Chu, Jue-Hui

1984-04-01

A new analytic theory is established for the Schrödinger equation with a rational potential, including a complete classification of the regular eigenfunctions into three different types, an exact method of obtaining wavefunctions, an explicit formulation of the spectral equation (3 x 3 determinant) etc. All representations are exhibited in a unifying way via function-theoretic methods and therefore given in explicit form, in contrast to the prevailing discussion appealing to perturbation or variation methods or continued-fraction techniques. The irregular eigenfunctions at infinity can be obtained analogously and will be discussed separately as another solvable case for singular potentials.

Educational Researchers' Personal Explicit Theories on Creativity and Its Development: A Qualitative Study

ERIC Educational Resources Information Center

Maksic, Slavica; Pavlovic, Jelena

2011-01-01

The aim of this paper is to investigate implicit theories of educational researchers on creativity and the potential to support creativity in schools. We used qualitative thematic analysis of material produced by 27 educational experts from Serbia. Personal explicit theories about manifestations of creativity are mainly based on qualities and…

Compact terahertz wave polarization beam splitter using photonic crystal.

PubMed

Mo, Guo-Qiang; Li, Jiu-Sheng

2016-09-01

Electromagnetic polarization conveys valuable information for signal processing. Manipulation of a terahertz wave polarization state exhibits tremendous potential in developing applications of terahertz science and technology. We propose an approach to efficiently split transverse-electric and transverse-magnetic polarized terahertz waves into different propagation directions over the frequency range from 0.9998 to 1.0007 THz. Both the plane wave expansion method and the finite-difference time-domain method are used to calculate and analyze the transmission characteristics of the proposed device. The present device is very compact and the total size is 1.02  mm×0.99  mm. This polarization beam splitter performance indicates that the structure has a potential application for forthcoming terahertz-wave integrated circuit fields.

Preliminary study of the use of the STAR-100 computer for transonic flow calculations

NASA Technical Reports Server (NTRS)

Keller, J. D.; Jameson, A.

1977-01-01

An explicit method for solving the transonic small-disturbance potential equation is presented. This algorithm, which is suitable for the new vector-processor computers such as the CDC STAR-100, is compared to successive line over-relaxation (SLOR) on a simple test problem. The convergence rate of the explicit scheme is slower than that of SLOR, however, the efficiency of the explicit scheme on the STAR-100 computer is sufficient to overcome the slower convergence rate and allow an overall speedup compared to SLOR on the CYBER 175 computer.

A chemo-mechanical free-energy-based approach to model durotaxis and extracellular stiffness-dependent contraction and polarization of cells.

PubMed

Shenoy, Vivek B; Wang, Hailong; Wang, Xiao

2016-02-06

We propose a chemo-mechanical model based on stress-dependent recruitment of myosin motors to describe how the contractility, polarization and strain in cells vary with the stiffness of their surroundings and their shape. A contractility tensor, which depends on the distribution of myosin motors, is introduced to describe the chemical free energy of the cell due to myosin recruitment. We explicitly include the contributions to the free energy that arise from mechanosensitive signalling pathways (such as the SFX, Rho-Rock and MLCK pathways) through chemo-mechanical coupling parameters. Taking the variations of the total free energy, which consists of the chemical and mechanical components, in accordance with the second law of thermodynamics provides equations for the temporal evolution of the active stress and the contractility tensor. Following this approach, we are able to recover the well-known Hill relation for active stresses, based on the fundamental principles of irreversible thermodynamics rather than phenomenology. We have numerically implemented our free energy-based approach to model spatial distribution of strain and contractility in (i) cells supported by flexible microposts, (ii) cells on two-dimensional substrates, and (iii) cells in three-dimensional matrices. We demonstrate how the polarization of the cells and the orientation of stress fibres can be deduced from the eigenvalues and eigenvectors of the contractility tensor. Our calculations suggest that the chemical free energy of the cell decreases with the stiffness of the extracellular environment as the cytoskeleton polarizes in response to stress-dependent recruitment of molecular motors. The mechanical energy, which includes the strain energy and motor potential energy, however, increases with stiffness, but the overall energy is lower for cells in stiffer environments. This provides a thermodynamic basis for durotaxis, whereby cells preferentially migrate towards stiffer regions of the extracellular environment. Our models also explain, from an energetic perspective, why the shape of the cells can change in response to stiffness of the surroundings. The effect of the stiffness of the nucleus on its shape and the orientation of the stress fibres is also studied for all the above geometries. Along with making testable predictions, we have estimated the magnitudes of the chemo-mechanical coupling parameters for myofibroblasts based on data reported in the literature.

A chemo-mechanical free-energy-based approach to model durotaxis and extracellular stiffness-dependent contraction and polarization of cells

PubMed Central

Shenoy, Vivek B.; Wang, Hailong; Wang, Xiao

2016-01-01

We propose a chemo-mechanical model based on stress-dependent recruitment of myosin motors to describe how the contractility, polarization and strain in cells vary with the stiffness of their surroundings and their shape. A contractility tensor, which depends on the distribution of myosin motors, is introduced to describe the chemical free energy of the cell due to myosin recruitment. We explicitly include the contributions to the free energy that arise from mechanosensitive signalling pathways (such as the SFX, Rho-Rock and MLCK pathways) through chemo-mechanical coupling parameters. Taking the variations of the total free energy, which consists of the chemical and mechanical components, in accordance with the second law of thermodynamics provides equations for the temporal evolution of the active stress and the contractility tensor. Following this approach, we are able to recover the well-known Hill relation for active stresses, based on the fundamental principles of irreversible thermodynamics rather than phenomenology. We have numerically implemented our free energy-based approach to model spatial distribution of strain and contractility in (i) cells supported by flexible microposts, (ii) cells on two-dimensional substrates, and (iii) cells in three-dimensional matrices. We demonstrate how the polarization of the cells and the orientation of stress fibres can be deduced from the eigenvalues and eigenvectors of the contractility tensor. Our calculations suggest that the chemical free energy of the cell decreases with the stiffness of the extracellular environment as the cytoskeleton polarizes in response to stress-dependent recruitment of molecular motors. The mechanical energy, which includes the strain energy and motor potential energy, however, increases with stiffness, but the overall energy is lower for cells in stiffer environments. This provides a thermodynamic basis for durotaxis, whereby cells preferentially migrate towards stiffer regions of the extracellular environment. Our models also explain, from an energetic perspective, why the shape of the cells can change in response to stiffness of the surroundings. The effect of the stiffness of the nucleus on its shape and the orientation of the stress fibres is also studied for all the above geometries. Along with making testable predictions, we have estimated the magnitudes of the chemo-mechanical coupling parameters for myofibroblasts based on data reported in the literature. PMID:26855753

Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions

NASA Astrophysics Data System (ADS)

Garimella, Sandilya V. B.; Webb, Ian K.; Prabhakaran, Aneesh; Attah, Isaac K.; Ibrahim, Yehia M.; Smith, Richard D.

2017-07-01

Here we describe instrumental approaches for performing dual polarity ion confinement, transport, ion mobility separations, and reactions in structures for lossless ion manipulations (SLIM). Previous means of ion confinement in SLIM, based upon rf-generated pseudopotentials and DC fields for lateral confinement, cannot trap ions of opposite polarity simultaneously. Here we explore alternative approaches to provide simultaneous lateral confinement of both ion polarities. Traveling wave ion mobility (IM) separations experienced in such SLIM cause ions of both polarities to migrate in the same directions and exhibit similar separations. The ion motion (and relative motion of the two polarities) under both surfing and IM separation conditions are discussed. In surfing conditions the two polarities are transported losslessly and non-reactively in their respective potential minima (higher absolute voltage regions confine negative polarities, and lower absolute potential regions are populated by positive polarities). In separation mode, where ions roll over an overtaking traveling wave, the two polarities can interact during the rollovers. Strategies to minimize overlap of the two ion populations to prevent reactive losses during separations are presented. A theoretical treatment of the time scales over which two populations (injected into a DC field-free region of the dual polarity SLIM device) interact is considered, and SLIM designs for allowing ion/ion interactions and other manipulations with dual polarities at 4 Torr are presented.

Three-dimensional imaging through turbid media based on polarization-difference liquid-crystal microlens array

NASA Astrophysics Data System (ADS)

Xin, Zhaowei; Wei, Dong; Li, Dapeng; Xie, Xingwang; Chen, Mingce; Zhang, Xinyu; Wang, Haiwei; Xie, Changsheng

2018-02-01

In this paper, a polarization difference liquid-crystal microlens array (PD-LCMLA) for three dimensional imaging application through turbid media is fabricated and demonstrated. This device is composed of a twisted nematic liquidcrystal cell (TNLCC), a polarizer and a liquid-crystal microlens array. The polarizer is sandwiched between the TNLCC and LCMLA to help the polarization difference system achieving the orthogonal polarization raw images. The prototyped camera for polarization difference imaging has been constructed by integrating the PD-LCMLA with an image sensor. The orthogonally polarized light-field images are recorded by switching the working state of the TNLCC. Here, by using a special microstructure in conjunction with the polarization-difference algorithm, we demonstrate that the three-dimensional information in the scattering media can be retrieved from the polarization-difference imaging system with an electrically tunable PD-LCMLA. We further investigate the system's potential function based on the flexible microstructure. The microstructure provides a wide operation range in the manipulation of incident beams and also emerges multiple operation modes for imaging applications, such as conventional planar imaging, polarization imaging mode, and polarization-difference imaging mode. Since the PD-LCMLA demonstrates a very low power consumption, multiple imaging modes and simple manufacturing, this kind of device presents a potential to be used in many other optical and electro-optical systems.

Quantum theoretical study of electron solvation dynamics in ice layers on a Cu(111) surface.

PubMed

Andrianov, I; Klamroth, T; Saalfrank, P; Bovensiepen, U; Gahl, C; Wolf, M

2005-06-15

Recent experiments using time- and angle-resolved two-photon photoemission (2PPE) spectroscopy at metal/polar adsorbate interfaces succeeded in time-dependent analysis of the process of electron solvation. A fully quantum mechanical, two-dimensional simulation of this process, which explicitly includes laser excitation, is presented here, confirming the origin of characteristic features, such as the experimental observation of an apparently negative dispersion. The inference of the spatial extent of the localized electron states from the angular dependence of the 2PPE spectra has been found to be non-trivial and system-dependent.

Lattice QCD and the timelike pion form factor.

PubMed

Meyer, Harvey B

2011-08-12

We present a formula that allows one to calculate the pion form factor in the timelike region 2m(π) ≤ √(s) ≤ 4m(π) in lattice QCD. The form factor quantifies the contribution of two-pion states to the vacuum polarization. It must be known very accurately in order to reduce the theoretical uncertainty on the anomalous magnetic moment of the muon. At the same time, the formula constitutes a rare example where, in a restricted kinematic regime, the spectral function of a conserved current can be determined from Euclidean observables without an explicit analytic continuation.

The role of attention during encoding in implicit and explicit memory.

PubMed

Mulligan, N W

1998-01-01

In 5 experiments, participants read study words under conditions of divided or full attention. Dividing attention reduced performance on the general knowledge test, a conceptual implicit test of memory. Likewise, dividing attention reduced conceptual priming on the word--association task, as well as on a matched explicit test, associate-cued recall. In contrast, even very strong division of attention did not reduce perceptual priming on word-fragment completion, although it did reduce recall on the matched explicit test of word-fragment-cued recall. Finally, dividing attention reduced recall on the perceptual explicit tests of graphemic-cued recall and graphemic recognition. The results indicate that perceptual implicit tests rely minimally on attention-demanding encoding processes relative to other types of memory tests. The obtained pattern of dissociations is not readily accommodated by the transfer-appropriate-processing (TAP) account of implicit and explicit memory. Potential extensions of the TAP view are discussed.

Vacuum Polarization by a Magnetic Flux Tube at Finite Temperature in the Cosmic String Space-Time

NASA Astrophysics Data System (ADS)

Spinelly, J.; Bezerra de Mello, E. R.

In this paper, we analyze the effect produced by the temperature in the vacuum polarization associated with a charged massless scalar field in the presence of a magnetic flux tube in the cosmic string space-time. Three different configurations of magnetic fields are taken into account: (i) a homogeneous field inside the tube, (ii) a field proportional to 1/r, and (iii) a cylindrical shell with δ-function. In these three cases, the axis of the infinitely long tube of radius R coincides with the cosmic string. Because of the complexity of this analysis in the region inside the tube, we consider the thermal effect in the region outside. In order to develop this analysis, we construct the thermal Green function associated with this system for the three above-mentioned situations considering points in the region outside the tube. We explicitly calculate, in the high-temperature limit, the thermal average of the field square and the energy-momentum tensor.

Analytical saturated domain orientation textures and electromechanical properties of ferroelectric ceramics due to electric/mechanical poling

NASA Astrophysics Data System (ADS)

Li, F. X.; Rajapakse, R. K. N. D.

2007-03-01

Saturated domain orientation textures of three types of pseudocubic (tetragonal, rhombohedral, and orthorhombic) ferroelectric ceramics after complete electric and uniaxial tension (compression) poling is studied analytically in this paper. A one-dimensional orientation distribution function (ODF) of the domain polar vectors is explicitly derived from the uniform inverse pole figures of the poling field axes on a stereographic projection with respect to the fixed crystallite coordinates. The analytical ODF is used to obtain the analytical solutions of saturated polarization and strain after electric/mechanical poling. Based on the closed form solution of the saturated domain orientation textures, the resultant intrinsic electromechanical properties of ferroelectric ceramics, which depend only on the ODF and properties of the corresponding single crystals, are obtained. The results show how the macroscopic symmetries of ferroelectric crystals change from 4mm (tetragonal), 3m (rhombohedral), and mm2 (orthorhombic) single crystals to a ∞mm (transversely isotropic) completely poled ceramic.

Robust Likelihoods for Inflationary Gravitational Waves from Maps of Cosmic Microwave Background Polarization

NASA Technical Reports Server (NTRS)

Switzer, Eric Ryan; Watts, Duncan J.

2016-01-01

The B-mode polarization of the cosmic microwave background provides a unique window into tensor perturbations from inflationary gravitational waves. Survey effects complicate the estimation and description of the power spectrum on the largest angular scales. The pixel-space likelihood yields parameter distributions without the power spectrum as an intermediate step, but it does not have the large suite of tests available to power spectral methods. Searches for primordial B-modes must rigorously reject and rule out contamination. Many forms of contamination vary or are uncorrelated across epochs, frequencies, surveys, or other data treatment subsets. The cross power and the power spectrum of the difference of subset maps provide approaches to reject and isolate excess variance. We develop an analogous joint pixel-space likelihood. Contamination not modeled in the likelihood produces parameter-dependent bias and complicates the interpretation of the difference map. We describe a null test that consistently weights the difference map. Excess variance should either be explicitly modeled in the covariance or be removed through reprocessing the data.

Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

PubMed

Bryce, Richard A

2011-04-01

The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.

Ethical Considerations Regarding the Biological Contamination of Climatically Recurrent Special Regions.

NASA Astrophysics Data System (ADS)

Clifford, S. M.

2014-04-01

With the dawn of planetary exploration, the international science community expressed concerns regarding the potential contamination of habitable planetary environments by the introduction of terrestrial organisms on robotic spacecraft. The initial concern was that such contamination would confound our efforts to find unambiguous evidence of life elsewhere in the Solar System, although, more recently, this concern has been expanded to include ethical considerations regarding the need to protect alien biospheres from potentially harmful and irreversible contamination. The international agreements which address this concern include the UN Space Treaty of 1967 and the Planetary Protection Policy of the International Council for Science's Committee on Space Research (COSPAR). In the context of Mars exploration, COSPAR calls a potentially habitable environment a 'Special Region', which it defines as: "A region within which terrestrial organisms are likely to propagate, or a region which is interpreted to have a high potential for the existence of extant Martian life forms." Specifically included in this definition are regions where liquid water is present or likely to occur and the Martian polar caps. Over the years, scientists have debated the level of cleanliness required for robotic spacecraft to investigate such environments with the goal of defining international standards that are strict enough to ensure the integrity of life-detection efforts during the period of 'biological exploration', which has been somewhat arbitrarily defined as 50 years from the arrival date of any given mission. More recently, NASA and ESA have adopted a definition of Special Regions as any Martian environment where liquid water is likely to exist within the next 500 years. While this appears to be a more conservative interpretation of the original COSPAR definition, it specifically excludes some environments where there is a high probability of liquid water on timescales greater than 500 years, such as in the Martian polar layered deposits (and other high-latitude, ice-rich environments), at times of high obliquity. Current climate models suggest that, for obliquities > 45°, summertime surface temperatures at polar and near-polar latitudes may approach or exceed the melting point of water for continuous periods of many months (Costard et al., 2001; Jakosky et al., 2003) - conditions that may be repeated annually throughout the maximum obliquity phase of the 105-year obliquity cycle. If so, these icerich, high-latitude environments may be considered climatically recurrent Special Regions - and may be among the most potentially habitable environments on Mars for the survival and growth of terrestrial microorganisms.A significant concern arising from this potential is that, whether by accident or the nominal operation of investigating spacecraft (cleaned to less than Special Region (IVc) standards), we might irreversibly contaminate these sensitive environments. While such contamination may not pose an immediate threat to the integrity of our spacecraft life-detection experiments, its potential impact on the long-term health and ultimate survival of a native Martian biosphere raises significant scientific and ethical concerns, as identified in the NRC report on Preventing the Forward Contamination 0f Mars [4]. Precedents for considering the adoption of planetary protection standards that minimize the potential impact of our exploration efforts on a native biosphere include the NRC report on Preventing the Forward Contamination of Europa, which noted that "future spacecraft missions to Europa must be subject to procedures designed to prevent its contamination by terrestrial organisms. This is necessary to safeguard the scientific integrity of future studies of Europa's biological potential and to protect against potential harm to Europan organisms, if they exist, and is mandated by obligations under the [Outer Space Treaty]" [5]). Virtually identical concerns were expressed by the NRC Committee on Planetary and Lunar Exploration [6] in its report A Science Strategy for the Exploration of Europa. Because microbial contaminants on spacecraft cleaned to less than IVc standards could introduce terrestrial organisms into polar and other ice-rich environments that current climate models and geologic evidence suggests are likely to become habitable on timescales of 105 - 107 years, PREVCOM argued that the definition of Special Regions should be extended to include such environments, in agreement with the original COSPAR definition. Our failure to do so could lead to the irreversible biological contamination of Mars and the potential extinction of the very first extraterrestrial biosphere we have attempted to detect. While there are those who believe that the advent of human exploration will make the irreversible biological contamination of Mars inevitable, it is an issue that should be addressed explicitly and in advance -- before the momentum of our robotic exploration activities renders the debate over the protection of such a Martian biosphere moot.

On the link between martian total ozone and potential vorticity

NASA Astrophysics Data System (ADS)

Holmes, James A.; Lewis, Stephen R.; Patel, Manish R.

2017-01-01

We demonstrate for the first time that total ozone in the martian atmosphere is highly correlated with the dynamical tracer, potential vorticity, under certain conditions. The degree of correlation is investigated using a Mars global circulation model including a photochemical model. Potential vorticity is the quantity of choice to explore the dynamical nature of polar vortices because it contains information on winds and temperature in a single scalar variable. The correlation is found to display a distinct seasonal variation, with a strong positive correlation in both northern and southern winter at poleward latitudes in the northern and southern hemisphere respectively. The identified strong correlation implies variations in polar total ozone during winter are predominantly controlled by dynamical processes in these spatio-temporal regions. The weak correlation in northern and southern summer is due to the dominance of photochemical reactions resulting from extended exposure to sunlight. The total ozone/potential vorticity correlation is slightly weaker in southern winter due to topographical variations and the preference for ozone to accumulate in Hellas basin. In northern winter, total ozone can be used to track the polar vortex edge. The ozone/potential vorticity ratio is calculated for both northern and southern winter on Mars for the first time. Using the strong correlation in total ozone and potential vorticity in northern winter inside the polar vortex, it is shown that potential vorticity can be used as a proxy to deduce the distribution of total ozone where satellites cannot observe for the majority of northern winter. Where total ozone observations are available on the fringes of northern winter at poleward latitudes, the strong relationship of total ozone and potential vorticity implies that total ozone anomalies in the surf zone of the northern polar vortex can potentially be used to determine the origin of potential vorticity filaments.

QCD evolution of (un)polarized gluon TMDPDFs and the Higgs q T -distribution

NASA Astrophysics Data System (ADS)

Echevarria, Miguel G.; Kasemets, Tomas; Mulders, Piet J.; Pisano, Cristian

2015-07-01

We provide the proper definition of all the leading-twist (un)polarized gluon transverse momentum dependent parton distribution functions (TMDPDFs), by considering the Higgs boson transverse momentum distribution in hadron-hadron collisions and deriving the factorization theorem in terms of them. We show that the evolution of all the (un)polarized gluon TMDPDFs is driven by a universal evolution kernel, which can be resummed up to next-to-next-to-leading-logarithmic accuracy. Considering the proper definition of gluon TMDPDFs, we perform an explicit next-to-leading-order calculation of the unpolarized ( f {1/ g }), linearly polarized ( h {1/⊥ g }) and helicity ( g {1/L g }) gluon TMDPDFs, and show that, as expected, they are free from rapidity divergences. As a byproduct, we obtain the Wilson coefficients of the refactorization of these TMDPDFs at large transverse momentum. In particular, the coefficient of g {1/L g }, which has never been calculated before, constitutes a new and necessary ingredient for a reliable phenomenological extraction of this quantity, for instance at RHIC or the future AFTER@LHC or Electron-Ion Collider. The coefficients of f {1/ g } and h {1/⊥ g } have never been calculated in the present formalism, although they could be obtained by carefully collecting and recasting previous results in the new TMD formalism. We apply these results to analyze the contribution of linearly polarized gluons at different scales, relevant, for instance, for the inclusive production of the Higgs boson and the C-even pseudoscalar bottomonium state η b . Applying our resummation scheme we finally provide predictions for the Higgs boson q T -distribution at the LHC.

Visualizing the Positive-Negative Interface of Molecular Electrostatic Potentials as an Educational Tool for Assigning Chemical Polarity

ERIC Educational Resources Information Center

Schonborn, Konrad; Host, Gunnar; Palmerius, Karljohan

2010-01-01

To help in interpreting the polarity of a molecule, charge separation can be visualized by mapping the electrostatic potential at the van der Waals surface using a color gradient or by indicating positive and negative regions of the electrostatic potential using different colored isosurfaces. Although these visualizations capture the molecular…

Direct visualization of polarization reversal of organic ferroelectric memory transistor by using charge modulated reflectance imaging

NASA Astrophysics Data System (ADS)

Otsuka, Takako; Taguchi, Dai; Manaka, Takaaki; Iwamoto, Mitsumasa

2017-11-01

By using the charge modulated reflectance (CMR) imaging technique, charge distribution in the pentacene organic field-effect transistor (OFET) with a ferroelectric gate insulator [P(VDF-TrFE)] was investigated in terms of polarization reversal of the P(VDF-TrFE) layer. We studied the polarization reversal process and the carrier spreading process in the OFET channel. The I-V measurement showed a hysteresis behavior caused by the spontaneous polarization of P(VDF-TrFE), but the hysteresis I-V curve changes depending on the applied drain bias, possibly due to the gradual shift of the polarization reversal position in the OFET channel. CMR imaging visualized the gradual shift of the polarization reversal position and showed that the electrostatic field formed by the polarization of P(VDF-TrFE) contributes to hole and electron injection into the pentacene layer and the carrier distribution is significantly dependent on the direction of the polarization. The polarization reversal position in the channel region is governed by the electrostatic potential, and it happens where the potential reaches the coercive voltage of P(VDF-TrFE). The transmission line model developed on the basis of the Maxwell-Wagner effect element analysis well accounts for this polarization reversal process in the OFET channel.

Retrieval of Concrete Words Involves More Contextual Information than Abstract Words: Multiple Components for the Concreteness Effect

ERIC Educational Resources Information Center

Xiao, Xin; Zhao, Di; Zhang, Qin; Guo, Chun-yan

2012-01-01

The current study used the directed forgetting paradigm in implicit and explicit memory to investigate the concreteness effect. Event-related potentials (ERPs) were recorded to explore the neural basis of this phenomenon. The behavioral results showed a clear concreteness effect in both implicit and explicit memory tests; participants responded…

Adolescents' Exposure to Sexually Explicit Internet Material and Sexual Satisfaction: A Longitudinal Study

ERIC Educational Resources Information Center

Peter, Jochen; Valkenburg, Patti M.

2009-01-01

The aim of this study was to investigate, within a social comparison framework, the causal relationship between adolescents' use of sexually explicit Internet material (SEIM) and their sexual satisfaction. In addition, we tested which adolescents were most susceptible to a potential influence of SEIM on sexual satisfaction. Between May 2006 and…

Effect of Long-Period Ocean Tides on the Earth's Polar Motion

NASA Technical Reports Server (NTRS)

Gross, R. S.; Chao, B. F.; Desai, S. D.

1997-01-01

The second-degree zonal tide raising potential is symmetric about the polar axis and hence can excite the Earth's polar motion only through its action upon nonaxisymmetric features of the Earth such as the oceans.

Tissue polarimetry: concepts, challenges, applications, and outlook.

PubMed

Ghosh, Nirmalya; Vitkin, I Alex

2011-11-01

Polarimetry has a long and successful history in various forms of clear media. Driven by their biomedical potential, the use of the polarimetric approaches for biological tissue assessment has also recently received considerable attention. Specifically, polarization can be used as an effective tool to discriminate against multiply scattered light (acting as a gating mechanism) in order to enhance contrast and to improve tissue imaging resolution. Moreover, the intrinsic tissue polarimetry characteristics contain a wealth of morphological and functional information of potential biomedical importance. However, in a complex random medium-like tissue, numerous complexities due to multiple scattering and simultaneous occurrences of many scattering and polarization events present formidable challenges both in terms of accurate measurements and in terms of analysis of the tissue polarimetry signal. In order to realize the potential of the polarimetric approaches for tissue imaging and characterization/diagnosis, a number of researchers are thus pursuing innovative solutions to these challenges. In this review paper, we summarize these and other issues pertinent to the polarized light methodologies in tissues. Specifically, we discuss polarized light basics, Stokes-Muller formalism, methods of polarization measurements, polarized light modeling in turbid media, applications to tissue imaging, inverse analysis for polarimetric results quantification, applications to quantitative tissue assessment, etc.

An analytical approach to the CMB polarization in a spatially closed background

NASA Astrophysics Data System (ADS)

Niazy, Pedram; Abbassi, Amir H.

2018-03-01

The scalar mode polarization of the cosmic microwave background is derived in a spatially closed universe from the Boltzmann equation using the line of sight integral method. The EE and TE multipole coefficients have been extracted analytically by considering some tolerable approximations such as considering the evolution of perturbation hydrodynamically and sudden transition from opacity to transparency at the time of last scattering. As the major advantage of analytic expressions, CEE,ℓS and CTE,ℓ explicitly show the dependencies on baryon density ΩB, matter density ΩM, curvature ΩK, primordial spectral index ns, primordial power spectrum amplitude As, Optical depth τreion, recombination width σt and recombination time tL. Using a realistic set of cosmological parameters taken from a fit to data from Planck, the closed universe EE and TE power spectrums in the scalar mode are compared with numerical results from the CAMB code and also latest observational data. The analytic results agree with the numerical ones on the big and moderate scales. The peak positions are in good agreement with the numerical result on these scales while the peak heights agree with that to within 20% due to the approximations have been considered for these derivations. Also, several interesting properties of CMB polarization are revealed by the analytic spectra.