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Sample records for kommenteerinud riho tamm

  1. Confined Visible Optical Tamm States

    NASA Astrophysics Data System (ADS)

    Feng, F.; Ouaret, K.; Portalupi, S.; Lafosse, X.; Nasilovski, M.; de Marcillac, W. Daney; Frigerio, J.-M.; Schwob, C.; Dubertret, B.; Maître, A.; Senellart, P.; Coolen, L.

    2016-05-01

    Optical Tamm states are two-dimensional (2D) electromagnetic modes propagating at the interface between a Bragg mirror and a metallic film. When a thin (a few tens of nm) metallic micron-radius disk is deposited on a Bragg mirror, optical Tamm states can be confined below the disk surface, creating a Tamm-states cavity. We describe here the photoluminescence properties of colloidal semiconductor nanocrystals embedded in a Tamm cavity. Tamm states confinement effects are demonstrated and analysed as a function of the disk diameter, and compared with finite-elements simulations.

  2. Transcutaneous Analyte Measuring Methods (TAMM), phase 2

    NASA Astrophysics Data System (ADS)

    Schlager, Kenneth J.

    1991-11-01

    The primary objectives of the first quarter of Phase 2 TAMM were the following: the design of a near infrared (NIR)-800 photodiode array spectrometer, two of which would be used in clinical testing during 1992; the development of advanced pattern recognition software for analyzing the data collected with the spectrometer; and the establishment of an ongoing, internal test program with the B1-102 infrared analyzer. The major effect during the first three months of the project was in developing the analytical software NETGEN. NETGEN is a set of analytical programs that combine the best features of neural networks and genetic algorithms. Artificial neural networks (ANNs) are a form of distributed parallel processing of information that attempts to simulate the human brain. For application in TAMM, ANNs are an alternative to previous pattern recognition methods used for predicting blood analyte concentrations from NIR spectra.

  3. Tamm plasmon polaritons in multilayered cylindrical structures

    NASA Astrophysics Data System (ADS)

    Little, C. E.; Anufriev, R.; Iorsh, I.; Kaliteevski, M. A.; Abram, R. A.; Brand, S.

    2012-12-01

    It is shown that cylindrical Bragg reflector structures with either a metal core, a metal cladding, or both can support Tamm plasmon polaritons (TPPs) that can propagate axially along the interface between the metallic layer and the adjacent dielectric. A transfer matrix formalism for cylindrical multilayered structures is used in association with cavity phase matching considerations to design structures that support Tamm plasmon polaritons at specified frequencies, and to explore the field distributions and the dispersion relations of the excitations. The cylindrical TPPs can exist in both the TE and TM polarizations for the special cases of modes with either azimuthal isotropy or zero axial propagation constant and also as hybrid cylindrical modes when neither of those conditions applies. In the cases considered the TPPs have low effective masses and low group velocities. Also, when there is both metallic core and cladding, near degenerate modes localized at each metallic interface can couple to produce symmetric and antisymmetric combinations whose frequency difference is in the terahertz regime.

  4. Properties of a glycopeptide isolated from human Tamm-Horsfall glycoprotein. Interaction with leucoagglutinin and anti-(human Tamm-Horsfall glycoprotein) antibodies.

    PubMed Central

    Abbondanza, A; Franceschi, C; Licastro, F; Serafini-Cessi, F

    1980-01-01

    A sialylated glycopeptide isolated after Pronase digestion of human Tamm-Horsfall glycoprotein behaves as a powerful monovalent hapten in the precipitin reaction between human Tamm-Horsfall glycoprotein and leucoagglutinin, but fails to inhibit the interaction of the glycoprotein with rabbit anti-(human Tamm-Horsfall glycoprotein) antibodies. The glycopeptide is much less active than the intact glycoprotein as an inhibitor of lymphocyte transformation induced by leucoagglutinin. PMID:6967312

  5. Confinement of gigahertz sound and light in Tamm plasmon resonators

    NASA Astrophysics Data System (ADS)

    Villafañe, V.; Bruchhausen, A. E.; Jusserand, B.; Senellart, P.; Lemaître, A.; Fainstein, A.

    2015-10-01

    We demonstrate theoretically and by pump-probe picosecond acoustics experiments the simultaneous confinement of light and gigahertz sound in Tamm plasmon resonators, formed by depositing a thin layer of Au onto a GaAs/AlGaAs Bragg reflector. The cavity has InGaAs quantum dots (QDs) embedded at the maximum of the confined optical field in the first GaAs layer. The different sound generation and detection mechanisms are theoretically analyzed. It is shown that the Au layer absorption and the resonant excitation of the QDs are the more efficient light-sound transducers for the coupling of near-infrared light with the confined acoustic modes, while the displacement of the interfaces is the main back-action mechanism at these energies. The prospects for the compact realization of optomechanical resonators based on Tamm plasmon cavities are discussed.

  6. Tamm State-Coupled Emission: Effect of Probe Location and Emission Wavelength

    PubMed Central

    2015-01-01

    We report the effect of the probe location and wavelength on the emission spatial distribution and spectral properties of fluorophores located on structures which display Tamm states. Our structure consists of a one-dimensional photonic crystal (1DPC)—that is, a multilayer structure of alternate high and low refractive index dielectrics—and a thin top silver film. Simulations show the presence of Tamm and surface plasmon modes in the structure. The electric field intensities for the Tamm modes are located mostly in the dielectric layer below the metal film. The corresponding field intensities for the surface plamon modes are located above the metal film in the distal side. Tamm states can be in resonance with the incident light normal or near normal to the surface, within the light line, and can be accessed without the use of a coupling prism or gratings. We investigated the emission spectra and angular distribution of the emission for probes located above and below the metal film to explore the interaction of fluorophores with Tamm plasmons and surface plasmons modes. Three probes were chosen with different overlap of the emission spectra with the Tamm modes. The fluorophores below the metal film coupled predominantly with the Tamm state and displayed more intense and only Tamm state-coupled emission (TSCE). Probes above the metal film display both surface plasmon-coupled emission (SPCE) and Tamm state-coupled emission. In contrast to SPCE, which shows only KR, P-polarized emission, the Tamm states can display both S- and P-polarized emission and can be populated using both RK and KR illuminations. The TSCE angle is highly sensitive to wavelength, which suggests the use of Tamm structures to provide both directional emission and wavelength dispersion. The combination of plasmonic and photonic structures with directional emission close to surface normal offers the opportunities for new design formats for clinical testing, portable devices, and other

  7. Hybrid states of Tamm plasmons and exciton polaritons

    SciTech Connect

    Kaliteevski, M.; Brand, S.; Abram, R. A.; Iorsh, I.; Kavokin, A. V.; Shelykh, I. A.

    2009-12-21

    Channeling of exciton polaritons in the plane of semiconductor microcavities can be achieved by the deposition of metallic mesas on the top of the semiconductor structure. We show theoretically that the regime of strong coupling between cavity polaritons and Tamm surface plasmons is possible in such structures. The effect is favorable for the spatial confinement of polaritons and the formation of hybrid one-dimensional plasmon-polariton modes.

  8. Novel sensing concept based on optical Tamm plasmon.

    PubMed

    Zhang, Wei Li; Wang, Fen; Rao, Yun Jiang; Jiang, Yao

    2014-06-16

    This paper proposes a novel concept of refractive index sensing taking advantage of a high-refractive-index-contrast optical Tamm plasmon (OTP) structure, i.e., an air/dielectric alternate-layered distributed Bragg reflector (DBR) coated with metal. In the reflection spectrum of the structure, a dip related to the formation of OTP appears. The wavelength and reflectivity of this dip are sensitive to variation of ambient refractive index, which provides a potential way to realize refractive index sensing with a large measuring range and high sensitivity. PMID:24977548

  9. Electro optical tuning of Tamm-plasmon exciton-polaritons

    SciTech Connect

    Gessler, J.; Baumann, V.; Emmerling, M.; Amthor, M.; Winkler, K.; Schneider, C.; Kamp, M.; Höfling, S.

    2014-11-03

    We report on electro optical tuning of the emission from GaAs quantum wells resonantly coupled to a Tamm-plasmon mode in a hybrid metal/dielectric structure. The structures were studied via momentum resolved photoluminescence and photoreflectance spectroscopy, and the surface metal layer was used as a top gate, which allowed for a precise tuning of the quantum well emission via the quantum confined Stark effect. By tuning the resonance, we were able to observe the characteristic anticrossing behavior of a polaritonic emission in the strong light-matter coupling regime, yielding a Rabi splitting of (9.2 ± 0.2) meV.

  10. Study of childhood renal tumours using a monoclonal antibody to Tamm-Horsfall protein.

    PubMed Central

    Kumar, S; Marsden, H B; Jasani, B; Kumar, P

    1987-01-01

    A monoclonal antibody to Tamm-Horsfall glycoprotein was used for the immuno-localization of Tamm-Horsfall protein in formalin fixed, paraffin embedded tissue sections of childhood renal tumours, normal children's kidneys, and human fetal kidneys. The procedure was a dinitrophenyl hapten sandwich staining method. The antibody, diluted 1/100,000, gave a very strong and specific staining of the loop of Henle and distal tubules of normal and fetal kidneys. No staining was seen in Wilms' tumour, mesoblastic nephroma, and bone metastasizing renal tumour of childhood. In contrast, two of seven renal carcinomas and three of four rhabdoid renal tumours were positive for Tamm-Horsfall protein. Images Fig 1 Fig 2 Fig 3 Fig 4 Fig 5 Fig 6 Fig 7 Fig 8 PMID:3429675

  11. Efficient out-coupling and beaming of Tamm optical states via surface plasmon polariton excitation

    SciTech Connect

    Lopez-Garcia, M.; Ho, Y.-L. D.; Taverne, M. P. C.; Chen, L.-F.; Rarity, J. G.; Oulton, R.; Murshidy, M. M.; Edwards, A. P.; Adawi, A. M.; Serry, M. Y.

    2014-06-09

    We present evidence of optical Tamm states to surface plasmon polariton (SPP) coupling. We experimentally demonstrate that for a Bragg stack with a thin metal layer on the surface, hybrid Tamm-SPP modes may be excited when a grating on the air-metal interface is introduced. Out-coupling via the grating to free space propagation is shown to enhance the transmission as well as the directionality and polarization selection for the transmitted beam. We suggest that this system will be useful on those devices, where a metallic electrical contact as well as beaming and polarization control is needed.

  12. Unconventional optical Tamm states in metal-terminated three-dimensional photonic crystals

    NASA Astrophysics Data System (ADS)

    Korovin, Alexander V.; Romanov, Sergei G.

    2016-03-01

    Unconventional optical Tamm surface states have been demonstrated in transmission and reflectance spectra of three-dimensional opal photonic crystals coated by thin metal films. These states appear in registry with diffraction resonances and localize the electromagnetic energy in asymmetric resonators formed by stacks of lattice planes and metal semishells. Tamm defect states provide the bypass for light at the edges of the Bragg diffraction resonances and thus reduce the diffraction efficiency. Despite the hidden nature of this effect, its magnitude is comparable to the extraordinary transmission associated with the surface-plasmon polaritons that are simultaneously excited at the surfaces of the corrugated metal films.

  13. Photoionization cross section of atomic cadmium using the multi-configuration Tamm-Dancoff approximation

    NASA Astrophysics Data System (ADS)

    Pradhan, G. B.; Jose, J.; Radojević, V.; Manson, S. T.; Deshmukh, P. C.

    2009-11-01

    The Multiconfiguration Tamm-Dancoff approximation (MCTD) is used to calculate the photoionization cross section of cadmium. Results are compared with available experimental data and also with earlier computations of the cross-section. We find that while earlier computations overestimated the photoionization cross section compared to experiment, the present MCTD computation underestimates the same.

  14. Inner Shell Photodetachment Of Na- Using The Multi-Configuration Tamm-Dancoff Approximation

    NASA Astrophysics Data System (ADS)

    Jose, J.; Pradhan, G. B.; Radojevic, V.; Manson, S. T.; Deshmukh, P. C.

    2010-07-01

    The multi-configuration Tamm-Dancoff approximation (MCTD) is used to calculate the inner shell photodetachment of the Na anion. The results reproduce a resonance peak in agreement with existing experimental and theoretical data. The current work emphasizes the importance of doing configuration interaction (CI) type calculations, and proves MCTD is an apt tool to investigate the photoionization/photodetachment process.

  15. Radiative Decay Engineering 7: Tamm State-Coupled Emission Using a Hybrid Plasmonic-Photonic Structure

    PubMed Central

    Badugu, Ramachandram; Descrovi, Emiliano; Lakowicz, Joseph R.

    2014-01-01

    There is a continuing need to increase the brightness and photostability of fluorophores for use in biotechnology, medical diagnostics and cell imaging. One approach developed during the past decade is to use metallic surfaces and nanostructures. It is now known that excited state fluorophores display interactions with surface plasmons, which can increase the radiative decay rates, modify the spatial distribution of emission and result in directional emission. One important example is Surface Plasmon-Coupled Emission (SPCE). In this phenomenon the fluorophores at close distances from a thin metal film, typically silver, display emission over a small range of angles into the substrate. A disadvantage of SPCE is that the emission occur at large angles relative to the surface normal, and at angles which are larger than the critical angle for the glass substrate. The large angles make it difficult to collect all the coupled emission and have prevented use of SPCE with high-throughput and/or array applications. In the present report we describe a simple multi-layer metal-dielectric structure which allows excitation with light that is perpendicular (normal) to the plane and provides emission within a narrow angular distribution that is normal to the plane. This structure consist of a thin silver film on top of a multi-layer dielectric Bragg grating, with no nanoscale features except for the metal or dielectric layer thicknesses. Our structure is designed to support optical Tamm states, which are trapped electromagnetic modes between the metal film and the underlying Bragg grating. We used simulations with the transfer matrix method to understand the optical properties of Tamm states and localization of the modes or electric fields in the structure. Tamm states can exist with zero in-plane wavevector components and can be created without the use of a coupling prism. We show that fluorophores on top of the metal film can interact with the Tamm state under the metal film

  16. Specific interaction of human Tamm-Horsfall gylcoprotein with leucoagglutinin, a lectin from Phaseolus vulgaris (red kidney bean).

    PubMed Central

    Serafini-Cessi, F; Franceschi, C; Sperti, S

    1979-01-01

    Human Tamm-Horsfall glycoprotein inhibits lymphocyte transformation induced by leucoagglutinin and haemagglutinin from Phaseolus vulgaris (red kidney bean). The glycoprotein interacts with the two lectins, giving insoluble precipitates. The interaction with leucoagglutinin is highly specific, and the shape of the precipitin curve is that of an antigen-antibody reaction; precipitation is specifically inhibited by N-acetyl-D-galactosamine. Results are discussed, and it is suggested that inhibition of lymphocyte transformation is due to competition between human Tamm-Horsfall glycoprotein and carbohydrate receptors on lymphocytes for the two lectins. The interaction between human Tamm-Horsfall glycoprotein and Phaseolus vulgaris lectins has been used to develop a one-step procedure for the separation of the two lectins by affinity chromatography on (human Tamm-Horsfall-glycoprotein)-Sepharose. Images Fig. 1. Fig. 5. PMID:118744

  17. Pairing and vibrational correlations in the higher Tamm-Dancoff approximation (HTDA) approach

    SciTech Connect

    Naiedja, H.; Quentin, P.; Samsoen, D.

    2010-04-15

    The higher Tamm-Dancoff Approximation (HTDA) is extended to include vibrational correlations with or without pairing correlations. The residual interaction in use is of the delta (in the T=1 channel) plus multipole-multipole type. In this paper we have limited our study to the mere case of isoscalar quadrupole correlations. The approach is illustrated by the consideration of ground state and isoscalar giant quadrupole resonance properties in the {sup 40}Ca nucleus.

  18. The Tamm-Dancoff Approximation as the Contraction Limit of the Richardson-Gaudin Equations

    NASA Astrophysics Data System (ADS)

    de Baerdemacker, S.

    2013-03-01

    A connection is made between the exact eigenstates of the level-independent Bardeen-Cooper-Schrieffer (BCS) Hamiltonian and its Tamm-Dancoff Approximation (TDA). This is done by means of a deformation of the quasi-spin algebra, which connects the Bethe Ansatz states with a unique multi-phonon mode of the TDA. The procedure is illustrated with a model describing neutron superluidity in 56Fe.

  19. Tuneable polaritonics at room temperature with strongly coupled Tamm plasmon polaritons in metal/air-gap microcavities

    NASA Astrophysics Data System (ADS)

    Grossmann, C.; Coulson, C.; Christmann, G.; Farrer, I.; Beere, H. E.; Ritchie, D. A.; Baumberg, J. J.

    2011-06-01

    We report strong coupling between Tamm plasmons and excitons in III-V quantum wells at room temperature in ultracompact sample designs. A high refractive index contrast air-gap mirror together with optical Tamm states at a metal/semiconductor interface tightly confines the intracavity field leading to substantial local field enhancements. Angular-resolved reflectivity spectra give clear evidence for anticrossing in the dispersion relation. Room temperature Rabi splittings of 10 meV are found in excellent agreement with simulations. Electrical control of the polariton modes is realized without need for doped mirror layers. Such air-gap microcavities open innovative possibilites for electrically tunable microcavities and polaritonic microelectromechanics.

  20. Meta-Optics with Nanowire Grid Arrays: Hyperbolic Fabry-Perot Modes and Hyperbolic Tamm Plasmons

    NASA Astrophysics Data System (ADS)

    Durach, Maxim; Keene, David; Lepain, Matthew

    2015-03-01

    In this talk we introduce a new class of structures - cavities formed by metal-dielectric metasurfaces. These cavities support a zoo of various resonances, including hyperbolic Tamm plasmons and hyperbolic Fabry-Perot modes, which feature anisotropic clover-leaf dispersion parallel to the metasurface and strong coupling between TM and TE polarizations in the modes. The properties and spectrum of the modes are highly tunable by the dimensional and material parameters of the structure and can be used for directional emission, modification of radiation produced by electric dipole emitters into magnetic dipole radiation as well as 90 degree polarization rotators and polarization rotation mirrors.

  1. Lasing effect enhanced by optical Tamm state with in-plane lattice plasmon

    NASA Astrophysics Data System (ADS)

    Zhang, Zhenqing; Li, Yunhui; Liu, Wenxing; Sun, Yong; Jiang, Haitao; Chen, Hong

    2016-02-01

    A new type of surface-emitting laser based on in-plane lattice plasmons (LPs) and optical Tamm states (OTSs) is proposed, with arrays of metallic micro-disks followed by a photonic crystal. Due to the presence of LP modes, the reflection properties of the combined LP-OTS structure, including the spectrum linewidth, Q-factor and electromagnetic field, can be optimized for better lasing behavior. When the combined LP-OTS structure with a gain medium is optically pumped, a much lower lasing threshold and higher emission intensity can be achieved simultaneously, compared with the individual LP structure. This phenomenon successfully demonstrates the enhancement of the lasing efficiency.

  2. Spectral engineering by flexible tunings of optical Tamm states and Fabry-Perot cavity resonance.

    PubMed

    Zhang, Xu-Lin; Song, Jun-Feng; Feng, Jing; Sun, Hong-Bo

    2013-11-01

    We present a design for spectral engineering in a metal dual distributed Bragg reflector (DBR)-based structure. Optical Tamm states and Fabry-Perot cavity mode, dual windows for light-matter interaction enhancement, can be excited simultaneously and tuned flexibly, including their respective bandwidth and resonant wavelength, due to the variable reflection phase from the outer DBR's internal surface. The design can find applications in solar cells for light trappings. Via calculations of overall absorptivity, the proposed simpler dual-states-based scheme is demonstrated to be almost as effective as the coherent-light-trapping scheme, owing to the dual-states-induced broader-band absorption enhancement. PMID:24177099

  3. Generalized q-deformed Tamm-Dancoff oscillator algebra and associated coherent states

    SciTech Connect

    Chung, Won Sang; Hounkonnou, Mahouton Norbert Arjika, Sama

    2014-08-15

    In this paper, we propose a full characterization of a generalized q-deformed Tamm-Dancoff oscillator algebra and investigate its main mathematical and physical properties. Specifically, we study its various representations and find the condition satisfied by the deformed q-number to define the algebra structure function. Particular Fock spaces involving finite and infinite dimensions are examined. A deformed calculus is performed as well as a coordinate realization for this algebra. A relevant example is exhibited. Associated coherent states are constructed. Finally, some thermodynamics aspects are computed and discussed.

  4. Spatial and Fourier-space distribution of confined optical Tamm modes

    NASA Astrophysics Data System (ADS)

    Feng, Fu; Daney de Marcillac, Willy; Lafosse, Xavier; Portalupi, Simone Luca; Nasilowski, Michel; Dubertret, Benoît; Frigerio, Jean-Marc; Schwob, Catherine; Maître, Agnès; Senellart, Pascale; Coolen, Laurent

    2016-08-01

    In this paper, we characterize the electric field distribution of confined optical modes in a 0D Tamm structure, consisting in a metallic disk deposited on a Bragg mirror. The modes are probed at room temperature, through the fluorescence of semiconductor colloidal nanocrystals. We perform a combined analysis of the resonant modes distribution in both direct space and Fourier space and show, in good agreement with numerical simulations, that a subportion of the structure will radiate with a different angular distribution depending on its position. Such analysis is shown to probe the gradient of the phase of the confined optical modes.

  5. Tamm plasmon-polariton with negative group velocity induced by a negative index meta-material capping layer at metal-Bragg reflector interface.

    PubMed

    Liu, Cunding; Kong, Mingdong; Li, Bincheng

    2014-05-01

    Influence of a negative refractive index meta-material (NIM) capping layer on properties of Tamm plasmon-polariton at the interface of metal-Bragg reflector structure is investigated. Conditions for excitation of the plasmon-polariton is determined from reflectivity mapping calculation and analyzed with cavity mode theory. For specific thicknesses of capping layers, Tamm plasmon-polariton with negative group velocity is revealed in a wide region of frequency. Different from backward optical propagation induced by negative effective-group-refractive-index in dispersive media, negative group velocity of Tamm plasmon-polariton results from opposite signs of cross-section-integrated field energy and Poynting vector. PMID:24921834

  6. Effect of metal film thickness on Tamm plasmon-coupled emission.

    PubMed

    Chen, Yikai; Zhang, Douguo; Zhu, Liangfu; Fu, Qiang; Wang, Ruxue; Wang, Pei; Ming, Hai; Badugu, Ramachandram; Lakowicz, Joseph R

    2014-12-14

    Tamm plasmons (TPs) are the result of trapping optical energy at the interface between a metal film and a one-dimensional photonic crystal. In contrast to surface plasmons, TPs display unique properties such as the ability to undergo direct optical excitation without the aid of prisms or gratings, being populated using both S- and P-polarized light, and importantly, they can be created with incident light normal to the surface. This latter property has recently been used to obtain Tamm plasmon-coupled emission (TPCE), which beams along a path directly perpendicular to the surface. In this paper the effects of metal film thickness on the TPCE are investigated using back focal plane (BFP) imaging and spectral resolutions. The observed experimental results are in agreement with the numerical simulations. The present work provides the basic understanding needed to design structures for TPCE, which in turn has potential applications in the fabrication of active materials for light emitting devices, fluorescence-based sensing, using microarrays, and imaging. PMID:25349013

  7. Transcutaneous analyte measuring method (TAMM): a reflective, noninvasive, near-infrared blood chemistry analyzer

    NASA Astrophysics Data System (ADS)

    Schlager, Kenneth J.; Ruchti, Timothy L.

    1995-04-01

    TAMM for Transcutaneous Analyte Measuring Method is a near infrared spectroscopic technique for the noninvasive measurement of human blood chemistry. A near infrared indium gallium arsenide (InGaAs) photodiode array spectrometer has been developed and tested on over 1,000 patients as a part of an SBIR program sponsored by the Naval Medical Research and Development Command. Nine (9) blood analytes have been measured and evaluated during pre-clinical testing: sodium, chloride, calcium, potassium, bicarbonate, BUN, glucose, hematocrit and hemoglobin. A reflective rather than a transmissive invasive approach to measurement has been taken to avoid variations resulting from skin color and sensor positioning. The current status of the instrumentation, neural network pattern recognition algorithms and test results will be discussed.

  8. Conical Intersections from Particle-Particle Random Phase and Tamm-Dancoff Approximations.

    PubMed

    Yang, Yang; Shen, Lin; Zhang, Du; Yang, Weitao

    2016-07-01

    The particle-particle random phase approximation (pp-RPA) and the particle-particle Tamm-Dancoff approximation (pp-TDA) are applied to the challenging conical intersection problem. Because they describe the ground and excited states on the same footing and naturally take into account the interstate interaction, these particle-particle methods, especially the pp-TDA, can correctly predict the dimensionality of the conical intersection seam as well as describe the potential energy surface in the vicinity of conical intersections. Though the bond length of conical intersections is slightly underestimated compared with the complete-active-space self-consistent field (CASSCF) theory, the efficient particle-particle methods are promising for conical intersections and nonadiabatic dynamics. PMID:27293013

  9. Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation

    SciTech Connect

    Kühn, Michael; Weigend, Florian

    2015-01-21

    We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy){sub 3} (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its “spin-forbidden” triplet-singlet transition.

  10. Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation

    NASA Astrophysics Data System (ADS)

    Kühn, Michael; Weigend, Florian

    2015-01-01

    We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy)3 (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its "spin-forbidden" triplet-singlet transition.

  11. Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation.

    PubMed

    Kühn, Michael; Weigend, Florian

    2015-01-21

    We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy)3 (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its "spin-forbidden" triplet-singlet transition. PMID:25612698

  12. Effects of freezing on the estimated amounts of Tamm--Horsfall glycoprotein in urine, as determined by radioimmunoassay.

    PubMed Central

    Goodall, A A; Marshall, R D

    1980-01-01

    Freeze-drying or freezing of salt-free solutions of human Tamm--Horsfall glycoprotein appeared to lead to changes in the structure of the latter, changes that increased its ability to bind with antibody raised, in rabbits, against it. This alteration in avidity of the glycoprotein was observed irrespective of whether antiserum was raised against freeze-dried or non-frozen antigen. The implications of this finding for the radioimmunoassay of the glycoprotein in urine samples were studied. Appropriate treatment for urine samples, before assay, was devised. The amount of Tamm--Horsfall glycoprotein excreted was shown to range from 30 to 138 mg in normal males and 43 to 126 mg in normal females per 24 h. PMID:7213344

  13. Cell-mediated Immunity to Human Tamm-Horsfall Glycoprotein in Autoimmune Liver Disease with Renal Tubular Acidosis

    PubMed Central

    Tsantoulas, D. C.; McFarlane, I. G.; Portmann, B.; Eddleston, A. L. W. F.; Williams, Roger

    1974-01-01

    Cell-mediated immune responses to Tamm-Horsfall glycoprotein isolated from human urine were investigated using the leucocyte migration test. Abnormal responses were found in 91% of patients with active chronic hepatitis or primary biliary cirrhosis with an associated renal tubular acidosis (R.T.A.) but in only 19% of those without R.T.A. In nearly all of a group of patients without autoimmune liver disease and in a control group of normal subjects results were within normal limits. In addition, using an immunofluorescent technique with rabbit antibody to human Tamm-Horsfall glycoprotein, it was possible to show the presence in human liver cell membrane of material reacting immunologically as Tamm-Horsfall. These findings suggest that the development of an immune response to this glycoprotein, initiated by release of cross-reacting antigens from damaged hepatocytes, could be the mechanism underlying the occurrence of R.T.A. in some patients with autoimmune liver disease. ImagesFIG. 3 PMID:4611578

  14. The optical Tamm states at the interface between a photonic crystal and a nanocomposite containing core–shell particles

    NASA Astrophysics Data System (ADS)

    Vetrov, S. Ya; Pankin, P. S.; Timofeev, I. V.

    2016-06-01

    We investigate the optical Tamm states (OTSs) localized at the interface between a photonic crystal (PC) and a nanocomposite consisting of spherical nanoparticles with a dielectric core and a metallic shell, which are dispersed in a transparent matrix, and is characterized by the resonance permittivity. Spectra of transmission, reflection, and absorption of normally incident light waves by the investigated structure are calculated. The spectral manifestation of the Tamm states caused by negative values of the real part of the effective permittivity in the visible spectral range is studied. It is demonstrated that, along with the significantly extended band gap of the PC, the transmission spectrum contains an additional stopband caused by nanocomposite absorption near the resonance frequency. It is shown that the OTSs can be implemented in two band gaps of the PCs, each corresponding to a certain plasmon resonance frequency of the nanocomposite. It is established that the characteristics of the Tamm state localized at the edge of the PCs significantly depend on the ratio between the particle core volume and the total particle volume.

  15. Tamm plasmon- and surface plasmon-coupled emission from hybrid plasmonic–photonic structures

    PubMed Central

    Chen, Yikai; Zhang, Douguo; Zhu, Liangfu; Wang, Ruxue; Wang, Pei; Ming, Hai; Badugu, Ramachandram; Lakowicz, Joseph R.

    2015-01-01

    Photonic and plasmon-coupled emissions present new opportunities for control on light emission from fluorophores, and have many applications in the physical and biological sciences. The mechanism of and the influencing factors for the coupling between the fluorescent molecules and plasmon and/or photonic modes are active areas of research. In this paper, we describe a hybrid photonic–plasmonic structure that simultaneously contains two plasmon modes: surface plasmons (SPs) and Tamm plasmons (TPs), both of which can modulate fluorescence emission. Experimental results show that both SP-coupled emission (SPCE) and TP-coupled emission (TPCE) can be observed simultaneously with this hybrid structure. Due to the different resonant angles of the TP and SP modes, the TPCE and SPCE can be beamed in different directions and can be separated easily. Back focal plane images of the fluorescence emission show that the relative intensities of the SPCE and TPCE can be changed if the probes are at different locations inside the hybrid structure, which reveals the probe location-dependent different coupling strengths of the fluorescent molecules with SPs and TPs. The different coupling strengths are ascribed to the electric field distribution of the two modes in the structure. Here, we present an understanding of these factors influencing mode coupling with probes, which is vital for structure design for suitable applications in sensing and diagnostics. PMID:26526929

  16. The interaction of Tamm-Horsfall protein with the extracellular matrix.

    PubMed Central

    Lambert, C; Brealey, R; Steele, J; Rook, G A

    1993-01-01

    Tamm-Horsfall protein (THP) is the major glycoprotein component of urine, yet its biological role remains obscure. Recent reports have suggested that a concanavalin A (Con A)-binding fraction of THP from pregnancy urine can bind the cytokines tumour necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1). In order to investigate this claim in relation to THP from normal adult urine we raised monoclonal antibodies to THP and sought THP/TNF-alpha interactions in three separate assay systems. We found no evidence that THP binds to TNF-alpha under physiological conditions, but we observed that it exerts a weak, probably not physiologically relevant, but reproducible inhibitory effect on the toxicity of TNF-alpha for monolayers of L929 cells, even when the cells are pretreated with the THP, and washed before addition of the cytokine. Since our preparations of THP do not interact directly with TNF-alpha we postulated an interaction with the cells themselves, or with their extracellular matrix. The THP was found by ELISA, immunoblotting and immunohistology, to bind to as yet unidentified components of the extracellular matrix in a manner dependent on cations, pH and carbohydrates. These data, considered in the light of the published amino acid sequence and biochemical properties, suggest that THP is a member of a structural glycoprotein family known to modulate cell adhesion. Images Figure 4 Figure 5 PMID:8344699

  17. Performance of Tamm-Dancoff approximation on nonadiabatic couplings by time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Hu, Chunping; Sugino, Osamu; Watanabe, Kazuyuki

    2014-02-01

    The Tamm-Dancoff approximation (TDA), widely used in physics to decouple excitations and de-excitations, is well known to be good for the calculation of excitation energies but not for oscillator strengths. In particular, the sum rule is violated in the latter case. The same concern arises within the TDA in the calculation of nonadiabatic couplings (NACs) by time-dependent density functional theory (TDDFT), due to the similarities in the TDDFT formulations of NACs and oscillator strengths [C. Hu, H. Hirai, and O. Sugino, J. Chem. Phys. 127, 064103 (2007)]. In this study, we present a systematic evaluation of the performance of TDDFT/TDA for the calculation of NACs. In the cases we considered, including a variety of systems possessing Jahn-Teller and Renner-Teller intersections, as well as an example with accidental conical intersections, it is found that the TDDFT/TDA performs better than the full TDDFT, contrary to the conjecture that the TDA might cause the NAC results to deteriorate and violate the sum rule. The surprisingly good performance of the TDA for NACs is probably because the TDA can partially compensate for the local-density-approximation error and give better excitation energies in the vicinity of intersections of potential energy surfaces. Our study also shows that it is important to use the TDA based on the rigorous full-TDDFT formulation of NACs, instead of using it based on an alternative approximate formulation.

  18. Molecular properties in the Tamm-Dancoff approximation: indirect nuclear spin-spin coupling constants

    NASA Astrophysics Data System (ADS)

    Cheng, Chi Y.; Ryley, Matthew S.; Peach, Michael J. G.; Tozer, David J.; Helgaker, Trygve; Teale, Andrew M.

    2015-07-01

    The Tamm-Dancoff approximation (TDA) can be applied to the computation of excitation energies using time-dependent Hartree-Fock (TD-HF) and time-dependent density-functional theory (TD-DFT). In addition to simplifying the resulting response equations, the TDA has been shown to significantly improve the calculation of triplet excitation energies in these theories, largely overcoming issues associated with triplet instabilities of the underlying reference wave functions. Here, we examine the application of the TDA to the calculation of another response property involving triplet perturbations, namely the indirect nuclear spin-spin coupling constant. Particular attention is paid to the accuracy of the triplet spin-dipole and Fermi-contact components. The application of the TDA in HF calculations leads to vastly improved results. For DFT calculations, the TDA delivers improved stability with respect to geometrical variations but does not deliver higher accuracy close to equilibrium geometries. These observations are rationalised in terms of the ground- and excited-state potential energy surfaces and, in particular, the severity of the triplet instabilities associated with each method. A notable feature of the DFT results within the TDA is their similarity across a wide range of different functionals. The uniformity of the TDA results suggests that some conventional evaluations may exploit error cancellations between approximations in the functional forms and those arising from triplet instabilities. The importance of an accurate treatment of correlation for evaluating spin-spin coupling constants is highlighted by this comparison.

  19. Restricted second random phase approximations and Tamm-Dancoff approximations for electronic excitation energy calculations

    SciTech Connect

    Peng, Degao; Yang, Yang; Zhang, Peng; Yang, Weitao

    2014-12-07

    In this article, we develop systematically second random phase approximations (RPA) and Tamm-Dancoff approximations (TDA) of particle-hole and particle-particle channels for calculating molecular excitation energies. The second particle-hole RPA/TDA can capture double excitations missed by the particle-hole RPA/TDA and time-dependent density-functional theory (TDDFT), while the second particle-particle RPA/TDA recovers non-highest-occupied-molecular-orbital excitations missed by the particle-particle RPA/TDA. With proper orbital restrictions, these restricted second RPAs and TDAs have a formal scaling of only O(N{sup 4}). The restricted versions of second RPAs and TDAs are tested with various small molecules to show some positive results. Data suggest that the restricted second particle-hole TDA (r2ph-TDA) has the best overall performance with a correlation coefficient similar to TDDFT, but with a larger negative bias. The negative bias of the r2ph-TDA may be induced by the unaccounted ground state correlation energy to be investigated further. Overall, the r2ph-TDA is recommended to study systems with both single and some low-lying double excitations with a moderate accuracy. Some expressions on excited state property evaluations, such as 〈S{sup ^2}〉 are also developed and tested.

  20. Beyond the Tamm-Dancoff approximation for extended systems using exact diagonalization

    NASA Astrophysics Data System (ADS)

    Sander, Tobias; Maggio, Emanuele; Kresse, Georg

    2015-07-01

    Linear optical properties can be accurately calculated using the Bethe-Salpeter equation. After introducing a suitable product basis for the electron-hole pairs, the Bethe-Salpeter equation is usually recast into a complex non-Hermitian eigenvalue problem that is difficult to solve using standard eigenvalue solvers. In solid-state physics, it is therefore common practice to neglect the problematic coupling between the positive- and negative-frequency branches, reducing the problem to a Hermitian eigenvalue problem [Tamm-Dancoff approximation (TDA)]. We use time-inversion symmetry to recast the full problem into a quadratic Hermitian eigenvalue problem, which can be solved routinely using standard eigenvalue solvers even at a finite wave vector q . This allows us to access the importance of the coupling between the positive- and negative-frequency branch for prototypical solids. As a starting point for the Bethe-Salpeter calculations, we use self-consistent Green's-function methods (GW ), making the present scheme entirely ab initio. We calculate the optical spectra of carbon (C), silicon (Si), lithium fluoride (LiF), and the cyclic dimer Li2F2 and discuss why the differences between the TDA and the full solution are tiny. However, at finite momentum transfer q , significant differences between the TDA and our exact treatment are found. The origin of these differences is explained.

  1. Restricted second random phase approximations and Tamm-Dancoff approximations for electronic excitation energy calculations

    NASA Astrophysics Data System (ADS)

    Peng, Degao; Yang, Yang; Zhang, Peng; Yang, Weitao

    2014-12-01

    In this article, we develop systematically second random phase approximations (RPA) and Tamm-Dancoff approximations (TDA) of particle-hole and particle-particle channels for calculating molecular excitation energies. The second particle-hole RPA/TDA can capture double excitations missed by the particle-hole RPA/TDA and time-dependent density-functional theory (TDDFT), while the second particle-particle RPA/TDA recovers non-highest-occupied-molecular-orbital excitations missed by the particle-particle RPA/TDA. With proper orbital restrictions, these restricted second RPAs and TDAs have a formal scaling of only O(N4). The restricted versions of second RPAs and TDAs are tested with various small molecules to show some positive results. Data suggest that the restricted second particle-hole TDA (r2ph-TDA) has the best overall performance with a correlation coefficient similar to TDDFT, but with a larger negative bias. The negative bias of the r2ph-TDA may be induced by the unaccounted ground state correlation energy to be investigated further. Overall, the r2ph-TDA is recommended to study systems with both single and some low-lying double excitations with a moderate accuracy. Some expressions on excited state property evaluations, such as < hat{S}2rangle are also developed and tested.

  2. Carotenoids and light-harvesting: from DFT/MRCI to the Tamm-Dancoff approximation.

    PubMed

    Andreussi, Oliviero; Knecht, Stefan; Marian, Christel M; Kongsted, Jacob; Mennucci, Benedetta

    2015-02-10

    Carotenoids are known to play a fundamental role in photosynthetic light-harvesting (LH) complexes; however, an accurate quantum-mechanical description of that is still missing. This is due to the multideterminant nature of the involved electronic states combined with an extended conjugation which limits the applicability of many of the most advanced approaches. In this study, we apply a multireference configuration interaction extension of density functional theory (DFT/MRCI) to describe transition energies and densities as well as the corresponding excitonic couplings, for the three lowest singlet excited states of nine carotenoids present in three different LH complexes of algae and plants. These benchmark results are used to find an approximated computational approach, which could be used to quantitatively reproduce the key quantities at a reduced computational cost. To this end, we tested the Tamm-Dancoff approximation (TDA) to time-dependent density functional theory in combination with different functionals. By analyzing the errors with respect to DFT/MRCI-TDA results for the full set of electronic properties, we conclude that TDA-TPSS with small basis sets indeed represents an effective approach to investigate LH processes that involve carotenoids. PMID:26579601

  3. Tamm-plasmon and surface-plasmon hybrid-mode based refractometry in photonic bandgap structures.

    PubMed

    Das, Ritwick; Srivastava, Triranjita; Jha, Rajan

    2014-02-15

    The transverse magnetic (TM) polarized hybrid modes formed as a consequence of coupling between Tamm plasmon polariton (TM-TPP) mode and surface plasmon polariton (SPP) mode exhibit interesting dispersive features for realizing a highly sensitive and accurate surface plasmon resonance (SPR) sensor. We found that the TM-TPP modes, formed at the interface of distributed Bragg reflector and metal, are strongly dispersive as compared to SPP modes at optical frequencies. This causes an appreciably narrow interaction bandwidth between TM-TPP and SPP modes, which leads to highly accurate sensing. In addition, appropriate tailoring of dispersion characteristics of TM-TPP as well as SPP modes could ensure high sensitivity of a novel SPR platform. By suitably designing the Au/TiO₂/SiO₂-based geometry, we propose a TM-TPP/SPP hybrid-mode sensor and achieve a sensitivity ≥900  nm/RIU with high detection accuracy (≥30  μm⁻¹) for analyte refractive indices varying between 1.330 and 1.345 in 600-700 nm wavelength range. The possibility to achieve desired dispersive behavior in any spectral band makes the sensing configuration an extremely attractive candidate to design sensors depending on the availability of optical sources. PMID:24562235

  4. Restricted second random phase approximations and Tamm-Dancoff approximations for electronic excitation energy calculations.

    PubMed

    Peng, Degao; Yang, Yang; Zhang, Peng; Yang, Weitao

    2014-12-01

    In this article, we develop systematically second random phase approximations (RPA) and Tamm-Dancoff approximations (TDA) of particle-hole and particle-particle channels for calculating molecular excitation energies. The second particle-hole RPA/TDA can capture double excitations missed by the particle-hole RPA/TDA and time-dependent density-functional theory (TDDFT), while the second particle-particle RPA/TDA recovers non-highest-occupied-molecular-orbital excitations missed by the particle-particle RPA/TDA. With proper orbital restrictions, these restricted second RPAs and TDAs have a formal scaling of only O(N(4)). The restricted versions of second RPAs and TDAs are tested with various small molecules to show some positive results. Data suggest that the restricted second particle-hole TDA (r2ph-TDA) has the best overall performance with a correlation coefficient similar to TDDFT, but with a larger negative bias. The negative bias of the r2ph-TDA may be induced by the unaccounted ground state correlation energy to be investigated further. Overall, the r2ph-TDA is recommended to study systems with both single and some low-lying double excitations with a moderate accuracy. Some expressions on excited state property evaluations, such as ⟨Ŝ(2)⟩ are also developed and tested. PMID:25481124

  5. An evaluation of Tamm-Horsfall protein glycans in kidney stone formers using novel techniques.

    PubMed

    Argade, Sulabha; Chen, Tony; Shaw, Timothy; Berecz, Zoltan; Shi, William; Choudhury, Biswa; Parsons, C Lowell; Sur, Roger L

    2015-08-01

    Tamm-Horsfall protein (THP) is theorized to play a critical role in preventing kidney stone formation. There is conflicting literature on THP analysis in kidney stone patients; therefore, this study was conducted using sensitive and specific bio-analytical techniques to better understand differences in THP, which play a potential role in nephrolithiasis pathogenesis. THP was isolated from urine samples of 34 male and 19 female kidney stone patients and 30 male and 24 female control subjects using diatomaceous earth. Protein was quantified by Superdex-200 size-exclusion chromatography. Sialic acid was determined by 1,2-diamino-4,5-methylenedioxybenzene high-performance liquid chromatography. Neutral and amino sugars were determined by high pH anion-exchange chromatography (HPAEC) with pulsed amperometric detection. THP N-glycans were derivatized with 2-aminobenzamide (2-AB) and profiled by HPAEC with fluorescence detection. N-glycan structures were confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Results indicate that kidney stone patients had 32% lower protein content compared to controls, while sialic acid content was lower by 29 and 24% in male and female kidney stone patients, respectively, compared to controls. The neutral and amino sugars were also lower by 18 and 20% for male and female kidney stone patients, respectively, compared to controls. All results were statistically significant (p<0.001). These results are supported by 2-AB profiling of THP N-glycans and by MALDI-TOF MS of highly sialylated N-glycans in the range of m/z 3000-6000. This study demonstrates quantitative and qualitative differences in THP, which can be crucial contributing factors for nephrolithiasis. PMID:25935139

  6. Numerical investigation of optical Tamm states in two-dimensional hybrid plasmonic-photonic crystal nanobeams

    SciTech Connect

    Meng, Zi-Ming E-mail: lizy@aphy.iphy.ac.cn; Hu, Yi-Hua; Ju, Gui-Fang; Zhong, Xiao-Lan; Ding, Wei; Li, Zhi-Yuan E-mail: lizy@aphy.iphy.ac.cn

    2014-07-28

    Optical Tamm states (OTSs) in analogy with its electronic counterpart confined at the surface of crystals are optical surface modes at the interfaces between uniform metallic films and distributed Bragg reflectors. In this paper, OTSs are numerically investigated in two-dimensional hybrid plasmonic-photonic crystal nanobeams (HPPCN), which are constructed by inserting a metallic nanoparticle into a photonic crystal nanobeam formed by periodically etching square air holes into dielectric waveguides. The evidences of OTSs can be verified by transmission spectra and the field distribution at resonant frequency. Similar to OTSs in one-dimensional multilayer structures OTSs in HPPCN can be excited by both TE and TM polarization. The physical origin of OTSs in HPPCN is due to the combined contribution of strong reflection imposed by the photonic band gap (PBG) of the photonic crystal (PC) nanobeam and strong backward scattering exerted by the nanoparticle. For TE, incidence OTSs can be obtained at the frequency near the center of the photonic band gap. The transmissivity and the resonant frequency can be finely tuned by the dimension of nanoparticles. While for TM incidence OTSs are observed for relatively larger metallic nanoparticles compared with TE polarization. The differences between TE and TM polarization can be explained by two reasons. For one reason stronger backward scattering of nanoparticles for TE polarization can be achieved by the excitation of localized surface plasmon polariton of nanoparticles. This assumption has been proved by examining the scattering, absorption, and extinction cross section of the metallic nanoparticle. The other can be attributed to the deep and wide PBG available for TE polarization with less number of air holes compared with TM polarization. Our results show great promise in extending the application scope of OTSs from one-dimensional structures to practical integrated photonic devices and circuits.

  7. Tunneling time in attosecond experiments, intrinsic-type of time. Keldysh, and Mandelstam–Tamm time

    NASA Astrophysics Data System (ADS)

    Kullie, Ossama

    2016-05-01

    Tunneling time in attosecond and strong-field experiments is one of the most controversial issues in current research, because of its importance to the theory of time, the time operator and the time–energy uncertainty relation in quantum mechanics. In Kullie (2015 Phys. Rev. A 92 052118) we derived an estimation of the (real) tunneling time, which shows an excellent agreement with the time measured in attosecond experiments, our derivation is found by utilizing the time–energy uncertainty relation, and it represents a quantum clock. In this work, we show different aspects of the tunneling time in attosecond experiments, we discuss and compare the different views and approaches, which are used to calculate the tunneling time, i.e. Keldysh time (as a real or imaginary quantity), Mandelstam–Tamm time, the classical view of the time measurement and our tunneling time relation(s). We draw some conclusions concerning the validity and the relation between the different types of the tunneling time with the hope that they will help to answer the question put forward by Orlando et al (2014 J. Phys. B 47 204002, 2014 Phys. Rev. A 89 014102): tunneling time, what does it mean? However, as we will see, the important question is a more general one: how to understand the time and the measurement of the time of a quantum system? In respect to our result, the time in quantum mechanics can be, in more general fashion, classified in two types, intrinsic dynamically connected, and external dynamically not connected to the system, and consequently (perhaps only) classical Newtonian time remains as a parametric type of time.

  8. Some factors affecting the production, by cultured baby-hamster kidney cells, of BHK glycoprotein I which cross-reacts immunologically with Tamm-Horsfall glycoprotein.

    PubMed Central

    Bloomfield, F J; Dunstan, D R; Foster, C L; Serafini-Cessi, F; Marshall, R D

    1977-01-01

    Cultured baby-hamster kidney cells (BHK-21/C13), which are adapted to grow in suspension (strain 2P), roduce a glycoprotein, termed BHK glycoprotein I, which cross-reacts immunologically with hamster urinary (Tamm-Horsfall glycoprotein. BHK glycoprotein I was isolated in an electrophoretically (sodium dodecyl sulphate/polyacrylamide gel) homogeneous form by application of affinity chromatography to the medium in which cells had been cultured. Insolubilized anti-(Tamm-Horsfall glycoprotein immunoglobulin G) was used as the adsorbent. The amount of BHK glycoprotein I associated with the cultured cells was found by both radioimmunoassay and immunofluorescence to be related to the amount of Ca2+ in the medium and to the particular stage of the cell cycle. 5'-Nucleotidase was also shed by the cells into the culture medium in amounts related to the stage of the cell cycle. The turnover of hamster Tamm-Horsfall glycoprotein in vivo appeared to be considerably more rapid than can be accounted for by cell turnover. Hamster Tamm-Horsfall glycoprotein was shown to be ineffective in inhibiting agglutination of chicken erythrocytes caused by influenza virus. Images PLATE 1 PLATE 2 PLATE 3 PLATE 4 PMID:328011

  9. Analytical Hessian of electronic excited states in time-dependent density functional theory with Tamm-Dancoff approximation.

    PubMed

    Liu, Jie; Liang, WanZhen

    2011-07-01

    We present the analytical expression and computer implementation for the second-order energy derivatives of the electronic excited state with respect to the nuclear coordinates in the time-dependent density functional theory (TDDFT) with Gaussian atomic orbital basis sets. Here, the Tamm-Dancoff approximation to the full TDDFT is adopted, and therefore the formulation process of TDDFT excited-state Hessian is similar to that of configuration interaction singles (CIS) Hessian. However, due to the replacement of the Hartree-Fock exchange integrals in CIS with the exchange-correlation kernels in TDDFT, many quantitative changes in the derived equations are arisen. The replacement also causes additional technical difficulties associated with the calculation of a large number of multiple-order functional derivatives with respect to the density variables and the nuclear coordinates. Numerical tests on a set of test molecules are performed. The simulated excited-state vibrational frequencies by the analytical Hessian approach are compared with those computed by CIS and the finite-difference method. It is found that the analytical Hessian method is superior to the finite-difference method in terms of the computational accuracy and efficiency. The numerical differentiation can be difficult due to root flipping for excited states that are close in energy. TDDFT yields more exact excited-state vibrational frequencies than CIS, which usually overestimates the values. PMID:21744894

  10. Estimation of a 2p2h effect on Gamow-Teller transitions within the second Tamm-Dancoff approximation

    NASA Astrophysics Data System (ADS)

    Minato, F.

    2016-04-01

    Two-particle two-hole (2p2h) effect on the Gamow-Teller (GT) transition for neutron-rich nuclei is studied by the second Tamm-Dancoff approximation (STDA) with the Skyrme interaction. Unstable 24O and 34Si and stable 48Ca nuclei are chosen to study the quenching and fragmentation of the GT strengths. Correlation of the 2p2h configurations causes about 20 % quenching and downward shift of GT giant resonances (GTGRs). The residual interaction changing relative angular momentum that appeared in the tensor force part gives a meaningful effect to the GT strength distributions. In this work, 17 - 26 % of the total GT strengths are brought to high-energy region above GTGRs. In particular, the tensor force brings strengths to high energy more than 50 MeV. STDA calculation within a small model space for 2p2h configuration is also performed and experimental data of 48Ca is reproduced reasonably.

  11. Direct determination of exciton couplings from subsystem time-dependent density-functional theory within the Tamm-Dancoff approximation

    NASA Astrophysics Data System (ADS)

    König, Carolin; Schlüter, Nicolas; Neugebauer, Johannes

    2013-01-01

    In subsystem time-dependent density functional theory (TDDFT) [J. Neugebauer, J. Chem. Phys. 126, 134116 (2007), 10.1063/1.2713754] localized excitations are used to calculate delocalized excitations in large chromophore aggregates. We have extended this formalism to allow for the Tamm-Dancoff approximation (TDA). The resulting response equations have a form similar to a perturbative configuration interaction singles (CIS) approach. Thus, the inter-subsystem matrix elements in subsystem TDA can, in contrast to the full subsystem-TDDFT case, directly be interpreted as exciton coupling matrix elements. Here, we present the underlying theory of subsystem TDDFT within the TDA as well as first applications. Since for some classes of pigments, such as linear polyenes and carotenoids, TDA has been reported to perform better than full TDDFT, we also report applications of this formalism to exciton couplings in dimers of such pigments and in mixed bacteriochlorophyll-carotenoid systems. The improved description of the exciton couplings can be traced back to a more balanced description of the involved local excitations.

  12. Going beyond the Tamm-Dancoff approximation in the Bethe-Salpeter approach to the optical properties of solids

    NASA Astrophysics Data System (ADS)

    Puschnig, Peter; Ambrosch-Draxl, Claudia

    2007-03-01

    The solution of the Bethe-Salpeter equation (BSE) has turned out to be the method of choice for the ab-initio calculation of optical properties of semiconductors and insulators which is capable of correctly accounting for excitonic effects. Commonly, however, the coupling between the resonant and anti-resonant excitations is neglected, referred to as the Tamm-Dancoff approximation (TDA). This is well justified in many cases, in particular, for the working horses of theoretical solid state physics, such as bulk Si and GaAs. Here, we report on a first-principles investigation of the optical properties of organic semiconductors which are highly anisotropic systems. We find that the TDA no longer holds in such low-dimensional systems, where the exciton binding energies are no longer small compared to the band gaps. Going beyond the TDA leads to an increase of the exciton binding energy in the order of several tenths of an eV thereby considerably improving the agreement with experiment.

  13. Tamm-Horsfall glycoprotein interacts with renal outer medullary potassium channel ROMK2 and regulates its function.

    PubMed

    Renigunta, Aparna; Renigunta, Vijay; Saritas, Turgay; Decher, Niels; Mutig, Kerim; Waldegger, Siegfried

    2011-01-21

    Tamm-Horsfall glycoprotein (THGP) or Uromodulin is a membrane protein exclusively expressed along the thick ascending limb (TAL) and early distal convoluted tubule (DCT) of the nephron. Mutations in the THGP encoding gene result in Familial Juvenile Hyperuricemic Nephropathy (FJHN), Medullary Cystic Kidney Disease type 2 (MCKD-2), and Glomerulocystic Kidney Disease (GCKD). The physicochemical and biological properties of THGP have been studied extensively, but its physiological function in the TAL remains obscure. We performed yeast two-hybrid screening employing a human kidney cDNA library and identified THGP as a potential interaction partner of the renal outer medullary potassium channel (ROMK2), a key player in the process of salt reabsorption along the TAL. Functional analysis by electrophysiological techniques in Xenopus oocytes showed a strong increase in ROMK current amplitudes when co-expressed with THGP. The effect of THGP was specific for ROMK2 and did not influence current amplitudes upon co-expression with Kir2.x, inward rectifier potassium channels related to ROMK. Single channel conductance and open probability of ROMK2 were not altered by co-expression of THGP, which instead increased surface expression of ROMK2 as determined by patch clamp analysis and luminometric surface quantification, respectively. Despite preserved interaction with ROMK2, disease-causing THGP mutants failed to increase its current amplitude and surface expression. THGP(-/-) mice exhibited increased ROMK accumulation in intracellular vesicular compartments when compared with WT animals. Therefore, THGP modulation of ROMK function confers a new role of THGP on renal ion transport and may contribute to salt wasting observed in FJHN/MCKD-2/GCKD patients. PMID:21081491

  14. Electronic circular dichroism of highly conjugated π-systems: breakdown of the Tamm-Dancoff/configuration interaction singles approximation.

    PubMed

    Bannwarth, Christoph; Grimme, Stefan

    2015-04-16

    We show that the electronic circular dichroism (ECD) of delocalized π-systems represents a worst-case scenario for Tamm-Dancoff approximated (TDA) linear response methods. We mainly consider density functional theory (TDA-DFT) variants together with range-separated hybrids, but the conclusions also apply for other functionals as well as the configuration interaction singles (CIS) approaches. We study the effect of the TDA for the computation of ECD spectra in some prototypical extended π-systems. The C76 fullerene, a chiral carbon nanotube fragment, and [11]helicene serve as model systems for inherently chiral, π-chromophores. Solving the full linear response problem is inevitable in order to obtain accurate ECD spectra for these systems. For the C76 fullerene and the nanotube fragment, TDA and CIS approximated methods yield spectra in the origin-independent velocity gauge formalism of incorrect sign which would lead to the assignment of the opposite (wrong) absolute configuration. As a counterexample, we study the ECD of an α-helix polypeptide chain. Here, the lowest-energy transitions are dominated by localized excitations within the individual peptide units, and TDA methods perform satisfactorily. The results may have far-reaching implications for simple semiempirical methods which often employ TDA and CIS for huge molecules. Our recently presented simplified time-dependent DFT approach proves to be an excellent low-cost linear response method which together with range-separated density functionals like ωB97X-D3 produces ECD spectra in very good agreement with experiment. PMID:25798823

  15. A simplified Tamm-Dancoff density functional approach for the electronic excitation spectra of very large molecules

    NASA Astrophysics Data System (ADS)

    Grimme, Stefan

    2013-06-01

    Two approximations in the Tamm-Dancoff density functional theory approach (TDA-DFT) to electronically excited states are proposed which allow routine computations for electronic ultraviolet (UV)- or circular dichroism (CD) spectra of molecules with 500-1000 atoms. Speed-ups compared to conventional time-dependent DFT (TD-DFT) treatments of about two to three orders of magnitude in the excited state part at only minor loss of accuracy are obtained. The method termed sTDA ("s" for simplified) employs atom-centered Löwdin-monopole based two-electron repulsion integrals with the asymptotically correct 1/R behavior and perturbative single excitation configuration selection. It is formulated generally for any standard global hybrid density functional with given Fock-exchange mixing parameter ax. The method performs well for two standard benchmark sets of vertical singlet-singlet excitations for values of ax in the range 0.2-0.6. The mean absolute deviations from reference data are only 0.2-0.3 eV and similar to those from standard TD-DFT. In three cases (two dyes and one polypeptide), good mutual agreement between the electronic spectra (up to 10-11 eV excitation energy) from the sTDA method and those from TD(A)-DFT is obtained. The computed UV- and CD-spectra of a few typical systems (e.g., C60, two transition metal complexes, [7]helicene, polyalanine, a supramolecular aggregate with 483 atoms and about 7000 basis functions) compare well with corresponding experimental data. The method is proposed together with medium-sized double- or triple-zeta type atomic-orbital basis sets as a quantum chemical tool to investigate the spectra of huge molecular systems at a reliable DFT level.

  16. The acid-base buffer capacity of podzolic soils and its changes under the impact of treatment with the Mehra-Jackson and Tamm reagents

    NASA Astrophysics Data System (ADS)

    Maksimova, Yu. G.; Maryakhina, N. N.; Tolpeshta, I. I.; Sokolova, T. A.

    2010-10-01

    The acid-base buffer capacity before and after the treatment with the Mehra-Jackson and Tamm reagents was assessed by continuous potentiometric titration for the main genetic horizons of two profiles of podzolic soils in the Central Forest State Reserve. The total buffer capacity was calculated in the pH range from the initial titration point (ITP) to 3 for the acid titration and from the ITP to 10 for the base titration, as well as the buffer capacities in the pH intervals of 0.25. It was found that both treatments abruptly decreased the base buffer capacity, which reached 70-90% in the E horizons. The high direct linear correlation of the difference between the total base buffer capacities before and after each treatment with the content of Fe in the Tamm extract was revealed. From the results obtained, a conclusion was drawn that finely dispersed Fe hydroxides were the main solid-phase constituents ensuring the base buffer capacity, and the deprotonation of hydroxyl groups on the surface of Fe hydroxides was the essential buffer reaction during the base titration.

  17. Configuration Interaction-Corrected Tamm-Dancoff Approximation: A Time-Dependent Density Functional Method with the Correct Dimensionality of Conical Intersections.

    PubMed

    Li, Shaohong L; Marenich, Aleksandr V; Xu, Xuefei; Truhlar, Donald G

    2014-01-16

    Linear response (LR) Kohn-Sham (KS) time-dependent density functional theory (TDDFT), or KS-LR, has been widely used to study electronically excited states of molecules and is the method of choice for large and complex systems. The Tamm-Dancoff approximation to TDDFT (TDDFT-TDA or KS-TDA) gives results similar to KS-LR and alleviates the instability problem of TDDFT near state intersections. However, KS-LR and KS-TDA share a debilitating feature; conical intersections of the reference state and a response state occur in F - 1 instead of the correct F - 2 dimensions, where F is the number of internal degrees of freedom. Here, we propose a new method, named the configuration interaction-corrected Tamm-Dancoff approximation (CIC-TDA), that eliminates this problem. It calculates the coupling between the reference state and an intersecting response state by interpreting the KS reference-state Slater determinant and linear response as if they were wave functions. Both formal analysis and test results show that CIC-TDA gives similar results to KS-TDA far from a conical intersection, but the intersection occurs with the correct dimensionality. We anticipate that this will allow more realistic application of TDDFT to photochemistry. PMID:26270707

  18. Exploring the nature of low-lying excited-states in molecular crystals from many-body perturbation theory beyond the Tamm-Dancoff Approximation

    NASA Astrophysics Data System (ADS)

    Rangel, Tonatiuh; Sharifzadeh, Sahar; Rinn, Andre; da Jornada, Felipe H.; Shao, Meiyue; Witte, Gregor; Yang, Chao; Louie, Steven G.; Chatterjee, Sangaam; Kronik, Leeor; Neaton, Jeffrey B.

    Organic semiconductors have attracted attention due to their potential for optoelectronics and novel phenomena, such as singlet fission. Here, we use many-body perturbation theory to simulate neutral excitations in acene and perylene crystals. By diagonalizing the full Bethe-Salpether (BSE) Hamiltonian beyond the Tamm Dancoff approximation (TDA), we find that both low-lying excitation energies and oscillator strengths are in improved agreement with experiments relative to the TDA. We characterize the low-lying excitons, focusing in the degree of charge-transfer and spatial delocalization, connecting their relevance to singlet fission. For perylene, we find overall good agreement with absorption measurements, and we see evidence for the formation of an ``exciton-polariton'' band in β-perylene. This work is supported by the DOE.

  19. Enhanced single photon emission from positioned InP/GaInP quantum dots coupled to a confined Tamm-plasmon mode

    SciTech Connect

    Braun, T.; Baumann, V.; Iff, O.; Schneider, C.; Kamp, M.; Höfling, S.

    2015-01-26

    We report on the enhancement of the spontaneous emission in the visible red spectral range from site-controlled InP/GaInP quantum dots by resonant coupling to Tamm-plasmon modes confined beneath gold disks in a hybrid metal/semiconductor structure. The enhancement of the emission intensity is confirmed by spatially resolved micro-photoluminescence area scans and temperature dependent measurements. Single photon emission from our coupled system is verified via second order autocorrelation measurements. We observe bright single quantum dot emission of up to ∼173 000 detected photons per second at a repetition rate of the excitation source of 82 MHz, and calculate an extraction efficiency of our device as high as 7%.

  20. Al, Fe, and Si compounds in Tamm and Mehra-Jackson extracts from mucky-peaty-podzolic gley soil: Contents, reserves, and profile and particle-size distributions

    NASA Astrophysics Data System (ADS)

    Sokolova, T. A.; Tolpeshta, I. I.; Maksimova, Yu. G.

    2014-05-01

    Equal or comparable contents of Fe and Al extractable by Tamm and Mehra-Jackson solutions have been revealed in all the horizons of a loamy mucky-peaty-podzolic gley soil on binary deposits. The content of Si extractable by the Mehra-Jackson solution has exceeded that of oxalate-soluble Si by an order of magnitude. The distributions of Al in the Tamm solutions from the entire soil and its fractions of 1-5 and >5 μm are of accumulative type with a maximum in the mucky H horizon and a gradual decrease of the content with depth in relation with the analogous distribution of Al-organic complexes. The maximum content of oxalate-soluble Al in the clay fraction has been found in the eluvial ELg horizon, which can be due to the partial dissolution of Al hydroxide interlayers in soil chlorites. The distribution of Fe in the entire soil has two maximums, in the H horizon due to the accumulation of Fe-organic complexes and in the concretion-rich ELnn,g horizon due to the accumulation of Fe hydroxides. Depletion of oxalate-soluble Fe in the eluvial ELg horizon has been observed in all the fractions, which can be related to its mobilization and removal under strongly acidic conditions and the development of reductive processes, as well as the enrichment of the concretion-rich horizon with these compounds because of an increase in pH and the development of conditions favorable for water stagnation and Fe segregation.

  1. Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB).

    PubMed

    Grimme, Stefan; Bannwarth, Christoph

    2016-08-01

    The computational bottleneck of the extremely fast simplified Tamm-Dancoff approximated (sTDA) time-dependent density functional theory procedure [S. Grimme, J. Chem. Phys. 138, 244104 (2013)] for the computation of electronic spectra for large systems is the determination of the ground state Kohn-Sham orbitals and eigenvalues. This limits such treatments to single structures with a few hundred atoms and hence, e.g., sampling along molecular dynamics trajectories for flexible systems or the calculation of chromophore aggregates is often not possible. The aim of this work is to solve this problem by a specifically designed semi-empirical tight binding (TB) procedure similar to the well established self-consistent-charge density functional TB scheme. The new special purpose method provides orbitals and orbital energies of hybrid density functional character for a subsequent and basically unmodified sTDA procedure. Compared to many previous semi-empirical excited state methods, an advantage of the ansatz is that a general eigenvalue problem in a non-orthogonal, extended atomic orbital basis is solved and therefore correct occupied/virtual orbital energy splittings as well as Rydberg levels are obtained. A key idea for the success of the new model is that the determination of atomic charges (describing an effective electron-electron interaction) and the one-particle spectrum is decoupled and treated by two differently parametrized Hamiltonians/basis sets. The three-diagonalization-step composite procedure can routinely compute broad range electronic spectra (0-8 eV) within minutes of computation time for systems composed of 500-1000 atoms with an accuracy typical of standard time-dependent density functional theory (0.3-0.5 eV average error). An easily extendable parametrization based on coupled-cluster and density functional computed reference data for the elements H-Zn including transition metals is described. The accuracy of the method termed sTDA-xTB is first

  2. Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB)

    NASA Astrophysics Data System (ADS)

    Grimme, Stefan; Bannwarth, Christoph

    2016-08-01

    The computational bottleneck of the extremely fast simplified Tamm-Dancoff approximated (sTDA) time-dependent density functional theory procedure [S. Grimme, J. Chem. Phys. 138, 244104 (2013)] for the computation of electronic spectra for large systems is the determination of the ground state Kohn-Sham orbitals and eigenvalues. This limits such treatments to single structures with a few hundred atoms and hence, e.g., sampling along molecular dynamics trajectories for flexible systems or the calculation of chromophore aggregates is often not possible. The aim of this work is to solve this problem by a specifically designed semi-empirical tight binding (TB) procedure similar to the well established self-consistent-charge density functional TB scheme. The new special purpose method provides orbitals and orbital energies of hybrid density functional character for a subsequent and basically unmodified sTDA procedure. Compared to many previous semi-empirical excited state methods, an advantage of the ansatz is that a general eigenvalue problem in a non-orthogonal, extended atomic orbital basis is solved and therefore correct occupied/virtual orbital energy splittings as well as Rydberg levels are obtained. A key idea for the success of the new model is that the determination of atomic charges (describing an effective electron-electron interaction) and the one-particle spectrum is decoupled and treated by two differently parametrized Hamiltonians/basis sets. The three-diagonalization-step composite procedure can routinely compute broad range electronic spectra (0-8 eV) within minutes of computation time for systems composed of 500-1000 atoms with an accuracy typical of standard time-dependent density functional theory (0.3-0.5 eV average error). An easily extendable parametrization based on coupled-cluster and density functional computed reference data for the elements H-Zn including transition metals is described. The accuracy of the method termed sTDA-xTB is first

  3. Tamm-Horsfall Protein Regulates Circulating and Renal Cytokines by Affecting Glomerular Filtration Rate and Acting as a Urinary Cytokine Trap*

    PubMed Central

    Liu, Yan; El-Achkar, Tarek M.; Wu, Xue-Ru

    2012-01-01

    Although few organ systems play a more important role than the kidneys in cytokine catabolism, the mechanism(s) regulating this pivotal physiological function and how its deficiency affects systemic cytokine homeostasis remain unclear. Here we show that elimination of Tamm-Horsfall protein (THP) expression from mouse kidneys caused a marked elevation of circulating IFN-γ, IL1α, TNF-α, IL6, CXCL1, and IL13. Accompanying this were enlarged spleens with prominent white-pulp macrophage infiltration. Lipopolysaccharide (LPS) exacerbated the increase of serum cytokines without a corresponding increase in their urinary excretion in THP knock-out (KO) mice. This, along with the rise of serum cystatin C and the reduced inulin and creatinine clearance from the circulation, suggested that diminished glomerular filtration may contribute to reduced cytokine clearance in THP KO mice both at the baseline and under stress. Unlike wild-type mice where renal and urinary cytokines formed specific in vivo complexes with THP, this “trapping” effect was absent in THP KO mice, thus explaining why cytokine signaling pathways were activated in renal epithelial cells in such mice. Our study provides new evidence implicating an important role of THP in influencing cytokine clearance and acting as a decoy receptor for urinary cytokines. Based on these and other data, we present a unifying model that underscores the role of THP as a major regulator of renal and systemic immunity. PMID:22451664

  4. A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm-Dancoff approximation

    NASA Astrophysics Data System (ADS)

    Liu, Fenglai; Gan, Zhengting; Shao, Yihan; Hsu, Chao-Ping; Dreuw, Andreas; Head-Gordon, Martin; Miller, Benjamin T.; Brooks, Bernard R.; Yu, Jian-Guo; Furlani, Thomas R.; Kong, Jing

    2010-10-01

    We derived the analytic gradient for the excitation energies from a time-dependent density functional theory calculation within the Tamm-Dancoff approximation (TDDFT/TDA) using Gaussian atomic orbital basis sets, and introduced an efficient serial and parallel implementation. Some timing results are shown from a B3LYP/6-31G**/SG-1-grid calculation on zincporphyrin. We also performed TDDFT/TDA geometry optimizations for low-lying excited states of 20 small molecules, and compared adiabatic excitation energies and optimized geometry parameters to experimental values using the B3LYP and ωB97 functionals. There are only minor differences between TDDFT and TDA optimized excited state geometries and adiabatic excitation energies. Optimized bond lengths are in better agreement with experiment for both functionals than either CC2 or SOS-CIS(D0), while adiabatic excitation energies are in similar or slightly poorer agreement. Optimized bond angles with both functionals are more accurate than CIS values, but less accurate than either CC2 or SOS-CIS(D0) ones.

  5. Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals

    SciTech Connect

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

    2015-11-28

    We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

  6. Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

  7. Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals.

    PubMed

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

    2015-11-28

    We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment. PMID:26627950

  8. Tamm-Horsfall protein in recurrent calcium kidney stone formers with positive family history: abnormalities in urinary excretion, molecular structure and function.

    PubMed

    Jaggi, Markus; Nakagawa, Yasushi; Zipperle, Ljerka; Hess, Bernhard

    2007-04-01

    Tamm-Horsfall protein (THP) powerfully inhibits calcium oxalate crystal aggregation, but structurally abnormal THPs from recurrent calcium stone formers may promote crystal aggregation. Therefore, increased urinary excretion of abnormal THP might be of relevance in nephrolithiasis. We studied 44 recurrent idiopathic calcium stone formers with a positive family history of stone disease (RCSF(fam)) and 34 age- and sex-matched healthy controls (C). Twenty-four-hour urinary THP excretion was measured by enzyme linked immunosorbent assay. Structural properties of individually purified THPs were obtained from analysis of elution patterns from a Sepharose 4B column. Sialic acid (SA) contents of native whole 24-h urines, crude salt precipitates of native urines and individually purified THPs were measured. THP function was studied by measuring inhibition of CaOx crystal aggregation in vitro (pH 5.7, 200 mM sodium chloride). Twenty-four-hour urine excretion of THP was higher in RCSF(fam) (44.0 +/- 4.0 mg/day) than in C (30.9 +/- 2.2 mg/day, P = 0.015). Upon salt precipitation and lyophilization, elution from a Sepharose 4B column revealed one major peak (peak A, cross-reacting with polyclonal anti-THP antibody) and a second minor peak (peak B, not cross-reacting). THPs from RCSF(fam) eluted later than those from C (P = 0.021), and maximum width of THP peaks was higher in RCSF(fam )than in C (P = 0.024). SA content was higher in specimens from RCSF(fam) than from C, in native 24-h urines (207.5 +/- 20.4 mg vs. 135.2 +/- 16.1 mg, P = 0.013) as well as in crude salt precipitates of 24-h urines (10.4 +/- 0.5 mg vs. 7.4 +/- 0.9 mg, P = 0.002) and in purified THPs (75.3 +/- 9.3 microg/mg vs. 48.8 +/- 9.8 microg/mg THP, P = 0.043). Finally, inhibition of calcium oxalate monohydrate crystal aggregation by 40 mg/L of THP was lower in RCSF(fam) (6.1 +/- 5.5%, range -62.0 to +84.2%) than in C (24.9 +/- 6.0%, range -39.8 to +82.7%), P = 0.022, and only 25 out of 44 (57%) THPs from RCSF

  9. Valence excitation energies of alkenes, carbonyl compounds, and azabenzenes by time-dependent density functional theory: Linear response of the ground state compared to collinear and noncollinear spin-flip TDDFT with the Tamm-Dancoff approximation

    NASA Astrophysics Data System (ADS)

    Isegawa, Miho; Truhlar, Donald G.

    2013-04-01

    Time-dependent density functional theory (TDDFT) holds great promise for studying photochemistry because of its affordable cost for large systems and for repeated calculations as required for direct dynamics. The chief obstacle is uncertain accuracy. There have been many validation studies, but there are also many formulations, and there have been few studies where several formulations were applied systematically to the same problems. Another issue, when TDDFT is applied with only a single exchange-correlation functional, is that errors in the functional may mask successes or failures of the formulation. Here, to try to sort out some of the issues, we apply eight formulations of adiabatic TDDFT to the first valence excitations of ten molecules with 18 density functionals of diverse types. The formulations examined are linear response from the ground state (LR-TDDFT), linear response from the ground state with the Tamm-Dancoff approximation (TDDFT-TDA), the original collinear spin-flip approximation with the Tamm-Dancoff (TD) approximation (SF1-TDDFT-TDA), the original noncollinear spin-flip approximation with the TDA approximation (SF1-NC-TDDFT-TDA), combined self-consistent-field (SCF) and collinear spin-flip calculations in the original spin-projected form (SF2-TDDFT-TDA) or non-spin-projected (NSF2-TDDFT-TDA), and combined SCF and noncollinear spin-flip calculations (SF2-NC-TDDFT-TDA and NSF2-NC-TDDFT-TDA). Comparing LR-TDDFT to TDDFT-TDA, we observed that the excitation energy is raised by the TDA; this brings the excitation energies underestimated by full linear response closer to experiment, but sometimes it makes the results worse. For ethylene and butadiene, the excitation energies are underestimated by LR-TDDFT, and the error becomes smaller making the TDA. Neither SF1-TDDFT-TDA nor SF2-TDDFT-TDA provides a lower mean unsigned error than LR-TDDFT or TDDFT-TDA. The comparison between collinear and noncollinear kernels shows that the noncollinear kernel

  10. The effect of basis set and exchange-correlation functional on time-dependent density functional theory calculations within the Tamm-Dancoff approximation of the x-ray emission spectroscopy of transition metal complexes.

    PubMed

    Roper, Ian P E; Besley, Nicholas A

    2016-03-21

    The simulation of X-ray emission spectra of transition metal complexes with time-dependent density functional theory (TDDFT) is investigated. X-ray emission spectra can be computed within TDDFT in conjunction with the Tamm-Dancoff approximation by using a reference determinant with a vacancy in the relevant core orbital, and these calculations can be performed using the frozen orbital approximation or with the relaxation of the orbitals of the intermediate core-ionised state included. Both standard exchange-correlation functionals and functionals specifically designed for X-ray emission spectroscopy are studied, and it is shown that the computed spectral band profiles are sensitive to the exchange-correlation functional used. The computed intensities of the spectral bands can be rationalised by considering the metal p orbital character of the valence molecular orbitals. To compute X-ray emission spectra with the correct energy scale allowing a direct comparison with experiment requires the relaxation of the core-ionised state to be included and the use of specifically designed functionals with increased amounts of Hartree-Fock exchange in conjunction with high quality basis sets. A range-corrected functional with increased Hartree-Fock exchange in the short range provides transition energies close to experiment and spectral band profiles that have a similar accuracy to those from standard functionals. PMID:27004859

  11. Work of the Tamm-Sakharov group on the first hydrogen bomb

    NASA Astrophysics Data System (ADS)

    Ritus, V. I.

    2014-09-01

    This review is an extended version of a report delivered at a session of the Department of Physical Sciences, the Department of Energetics, Mechanical Engineering, Mechanics, and Control Processes, and the Coordination Council on Technical Sciences of the RAS devoted to the 60th anniversary of the first hydrogen bomb test. The significant physical ideas suggested by A D Sakharov and V L Ginzburg underlying our first hydrogen bomb, RDS-6s, and numerous concrete problems and difficulties that had to be solved and overcome in designing thermonuclear weapons are presented. The understanding of the country's leaders and the Atomic Project managers of the exceptional role of fundamental science in the appearance and implementation of our scientists' concrete ideas and suggestions is emphasized.

  12. The development of an air motion measurement system for NASA's Electra aircraft

    NASA Technical Reports Server (NTRS)

    Ritter, J.; Beck, S.; Hedgepeth, R.; Barrick, J.; Butler, C.

    1987-01-01

    The development of the Turbulent Air Motion Measurement System (TAMMS), which is to measure dynamical and photochemical processes over a wide range of spatial and temporal scales, is examined. The composition and operation of the TAMMS subsystems, which include (1) fast-response meteorological sensors; (2) a boom/inertial navigation system; (3) baseline meteorological sensors; (4) an analog/digital interface; (5) control and data acquisition; and (6) data/reduction and spectral analysis software, are described. The planned flight testing and calibration of the TAMMS are discussed. The TAMMS platform wil be able to estimate the turbulent fluxes of heat, moisture, momentum, and any chemical species for which fast-response instrumentation is available.

  13. The nature of urinary casts

    PubMed Central

    McQueen, E. G.

    1962-01-01

    The composition of hyaline casts has been investigated. The major constituent appears to be the urinary mucoprotein described by Tamm and Horsfall. Small amounts only of serum proteins are present. Neither the amounts excreted nor the concentration of Tamm-Horsfall protein appeared to determine the rate of cast formation. The only invariable association of hyaline cast formation was with the presence of significant amounts of serum proteins in the urine. In vitro it was found that aqueous solutions of serum albumin were particularly effective in producing precipitation of Tamm-Horsfall protein. This interaction was inhibited in normal urine but occurred to a greater extent in nephrotic urine and is suggested as the possible mechanism of hyaline cast formation. Images PMID:16810981

  14. New Microscopic Approach to Multiphonon Nuclear Spectra

    NASA Astrophysics Data System (ADS)

    Andreozzi, F.; Knapp, F.; Lo Iudice, N.; Porrino, A.; Kvasil, J.

    2008-04-01

    The method outlined here consists in generating a multiphonon basis by constructing and solving iteratively a set of equations of motion within a subspace spanned by states which are tensor products of n Tamm Dancoff phonons. In such a basis, the Hamiltonian takes on a simple form and can be easily diagonalized. For illustrative purposes, the method is applied to 16O.

  15. Ray trajectories for Alcubierre spacetime

    NASA Astrophysics Data System (ADS)

    Anderson, Tom H.; Mackay, Tom G.; Lakhtakia, Akhlesh

    2011-05-01

    The Alcubierre spacetime was simulated by means of a Tamm medium which is asymptotically identical to vacuum and has constitutive parameters which are continuous functions of the spatial coordinates. Accordingly, the Tamm medium is amenable to physical realization as a micro- or nanostructured metamaterial. A comprehensive characterization of ray trajectories in the Tamm medium was undertaken, within the geometric-optics regime. Propagation directions corresponding to evanescent waves were identified: these occur in the region of the Tamm medium which corresponds to the warp bubble of the Alcubierre spacetime, especially for directions perpendicular to the velocity of the warp bubble at high speeds of that bubble. Ray trajectories are acutely sensitive to the magnitude and direction of the warp bubble's velocity, but rather less sensitive to the thickness of the transition zone between the warp bubble and its background. In particular, for rays which travel in the same direction as the warp bubble, the latter acts as a focusing lens, most notably at high speeds.

  16. Geometric-optical studies for metamaterial representations of curved spacetime

    NASA Astrophysics Data System (ADS)

    Anderson, Tom H.; Mackay, Tom G.; Lakhtakia, Akhlesh

    2011-10-01

    Metamaterials offer opportunities to explore curved-spacetime scenarios which would otherwise be impractical or impossible to study. These opportunities arise from the formal analogy that exists between light propagation in vacuous curved spacetime and in a certain nonhomogeneous bianisotropic medium, called a Tamm medium. As the science and technology of nanostructured metamaterials continues its rapid development, the practical realization of Tamm mediums is edging ever closer. We considered two particular curved spacetimes associated with: (a) spinning cosmic strings, and (b) the Alcubierre drive. For both examples, a Tamm medium formulation was developed which is asymptotically identical to vacuum and is therefore amenable to physical realization. A study of ray trajectories for both Tamm mediums was undertaken, within the geometric optics regime. For the spinning cosmic string, it was observed that: (i) rays do not cross the string's boundary; (ii) evanescent waves are supported in regions of phase space that correspond to those regions of the string's spacetime wherein closed timelike curves may arise; and (iii) a non-spinning string is nearly invisible whereas a spinning string may be rather more visible. For the Alcubierre drive, it was observed that: (i) ray trajectories are highly sensitive to the magnitude and direction of the warp bubble's velocity, but less sensitive to the thickness of the transition zone between the warp bubble and its background; and (ii) the warp bubble acts as a focusing lens for rays which travel in the same direction as the bubble, especially at high speeds.

  17. Adaptations of a deep sea scavenger: high ammonia tolerance and active NH₄⁺ excretion by the Pacific hagfish (Eptatretus stoutii).

    PubMed

    Clifford, Alexander M; Goss, Greg G; Wilkie, Michael P

    2015-04-01

    The Pacific hagfish (Eptatretus stoutii) has an exceptional ability to both withstand and recover from exposure to high external ammonia (HEA). This tolerance is likely due to the feeding behavior of this scavenger, which feeds on intermittent food falls of carrion (e.g. fish, large marine mammals) during which time it may be exposed to high concentrations of total ammonia (T(Amm)=NH3+NH4(+)) while burrowed inside the decomposing carcass. Here we exposed hagfish to 20 mmol L(-1) T(Amm) for periods of up to 48 h and then let animals recover in ammonia-free seawater. During the 48 h HEA exposure period, plasma T(Amm) increased 100-fold to over 5000 μmol L(-1) while ammonia excretion (J(amm)) was transiently inhibited. This increase in plasma T(Amm) resulted from NH3 influx down massive inwardly directed ΔP(NH3) gradients, which also led to a short-lived metabolic alkalosis. Plasma [T(Amm)] stabilized after 24-48 h, possibly through a reduction in NH3 permeability across the body surface, which lowered NH3 influx. Ammonia balance was subsequently maintained through the re-establishment of J(amm) against an inwardly directed ΔP(NH3). Calculations of the Nernst potential for ammonia strongly indicated that J(amm) was also taking place against a large inwardly directed NH4(+) electrochemical gradient. Recovery from HEA in ammonia-free water was characterized by a large ammonia washout, and the restoration of plasma TAmm concentrations to near control concentrations. Ammonia clearance was also accompanied by a residual metabolic acidosis, which likely offset the ammonia-induced metabolic alkalosis seen in the early stages of HEA exposure. We conclude that restoration of J(amm) by the Pacific hagfish during ammonia exposure likely involves secondary active transport of NH4(+), possibly mediated by Na(+)/NH4(+) (H(+)) exchange. PMID:25499242

  18. Transport of massless Dirac fermions in non-topological type edge states.

    PubMed

    Latyshev, Yu I; Orlov, A P; Volkov, V A; Enaldiev, V V; Zagorodnev, I V; Vyvenko, O F; Petrov, Yu V; Monceau, P

    2014-01-01

    There are two types of intrinsic surface states in solids. The first type is formed on the surface of topological insulators. Recently, transport of massless Dirac fermions in the band of "topological" states has been demonstrated. States of the second type were predicted by Tamm and Shockley long ago. They do not have a topological background and are therefore strongly dependent on the properties of the surface. We study the problem of the conductivity of Tamm-Shockley edge states through direct transport experiments. Aharonov-Bohm magneto-oscillations of resistance are found on graphene samples that contain a single nanohole. The effect is explained by the conductivity of the massless Dirac fermions in the edge states cycling around the nanohole. The results demonstrate the deep connection between topological and non-topological edge states in 2D systems of massless Dirac fermions. PMID:25524881

  19. The role of the fano resonance in multiple exciton generation in quantum dots

    NASA Astrophysics Data System (ADS)

    Oksengendler, B. L.; Marasulov, M. B.; Nikiforov, V. N.

    2016-02-01

    The phenomenon of interference between two pathways of electron transfer from the valence to the conduction band at a quantum dot is considered. The first way is the conventional "valence band-conduction band" transition, while the second is the transition via a virtual two-electron state on the Tamm level in a quantum dot (QD) followed by the Auger effect, which ejects one electron from the Tamm level to the conduction band. In the case of a coherent addition of these ionization pathways, the Fano resonance can take place, this leading to an increase in the coefficient of photon absorption. This results in increasing internal efficiency of light conversion and can provide a basis for increasing the efficiency of solar cells due to the phenomenon of multiple exciton generation.

  20. Theory and operation of the Gould 32/27 programs ABLE-2A and EBLE for the tropospheric air motion measurement system

    NASA Technical Reports Server (NTRS)

    Butler, C.

    1986-01-01

    Software development for the Trospheric Air Motion Measurement Systems (TAMMS) is documented. In July/August the TAMMS was flown on the NASA/Goddard Flight Center Electra aircraft for 19 mission for the ABLE-2A (Amazon Boundary Layer Experiment) in Brazil. In December 1985, several flights were performed to assess the contamination and boundary layer of the Electra. Position data, flow angles, pressure transducer measurements were recorded. The programs written for the ABLE-2A were modified due to timing considerations for this particular program. The 3-step programs written for EBLE (Electra Boundary Layer Experiment) are described. Power up and log-on procedures are discussed. A few editing techniques are described for modification of the programs.

  1. Transport of Massless Dirac Fermions in Non-topological Type Edge States

    PubMed Central

    Latyshev, Yu I.; Orlov, A. P.; Volkov, V. A.; Enaldiev, V. V.; Zagorodnev, I. V.; Vyvenko, O. F.; Petrov, Yu V.; Monceau, P.

    2014-01-01

    There are two types of intrinsic surface states in solids. The first type is formed on the surface of topological insulators. Recently, transport of massless Dirac fermions in the band of “topological” states has been demonstrated. States of the second type were predicted by Tamm and Shockley long ago. They do not have a topological background and are therefore strongly dependent on the properties of the surface. We study the problem of the conductivity of Tamm-Shockley edge states through direct transport experiments. Aharonov-Bohm magneto-oscillations of resistance are found on graphene samples that contain a single nanohole. The effect is explained by the conductivity of the massless Dirac fermions in the edge states cycling around the nanohole. The results demonstrate the deep connection between topological and non-topological edge states in 2D systems of massless Dirac fermions. PMID:25524881

  2. Nuclear Response Within a New Microscopic Multiphonon Approach

    NASA Astrophysics Data System (ADS)

    Lo Iudice, N.; Bianco, D.; Knapp, F.; Andreozzi, F.; Porrino, A.; Vesely, P.

    2013-03-01

    We have revised an equation of motion method for generating a basis of microscopic multiphonon states built of Tamm-Dancoff phonons. This new version removes the inconsistencies of the previous formulation and yields eigenvalue equations of simple structure. To test the method we have computed the electric dipole response of the neutron rich 20O in a space extending up to the three-phonon subspace.

  3. A comparative study on two extraction procedures in speciation of iron in municipal solid waste.

    PubMed

    Li, Wen-Bing; Yao, Jun; Tao, Ping-Ping; Guo, Meng-Ting; Feng, Xiao-Yan; He, Yan-Ni; Fang, Cheng-Ran; Shen, Dong-Sheng

    2010-10-15

    Two extraction reagents, hydrochloric acid (HCl) and acid ammonium oxalate solution (Tamm's reagent), were used to evaluate the redox state of iron in municipal solid waste (MSW) with different deposit ages. Orthogonal experiments were conducted to optimize the extraction conditions for extractable iron speciation (ferric and ferrous) in MSW. The optimal extraction conditions for HCl were determined as follows: the liquid-to-solid ratio was set at 100, and then the samples were extracted at the shaking speed of 200 rpm at 35 degrees C for 60 min by 1.00 M HCl. For Tamm's reagent, the optimal extraction conditions were extracted at the shaking speed of 175 rpm at 30 degrees C for 12 h with the same liquid-to-solid ratio. However, Tamm's reagent extraction is much more laborious and time-consuming. Thus the HC1 extraction might be a better choice for the evaluation of the redox state of iron in MSW. The results also showed that the yield of extractable iron increased with deposited age. About 60-83% of extractable iron was presented as ferrous in the MSW deposited for 1-8 years. This study supplied a tool for investigating the role of iron on the fate of pollutants in the landfill. PMID:20638175

  4. Effect of hydrochloric acid on sound absorption and relaxation frequency in magnesium sulfate solutions

    NASA Astrophysics Data System (ADS)

    Fisher, F. H.

    2002-05-01

    The epic work of Kurtze and Tamm on sound absorption spectroscopy in divalent sulfate electrolyte solutions (1953) from the low-kHz region up to over 200 MHz revealed astonishing variability at frequencies below 10 MHz and a common relaxation frequency at about 200 MHz. For magnesium sulfate [Epsom salts] solutions, the salt producing 30× the absorption of fresh water below the 100-kHz region in the oceans at low concentrations [~0.02 moles/liter], Kurtze and Tamm investigated the effects of adding HC1 or H2SO4. They found that as formal pH increased, the results were different for these acids in reducing the sound absorption. Fisher (1983) found that if the absorption was plotted against free hydrogen, ion concentration was the same. We used the 100-liter titanium sphere, a spare ballast tank from the WHOI submarine ALVIN. With precise temperature control, we found an increase in the relaxation frequency as HC1 was added in conjunction with the reduction in sound absorption. The results will be presented and an explanation will be proposed in the context of the Eigen and Tamm multistate dissociation model for MgSO4 (1962) which explains the effects of pressure on both absorption and conductance. [Work supported by ONR.] The author acknowledges C. C. Hsu for his work on this project.

  5. Devescovinid trichomonad with axostyle-based rotary motor ("Rubberneckia"): taxonomic assignment as Caduceia versatilis sp. nov

    NASA Technical Reports Server (NTRS)

    d'Ambrosio, U.; Dolan, M.; Wier, A. M.; Margulis, L.

    1999-01-01

    An amitochondriate trichomonad cell of the family Devescovinidae (Class Parabasalia), helped demonstrate the fluid model of lipoprotein cell membranes. This wood-ingesting symbiont in the hindgut of the dry wood-eating termite Cryptotermes cavifrons is informally known to cell biologists as "Rubberneckia". As the microtubular axo-style complex generates force causing clockwise movement of the entire anterior portion of the cell at the shear zone the protist displays "head" rotation. Studies by phase contrast and videomicroscopy of live cells, of whole mounts by scanning, and thin sections by transmission electron microscopy extend the observations of Tamm and Tamm [24-26] and Tamm [19-23]. Habitat, cell shape, size, nuclear features, parabasal apparatus and other morphological details permit the assignment of "Rubberneckia" to Kirby's cosmopolitan genus Caduceia. This large-sized devescovinid has distinctive parabasal gyres, an axostylar rotary, motor, and regularly-associated nonflagellated, fusiform and flagellated rod epibiotic surface bacteria. In addition to regularly aligned epibionts intranuclear and endocytoplasmic bacteria are abundant and hydrogenosomes are Present. "Rubberneckia" is compared here to the other seven species of Caduceia. Since it is clearly sufficiently distinctive to warrant new species status, we named it C. versatilis.

  6. The relationship between NMDA receptor function and the high ammonia tolerance of anoxia-tolerant goldfish.

    PubMed

    Wilkie, Michael P; Pamenter, Matthew E; Duquette, Stephanie; Dhiyebi, Hadi; Sangha, Navjeet; Skelton, Geoffrey; Smith, Matthew D; Buck, Leslie T

    2011-12-15

    Acute ammonia toxicity in vertebrates is thought to be characterized by a cascade of deleterious events resembling those associated with anoxic/ischemic injury in the central nervous system. A key event is the over-stimulation of neuronal N-methyl-D-aspartate (NMDA) receptors, which leads to excitotoxic cell death. The similarity between the responses to acute ammonia toxicity and anoxia suggests that anoxia-tolerant animals such as the goldfish (Carassius auratus Linnaeus) may also be ammonia tolerant. To test this hypothesis, the responses of goldfish were compared with those of the anoxia-sensitive rainbow trout (Oncorhynchus mykiss Walbaum) during exposure to high external ammonia (HEA). Acute toxicity tests revealed that goldfish are ammonia tolerant, with 96 h median lethal concentration (LC(50)) values of 199 μmol l(-1) and 4132 μmol l(-1) for NH(3) and total ammonia ([T(Amm)]=[NH(3)]+[NH(4)(+)]), respectively. These values were ~5-6 times greater than corresponding NH(3) and T(Amm) LC(50) values measured in rainbow trout. Further, the goldfish readily coped with chronic exposure to NH(4)Cl (3-5 mmol l(-1)) for 5 days, despite 6-fold increases in plasma [T] to ~1300 μmol l(-1) and 3-fold increases in brain [T(Amm)] to 6700 μmol l(-1). Muscle [T(Amm)] increased by almost 8-fold from ~900 μmol kg(-1) wet mass (WM) to greater than 7000 μmol kg(-1) WM by 48 h, and stabilized. Although urea excretion rates (J(Urea)) increased by 2-3-fold during HEA, the increases were insufficient to offset the inhibition of ammonia excretion that occurred, and increases in urea were not observed in the brain or muscle. There was a marked increase in brain glutamine concentration at HEA, from ~3000 μmol kg(-1) WM to 15,000 μmol kg(-1) WM after 48 h, which is consistent with the hypothesis that glutamine production is associated with ammonia detoxification. Injection of the NMDA receptor antagonists MK801 (0.5-8 mg kg(-1)) or ethanol (1-8 mg kg(-1)) increased trout

  7. Memories of David Kirzhnits

    NASA Astrophysics Data System (ADS)

    Bolotovsky, B. M.

    2013-06-01

    In the mid-1950s, a new staff member appeared at the Theory Division of the Physical Institute of the Academy of Sciences (FIAN): David Abramovich Kirzhnits. A Moscow State University alumnus, after graduation he had been assigned to a large defense plant in the city of Gorky, where he had worked for several years as an engineer. He was "liberated" from there by Igor Evgenyevich Tamm, our department head, who managed to transfer him to FIAN. Igor Evgenyevich knew D. A. Kirzhnits - they had met in Moscow before Kirzhnits finished university. At that time Kirzhnits was performing thesis work with professor A. S. Kompaneyets as academic adviser. At his adviser's suggestion, D. Kirzhnits consulted with I. E. Tamm on questions pertaining to the thesis topic. I. E. Tamm took a great liking for the diploma student, and he even wanted to recruit D. A. Kirzhnits for the Theory Division immediately after graduation. But at that time (1949) this proved impossible for several reasons. First, D. Kirzhnits was, as they say, an "invalid of the fifth group" - a Jew - which during those years of violent struggle against cosmopolitanismb often proved an obstacle in looking for work. Second, during the years of mass repressions D. Kirzhnits' father had been arrested on treason charges (according to the charges, he had wanted to sell the Far East to Japan). After intensive investigation his father was released, but he lived only a little longer. Reports of this also could have impeded his acceptance. Third, Igor Evgenyevich didn't have enough weight in officials' eyes at that time and so was unable to overcome "first" and "second."...

  8. Non-perturbative Calculation of the Scalar Yukawa Theory in Four-Body Truncation

    NASA Astrophysics Data System (ADS)

    Li, Yang; Karmanov, V. A.; Maris, P.; Vary, J. P.

    2015-09-01

    The quenched scalar Yukawa theory is solved in the light-front Tamm-Dancoff approach including up to four constituents (one scalar nucleon, three scalar pions). The Fock sector dependent renormalization is implemented. By studying the Fock sector norms, we find that the lowest two Fock sectors dominate the state even in the large-coupling region. The one-body sector shows convergence with respect to the Fock sector truncation. However, the four-body norm exceeds the three-body norm at the coupling.

  9. Theoretical investigation on dye sensitizer solar cell: Spin-forbidden transition

    SciTech Connect

    Imamura, Yutaka

    2015-12-31

    We studied spin-forbidden transitions of metal polypyridyl sensitizers by two-component relativistic time-dependent density functional theory with the spin-orbit interaction based on Tamm-Dancoff approximation. The singlet-to-triplet transition, which is assigned to a metal-to-ligand charge-transfer type excitation, appears for a phosphine-coordinated Ru(II), DX1. Absorption spectra of the modified DX1 molecules, whose Ru is replaced with Fe and Os, were also calculated for examining the effects of metals on the spin-orbit interaction.

  10. Investigations of the g{sub K}-factors in the {sup 175,177,179}Hf Isotopes

    SciTech Connect

    Yakut, Hakan; Kuliev, Ali; Guliyev, Ekber

    2008-11-11

    In this paper the intrinsic g{sub K} and effective spin g{sub s} factors of the odd-mass {sup 175-179}Hf isotopes have been investigated within the Tamm-Dancoff approximation by using the realistic Saxon-Woods potential. The theoretically calculated g{sub K} and g{sub s}{sup eff} values are compared with experimental data. The comparison of the measured and calculated values of the effective g{sub s} factor shows that the spin polarization explains quite well the observed reduction of g{sub s} from its free-nucleon value.

  11. Valence photodetachment of Li- and Na- using relativistic many-body techniques

    NASA Astrophysics Data System (ADS)

    Jose, J.; Pradhan, G. B.; Radojević, V.; Manson, S. T.; Deshmukh, P. C.

    2011-05-01

    The multiconfiguration Tamm-Dancoff technique (MCTD) is applied to study photodetachment of negative ions of lithium and sodium. A cusplike structure is found in the photodetachment cross section just below the first detachment-plus-excitation threshold of Li- (Li 2p), and of Na- (Na 3p), in qualitative agreement with existing theoretical and experimental results. The current work emphasizes the importance of correlation in the form of configuration interaction in the photodetachment process and demonstrates the utility of MCTD in dealing with highly correlated systems.

  12. Dynamics of Sulfur Dioxide in the Marine Boundary During Trace P

    NASA Astrophysics Data System (ADS)

    Thornton, D. C.; Tu, F.; Bandy, A. R.; Kim, M.; Thornhill, L.; Barrick, J. D.; Anderson, B.

    2002-12-01

    An atmospheric pressure ionization mass spectrometer (APIMS) was employed to obtain 25 Hz sulfur dioxide (SO2) meausrements during the NASA Trace P field experiment. The APIMS was deployed on the NASA Wallops P-3B, which was equiped with the total air motion measurement system (TAMMS). The APIMS SO2 signal was recorded on the TAMMS data system to insure that the data was recorded on the same time base to allow processing of the data for eddy correlation measurements of SO2 with the vertical wind velocity from TAMMS. A preliminary estimate of the SO2 deposition velocity will be presented. At the high data sampling rates the dynamics of boundary layer could be studied for the effects on the SO2 distribution in conjunction with high data rate water vapor and temperature data from TAMMS. The turbulence data showed that the well mixed layer (within the planetary boundary layer) often was approximately 500 m with an intermittently turbulent layer above. The vertical distribution of SO2 was often constrained by the dynamics of these layers. In some cases the highest SO2 concentrations were in the well mixed layer and at other times the highest SO2 concentrations were in the less well mixed layer above. This partitioning could also be seen for water vapor and sometimes for carbon monoxide. In some cases it appeared that the continental boundary layer air had overrun the marine mixed layer during frontal progress through the experiment area. This partitioning can greatly affect the loss rates and mechanisms of SO2 in the absence of convection. When SO2 is predominantly above the well mixed layer, SO2 loss to the sea surface is primarily controlled by entraiment into the well mixed layer, which is a relatively slow process. When the SO2 is primarily in the well mixed layer its lifetime during transport can be much shorter than during transport aloft unless convection through the boundary layer occurs. The transport of SO2 in and around clouds was also observed during Trace P

  13. A Local CC2 and TDA-DFT Double Hybrid Study on BODIPY/aza-BODIPY Dimers as Heavy Atom Free Triplet Photosensitizers for Photodynamic Therapy Applications.

    PubMed

    Momeni, Mohammad R; Brown, Alex

    2016-04-28

    A series of 11 different boron-dipyrromethene (BODIPY) dimers is carefully examined by means of ab initio and Tamm-Dancoff approximated density functional theory methods. Vertical and 0-0 excitation energies along with the tetraradical character of these dimers are determined. Possible application of a series of linked dimers for photodynamic therapy (PDT) was investigated through computing their excitation energies, spin-orbit coupling matrix elements, and singlet-triplet energy gaps. Finally through a systematic investigation of a series of 36 different BODIPY and aza-BODIPY dimers, a new class of near-IR heavy atom free photosensitizers for PDT action is introduced. PMID:27035753

  14. Richardson-Gaudin description of pairing in atomic nuclei

    NASA Astrophysics Data System (ADS)

    De Baerdemacker, Stijn

    2012-05-01

    The present contribution discusses a connection between the exact Bethe Ansatz eigenstates of the reduced Bardeen-Cooper-Schrieffer (BCS) Hamiltonian and the multi-phonon states of the Tamm-Dancoff Approximation (TDA). The connection is made on the algebraic level, by means of a deformed quasi-spin algebra with a bosonic Heisenberg-Weyl algebra in the contraction limit of the deformation parameter. Each exact Bethe Ansatz eigenstate is mapped on a unique TDA multi-phonon state, shedding light on the physics behind the Bethe Ansatz structure of the exact wave function. The procedure is illustrated with a model describing neutron pairing in 56Fe.

  15. Meson Structure in a Relativistic Many-Body Approach

    SciTech Connect

    Llanes-Estrada, Felipe J.; Cotanch, Stephen R.

    2000-02-07

    Results from an extensive relativistic many-body analysis utilizing a realistic effective QCD Hamiltonian are presented for the meson spectrum. A comparative numerical study of the BCS, Tamm-Dancoff (TDA), and RPA treatments provides new, significant insight into the condensate structure of the vacuum, the chiral symmetry governance of the pion, and the meson spin, orbital, and flavor mass splitting contributions. In contrast to a previous glueball application, substantial quantitative differences are computed between TDA and RPA for the light quark sector with the pion emerging as a Goldstone boson only in the RPA. (c) 2000 The American Physical Society.

  16. Projected quasiparticle calculations for the N =82 odd-proton isotones

    SciTech Connect

    Losano, L. ); Dias, H. )

    1991-12-01

    The structure of low-lying states in odd-mass {ital N}=82 isotones (135{le}{ital A}{le}145) is investigated in terms of a number-projected one- and three-quasiparticles Tamm-Dancoff approximation. A surface-delta interaction is taken as the residual nucleon-nucleon interaction. Excitation energies, dipole and quadrupole moments, and {ital B}({ital M}1) and {ital B}({ital E}2) values are calculated and compared with the experimental data.

  17. Geometric derivation of the quantum speed limit

    SciTech Connect

    Jones, Philip J.; Kok, Pieter

    2010-08-15

    The Mandelstam-Tamm and Margolus-Levitin inequalities play an important role in the study of quantum-mechanical processes in nature since they provide general limits on the speed of dynamical evolution. However, to date there has been only one derivation of the Margolus-Levitin inequality. In this paper, alternative geometric derivations for both inequalities are obtained from the statistical distance between quantum states. The inequalities are shown to hold for unitary evolution of pure and mixed states, and a counterexample to the inequalities is given for evolution described by completely positive trace-preserving maps. The counterexample shows that there is no quantum speed limit for nonunitary evolution.

  18. Quantum speed limits—primer, perspectives, and potential future directions

    NASA Astrophysics Data System (ADS)

    Frey, Michael R.

    2016-07-01

    Fundamental physical limits on the speed of state evolution in quantum systems exist in the form of the Mandelstam-Tamm and the Margolus-Levitin inequalities. We give an expository review of the development of these quantum speed limit (QSL) inequalities, including extensions to different energy statistics and generalizations to mixed system states and open and multipartite systems. The QSLs expressed by these various inequalities have implications for quantum computation, quantum metrology, and control of quantum systems. These connections are surveyed, and some important open questions are noted.

  19. Hyperbolic resonances of metasurface cavities.

    PubMed

    Keene, D; Durach, M

    2015-07-13

    We propose a new class of optical resonator structures featuring one or two metasurface reflectors or metacavities and predict that such resonators support novel hyperbolic resonances. As an example of such resonances we introduce hyperbolic Tamm plasmons (HTPs) and hyperbolic Fabry-Perot resonances (HFPs). The hyperbolic optical modes feature low-loss incident power re-distribution over TM and TE polarization output channels, clover-leaf anisotropic dispersion, and other unique properties which are tunable and are useful for multiple applications. PMID:26191916

  20. Mobile aluminum compounds in soils of the southern taiga (soils of the central forest reserve as an example)

    NASA Astrophysics Data System (ADS)

    Tolpeshta, I. I.; Sokolova, T. A.

    2010-08-01

    The profile distributions of aluminum extracted by the Tamm and Bascomb reagents and of the exchangeable aluminum were studied in soils of automorphic, transitive, and accumulative positions in the landscapes of the southern taiga. In the mineral horizons of the gleyic peaty-podzolic soils developed on poorly drained flat surfaces and in the floodplain soils, the distribution of oxalate- and pyrophosphate-soluble aluminum has a strongly pronounced accumulative character. In the podzolic soils of the automorphic positions and slopes, an eluvial-illuvial distribution was characteristic with the maximal aluminum content in the podzolic horizons. The strong differentiation of the upper part of the profile in the automorphic podzolic soils in terms of the Al content in the Tamm and Bascomb extracts is mainly related to an increase of the pedogenic chlorite content upon the transition from the AE to the E horizon. In the podzolic horizons of these soils, aluminum can accumulate in the form of proto-imogolite structures. The exchangeable aluminum displays an accumulative type of distribution. On the basis of calculating the reserves of the different aluminum compounds, two main accumulative zones for the mobile compounds of this element were recorded in the soils of the landscapes studied: the E horizon in the automorphic podzolic soils, where Al accumulates as soil chlorite or, probably, as proto-imogolite, and the A1 horizon of the floodplain soils, where Al accumulates in aluminoorganic complexes.

  1. Calibration of NASA Turbulent Air Motion Measurement System

    NASA Technical Reports Server (NTRS)

    Barrick, John D. W.; Ritter, John A.; Watson, Catherine E.; Wynkoop, Mark W.; Quinn, John K.; Norfolk, Daniel R.

    1996-01-01

    A turbulent air motion measurement system (TAMMS) was integrated onboard the Lockheed 188 Electra airplane (designated NASA 429) based at the Wallops Flight Facility in support of the NASA role in global tropospheric research. The system provides air motion and turbulence measurements from an airborne platform which is capable of sampling tropospheric and planetary boundary-layer conditions. TAMMS consists of a gust probe with free-rotating vanes mounted on a 3.7-m epoxy-graphite composite nose boom, a high-resolution inertial navigation system (INS), and data acquisition system. A variation of the tower flyby method augmented with radar tracking was implemented for the calibration of static pressure position error and air temperature probe. Additional flight calibration maneuvers were performed remote from the tower in homogeneous atmospheric conditions. System hardware and instrumentation are described and the calibration procedures discussed. Calibration and flight results are presented to illustrate the overall ability of the system to determine the three-component ambient wind fields during straight and level flight conditions.

  2. Quantum Localization in Laser-Driven Molecular Rotation

    NASA Astrophysics Data System (ADS)

    Averbukh, Ilya

    2016-05-01

    Recently we predicted that several celebrated solid state quantum localization phenomena - Anderson localization, Bloch oscillations, and Tamm-Shockley surface states - may manifest themselves in the rotational dynamics of laser-kicked molecules. In this talk, I will present these new rotational effects in a gas of linear molecules subject to a moderately long periodic train of femtosecond laser pulses. A small detuning of the train period from the rotational revival time causes Anderson localization in the angular momentum space above some critical value of J - the Anderson wall. This wall marks an impenetrable border stopping any further rotational excitation. Below the Anderson wall, the rotational excitation oscillates with the number of pulses due to a mechanism similar to Bloch oscillations in crystalline solids. I will present the results of the first experimental observation of the laser-induced rotational Bloch oscillations in molecular nitrogen at ambient conditions (Stanford & Weizmann, 2015). We will also discuss the prospects of observing the rotational analogues of the Tamm surface states in a similar experimental setup. Our results offer laser-driven molecular rotation as a new platform for studies on the localization phenomena in quantum transport. These effects are important for many processes involving highly excited rotational states, including coherent optical manipulations in molecular mixtures, and propagation of powerful laser pulses in atmosphere.

  3. Quantum speed limits, coherence, and asymmetry

    NASA Astrophysics Data System (ADS)

    Marvian, Iman; Spekkens, Robert W.; Zanardi, Paolo

    2016-05-01

    The resource theory of asymmetry is a framework for classifying and quantifying the symmetry-breaking properties of both states and operations relative to a given symmetry. In the special case where the symmetry is the set of translations generated by a fixed observable, asymmetry can be interpreted as coherence relative to the observable eigenbasis, and the resource theory of asymmetry provides a framework to study this notion of coherence. We here show that this notion of coherence naturally arises in the context of quantum speed limits. Indeed, the very concept of speed of evolution, i.e., the inverse of the minimum time it takes the system to evolve to another (partially) distinguishable state, is a measure of asymmetry relative to the time translations generated by the system Hamiltonian. Furthermore, the celebrated Mandelstam-Tamm and Margolus-Levitin speed limits can be interpreted as upper bounds on this measure of asymmetry by functions which are themselves measures of asymmetry in the special case of pure states. Using measures of asymmetry that are not restricted to pure states, such as the Wigner-Yanase skew information, we obtain extensions of the Mandelstam-Tamm bound which are significantly tighter in the case of mixed states. We also clarify some confusions in the literature about coherence and asymmetry, and show that measures of coherence are a proper subset of measures of asymmetry.

  4. Recent progress in density functional theory

    NASA Astrophysics Data System (ADS)

    Truhlar, Donald

    2014-03-01

    Ongoing work involves several areas of density functional theory: new methods for computing electronic excitation energies, including a new way to remove spin contamination in the spin-flip Tamm-Dancoff approximation and a configuration-interaction-corrected Tamm-Dancoff Approximation for treating conical intersections; new ways to treat open-shell states, including a reinterpreted broken-symmetry method and multi-configuration Kohn-Sham theory; a new exchange-correlation functional; new tests of density functional theory against databases for electronic transition energies and molecules and solids containing metal atoms; and applications. A selection of results will be presented. I am grateful to the following collaborators for contributions to the ongoing work: Boris Averkiev, Rebecca Carlson, Laura Fernandez, Laura Gagliardi, Chad Hoyer, Francesc Illas, Miho Isegawa, Shaohong Li, Giovanni Li Manni, Sijie Luo, Dongxia Ma, Remi Maurice, Rubén Means-Pañeda, Roberto Peverati, Nora Planas, Prasenjit Seal, Pragya Verma, Bo Wang, Xuefei Xu, Ke R. Yang, Haoyu Yu, Wenjing Zhang, and Jingjing Zheng. Supported in part by the AFOSR and U.S. DOE.

  5. On the relation between time-dependent and variational density functional theory approaches for the determination of excitation energies and transition moments.

    PubMed

    Ziegler, Tom; Seth, Michael; Krykunov, Mykhaylo; Autschbach, Jochen; Wang, Fan

    2009-04-21

    It is shown that it is possible to derive the basic eigenvalue equation of adiabatic time-dependent density functional theory within the Tamm-Dancoff approximation (TD-DFT/TD) from a variational principle. The variational principle is applied to the regular Kohn-Sham formulation of DFT energy expression for a single Slater determinant and leads to the same energy spectrum as TD-DFT/TD. It is further shown that this variational approach affords the same electric and magnetic transition moments as TD-DFT/TD. The variational scheme can also be applied without the Tamm-Dancoff approximation. Practical implementations of TD-DFT are limited to second order response theory which introduces errors in transition energies for charge transfer and Rydberg excitations. It is indicated that higher order terms can be incorporated into the variational approach. It is also discussed how the current variational method is related to traditional DFT schemes based on variational principles such as DeltaSCF-DFT, and how they can be combined. PMID:19388731

  6. Spin-polarised edge states in atomic Mn chains supported on Cu2N/Cu (100)

    NASA Astrophysics Data System (ADS)

    Choi, Deung-Jang; Robles, Roberto; Gauyacq, Jean-Pierre; Rubio-Verdú, Carmen; Lorente, Nicolás; Pascual, José Ignacio

    2016-06-01

    Scanning tunnelling microscopy and density functional theory studies of manganese chains adsorbed on Cu2N/Cu (100) reveal an unsuspected electronic edge state at ∼ 1 eV above the Fermi energy. This Tamm-like state is strongly localised to the terminal Mn atoms of the chain and fully spin polarised. However, no equivalence is found for occupied states, and the electronic structure at ∼   ‑1 eV is mainly spin unpolarised due to the extended p-states of the N atoms that mediate the coupling between the Mn atoms in the chain. The spin polarisation of the edge state is affected by the antiferromagnetic ordering of the chains leading to non-trivial consequences.

  7. Cylindruria.

    PubMed

    Caleffi, Alberta; Lippi, Giuseppe

    2015-11-01

    The morphological analysis of urine sediment is an essential part of urinalysis and casts are important elements of urinary sediment. Their shape is typically cylindrical, with extremities often rounded. Casts form within the renal tubules and are made of Tamm-Horsfall glycoprotein (THG). Under some physiological or pathological conditions THG fibrils aggregate giving rise to casts, whose formation is favoured by a number of factors including high urine osmolality and/or low pH. Casts can be found in normal subjects, in non-renal conditions, such as fever, dehydration, and acute heart failure as well as in virtually all renal diseases. Casts can be classified on the basis of their morphology as hyaline, granular, waxy, fatty, cellular (leukocytic, erythrocytic, epithelial), containing crystals or microorganisms, pigmented and mixed. As the correct identification of casts is crucial for an accurate and timely diagnosis of renal disorders, laboratory professionals should be trained to identify and classify casts properly. PMID:26079824

  8. First-Principles Studies of the Excited States of Chromophore Monomers and Dimers

    NASA Astrophysics Data System (ADS)

    Hamed, Samia; Sharifzadeh, Sahar; Neaton, Jeffrey

    2015-03-01

    Elucidation of the energy transfer mechanism in natural photosynthetic systems remains an exciting challenge. Through the careful analysis of excited states on individual chromophores and dimers - and the predictive first-principles methods used to compute them - we are building towards an understanding of the nature of excitation transfer among arrays of chromophores embedded in protein environments. Excitation energies, transition dipoles, and natural transition orbitals for the important low-lying singlet and triplet states of experimentally-relevant chromophores are obtained from first-principles time-dependent density functional theory (TDDFT) and many body perturbation theory. The effect of the Tamm-Dancoff approximation and the performance of several exchange-correlation functionals, including an optimally-tuned range-separated hybrid, are evaluated with TDDFT, and compared to MBPT calculations and experiments. This work has been supported by the DOE; computational resources have been provided by NERSC.

  9. Contact conductance of a graphene nanoribbon with its graphene nano-electrodes

    NASA Astrophysics Data System (ADS)

    Srivastava, Saurabh; Kino, Hiori; Joachim, Christian

    2016-04-01

    Electronically contacted between two graphene nano-electrodes, the contact conductance (G0) of a graphene nanoribbon (GNR) molecular wire is calculated using mono-electronic Elastic Scattering Quantum Chemistry (ESQC) theory. Different nano-electrode contact geometries are considered ranging from a top face to face van der Waals contact to an adiabatic funnel like planar chemical bonding. The Tamm state contributions to the GNR-graphene nano-electrode electronic interactions are discussed as a function of the molecular orbital hybridization. Contrary to the common belief, the adiabatic-like triangle shaped contact nano-graphene electrode does not provide a large G0 as compared to the abrupt contact geometry. The abrupt contact geometry is even worth than a top face to face van der Waals electronic contact with a metal.

  10. Correlation energy for the homogeneous electron gas: Exact Bethe-Salpeter solution and an approximate evaluation

    NASA Astrophysics Data System (ADS)

    Maggio, Emanuele; Kresse, Georg

    2016-06-01

    The correlation energy of the homogeneous electron gas is evaluated by solving the Bethe-Salpeter equation (BSE) beyond the Tamm-Dancoff approximation for the electronic polarization propagator. The BSE is expected to improve on the random-phase approximation, owing to the inclusion of exchange diagrams. For instance, since the BSE reduces in second order to Møller-Plesset perturbation theory, it is self-interaction free in second order. Results for the correlation energy are compared with quantum Monte Carlo benchmarks and excellent agreement is observed. For low densities, however, we find imaginary eigenmodes in the polarization propagator. To avoid the occurrence of imaginary eigenmodes, an approximation to the BSE kernel is proposed that allows us to completely remove this issue in the low-electron-density region. We refer to this approximation as the random-phase approximation with screened exchange (RPAsX). We show that this approximation even slightly improves upon the standard BSE kernel.

  11. Photoionization study of Xe 5s: ionization cross sections and photoelectron angular distributions

    NASA Astrophysics Data System (ADS)

    Aarthi, G.; Jose, J.; Deshmukh, S.; Radojevic, V.; Deshmukh, P. C.; Manson, S. T.

    2014-01-01

    We report studies of photoelectron angular distribution and cross-section for photoionization of xenon 5s electrons using the relativistic multiconfiguration Tamm-Dancoff (MCTD) approximation. We find that MCTD provides a significantly improved agreement with experiment, compared to some of the other relativistic many body approximations such as the relativistic random phase approximation and the relativistic random phase approximation with relaxation, over the entire photon energy region bracketing the near-threshold 5s Cooper minimum, from the 5s threshold up to about 70 eV. The MCTD results in the length form are in much better agreement with the experiment than those in the velocity form, suggesting residual correlations that must be of importance.

  12. Time delay in photoionization in Ne: Effect of different types of correlation

    NASA Astrophysics Data System (ADS)

    Mandal, Ankur; Saha, Soumyajit; Dutta, Narenda Nath; Ganesan, Aarthi; Deshmukh, P. C.; Dolmatov, V. K.; Kheifets, A. S.; Manson, S. T.

    2015-05-01

    Various effects on time delay in photoionization, such as many body correlations, relativity, Cooper minima, autoionizing resonances, etc.,. have been studied. Here we investigate the effects of correlation on time delay using relativistic randon phase approximation (RRPA), RRPA with relaxation (RRPA-R) muticonfiguration Tamm Dancoff (MCTD) (configuration interaction) and many-body perturbation theory (MBPT). Ne is chosen since it has been studied extensively. In an earlier study a truncated RRPA calculation on Ne showed an increase in time delay near the 2s threshold as compared to a nonrelativistic calculation. In the present work, a full RRPA calculation is studied to explore the interchannel coupling effects in the vicinity of the 1s threshold.

  13. Mixed optical Cherenkov-Bremsstrahlung radiation in vicinity of the Cherenkov cone from relativistic heavy ions: Unusual dependence of the angular distribution width on the radiator thickness

    NASA Astrophysics Data System (ADS)

    Rozhkova, E. I.; Pivovarov, Yu. L.

    2016-07-01

    The Cherenkov radiation (ChR) angular distribution is usually described by the Tamm-Frank (TF) theory, which assumes that relativistic charged particle moves uniformly and rectilinearly in the optically transparent radiator. According to the TF theory, the full width at half maximum (FWHM) of the ChR angular distribution inversely depends on the radiator thickness. In the case of relativistic heavy ions (RHI) a slowing-down in the radiator may sufficiently change the angular distribution of optical radiation in vicinity of the Cherenkov cone, since there appears a mixed ChR-Bremsstrahlung radiation. As a result, there occurs a drastic transformation of the FWHM of optical radiation angular distribution in dependence on the radiator thickness: from inversely proportional (TF theory) to the linearly proportional one. In our paper we present the first analysis of this transformation taking account of the gradual velocity decrease of RHI penetrating through a radiator.

  14. Electric dipole transitions between Gamow-Teller and spin-dipole states

    SciTech Connect

    Suzuki, T.; Sagawa, H.; Van Giai, N.

    1998-01-01

    We study electric dipole transitions between Gamow-Teller (GT) and spin-dipole (SD) states. SD and GT excitations are calculated within the Hartree-Fock+Tamm-Dancoff approximation for {sup 48}Sc and {sup 90}Nb. The electric dipole transitions are found to be rather selective, and strong E1 transitions occur to some specific spin-dipole states. Calculated E1 transition strengths between GT and SD states are compared with the analytic sum rules within one-particle{endash}one-hole (1p-1h) configuration space and within both 1p-1h and 2p-2h model space. Possible implications for charge-exchange reactions may help to understand the quenching problem of spin excitations. {copyright} {ital 1998} {ital The American Physical Society}

  15. Gamow-Teller {beta}{sup +} decay of deformed nuclei near the proton drip line

    SciTech Connect

    Frisk, F.; Hamamoto, I.; Zhang, X.Z. |

    1995-11-01

    Using a quasiparticle Tamm-Dancoff approximation (TDA) based on deformed Hartree-Fock (HF) calculations with Skyrme interactions, the distribution of the Gamow-Teller (GT) {beta}{sup +} decay strength is estimated for the HF local minima of even-even deformed nuclei near the proton drip line in the region of 28{lt}{ital Z}{lt}66. The distribution often depends sensitively on the nuclear shape (namely, oblate or prolate). In the region of {ital Z}{lt}50 the possibility of observing {beta}-delayed proton emission depends sensitively on the excess of {ital Z} over {ital Z}={ital N}. In the region of {ital Z}{gt}50 almost the entire estimated GT strength is found to lie below the ground states of the even-even mother nuclei, and the observation of the total GT strength by {beta}-delayed charged-particle(s) emission will be of essential importance.

  16. Double, Rydberg and Charge Transfer Excitations from Pairing Matrix Fluctuation and Particle-Particle Random Phase Approximation

    NASA Astrophysics Data System (ADS)

    Yang, Yang; van Aggelen, Helen; Yang, Weitao

    2014-03-01

    Double, Rydberg and charge transfer (CT) excitations have been great challenges for time-dependent density functional theory (TDDFT). Starting from an (N +/- 2) -electron single-determinant reference, we investigate excitations for the N-electron system through the pairing matrix fluctuation, which contains information on two-electron addition/removal processes. We adopt the particle-particle random phase approximation (pp-RPA) and the particle-particle Tamm-Dancoff approximation (pp-TDA) to approximate the pairing matrix fluctuation and then determine excitation energies by the differences of two-electron addition/removal energies. This approach captures all types of interesting excitations: single and double excitations are described accurately, Rydberg excitations are in good agreement with experimental data and CT excitations display correct 1/R dependence. Furthermore, the pp-RPA and the pp-TDA have a computational cost similar to TDDFT and consequently are promising for practical calculations.

  17. Pseudospectral time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Ko, Chaehyuk; Malick, David K.; Braden, Dale A.; Friesner, Richard A.; Martínez, Todd J.

    2008-03-01

    Time-dependent density functional theory (TDDFT) is implemented within the Tamm-Dancoff approximation (TDA) using a pseudospectral approach to evaluate two-electron repulsion integrals. The pseudospectral approximation uses a split representation with both spectral basis functions and a physical space grid to achieve a reduction in the scaling behavior of electronic structure methods. We demonstrate here that exceptionally sparse grids may be used in the excitation energy calculation, following earlier work employing the pseudospectral approximation for determining correlation energies in wavefunction-based methods with similar conclusions. The pseudospectral TDA-TDDFT method is shown to be up to ten times faster than a conventional algorithm for hybrid functionals without sacrificing chemical accuracy.

  18. Double, Rydberg and charge transfer excitations from pairing matrix fluctuation and particle-particle random phase approximation

    SciTech Connect

    Yang, Yang; Aggelen, Helen van; Yang, Weitao

    2013-12-14

    Double, Rydberg, and charge transfer (CT) excitations have been great challenges for time-dependent density functional theory (TDDFT). Starting from an (N ± 2)-electron single-determinant reference, we investigate excitations for the N-electron system through the pairing matrix fluctuation, which contains information on two-electron addition/removal processes. We adopt the particle-particle random phase approximation (pp-RPA) and the particle-particle Tamm-Dancoff approximation (pp-TDA) to approximate the pairing matrix fluctuation and then determine excitation energies by the differences of two-electron addition/removal energies. This approach captures all types of interesting excitations: single and double excitations are described accurately, Rydberg excitations are in good agreement with experimental data and CT excitations display correct 1/R dependence. Furthermore, the pp-RPA and the pp-TDA have a computational cost similar to TDDFT and consequently are promising for practical calculations.

  19. Representation independent algorithms for molecular response calculations in time-dependent self-consistent field theories

    NASA Astrophysics Data System (ADS)

    Tretiak, Sergei; Isborn, Christine M.; Niklasson, Anders M. N.; Challacombe, Matt

    2009-02-01

    Four different numerical algorithms suitable for a linear scaling implementation of time-dependent Hartree-Fock and Kohn-Sham self-consistent field theories are examined. We compare the performance of modified Lanczos, Arooldi, Davidson, and Rayleigh quotient iterative procedures to solve the random-phase approximation (RPA) (non-Hermitian) and Tamm-Dancoff approximation (TDA) (Hermitian) eigenvalue equations in the molecular orbital-free framework. Semiempirical Hamiltonian models are used to numerically benchmark algorithms for the computation of excited states of realistic molecular systems (conjugated polymers and carbon nanotubes). Convergence behavior and stability are tested with respect to a numerical noise imposed to simulate linear scaling conditions. The results single out the most suitable procedures for linear scaling large-scale time-dependent perturbation theory calculations of electronic excitations.

  20. Linear scaling solution of the time-dependent self-consistent-field equations with quasi-independent Rayleigh quotient iteration

    SciTech Connect

    Challacombe, Matt

    2009-01-01

    An algorithm for solution of the Time-Dependent Self-Consistent-Field (TD-SCF) equations is developed, based on dual solution channels for non-linear optimization of the Tsiper functional [J.Phys.B, 34 L401 (2001)]. This formulation poses the TD-SCF problem as two Rayleigh quotients, coupled weakly through biorthogonality. Convergence rates for the Random Phase Approximation (RPA) are found to be equivalent to the Tamm-Dancoff approximation (TDA). Moreover, the variational nature of the quotient is robust to approximation errors, allowing linear scaling solution to the bulk limit of the RPA matrix-eigenvalue and exchange operator problem for molecular wires with extended conjugation, including polyphenylene vinylene and the (4,3) nanotube.

  1. First order nonadiabatic coupling matrix elements between excited states: Implementation and application at the TD-DFT and pp-TDA levels

    NASA Astrophysics Data System (ADS)

    Li, Zhendong; Suo, Bingbing; Liu, Wenjian

    2014-12-01

    The recently proposed rigorous yet abstract theory of first order nonadiabatic coupling matrix elements (fo-NACME) between electronically excited states [Z. Li and W. Liu, J. Chem. Phys. 141, 014110 (2014)] is specified in detail for two widely used models: The time-dependent density functional theory and the particle-particle Tamm-Dancoff approximation. The actual implementation employs a Lagrangian formalism with atomic-orbital based direct algorithms, which makes the computation of fo-NACME very similar to that of excited-state gradients. Although the methods have great potential in investigating internal conversions and nonadiabatic dynamics between excited states of large molecules, only prototypical systems as a first pilot application are considered here to illustrate some conceptual aspects.

  2. Double, Rydberg and charge transfer excitations from pairing matrix fluctuation and particle-particle random phase approximation

    NASA Astrophysics Data System (ADS)

    Yang, Yang; van Aggelen, Helen; Yang, Weitao

    2013-12-01

    Double, Rydberg, and charge transfer (CT) excitations have been great challenges for time-dependent density functional theory (TDDFT). Starting from an (N ± 2)-electron single-determinant reference, we investigate excitations for the N-electron system through the pairing matrix fluctuation, which contains information on two-electron addition/removal processes. We adopt the particle-particle random phase approximation (pp-RPA) and the particle-particle Tamm-Dancoff approximation (pp-TDA) to approximate the pairing matrix fluctuation and then determine excitation energies by the differences of two-electron addition/removal energies. This approach captures all types of interesting excitations: single and double excitations are described accurately, Rydberg excitations are in good agreement with experimental data and CT excitations display correct 1/R dependence. Furthermore, the pp-RPA and the pp-TDA have a computational cost similar to TDDFT and consequently are promising for practical calculations.

  3. Representation independent algorithms for molecular response calculations in time-dependent self-consistent field theories

    SciTech Connect

    Tretiak, Sergei

    2008-01-01

    Four different numerical algorithms suitable for a linear scaling implementation of time-dependent Hartree-Fock and Kohn-Sham self-consistent field theories are examined. We compare the performance of modified Lanczos, Arooldi, Davidson, and Rayleigh quotient iterative procedures to solve the random-phase approximation (RPA) (non-Hermitian) and Tamm-Dancoff approximation (TDA) (Hermitian) eigenvalue equations in the molecular orbital-free framework. Semiempirical Hamiltonian models are used to numerically benchmark algorithms for the computation of excited states of realistic molecular systems (conjugated polymers and carbon nanotubes). Convergence behavior and stability are tested with respect to a numerical noise imposed to simulate linear scaling conditions. The results single out the most suitable procedures for linear scaling large-scale time-dependent perturbation theory calculations of electronic excitations.

  4. Charge-changing particle-hole excitation of 16N and 16F nuclei

    NASA Astrophysics Data System (ADS)

    Taqi Al-Bayati, Ali H.; Darwesh, Sarah S.

    2013-12-01

    The nuclear structure of 16N (closed shell + ν - π) and 16F (closed shell + π - ν) nuclei is studied using particle-hole proton-neutron Tamm-Dancoff Approximation pn TDA and particle-hole proton-neutron Random Phase Approximation pn RPA. The particle-hole Hamiltonian of PSD model space is to be diagonalized in the presence of the PSDMWKPN interaction: for P-space the Cohen-Kurath interaction, for SD-space the Wildenthal Interaction, for the coupling matrix elements between P- and SD-spaces the Millener-Kurath interaction is used, spurious components were eliminated with CM contribution. The results containing energy level schemes and electromagnetic transition strength are compared with the available experimental data.

  5. Charge-changing particle-hole excitation of {sup 16}N and {sup 16}F nuclei

    SciTech Connect

    Taqi Al-Bayati, Ali H.; Darwesh, Sarah S.

    2013-12-16

    The nuclear structure of {sup 16}N (closed shell + ν − π) and {sup 16}F (closed shell + π − ν) nuclei is studied using particle-hole proton-neutron Tamm-Dancoff Approximation pn TDA and particle-hole proton-neutron Random Phase Approximation pn RPA. The particle-hole Hamiltonian of PSD model space is to be diagonalized in the presence of the PSDMWKPN interaction: for P-space the Cohen-Kurath interaction, for SD-space the Wildenthal Interaction, for the coupling matrix elements between P- and SD-spaces the Millener-Kurath interaction is used, spurious components were eliminated with CM contribution. The results containing energy level schemes and electromagnetic transition strength are compared with the available experimental data.

  6. First order nonadiabatic coupling matrix elements between excited states: Implementation and application at the TD-DFT and pp-TDA levels

    SciTech Connect

    Li, Zhendong; Suo, Bingbing; Liu, Wenjian

    2014-12-28

    The recently proposed rigorous yet abstract theory of first order nonadiabatic coupling matrix elements (fo-NACME) between electronically excited states [Z. Li and W. Liu, J. Chem. Phys. 141, 014110 (2014)] is specified in detail for two widely used models: The time-dependent density functional theory and the particle-particle Tamm-Dancoff approximation. The actual implementation employs a Lagrangian formalism with atomic-orbital based direct algorithms, which makes the computation of fo-NACME very similar to that of excited-state gradients. Although the methods have great potential in investigating internal conversions and nonadiabatic dynamics between excited states of large molecules, only prototypical systems as a first pilot application are considered here to illustrate some conceptual aspects.

  7. Faddeev random-phase approximation for molecules

    SciTech Connect

    Degroote, Matthias; Van Neck, Dimitri; Barbieri, Carlo

    2011-04-15

    The Faddeev random-phase approximation is a Green's function technique that makes use of Faddeev equations to couple the motion of a single electron to the two-particle-one-hole and two-hole-one-particle excitations. This method goes beyond the frequently used third-order algebraic diagrammatic construction method: all diagrams involving the exchange of phonons in the particle-hole and particle-particle channel are retained, but the phonons are now described at the level of the random-phase approximation, which includes ground-state correlations, rather than at the Tamm-Dancoff approximation level, where ground-state correlations are excluded. Previously applied to atoms, this paper presents results for small molecules at equilibrium geometry.

  8. Spin-polarised edge states in atomic Mn chains supported on Cu2N/Cu (100).

    PubMed

    Choi, Deung-Jang; Robles, Roberto; Gauyacq, Jean-Pierre; Rubio-Verdú, Carmen; Lorente, Nicolás; Ignacio Pascual, José

    2016-06-15

    Scanning tunnelling microscopy and density functional theory studies of manganese chains adsorbed on Cu2N/Cu (100) reveal an unsuspected electronic edge state at [Formula: see text] eV above the Fermi energy. This Tamm-like state is strongly localised to the terminal Mn atoms of the chain and fully spin polarised. However, no equivalence is found for occupied states, and the electronic structure at [Formula: see text]  -1 eV is mainly spin unpolarised due to the extended p-states of the N atoms that mediate the coupling between the Mn atoms in the chain. The spin polarisation of the edge state is affected by the antiferromagnetic ordering of the chains leading to non-trivial consequences. PMID:27158116

  9. Tokamaks: from A D Sakharov to the present (the 60-year history of tokamaks)

    NASA Astrophysics Data System (ADS)

    Azizov, E. A.

    2012-02-01

    The paper is prepared on the basis of the report presented at the session of the Physical Sciences Division of the Russian Academy of Sciences (RAS) at the Lebedev Physical Institute, RAS on 25 May 2011, devoted to the 90-year jubilee of Academician Andrei D Sakharov - the initiator of controlled nuclear fusion research in the USSR. The 60-year history of plasma research work in toroidal devices with a longitudinal magnetic field suggested by Andrei D Sakharov and Igor E Tamm in 1950 for the confinement of fusion plasma and known at present as tokamaks is described in brief. The recent (2006) agreement among Russia, the EU, the USA, Japan, China, the Republic of Korea, and India on the joint construction of the international thermonuclear experimental reactor (ITER) in France based on the tokamak concept is discussed. Prospects for using the tokamak as a thermonuclear (14 MeV) neutron source are examined.

  10. A particle-hole calculation for pion production in relativistic heavy-ion collisions

    NASA Technical Reports Server (NTRS)

    Norbury, J. W.; Deutchman, P. A.; Townsend, L. W.

    1985-01-01

    A differential cross section for pi-meson production in peripheral heavy-ion collisions is formulated within the context of a particle-hole model in the Tamm-Dancoff approximation. This is the first attempt at a fully quantum-mechanical particle-hole calculation for pion production in relativistic heavy-ion collisions. The particular reaction studied is an O-16 projectile colliding with a C-12 target at rest. In the projectile a linear combination of isobar-hole states is formed, with the possibility of a coherent isobar giant resonance. The target can be excited to its giant M1 resonance (J-pi = 1(+), T = 1) at 15.11 MeV, or to its isobar analog neighbors, B-12 at 13.4 MeV and N-12 at 17.5 MeV. The theory is compared to recent experimental results.

  11. Contact conductance of a graphene nanoribbon with its graphene nano-electrodes.

    PubMed

    Srivastava, Saurabh; Kino, Hiori; Joachim, Christian

    2016-04-28

    Electronically contacted between two graphene nano-electrodes, the contact conductance (G0) of a graphene nanoribbon (GNR) molecular wire is calculated using mono-electronic Elastic Scattering Quantum Chemistry (ESQC) theory. Different nano-electrode contact geometries are considered ranging from a top face to face van der Waals contact to an adiabatic funnel like planar chemical bonding. The Tamm state contributions to the GNR-graphene nano-electrode electronic interactions are discussed as a function of the molecular orbital hybridization. Contrary to the common belief, the adiabatic-like triangle shaped contact nano-graphene electrode does not provide a large G0 as compared to the abrupt contact geometry. The abrupt contact geometry is even worth than a top face to face van der Waals electronic contact with a metal. PMID:27089225

  12. A D Sakharov: personality and fate

    NASA Astrophysics Data System (ADS)

    Ritus, Vladimir I.

    2012-02-01

    A D Sakharov was an amazingly gifted person for whom, with his combined talents as a physicist and inventor, "physical laws and the relation among phenomena were directly visualized and tangible in all their inherent simplicity" (I E Tamm). The author of the key ideas involved in the hydrogen weapons and fusion reactor programs, and well aware of his scientific and public status, Sakharov was, nevertheless, a modest and highly decent man, always trustful of people in discussing their or his problems. Although his greatest satisfaction lay in successfully solving fundamental problems in physics and cosmology, fate and duty made him turn to matters of universal human significance, particularly human rights, to the gruelling struggle to which he devoted many years of his life.

  13. Equation-of-motion approach to frequency-dependent nuclear electric shielding tensors in the HF molecule

    NASA Astrophysics Data System (ADS)

    Lazzeretti, P.; Rossi, E.; Zanasi, R.

    1983-03-01

    The frequency dependence of the dipole electric polarizability and electric shielding tensors of hydrogen and fluorine nuclei in the HF molecule has been investigated by means of the lower approximations to the equation-of-motion method-namely, the single-transition approximation (STA), the Tamm-Dancoff approximation (TDA), and the random-phase approximation (RPA)-within the framework of dipole length, velocity, acceleration, and mixed formalisms. Some relations are proved, concerning the relative magnitude of TDA and RPA polarizabilities and Thomas-Reich-Kuhn sum rules in the various formalisms. An interdependence between dynamic polarizabilities and nuclear shielding factors has been found. Good agreement with experimental static shielding factors has been obtained in the RPA calculation.

  14. Correlation studies in weakly confining quantum dot potentials

    NASA Astrophysics Data System (ADS)

    Kimani, Peter; Jones, Preston; Winkler, Peter

    We investigate the electron correlation in few-electron closed-shell atomic systems and similarly in few-electron quantum dots under weak confinement. As usual we start with restricted Hartree-Fock (HF) calculations and add electron correlation in steps in a series of approximations based on the single particle Green's function approach: (i) second-order Green function (GF); (ii) 2ph-Tamm-Dancoff approximation (TDA); and (iii) an extended version thereof which introduces ground-state correlation into the TDA. Our studies exhibit similarities and differences between weakly confined quantum dots and standard atomic systems. The calculations support the application of HF, GF, and TDA techniques in the modeling of three-dimensional quantum dot systems. The observed differences emphasize the significance of confinement and electronic features unique to quantum dots, such as the increased binding of electrons with higher angular momentum and thus - compared to atomic systems - modified shell-filling sequences.

  15. First order nonadiabatic coupling matrix elements between excited states: implementation and application at the TD-DFT and pp-TDA levels.

    PubMed

    Li, Zhendong; Suo, Bingbing; Liu, Wenjian

    2014-12-28

    The recently proposed rigorous yet abstract theory of first order nonadiabatic coupling matrix elements (fo-NACME) between electronically excited states [Z. Li and W. Liu, J. Chem. Phys. 141, 014110 (2014)] is specified in detail for two widely used models: The time-dependent density functional theory and the particle-particle Tamm-Dancoff approximation. The actual implementation employs a Lagrangian formalism with atomic-orbital based direct algorithms, which makes the computation of fo-NACME very similar to that of excited-state gradients. Although the methods have great potential in investigating internal conversions and nonadiabatic dynamics between excited states of large molecules, only prototypical systems as a first pilot application are considered here to illustrate some conceptual aspects. PMID:25554131

  16. Reversible brain swelling in crucian carp (Carassius carassius) and goldfish (Carassius auratus) in response to high external ammonia and anoxia.

    PubMed

    Wilkie, Michael P; Stecyk, Jonathan A W; Couturier, Christine S; Sidhu, Sanya; Sandvik, Guro K; Nilsson, Göran E

    2015-06-01

    Increased internal ammonia (hyperammonemia) and ischemic/anoxic insults are known to result in a cascade of deleterious events that can culminate in potentially fatal brain swelling in mammals. It is less clear, however, if the brains of fishes respond to ammonia in a similar manner. The present study demonstrated that the crucian carp (Carassius carassius) was not only able to endure high environmental ammonia exposure (HEA; 2 to 22 mmol L(-1)) but that they experienced 30% increases in brain water content at the highest ammonia concentrations. This swelling was accompanied by 4-fold increases in plasma total ammonia (TAmm) concentration, but both plasma TAmm and brain water content were restored to pre-exposure levels following depuration in ammonia-free water. The closely related, ammonia-tolerant goldfish (Carassius auratus) responded similarly to HEA (up to 3.6 mmol L(-1)), which was accompanied by 4-fold increases in brain glutamine. Subsequent administration of the glutamine synthetase inhibitor, methionine sulfoximine (MSO), reduced brain glutamine accumulation by 80% during HEA. However, MSO failed to prevent ammonia-induced increases in brain water content suggesting that glutamine may not be directly involved in initiating ammonia-induced brain swelling in fishes. Although the mechanisms of brain swelling are likely different, exposure to anoxia for 96 h caused similar, but lesser (10%) increases in brain water content in crucian carp. We conclude that brain swelling in some fishes may be a common response to increased internal ammonia or lower oxygen but further research is needed to deduce the underlying mechanisms behind such responses. PMID:25582543

  17. Does ammonia trigger hyperventilation in the elasmobranch, Squalus acanthias suckleyi?

    PubMed

    De Boeck, Gudrun; Wood, Chris M

    2015-01-15

    We examined the ventilatory response of the spiny dogfish, to elevated internal or environmental ammonia. Sharks were injected via arterial catheters with ammonia solutions or their Na salt equivalents sufficient to increase plasma total ammonia concentration [TAmm]a by 3-5 fold from 145±21μM to 447±150μM using NH4HCO3 and a maximum of 766±100μM using (NH4)2SO4. (NH4)2SO4 caused a small increase in ventilation frequency (+14%) and a large increase in amplitude (+69%), while Na2SO4 did not. However, CO2 partial pressure (PaCO2) also increased and arterial pHa and plasma bicarbonate concentration ([HCO3(-)]a) decreased. NH4HCO3 caused a smaller increase in plasma ammonia resulting in a smaller but significant, short lived increases in ventilation frequency (+6%) and amplitude (36%), together with a rise in PaCO2 and [HCO3(-)]a. Injection with NaHCO3 which increased pHa and [HCO3(-)]a did not change ventilation. Plasma ammonia concentration correlated significantly with ventilation amplitude, while ventilation frequency showed a (negative) correlation with pHa. Exposure to high environmental ammonia (1500μM NH4HCO3) did not induce changes in ventilation until plasma [TAmm]a increased and ventilation amplitude (but not frequency) increased in parallel. We conclude that internal ammonia stimulates ventilation in spiny dogfish, especially amplitude or stroke volume, while environmental ammonia only stimulates ventilation after ammonia diffuses into the bloodstream. PMID:25462837

  18. Novel Urinary Protein Biomarkers Predicting the Development of Microalbuminuria and Renal Function Decline in Type 1 Diabetes

    PubMed Central

    Schlatzer, Daniela; Maahs, David M.; Chance, Mark R.; Dazard, Jean-Eudes; Li, Xiaolin; Hazlett, Fred; Rewers, Marian; Snell-Bergeon, Janet K.

    2012-01-01

    OBJECTIVE To define a panel of novel protein biomarkers of renal disease. RESEARCH DESIGN AND METHODS Adults with type 1 diabetes in the Coronary Artery Calcification in Type 1 Diabetes study who were initially free of renal complications (n = 465) were followed for development of micro- or macroalbuminuria (MA) and early renal function decline (ERFD, annual decline in estimated glomerular filtration rate of ≥3.3%). The label-free proteomic discovery phase was conducted in 13 patients who progressed to MA by the 6-year visit and 11 control subjects, and four proteins (Tamm-Horsfall glycoprotein, α-1 acid glycoprotein, clusterin, and progranulin) identified in the discovery phase were measured by enzyme-linked immunosorbent assay in 74 subjects: group A, normal renal function (n = 35); group B, ERFD without MA (n = 15); group C, MA without ERFD (n = 16); and group D, both ERFD and MA (n = 8). RESULTS In the label-free analysis, a model of progression to MA was built using 252 peptides, yielding an area under the curve (AUC) of 84.7 ± 5.3%. In the validation study, ordinal logistic regression was used to predict development of ERFD, MA, or both. A panel including Tamm-Horsfall glycoprotein (odds ratio 2.9, 95% CI 1.3–6.2, P = 0.008), progranulin (1.9, 0.8–4.5, P = 0.16), clusterin (0.6, 0.3–1.1, P = 0.09), and α-1 acid glycoprotein (1.6, 0.7–3.7, P = 0.27) improved the AUC from 0.841 to 0.889. CONCLUSIONS A panel of four novel protein biomarkers predicted early renal damage in type 1 diabetes. These findings require further validation in other populations for prediction of renal complications and treatment monitoring. PMID:22238279

  19. SU-E-T-238: Monte Carlo Estimation of Cerenkov Dose for Photo-Dynamic Radiotherapy

    SciTech Connect

    Chibani, O; Price, R; Ma, C; Eldib, A; Mora, G

    2014-06-01

    Purpose: Estimation of Cerenkov dose from high-energy megavoltage photon and electron beams in tissue and its impact on the radiosensitization using Protoporphyrine IX (PpIX) for tumor targeting enhancement in radiotherapy. Methods: The GEPTS Monte Carlo code is used to generate dose distributions from 18MV Varian photon beam and generic high-energy (45-MV) photon and (45-MeV) electron beams in a voxel-based tissueequivalent phantom. In addition to calculating the ionization dose, the code scores Cerenkov energy released in the wavelength range 375–425 nm corresponding to the pick of the PpIX absorption spectrum (Fig. 1) using the Frank-Tamm formula. Results: The simulations shows that the produced Cerenkov dose suitable for activating PpIX is 4000 to 5500 times lower than the overall radiation dose for all considered beams (18MV, 45 MV and 45 MeV). These results were contradictory to the recent experimental studies by Axelsson et al. (Med. Phys. 38 (2011) p 4127), where Cerenkov dose was reported to be only two orders of magnitude lower than the radiation dose. Note that our simulation results can be corroborated by a simple model where the Frank and Tamm formula is applied for electrons with 2 MeV/cm stopping power generating Cerenkov photons in the 375–425 nm range and assuming these photons have less than 1mm penetration in tissue. Conclusion: The Cerenkov dose generated by high-energy photon and electron beams may produce minimal clinical effect in comparison with the photon fluence (or dose) commonly used for photo-dynamic therapy. At the present time, it is unclear whether Cerenkov radiation is a significant contributor to the recently observed tumor regression for patients receiving radiotherapy and PpIX versus patients receiving radiotherapy only. The ongoing study will include animal experimentation and investigation of dose rate effects on PpIX response.

  20. Nitrogen metabolism, acid-base regulation, and molecular responses to ammonia and acid infusions in the spiny dogfish shark (Squalus acanthias).

    PubMed

    Nawata, C Michele; Walsh, Patrick J; Wood, Chris M

    2015-07-01

    Although they are ureotelic, marine elasmobranchs express Rh glycoproteins, putative ammonia channels. To address questions raised by a recent study on high environmental ammonia (HEA) exposure, dogfish were intravascularly infused for 24 h at 3 ml kg(-1) h(-1) with isosmotic NaCl (500 mmol l(-1), control), NH4HCO3 (500 mmol l(-1)), NH4Cl (500 mmol l(-1)), or HCl (as 125 mmol l(-1) HCl + 375 mmol l(-1) NaCl). While NaCl had no effect on arterial acid-base status, NH4HCO3 caused mild alkalosis, NH4Cl caused strong acidosis, and HCl caused lesser acidosis, all predominantly metabolic in nature. Total plasma ammonia (T(Amm)) and excretion rates of ammonia (J(Amm)) and urea-N (J(Urea-N)) were unaffected by NaCl or HCl. However, despite equal loading rates, plasma T(Amm) increased to a greater extent with NH4Cl, while J(Amm) increased to a greater extent with NH4HCO3 due to much greater increases in blood-to-water PNH3 gradients. As with HEA, both treatments caused large (90%) elevations of J(Urea-N), indicating that urea-N synthesis by the ornithine-urea cycle (OUC) is driven primarily by ammonia rather than HCO3(-). Branchial mRNA expressions of Rhbg and Rhp2 were unaffected by NH4HCO3 or NH4Cl, but v-type H(+)-ATPase was down-regulated by both treatments, and Rhbg and Na(+)/H(+) exchanger NHE2 were up-regulated by HCl. In the kidney, Rhbg was unresponsive to all treatments, but Rhp2 was up-regulated by HCl, and the urea transporter UT was up-regulated by HCl and NH4Cl. These responses are discussed in the context of current ideas about branchial, renal, and OUC function in this nitrogen-limited predator. PMID:25794843

  1. Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules.

    PubMed

    Cao, Yixiang; Hughes, Thomas; Giesen, Dave; Halls, Mathew D; Goldberg, Alexander; Vadicherla, Tati Reddy; Sastry, Madhavi; Patel, Bhargav; Sherman, Woody; Weisman, Andrew L; Friesner, Richard A

    2016-06-15

    We have developed and implemented pseudospectral time-dependent density-functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm-Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time-dependent density-functional theory with full linear response (PS-FLR-TDDFT) and within the Tamm-Dancoff approximation (PS-TDA-TDDFT) for G2 set molecules using B3LYP/6-31G*(*) show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS-FLR-TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS-FLR-TDDFT and best estimations demonstrate that the accuracy of both PS-FLR-TDDFT and PS-TDA-TDDFT. Calculations for a set of medium-sized molecules, including Cn fullerenes and nanotubes, using the B3LYP functional and 6-31G(**) basis set show PS-TDA-TDDFT provides 19- to 34-fold speedups for Cn fullerenes with 450-1470 basis functions, 11- to 32-fold speedups for nanotubes with 660-3180 basis functions, and 9- to 16-fold speedups for organic molecules with 540-1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46-residue crambin protein, fullerenes up to C540 and nanotubes up to 14×(6,6), using the B3LYP functional and 6-31G

  2. Application of recent double-hybrid density functionals to low-lying singlet-singlet excitation energies of large organic compounds

    NASA Astrophysics Data System (ADS)

    Meo, F. Di; Trouillas, P.; Adamo, C.; Sancho-García, J. C.

    2013-10-01

    The present work assesses some recently developed double-hybrid density functionals (B2π-PLYP, PBE0-DH, and PBE0-2) using linear-response Tamm-Dancoff Time-Dependent Density Functional Theory. This assessment is achieved against experimentally derived low-lying excitation energies of large organic dyes of recent interest, including some excitations dominated by charge-transfer transitions. Comparisons are made with some of the best-performing methods established from the literature, such as PBE0 or B3LYP hybrid or the recently proposed B2-PLYP and B2GP-PLYP double-hybrid models, to ascertain their quality and robustness on equal footing. The accuracy of parameter-free or empirical forms of double-hybrid functionals is also briefly discussed. Generally speaking, it turns out that double-hybrid expressions always provide more accurate estimates than corresponding hybrid methods. Double-hybrid functionals actually reach averaged accuracies of 0.2 eV, that can be admittedly considered close to any intended accuracy limit within the present theoretical framework.

  3. Electronic structure and electron correlation in weakly confining spherical quantum dot potentials

    NASA Astrophysics Data System (ADS)

    Kimani, Peter Borgia Ndungu

    The electronic structure and electron correlations in weakly confining spherical quantum dots potentials are investigated. Following a common practice, the investigation starts with the restricted Hartree-Fock (HF) approximation. Then electron correlation is added in steps in a series of approximations based on the single particle Green's function approach: (i) Second-order Green function (GF) (ii) 2ph-Tamm-Dancoff approximation (TDA) and (iii) an extended version thereof (XTDA) which introduces ground-state correlation into the TDA. The study includes as well Hartree-Fock V (N-1) potential approximation in which framework the Hartree-Fock virtual orbitals are calculated in the field of the N-1 electrons as opposed to the regular but unphysical N-electron field Hartree-Fock calculation of virtual orbitals. For contrast and comparison, the same approximation techniques are applied to few-electron closed-shell atoms and few-electron negative ions for which pertinent data is readily available. The results for the weakly confining spherical quantum dot potentials and the standard atomic systems exhibit fundamental similarities as well as significant differences. For the most part the results of these calculations are in favor of application of HF, GF, and TDA techniques in the modeling of three-dimensional weakly confining quantum dot potentials. The observed differences emphasize the significance of confinement and electronic features unique to quantum dots such as the increased binding of electrons with higher angular momentum and the modified shell filling sequences.

  4. Crystal aggregation in kidney stones; a polymer aggregation problem?

    NASA Astrophysics Data System (ADS)

    Wesson, J.; Beshensky, A.; Viswanathan, P.; Zachowicz, W.; Kleinman, J.

    2008-03-01

    Kidney stones most frequently form as aggregates of calcium oxalate monohydrate (COM) crystals with organic layers between them, and the organic layers contain principally proteins. The pathway leading to the formation of these crystal aggregates in affected people has not been identified, but stone forming patients are thought to have a defect in the structure or distribution of urinary proteins, which normally protect against stone formation. We have developed two polyelectrolyte models that will induce COM crystal aggregation in vitro, and both are consistent with possible urinary protein compositions. The first model was based on mixing polyanionic and polycationic proteins, in portions such that the combined protein charge is near zero. The second model was based on reducing the charge density on partially charged polyanionic proteins, specifically Tamm-Horsfall protein, the second most abundant protein in urine. Both models demonstrated polymer phase separation at solution conditions where COM crystal aggregation was observed. Correlation with data from other bulk crystallization measurements suggest that the anionic side chains form critical binding interactions with COM surfaces that are necessary along with the phase separation process to induce COM crystal aggregation.

  5. Tokamak foundation in USSR/Russia 1950-1990

    NASA Astrophysics Data System (ADS)

    Smirnov, V. P.

    2010-01-01

    In the USSR, nuclear fusion research began in 1950 with the work of I.E. Tamm, A.D. Sakharov and colleagues. They formulated the principles of magnetic confinement of high temperature plasmas, that would allow the development of a thermonuclear reactor. Following this, experimental research on plasma initiation and heating in toroidal systems began in 1951 at the Kurchatov Institute. From the very first devices with vessels made of glass, porcelain or metal with insulating inserts, work progressed to the operation of the first tokamak, T-1, in 1958. More machines followed and the first international collaboration in nuclear fusion, on the T-3 tokamak, established the tokamak as a promising option for magnetic confinement. Experiments continued and specialized machines were developed to test separately improvements to the tokamak concept needed for the production of energy. At the same time, research into plasma physics and tokamak theory was being undertaken which provides the basis for modern theoretical work. Since then, the tokamak concept has been refined by a world-wide effort and today we look forward to the successful operation of ITER.

  6. Quantitative modeling of Cerenkov light production efficiency from medical radionuclides.

    PubMed

    Beattie, Bradley J; Thorek, Daniel L J; Schmidtlein, Charles R; Pentlow, Keith S; Humm, John L; Hielscher, Andreas H

    2012-01-01

    There has been recent and growing interest in applying Cerenkov radiation (CR) for biological applications. Knowledge of the production efficiency and other characteristics of the CR produced by various radionuclides would help in accessing the feasibility of proposed applications and guide the choice of radionuclides. To generate this information we developed models of CR production efficiency based on the Frank-Tamm equation and models of CR distribution based on Monte-Carlo simulations of photon and β particle transport. All models were validated against direct measurements using multiple radionuclides and then applied to a number of radionuclides commonly used in biomedical applications. We show that two radionuclides, Ac-225 and In-111, which have been reported to produce CR in water, do not in fact produce CR directly. We also propose a simple means of using this information to calibrate high sensitivity luminescence imaging systems and show evidence suggesting that this calibration may be more accurate than methods in routine current use. PMID:22363636

  7. Improved Čerenkov counting techniques based on a free parameter model.

    PubMed

    Kossert, K; Grau Carles, A; Nähle, O J

    2014-04-01

    In the past few years, two Čerenkov methods were developed to make activity measurements of high-energy beta emitters in liquid scintillation counters with two or three photomultiplier tubes (PMTs) possible. Both methods are based on a free parameter model and make use of the Frank and Tamm theory for the emission of Čerenkov light. In this article, additional effects are discussed and further improvements are presented. The dependence of the refractive index of water on the wavelength can now be taken into account, which has also an influence on the upper limit of the wavelength region for the production of Čerenkov light. In addition, the dependence of the PMT response on the wavelength is taken into account. Finally, it is possible to take a potential asymmetry of efficiencies in a system with three PMTs into account. To this end, three free parameters are assigned to each individual PMT and then determined by means of a downhill simplex optimization algorithm. The computed counting efficiencies for a triple-to-double coincidence ratio (TDCR) system were compared with experimental data for (32)P, (89)Sr, and (90)Y. PMID:24457420

  8. Charge-transfer correction for improved time-dependent local density approximation excited-state potential energy curves: Analysis within the two-level model with illustration for H2 and LiH

    NASA Astrophysics Data System (ADS)

    Casida, Mark E.; Gutierrez, Fabien; Guan, Jingang; Gadea, Florent-Xavier; Salahub, Dennis; Daudey, Jean-Pierre

    2000-11-01

    Time-dependent density-functional theory (TDDFT) is an increasingly popular approach for calculating molecular excitation energies. However, the TDDFT lowest triplet excitation energy, ωT, of a closed-shell molecule often falls rapidly to zero and then becomes imaginary at large internuclear distances. We show that this unphysical behavior occurs because ωT2 must become negative wherever symmetry breaking lowers the energy of the ground state solution below that of the symmetry unbroken solution. We use the fact that the ΔSCF method gives a qualitatively correct first triplet excited state to derive a "charge-transfer correction" (CTC) for the time-dependent local density approximation (TDLDA) within the two-level model and the Tamm-Dancoff approximation (TDA). Although this correction would not be needed for the exact exchange-correlation functional, it is evidently important for a correct description of molecular excited state potential energy surfaces in the TDLDA. As a byproduct of our analysis, we show why TDLDA and LDA ΔSCF excitation energies are often very similar near the equilibrium geometries. The reasoning given here is fairly general and it is expected that similar corrections will be needed in the case of generalized gradient approximations and hybrid functionals.

  9. What's on the Surface? Physics and Chemistry of Delta-Doped Surfaces

    NASA Technical Reports Server (NTRS)

    Hoenk, Michael

    2011-01-01

    Outline of presentation: 1. Detector surfaces and the problem of stability 2. Delta-doped detectors 3. Physics of Delta-doped Silicon 4. Chemistry of the Si-SiO2 Interface 5. Physics and Chemistry of Delta-doped Surfaces a. Compensation b. Inversion c. Quantum exclusion. Conclusions: 1. Quantum confinement of electrons and holes dominates the behavior of delta-doped surfaces. 2. Stability of delta-doped detectors: Delta-layer creates an approx 1 eV tunnel barrier between bulk and surface. 3. At high surface charge densities, Tamm-Shockley states form at the surface. 4. Surface passivation by quantum exclusion: Near-surface delta-layer suppresses T-S trapping of minority carriers. 5. The Si-SiO2 interface compensates the surface 6. For delta-layers at intermediate depth, surface inversion layer forms 7. Density of Si-SiO2 interface charge can be extremely high (>10(exp 14)/sq cm)

  10. [Urine protein analysis with the sodium-dodecyl-sulfate-polyacrylamide gel-electrophoresis (SDS-PAGE) in healthy cats and cats with kidney diseases].

    PubMed

    Meyer-Lindenberg, A; Wohlsein, P; Trautwein, G; Nolte, I

    1997-03-01

    In this investigation, the value of urine protein analysis by means of molecular-weight related sodium dodecyl-polyacryl gradient gel electrophoresis (SDS-PAGE) was examined with regard to its applicability and diagnostic significance in nephropathy in the cat. A total of 87 cats was included in the study, 30 of them that were clinically healthy served as the control group. The urine protein pattern of this group had, besides the band representing the market albumin, and additional broad band within the size of the marker transferrin. In some cases, weak bands were present within the range of the Tamm-Horsfall-protein and immunoglobulin G. Micromolecular protein bands were not demonstrable. The remaining 57 animals had a histologically proven nephropathy. Thirty-eight cats had elevated urea and/or creatinine values in the plasma (group 1), and 19 animals had values within the reference range (group 2). The urine protein pattern as evidenced by SDS-urine electrophoresis was altered in all cats with histologically proven nephropathy, and it is thus concluded that with this technique a nephropathy can be diagnosed very early and prior to changes of plasma urea and creatinine (group 2). Moreover, in most of the cases, the nephrological changes can be classified as glomerular or tubulo-interstitial (group 1 and group 2). However, it is not possible to draw exact conclusions concerning the underlying morphological changes, nor can the severity of the disease be correctly assessed. PMID:9123982

  11. Lifetime Measurements of Trapped ^232Th^3+

    NASA Astrophysics Data System (ADS)

    Depalatis, Michael; Chapman, Michael

    2012-06-01

    In recent years, there has been considerable interest in the low lying nuclear isomer state of ^229Th which is only several eV above the nuclear ground state [1]. To date, several groups are taking a variety of approaches to finding and exciting this unique state [2], including the use of trapped Th^3+ ions. Despite this attention, few precise measurements have been made of atomic lifetimes. In this work we present experiments to measure the 6D3/2 and 6D5/2 states using laser cooled ^232Th^3+ confined in a linear Paul trap.[4pt] [1] E. Peik and Chr. Tamm, Europhys. Lett. 61, 181 (2003); V. V. Flambaum, Phys. Rev. Lett. 97, 092502 (2006); B. R. Beck et al., Phys. Rev. Lett. 98, 142501 (2007).[0pt] [2] W. G. Rellergert et al., Phys. Rev. Lett. 104, 200802 (2010); S. G. Porsev et al., Phys. Rev. Lett. 105, 182501 (2010); C. J. Campbell et al., Phys. Rev. Let. 106, 223001 (2011).

  12. Long-range doublon transfer in a dimer chain induced by topology and ac fields.

    PubMed

    Bello, M; Creffield, C E; Platero, G

    2016-01-01

    The controlled transfer of particles from one site of a spatial lattice to another is essential for many tasks in quantum information processing and quantum communication. In this work we study how to induce long-range transfer between the two ends of a dimer chain, by coupling states that are localized just on the chain's end-points. This has the appealing feature that the transfer occurs only between the end-points - the particle does not pass through the intermediate sites-making the transfer less susceptible to decoherence. We first show how a repulsively bound-pair of fermions, known as a doublon, can be transferred from one end of the chain to the other via topological edge states. We then show how non-topological surface states of the familiar Shockley or Tamm type can be used to produce a similar form of transfer under the action of a periodic driving potential. Finally we show that combining these effects can produce transfer by means of more exotic topological effects, in which the driving field can be used to switch the topological character of the edge states, as measured by the Zak phase. Our results demonstrate how to induce long range transfer of strongly correlated particles by tuning both topology and driving. PMID:26932406

  13. Long-range doublon transfer in a dimer chain induced by topology and ac fields

    NASA Astrophysics Data System (ADS)

    Bello, M.; Creffield, C. E.; Platero, G.

    2016-03-01

    The controlled transfer of particles from one site of a spatial lattice to another is essential for many tasks in quantum information processing and quantum communication. In this work we study how to induce long-range transfer between the two ends of a dimer chain, by coupling states that are localized just on the chain’s end-points. This has the appealing feature that the transfer occurs only between the end-points - the particle does not pass through the intermediate sites-making the transfer less susceptible to decoherence. We first show how a repulsively bound-pair of fermions, known as a doublon, can be transferred from one end of the chain to the other via topological edge states. We then show how non-topological surface states of the familiar Shockley or Tamm type can be used to produce a similar form of transfer under the action of a periodic driving potential. Finally we show that combining these effects can produce transfer by means of more exotic topological effects, in which the driving field can be used to switch the topological character of the edge states, as measured by the Zak phase. Our results demonstrate how to induce long range transfer of strongly correlated particles by tuning both topology and driving.

  14. Visibly transparent organic photovoltaic with improved transparency and absorption based on tandem photonic crystal for greenhouse application.

    PubMed

    Yang, Fan; Zhang, Ye; Hao, Yuying; Cui, Yanxia; Wang, Wenyan; Ji, Ting; Shi, Fang; Wei, Bin

    2015-12-01

    We demonstrate a visible transparent organic photovoltaic (OPV) with improved transmission and absorption based on tandem photonic crystals (TPCs) for greenhouse applications. The proposed device has an average transmittance of 40.3% in the visible range of 400-700 nm and a high quality transparency spectrum for plant growth with a crop growth factor of 41.9%, considering the weight of the AM 1.5G solar spectrum. Compared with the corresponding transparent OPV without photonic crystals, an enhancement of 20.7% in the average transmittance and of 24.5% in the crop growth factor are achieved. Detailed investigations reveal that the improved transmittance is attributed to the excitation of the optical Tamm state and the light interference effect in TPC. Concomitantly, the total absorption efficiency in the active layer of the designed TPC based transparent OPV reaches 51.5%, being 1.78% higher than that of the transparent OPV without PC and 76% of that of the opaque counterpart. The improved absorption originates from the Bragg forbidden reflectance of TPC. Overall, our proposal achieves the optimized utilization of sunlight by light manipulation of TPC. PMID:26836682

  15. A Preliminary Study Into the Significance of Intrarenal Reflux in BK Virus Nephropathy After Kidney Transplantation

    PubMed Central

    Kawanishi, Kunio; Honda, Kazuho; Koike, Junki; Hattori, Motoshi; Fuchinoue, Shouhei; Tanabe, Kazunari; Oda, Hideaki; Nagashima, Yoji

    2016-01-01

    Background The BK virus typically colonizes the lower urinary tract and is the causative agent in BK virus nephropathy (BKVN), which can progress to allograft dysfunction and graft loss. Urinary reflux in kidney allografts is induced by vesicoureteral reflux or disturbances in intrarenal reflux (IRR), believed to be associated with BKVN. This study was designed to elucidate the relationship between BKVN and IRR. Methods We examined 30 renal transplant recipients histologically diagnosed with BKVN using anti-Simian virus 40 immunohistochemistry and 60 clinically matched control recipients. The BKVN patients were divided into stable (n = 12) and progressive (n = 18) groups according to allograft kidney function 1 year after diagnosis. Histological rejection scores according to the pathological classification of rejection in renal allografts (Banff classification), histological BKVN stages, and histological polyomavirus load levels (pvl) proposed by the Banff working group were evaluated. The IRR was quantified by histological reflux scores defined with retention and reflux of immunostained Tamm-Horsfall protein in renal tubules and glomeruli. Results Higher reflux scores were observed in the BKVN group compared with that in the control group. No differences in clinical parameters were observed between the BKVN and control groups. Reflux scores and pvl were significantly higher in the progressive group than in the stable BKVN group with no significant difference in BK stage observed between groups. Reflux scores were found to be significantly correlated with pvl. Conclusions Our preliminary study suggested that IRR might be a predisposing and prognostic factor in BKVN.

  16. Biogeochemical role of magnetite in urban soils (Review of publications)

    NASA Astrophysics Data System (ADS)

    Vodyanitskii, Yu. N.

    2013-03-01

    The surface horizons of urban soils are enriched in technogenic magnetite Fe3O4 accumulated from emissions. Its content there reaches 3-4% and more, whereas it does not exceed 0.1% in the back-ground soils. In urban soils, large spherical magnetite particles of pseudo-single-domain and multidomain fabric predominate; the cavities in magnetic spherules decrease their chemical stability and increase their reactivity. Magnetite is most often destroyed in urban soils due to complexing; its destruction may be initiated by mineral salts entering the soil with deicing mixtures and by organic acids excreted by roots (e.g., by oxalic acid). The high solubility of magnetite with ammonium oxalate should be taken into account when using Tamm's reagent for the analysis of urban soils. Magnetite is a mineral carrier of some heavy metals. Therefore, its content (as determined from the magnetic susceptibility) serves as an indirect index of soil pollution. In addition, magnetite may affect many soil properties as a reducer and sorbent. It adsorbs phosphorus thus preventing the penetration of this nutrient into rivers and lakes. Magnetite also oxidizes Cl-containing aliphatic hydrocarbons and purifies the soil. Although magnetite enters urban soils as a pollutant, its influence on the soil properties cannot be unambiguously judged as only negative.

  17. Quantitative Modeling of Cerenkov Light Production Efficiency from Medical Radionuclides

    PubMed Central

    Beattie, Bradley J.; Thorek, Daniel L. J.; Schmidtlein, Charles R.; Pentlow, Keith S.; Humm, John L.; Hielscher, Andreas H.

    2012-01-01

    There has been recent and growing interest in applying Cerenkov radiation (CR) for biological applications. Knowledge of the production efficiency and other characteristics of the CR produced by various radionuclides would help in accessing the feasibility of proposed applications and guide the choice of radionuclides. To generate this information we developed models of CR production efficiency based on the Frank-Tamm equation and models of CR distribution based on Monte-Carlo simulations of photon and β particle transport. All models were validated against direct measurements using multiple radionuclides and then applied to a number of radionuclides commonly used in biomedical applications. We show that two radionuclides, Ac-225 and In-111, which have been reported to produce CR in water, do not in fact produce CR directly. We also propose a simple means of using this information to calibrate high sensitivity luminescence imaging systems and show evidence suggesting that this calibration may be more accurate than methods in routine current use. PMID:22363636

  18. Evaluation of nephrotoxicity in vitro using a suspension of highly purified porcine proximal tubular cells and characterization of the cells in primary culture.

    PubMed

    Kruidering, M; Maasdam, D H; Prins, F A; de Heer, E; Mulder, G J; Nagelkerke, J F

    1994-01-01

    Proximal tubular cells (PTC) were isolated from porcine kidney by collagenase treatment, subsequently purified on a discontinuous density gradient and finally cultured. Porcine PTC (PPTC) in primary culture expressed keratin, characteristics of epithelia and brush border specific glycoproteins (FX1A). In addition, vimentin was present. All cells were negative for the endothelial marker pal-E. Less than 0.1% expressed the Tamm-Horsfall protein, characteristic of the distal tubule, while less than 0.3% of all cells in culture expressed desmin, characteristic of connective tissue (i.e. fibroblasts) and mesangial cells. Ultrastructural analysis revealed microvilli, tight junctions and abundant mitochondrial and lysosomes, all characteristics of proximal tubular cells. Freshly isolated PPTC were validated as in vitro model to detect nephrotoxicity by studying the effect of mercuric chloride, cis-platin, p-aminophenol and the halogenated alkenes 1,2 dichlorovinyl-l-cysteine, S-(1,1-difluoro-2,2-dichloroethyl)-L-cysteine (DCDFE-cys) and the glutathione conjugate of DCDFE on viability and mitochondrial membrane potential. The cells responded, time- and dose-dependently, to the nephrotoxic compounds with a decrease in mitochondrial membrane potential and loss of viability. The sensitivity of the porcine cells in detecting toxic effects corresponded favorably with in vitro systems derived from other animals. PMID:7859034

  19. From the inverted pendulum to the periodic interface modes

    NASA Astrophysics Data System (ADS)

    Combe, Nicolas

    2013-01-01

    The physics of the spatial propagation of monochromatic waves in periodic media is related to the temporal evolution of the parametric oscillators. We transpose the possibility that a parametric pendulum oscillates in the vicinity of its unstable equilibrium position to the case of monochromatic waves in a lossless unidimensional periodic medium. We develop this concept, that can formally applies to any kind of waves, to the case of longitudinal elastic wave. Our analysis yields us to study the propagation of monochromatic waves in a periodic structure involving two main periods. We evidence a class of phonons we refer to as periodic interface modes that propagate in these structures. These modes are similar to the optical Tamm states exhibited in photonic crystals. Our analysis is based on both a formal and an analytical approach. The application of the concept to the case of phonons in an experimentally realizable structure is given. We finally show how to control the frequencies of these phonons from the engineering of the periodic structure.

  20. Einstein studies in Russia

    NASA Astrophysics Data System (ADS)

    Balashov, Yuri; Vizgin, Vladimir

    This volume presents a selection of the best contributions by Russian scholars - historians and philosophers of science - to the Einstein Studies industry, broadly construed. Many of the papers were first published in Russian, in the Einshteinovskiy Sbornik series (Einstein Studies) initiated by I. Tamm in 1966. This book explores the historical and foundational issues in general relativity and relativistic cosmology, Einstein's contributions to quantum theory of radiation, and the rise of Dirac's quantum electrodynamics. It also includes a detailed description of the physics colloquium Einstein established and coordinated in 1912- 1914 in Zürich. The contributors draw extensively on documentation previously unavailable to most scholars. Materials from various Russian archives shed new light on the famous exchange (regarding the first evolutionary cosmological models) between Einstein and Alexander Friedmann in the early 1920's and on the role of Boris Podolsky and Vladimir Fock in the emergence of quantum electrodynamics. The little-known correspondence between Einstein and a famous German pilot Paul Erhardt suggests that during World War I, the former was involved with aero- and hydrodynamics research and ways of improving airplane design. Other articles introduce new approaches to important foundational questions in general relativity and cosmology. Historians, philosophers, and sociologists of science will find much new and unexpected material in this engaging volume presenting the best of recent Russian scholarship in the field. The book is also very accessible to the general reader.

  1. Computed Cerenkov luminescence yields for radionuclides used in biology and medicine.

    PubMed

    Gill, Ruby K; Mitchell, Gregory S; Cherry, Simon R

    2015-06-01

    Cerenkov luminescence imaging is an emerging biomedical imaging modality that takes advantage of the optical Cerenkov photons emitted following the decay of radionuclides in dielectric media such as tissue. Cerenkov radiation potentially allows many biomedically-relevant radionuclides, including all positron-emitting radionuclides, to be imaged in vivo using sensitive CCD cameras. Cerenkov luminescence may also provide a means to deliver light deep inside tissue over a sustained period of time using targeted radiotracers. This light could be used for photoactivation, including photorelease of therapeutics, photodynamic therapy and photochemical internalization. Essential to assessing the feasibility of these concepts, and the design of instrumentation designed for detecting Cerenkov radiation, is an understanding of the light yield of different radionuclides in tissue. This is complicated by the dependence of the light yield on refractive index and the volume of the sample being interrogated. Using Monte Carlo simulations, in conjunction with step-wise use of the Frank-Tamm equation, we studied forty-seven different radionuclides and show that Cerenkov light yields in tissue can be as high as a few tens of photons per nuclear decay for a wavelength range of 400-800 nm. The dependency on refractive index and source volume is explored, and an expression for the scaling factor necessary to compute the Cerenkov yield in any arbitrary spectral band is given. This data will be of broad utility in guiding the application of Cerenkov radiation emitted from biomedical radionuclides. PMID:25973972

  2. Tailoring the optical properties of wide-bandgap based microcavities via metal films

    SciTech Connect

    Sebald, K. Rahman, SK. S.; Cornelius, M.; Gutowski, J.; Klein, T.; Klembt, S.; Kruse, C.; Hommel, D.

    2015-08-10

    We report on the tuning of the optical properties of II-VI-material-based microcavity samples, which is achieved by depositing Ag films on top of the structures. The micro-reflectivity spectra show a spectral shift of the sample resonance dependent on the metal layer thickness. By comparison of the experimental findings with the theoretical calculations applying the transfer matrix method on a metal-dielectric mirror structure, the influence of the metal layer particularly with regard to its partial oxidation was explored. Tamm plasmon modes are created at the interface between an open cavity with three ZnSe quantum wells and a metal layer on top. When tuning the excitonic emission relative to the mode by changing the sample temperature, an anticrossing of the resonances was observed. This is a clear indication that the strong coupling regime has been achieved in that sample configuration yielding a Rabi splitting of 18.5 meV. These results are promising for the realization of polariton-based optical devices with a rather simple sample configuration.

  3. Photonic lattices in organic microcavities: Bloch states and control of lasing

    NASA Astrophysics Data System (ADS)

    Mischok, Andreas; Brückner, Robert; Fröb, Hartmut; Lyssenko, Vadim G.; Leo, Karl

    2015-09-01

    Organic microcavities comprising the host:guest emitter system Alq3:DCM offer an interesting playground to experimentally study the dispersion characteristics of laterally patterned microlasers due to the broad emission spectrum and large oscillator strength of the organic dye. By structuring of metallic or dielectric sublayers directly on top of the bottom mirror, we precisely manipulate the mode structure and influence the coherent emission properties of the device. Embedding silver layers into a microcavity leads to an interaction of the optical cavity-state in the organic layer and the neighboring metal which red-shifts the cavity resonance, creating a Tamm-plasmon-polariton state. A patterning of the metal can in turn be exploited to fabricate deep photonic wells of micron-size, efficiently confining light in lateral direction. In periodic arrays of silver wires, we create a Kronig-Penney-like optical potential in the cavity and in turn observe optical Bloch states spanning over several photonic wires. We modify the Kronig-Penney theory to analytically describe the full far-field emission dispersion of our cavities and show the emergence of either zero- , π-, or 2π- phase-locking in the system. By investigating periodic SiO2 patterns, we experimentally observe stimulated emission from the ground and different excited discrete states at room temperature and are able to directly control the laser emission from both extended and confined modes of the photonic wires at room-temperature.

  4. Identifying and tracing potential energy surfaces of electronic excitations with specific character via their transition origins: application to oxirane.

    PubMed

    Li, Jian-Hao; Zuehlsdorff, T J; Payne, M C; Hine, N D M

    2015-05-14

    We show that the transition origins of electronic excitations identified by quantified natural transition orbital (QNTO) analysis can be employed to connect potential energy surfaces (PESs) according to their character across a wide range of molecular geometries. This is achieved by locating the switching of transition origins of adiabatic potential surfaces as the geometry changes. The transition vectors for analysing transition origins are provided by linear response time-dependent density functional theory (TDDFT) calculations under the Tamm-Dancoff approximation. We study the photochemical CO ring opening of oxirane as an example and show that the results corroborate the traditional Gomer-Noyes mechanism derived experimentally. The knowledge of specific states for the reaction also agrees well with that given by previous theoretical work using TDDFT surface-hopping dynamics that was validated by high-quality quantum Monte Carlo calculations. We also show that QNTO can be useful for considerably larger and more complex systems: by projecting the excitations to those of a reference oxirane molecule, the approach is able to identify and analyse specific excitations of a trans-2,3-diphenyloxirane molecule. PMID:25875632

  5. General description of electromagnetic radiation processes based on instantaneous charge acceleration in ''endpoints''

    SciTech Connect

    James, Clancy W.; Falcke, Heino; Huege, Tim; Ludwig, Marianne

    2011-11-15

    We present a methodology for calculating the electromagnetic radiation from accelerated charged particles. Our formulation - the 'endpoint formulation' - combines numerous results developed in the literature in relation to radiation arising from particle acceleration using a complete, and completely general, treatment. We do this by describing particle motion via a series of discrete, instantaneous acceleration events, or 'endpoints', with each such event being treated as a source of emission. This method implicitly allows for particle creation and destruction, and is suited to direct numerical implementation in either the time or frequency domains. In this paper we demonstrate the complete generality of our method for calculating the radiated field from charged particle acceleration, and show how it reduces to the classical named radiation processes such as synchrotron, Tamm's description of Vavilov-Cherenkov, and transition radiation under appropriate limits. Using this formulation, we are immediately able to answer outstanding questions regarding the phenomenology of radio emission from ultra-high-energy particle interactions in both the earth's atmosphere and the moon. In particular, our formulation makes it apparent that the dominant emission component of the Askaryan effect (coherent radio-wave radiation from high-energy particle cascades in dense media) comes from coherent 'bremsstrahlung' from particle acceleration, rather than coherent Vavilov-Cherenkov radiation.

  6. Observation of unconventional edge states in 'photonic graphene'.

    PubMed

    Plotnik, Yonatan; Rechtsman, Mikael C; Song, Daohong; Heinrich, Matthias; Zeuner, Julia M; Nolte, Stefan; Lumer, Yaakov; Malkova, Natalia; Xu, Jingjun; Szameit, Alexander; Chen, Zhigang; Segev, Mordechai

    2014-01-01

    Graphene, a two-dimensional honeycomb lattice of carbon atoms, has been attracting much interest in recent years. Electrons therein behave as massless relativistic particles, giving rise to strikingly unconventional phenomena. Graphene edge states are essential for understanding the electronic properties of this material. However, the coarse or impure nature of the graphene edges hampers the ability to directly probe the edge states. Perhaps the best example is given by the edge states on the bearded edge that have never been observed-because such an edge is unstable in graphene. Here, we use the optical equivalent of graphene-a photonic honeycomb lattice-to study the edge states and their properties. We directly image the edge states on both the zigzag and bearded edges of this photonic graphene, measure their dispersion properties, and most importantly, find a new type of edge state: one residing on the bearded edge that has never been predicted or observed. This edge state lies near the Van Hove singularity in the edge band structure and can be classified as a Tamm-like state lacking any surface defect. The mechanism underlying its formation may counterintuitively appear in other crystalline systems. PMID:24193661

  7. Time-dependent projected Hartree-Fock

    SciTech Connect

    Tsuchimochi, Takashi; Van Voorhis, Troy

    2015-03-28

    Projected Hartree-Fock (PHF) has recently emerged as an alternative approach to describing degenerate systems where static correlation is abundant, when the spin-symmetry is projected. Here, we derive a set of linearized time-dependent equations for PHF in order to be able to access excited states. The close connection of such linear-response time-dependent PHF (TDPHF) to the stability condition of a PHF wave function is discussed. Expanding this analysis also makes it possible to give analytical expressions for the projected coupling terms of Hamiltonian and overlaps between excited Slater determinants. TDPHF with spin-projection (TDSUHF) and its Tamm-Dancoff approximation are benchmarked for several electronically degenerate molecules including the dissociating H{sub 2}, F{sub 2} and O{sub 3} at equilibrium, and the distorted ethylene. It is shown that they give consistently better descriptions of excited states than does time-dependent HF (TDHF). Furthermore, we demonstrate that they offer not only singly but also doubly excited states, which naturally arise upon spin-projection. We also address the thermodynamic limit of TDSUHF, using non-interacting He gas. While TDPHF singly excited states tend to converge to those of HF with the size of the system due to the lack of size-extensivity of PHF, doubly excited states remain reasonable even at the thermodynamic limit. We find that the overall performance of our method is systematically better than the regular TDHF in many cases at the same computational scaling.

  8. Localized end states in density modulated quantum wires and rings.

    PubMed

    Gangadharaiah, Suhas; Trifunovic, Luka; Loss, Daniel

    2012-03-30

    We study finite quantum wires and rings in the presence of a charge-density wave gap induced by a periodic modulation of the chemical potential. We show that the Tamm-Shockley bound states emerging at the ends of the wire are stable against weak disorder and interactions, for discrete open chains and for continuum systems. The low-energy physics can be mapped onto the Jackiw-Rebbi equations describing massive Dirac fermions and bound end states. We treat interactions via the continuum model and show that they increase the charge gap and further localize the end states. The electrons placed in the two localized states on the opposite ends of the wire can interact via exchange interactions and this setup can be used as a double quantum dot hosting spin qubits. The existence of these states could be experimentally detected through the presence of an unusual 4π Aharonov-Bohm periodicity in the spectrum and persistent current as a function of the external flux. PMID:22540720

  9. Introducing constricted variational density functional theory in its relaxed self-consistent formulation (RSCF-CV-DFT) as an alternative to adiabatic time dependent density functional theory for studies of charge transfer transitions

    SciTech Connect

    Krykunov, Mykhaylo; Seth, Mike; Ziegler, Tom

    2014-05-14

    We have applied the relaxed and self-consistent extension of constricted variational density functional theory (RSCF-CV-DFT) for the calculation of the lowest charge transfer transitions in the molecular complex X-TCNE between X = benzene and TCNE = tetracyanoethylene. Use was made of functionals with a fixed fraction (α) of Hartree-Fock exchange ranging from α = 0 to α = 0.5 as well as functionals with a long range correction (LC) that introduces Hartree-Fock exchange for longer inter-electronic distances. A detailed comparison and analysis is given for each functional between the performance of RSCF-CV-DFT and adiabatic time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation. It is shown that in this particular case, all functionals afford the same reasonable agreement with experiment for RSCF-CV-DFT whereas only the LC-functionals afford a fair agreement with experiment using TDDFT. We have in addition calculated the CT transition energy for X-TCNE with X = toluene, o-xylene, and naphthalene employing the same functionals as for X = benzene. It is shown that the calculated charge transfer excitation energies are in as good agreement with experiment as those obtained from highly optimized LC-functionals using adiabatic TDDFT. We finally discuss the relation between the optimization of length separation parameters and orbital relaxation in the RSCF-CV-DFT scheme.

  10. Surface aggregation of urinary proteins and aspartic acid-rich peptides on the faces of calcium oxalate monohydrate investigated by in situ force microscopy

    SciTech Connect

    Weaver, M L; Qiu, S R; Hoyer, J R; Casey, W H; Nancollas, G H; De Yoreo, J J

    2008-05-28

    The growth of calcium oxalate monohydrate in the presence of Tamm-Horsfall protein (THP), osteopontin (OPN), and the 27-residue synthetic peptides (DDDS){sub 6}DDD and (DDDG){sub 6}DDD [where D = aspartic acid and X = S (serine) or G (glycine)] was investigated via in situ atomic force microscopy (AFM). The results show that these three growth modulators create extensive deposits on the crystal faces. Depending on the modulator and crystal face, these deposits can occur as discrete aggregates, filamentary structures, or uniform coatings. These proteinaceous films can lead to either the inhibition or increase of the step speeds (with respect to the impurity-free system) depending on a range of factors that include peptide or protein concentration, supersaturation and ionic strength. While THP and the linear peptides act, respectively, to exclusively increase and inhibit growth on the (-101) face, both exhibit dual functionality on the (010) face, inhibiting growth at low supersaturation or high modulator concentration and accelerating growth at high supersaturation or low modulator concentration. Based on analyses of growth morphologies and dependencies of step speeds on supersaturation and protein or peptide concentration, we argue for a picture of growth modulation that accounts for the observations in terms of the strength of binding to the surfaces and steps and the interplay of electrostatic and solvent-induced forces at crystal surface.

  11. Composite surface-plasmon-polariton waves guided by a thin metal layer sandwiched between a homogeneous isotropic dielectric material and a periodically multilayered isotropic dielectric material

    NASA Astrophysics Data System (ADS)

    Chiadini, Francesco; Fiumara, Vincenzo; Scaglione, Antonio; Lakhtakia, Akhlesh

    2015-01-01

    Multiple p- and s-polarized compound surface-plasmon-polariton (SPP) waves at a fixed frequency can be guided by a structure consisting of a metal layer sandwiched between a homogeneous isotropic dielectric (HID) material and a periodic multilayered isotropic dielectric (PMLID) material. For any thickness of the metal layer, at least one compound SPP wave must exist. It possesses the p-polarization state, and is strongly bound to the metal/HID interface when the metal thickness is large but to both metal/dielectric interfaces when the metal thickness is small. When the metal layer vanishes, this compound SPP wave transmutes into a Tamm wave. Additional compound SPP waves exist, depending on the thickness of the metal layer, the relative permittivity of the HID material, and the period and composition of the PMLID material. Some of these are p-polarized, the others are s-polarized. All of them differ in phase speed, attenuation rate, and field profile, even though all are excitable at the same frequency. The multiplicity and dependence of the number of compound SPP waves on the relative permittivity of the HID material when the metal layer is thin could be useful for optical sensing applications and intrachip plasmonic optical communication.

  12. Loss of Urinary Macromolecules in Mice Causes Interstitial and Intratubular Renal Calcification Dependent on the Underlying Conditions

    NASA Astrophysics Data System (ADS)

    Wu, Xue-Ru; Lieske, John C.; Evan, Andrew P.; Sommer, Andre J.; Liaw, Lucy; Mo, Lan

    2008-09-01

    Urinary protein macromolecules have long been thought to play a role in influencing the various phases of urolithiasis including nucleation, growth, aggregation of mineral crystals and their subsequent adhesion to the renal epithelial cells. However, compelling evidence regarding their precise role was lacking, due partly to the fact that most prior studies were done in vitro and results were highly variable depending on the experimental conditions. The advent of genetic engineering technology has made it possible to study urinary protein macromolecules within an in vivo biological system. Indeed, recent studies have begun to shed light on the net effects of loss of one or more macromolecules on the earliest steps of urolithiasis. This paper focuses on the in vivo consequences of inactivating Tamm-Horsfall protein and/or osteopontin, two major urinary glycoproteins, using the knockout approach. The renal phenotypes of both single and double knockout mice under spontaneous or hyperoxaluric conditions will be described. The functional significance of the urinary macromolecules as critical defense factors against renal calcification will also be discussed.

  13. Theoretical rationalization of the singlet-triplet gap in OLEDs materials: impact of charge-transfer character.

    PubMed

    Moral, M; Muccioli, L; Son, W-J; Olivier, Y; Sancho-García, J C

    2015-01-13

    New materials for OLED applications with low singlet-triplet energy splitting have been recently synthesized in order to allow for the conversion of triplet into singlet excitons (emitting light) via a Thermally Activated Delayed Fluorescence (TADF) process, which involves excited-states with a non-negligible amount of Charge-Transfer (CT). The accurate modeling of these states with Time-Dependent Density Functional Theory (TD-DFT), the most used method so far because of the favorable trade-off between accuracy and computational cost, is however particularly challenging. We carefully address this issue here by considering materials with small (high) singlet-triplet gap acting as emitter (host) in OLEDs and by comparing the accuracy of TD-DFT and the corresponding Tamm-Dancoff Approximation (TDA), which is found to greatly reduce error bars with respect to experiments thanks to better estimates for the lowest singlet-triplet transition. Finally, we quantitatively correlate the singlet-triplet splitting values with the extent of CT, using for it a simple metric extracted from calculations with double-hybrid functionals, that might be applied in further molecular engineering studies. PMID:26574215

  14. Analytical approach for the excited-state Hessian in time-dependent density functional theory: Formalism, implementation, and performance

    NASA Astrophysics Data System (ADS)

    Liu, Jie; Liang, WanZhen

    2011-11-01

    The paper presents the formalism, implementation, and performance of the analytical approach for the excited-state Hessian in the time-dependent density functional theory (TDDFT) that extends our previous work [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011)] on the analytical Hessian in TDDFT within Tamm-Dancoff approximation (TDA) to full TDDFT. In contrast to TDA-TDDFT, an appreciable advantage of full TDDFT is that it maintains the oscillator strength sum rule, and therefore yields more precise results for the oscillator strength and other related physical quantities. For the excited-state harmonic vibrational frequency calculation, however, full TDDFT does not seem to be advantageous since the numerical tests demonstrate that the accuracy of TDDFT with and without TDA are comparable to each other. As a common practice, the computed harmonic vibrational frequencies are scaled by a suitable scale factor to yield good agreement with the experimental fundamental frequencies. Here we apply both the optimized ground-state and excited-state scale factors to scale the calculated excited-state harmonic frequencies and find that the scaling decreases the root-mean-square errors. The optimized scale factors derived from the excited-state calculations are slightly smaller than those from the ground-state calculations.

  15. Linear response theory for the density matrix renormalization group: Efficient algorithms for strongly correlated excited states

    NASA Astrophysics Data System (ADS)

    Nakatani, Naoki; Wouters, Sebastian; Van Neck, Dimitri; Chan, Garnet Kin-Lic

    2014-01-01

    Linear response theory for the density matrix renormalization group (DMRG-LRT) was first presented in terms of the DMRG renormalization projectors [J. J. Dorando, J. Hachmann, and G. K.-L. Chan, J. Chem. Phys. 130, 184111 (2009)]. Later, with an understanding of the manifold structure of the matrix product state (MPS) ansatz, which lies at the basis of the DMRG algorithm, a way was found to construct the linear response space for general choices of the MPS gauge in terms of the tangent space vectors [J. Haegeman, J. I. Cirac, T. J. Osborne, I. Pižorn, H. Verschelde, and F. Verstraete, Phys. Rev. Lett. 107, 070601 (2011)]. These two developments led to the formulation of the Tamm-Dancoff and random phase approximations (TDA and RPA) for MPS. This work describes how these LRTs may be efficiently implemented through minor modifications of the DMRG sweep algorithm, at a computational cost which scales the same as the ground-state DMRG algorithm. In fact, the mixed canonical MPS form implicit to the DMRG sweep is essential for efficient implementation of the RPA, due to the structure of the second-order tangent space. We present ab initio DMRG-TDA results for excited states of polyenes, the water molecule, and a [2Fe-2S] iron-sulfur cluster.

  16. QPNM calculation for the ground state magnetic moments of odd-mass deformed nuclei: 157-167Er isotopes

    NASA Astrophysics Data System (ADS)

    Yakut, H.; Guliyev, E.; Guner, M.; Tabar, E.; Zenginerler, Z.

    2012-08-01

    A new microscopic method has been developed in the framework of the Quasiparticle-Phonon Nuclear Model (QPNM) in order to investigate spin polarization effects on the magnetic properties such as magnetic moment, intrinsic magnetic moment and effective gs factor of the ground state of odd-mass 157-167Er isotopes. The calculations were performed using both Tamm-Dancoff Approximation (TDA) and Quasiparticle Random-Phase Approximation (QRPA). Reasonably good agreement has been obtained between the QRPA results and the relevant experimental data. Furthermore the variation of the intrinsic magnetic moment gK values with the mass number A exhibits similar behavior for both theoretical and experimental results. From the compression of the calculated intrinsic magnetic moment values with the experimental data the spin-spin interaction parameter has been found as χ=(30/A) MeV for odd-mass 157-167Er isotopes. Our results clarify the possibility of using this new method to describe the magnetic properties of odd-mass deformed nuclei.

  17. Computational simulation and interpretation of the low-lying excited electronic states and electronic spectrum of thioanisole.

    PubMed

    Li, Shaohong L; Xu, Xuefei; Truhlar, Donald G

    2015-08-21

    Three singlet states, namely a closed-shell ground state and two excited states with (1)ππ* and (1)nσ* character, have been suggested to be responsible for the radiationless decay or photochemical reaction of photoexcited thioanisole. The correct interpretation of the electronic spectrum is critical for understanding the character of these low-lying excited states, but the experimental spectrum is yet to be fully interpreted. In the work reported here, we investigated the nature of those three states and a fourth singlet state of thioanisole using electronic structure calculations by multireference perturbation theory, by completely-renormalized equation-of-motion coupled cluster theory with single and double excitations and noniterative inclusion of connected triples (CR-EOM-CCSD(T)), and by linear-response time-dependent density functional theory (TDDFT). We clarified the assignment of the electronic spectrum by simulating it using a normal-mode sampling approach combined with TDDFT in the Tamm-Dancoff approximation (TDA). The understanding of the electronic states and of the accuracy of the electronic structure methods lays the foundation of our future work of constructing potential energy surfaces. PMID:26088195

  18. Calculation Method for Exciton Wavefunctions with Electron--Hole Exchange Interaction: Application to Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Ajiki, Hiroshi

    2013-05-01

    A new method for calculating exciton wavefunctions in the presence of a long-range electron--hole (e--h) exchange interaction (EXI) is presented. The e--h EXI arises, for example, for cross-polarized excitons in a single-walled carbon nanotube (SWNT). Cross-polarized excitons have previously been calculated as an eigenvalue problem of a Bethe--Salpeter equation (BSE) within the Tamm--Dancoff-type approximation (TDA). The resulting wavefunctions provide quite different absorption spectra in comparison with those calculated in the self-consistent-field method [S. Uryu and T. Ando, J. Phys.: Conf. Ser. 302 (2011) 012004]. Although the self-consistent-field method is more reliable, exciton wavefunctions cannot be obtained from this method. A general method is derived here to obtain exciton wavefunctions that take the e--h EXI into account within the TDA, and the method is applied to the cross-polarized excitons of a SWNT. The absorption spectra calculated from the resulting exciton wavefunctions agree well with the spectra calculated from the self-consistent-field method within a rotating-wave approximation.

  19. Thouless theorem for matrix product states and subsequent post density matrix renormalization group methods

    NASA Astrophysics Data System (ADS)

    Wouters, Sebastian; Nakatani, Naoki; Van Neck, Dimitri; Chan, Garnet Kin-Lic

    2013-08-01

    The similarities between Hartree-Fock (HF) theory and the density matrix renormalization group (DMRG) are explored. Both methods can be formulated as the variational optimization of a wave-function Ansatz. Linearization of the time-dependent variational principle near a variational minimum allows to derive the random phase approximation (RPA). We show that the nonredundant parameterization of the matrix product state (MPS) tangent space [J. Haegeman, J. I. Cirac, T. J. Osborne, I. Pižorn, H. Verschelde, and F. Verstraete, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.107.070601 107, 070601 (2011)] leads to the Thouless theorem for MPS, i.e., an explicit nonredundant parameterization of the entire MPS manifold, starting from a specific MPS reference. Excitation operators are identified, which extends the analogy between HF and DMRG to the Tamm-Dancoff approximation (TDA), the configuration interaction (CI) expansion, and coupled cluster theory. For a small one-dimensional Hubbard chain, we use a CI-MPS Ansatz with single and double excitations to improve on the ground state and to calculate low-lying excitation energies. For a symmetry-broken ground state of this model, we show that RPA-MPS allows to retrieve the Goldstone mode. We also discuss calculations of the RPA-MPS correlation energy. With the long-range quantum chemical Pariser-Parr-Pople Hamiltonian, low-lying TDA-MPS and RPA-MPS excitation energies for polyenes are obtained.

  20. All-electron G W +Bethe-Salpeter calculations on small molecules

    NASA Astrophysics Data System (ADS)

    Hirose, Daichi; Noguchi, Yoshifumi; Sugino, Osamu

    2015-05-01

    Accuracy of the first-principles G W +Bethe-Salpeter equation (BSE) method is examined for low-energy excited states of small molecules. The standard formalism, which is based on the one-shot G W approximation and the Tamm-Dancoff approximation (TDA), is found to underestimate the optical gap of N2, CO, H2O ,C2H4 , and CH2O by about 1 eV. Possible origins are investigated separately for the effect of TDA and for the approximate schemes of the self-energy operator, which are known to cause overbinding of the electron-hole pair and overscreening of the interaction. By applying the known correction formula, we find the amount of the correction is too small to overcome the underestimated excitation energy. This result indicates a need for fundamental revision of the G W +BSE method rather than adjustment of the standard one. We expect that this study makes the problems in the current G W +BSE formalism clearer and provides useful information for further intrinsic development beyond the current framework.

  1. Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

    PubMed

    Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

    2016-03-21

    We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution. PMID:26907588

  2. Relativistic Continuum Shell Model

    NASA Astrophysics Data System (ADS)

    Grineviciute, Janina; Halderson, Dean

    2011-04-01

    The R-matrix formalism of Lane and Thomas has been extended to the relativistic case so that the many-coupled channels problem may be solved for systems in which binary breakup channels satisfy a relative Dirac equation. The formalism was previously applied to the relativistic impulse approximation RIA and now we applied it to Quantum Hadrodynamics QHD in the continuum Tamm-Dancoff approximation TDA with the classical meson fields replaced by one-meson exchange potentials. None of the published QHD parameters provide a decent fit to the 15 N + p elastic cross section. The deficiency is also evident in inability of the QHD parameters with the one meson exchange potentials to reproduce the QHD single particle energies. Results with alternate parameters sets are presented. A. M. Lane and R. G. Thomas, R-Matrix Theory of Nuclear Reactions, Reviews of Modern Physics, 30 (1958) 257

  3. Reliable Prediction with Tuned Range-Separated Functionals of the Singlet-Triplet Gap in Organic Emitters for Thermally Activated Delayed Fluorescence.

    PubMed

    Sun, Haitao; Zhong, Cheng; Brédas, Jean-Luc

    2015-08-11

    The thermally activated delayed fluorescence (TADF) mechanism has recently attracted significant interest in the field of organic light-emitting diodes (OLEDs). TADF relies on the presence of a very small energy gap between the lowest singlet and triplet excited states. Here, we demonstrate that time-dependent density functional theory in the Tamm-Dancoff approximation can be very successful in calculations of the lowest singlet and triplet excitation energies and the corresponding singlet-triplet gap when using nonempirically tuned range-separated functionals. Such functionals provide very good estimates in a series of 17 molecules used in TADF-based OLED devices with mean absolute deviations of 0.15 eV for the vertical singlet excitation energies and 0.09 eV [0.07 eV] for the adiabatic [vertical] singlet-triplet energy gaps as well as low relative errors and high correlation coefficients compared to the corresponding experimental values. They significantly outperform conventional functionals, a feature which is rationalized on the basis of the amount of exact-exchange included and the delocalization error. The present work provides a reliable theoretical tool for the prediction and development of novel TADF-based materials with low singlet-triplet energetic splittings. PMID:26574466

  4. Derivation of the RPA (Random Phase Approximation) Equation of ATDDFT (Adiabatic Time Dependent Density Functional Ground State Response Theory) from an Excited State Variational Approach Based on the Ground State Functional.

    PubMed

    Ziegler, Tom; Krykunov, Mykhaylo; Autschbach, Jochen

    2014-09-01

    The random phase approximation (RPA) equation of adiabatic time dependent density functional ground state response theory (ATDDFT) has been used extensively in studies of excited states. It extracts information about excited states from frequency dependent ground state response properties and avoids, thus, in an elegant way, direct Kohn-Sham calculations on excited states in accordance with the status of DFT as a ground state theory. Thus, excitation energies can be found as resonance poles of frequency dependent ground state polarizability from the eigenvalues of the RPA equation. ATDDFT is approximate in that it makes use of a frequency independent energy kernel derived from the ground state functional. It is shown in this study that one can derive the RPA equation of ATDDFT from a purely variational approach in which stationary states above the ground state are located using our constricted variational DFT (CV-DFT) method and the ground state functional. Thus, locating stationary states above the ground state due to one-electron excitations with a ground state functional is completely equivalent to solving the RPA equation of TDDFT employing the same functional. The present study is an extension of a previous work in which we demonstrated the equivalence between ATDDFT and CV-DFT within the Tamm-Dancoff approximation. PMID:26588541

  5. Effects of urine composition on epithelial Na+ channel-targeted protease activity.

    PubMed

    Berman, Jonathan M; Awayda, Ryan G; Awayda, Mouhamed S

    2015-11-01

    We examined human urinary proteolytic activity toward the Epithelial Sodium Channel (ENaC). We focused on two sites in each of alpha and gamma ENaC that are targets of endogenous and exogenous proteases. We examined the effects of ionic strength, pH and urinary H(+)-buffers, metabolic intermediates, redox molecules, and large urinary proteins. Monoatomic cations caused the largest effect, with sodium inhibiting activity in the 15-515 mEq range. Multivalent cations zinc and copper inhibited urinary proteolytic activity at concentrations below 100 μmol/L. Similar to sodium, urea caused a 30% inhibition in the 0-500 mmol/L range. This was not observed with acetone and ethanol. Modulating urinary redox status modified activity with H2O2 stimulated and ascorbate inhibited activity. Minimal effects (<10%) were observed with caffeine, glucose, several TCA cycle intermediates, salicylic acid, inorganic phosphate, albumin, creatinine, and Tamm-Horsfall protein. The cumulative activity of ENaC-cleaving proteases was highest at neutral pH, however, alpha and gamma proteases exhibited an inverse dependence with alpha stimulated at acidic and gamma stimulated at alkaline pH. These data indicate that ENaC-targeting urinary proteolytic activity is sensitive to sodium, urea and pH and changes in these components can modify channel cleavage and activation status, and likely downstream sodium absorption unrelated to changes in protein or channel density. PMID:26564065

  6. Modified non-Euclidean transformation on the SO(2N+2) U(N+1) Grassmannian and SO(2N + 1) random phase approximation for unified description of Bose and Fermi type collective excitations

    NASA Astrophysics Data System (ADS)

    Nishiyama, Seiya; da Providência, João

    2016-02-01

    In a slight different way from the previous one, we propose a modified non-Euclidean transformation on the SO(2N+2) U(N+1) Grassmannian which gives the projected SO(2N+1) Tamm-Dancoff equation. We derive a classical time-dependent (TD) SO(2N + 1) Lagrangian which, through the Euler-Lagrange equation of motion for SO(2N+2) U(N+1) coset variables, brings another form of the previous extended-TD Hartree-Bogoliubov (HB) equation. The SO(2N + 1) random phase approximation (RPA) is derived using Dyson representation for paired and unpaired operators. In the SO(2N) HB case, one boson and two boson excited states are realized. We, however, stress non-existence of a higher RPA vacuum. An integrable system is given by a geometrical concept of zero-curvature, i.e. integrability condition of connection on the corresponding Lie group. From the group theoretical viewpoint, we show the existence of a symplectic two-form ω.

  7. Subfractionation, characterization and in-depth proteomic analysis of glomerular membrane vesicles in human urine

    PubMed Central

    Hogan, Marie C.; Johnson, Kenneth L.; Zenka, Roman M.; Charlesworth, M. Cristine; Madden, Benjamin J.; Mahoney, Doug W.; Oberg, Ann L.; Huang, Bing Q.; Nesbitt, Lisa L.; Bakeberg, Jason L.; Bergen, H. Robert; Ward, Christopher J.

    2014-01-01

    Urinary exosome-like vesicles (ELVs) are a heterogenous mixture (diameter 40–200nm) containing vesicles shed from all segments of the nephron including glomerular podocytes. Contamination with Tamm Horsfall protein (THP) oligomers has hampered their isolation and proteomic analysis. Here we improved ELV isolation protocols employing density centrifugation to remove THP and albumin, and isolated a glomerular membranous vesicle (GMV) enriched subfraction from 7 individuals identifying 1830 proteins and in 3 patients with glomerular disease identifying 5657 unique proteins. The GMV fraction was composed of podocin/podocalyxin positive irregularly shaped membranous vesicles and podocin/podocalyxin negative classical exosomes. Ingenuity pathway analysis identified integrin, actin cytoskeleton and RhoGDI signaling in the top three canonical represented signaling pathways and 19 other proteins associated with inherited glomerular diseases. The GMVs are of podocyte origin and the density gradient technique allowed isolation in a reproducible manner. We show many nephrotic syndrome proteins, proteases and complement proteins involved in glomerular disease are in GMVs and some were shed in the disease state (nephrin, TRPC6 and INF2 and PLA2R). We calculated sample sizes required to identify new glomerular disease biomarkers, expand the ELV proteome and provide a reference proteome in a database that may prove useful in the search for biomarkers of glomerular disease. PMID:24196483

  8. Long-range doublon transfer in a dimer chain induced by topology and ac fields

    PubMed Central

    Bello, M.; Creffield, C. E.; Platero, G.

    2016-01-01

    The controlled transfer of particles from one site of a spatial lattice to another is essential for many tasks in quantum information processing and quantum communication. In this work we study how to induce long-range transfer between the two ends of a dimer chain, by coupling states that are localized just on the chain’s end-points. This has the appealing feature that the transfer occurs only between the end-points – the particle does not pass through the intermediate sites–making the transfer less susceptible to decoherence. We first show how a repulsively bound-pair of fermions, known as a doublon, can be transferred from one end of the chain to the other via topological edge states. We then show how non-topological surface states of the familiar Shockley or Tamm type can be used to produce a similar form of transfer under the action of a periodic driving potential. Finally we show that combining these effects can produce transfer by means of more exotic topological effects, in which the driving field can be used to switch the topological character of the edge states, as measured by the Zak phase. Our results demonstrate how to induce long range transfer of strongly correlated particles by tuning both topology and driving. PMID:26932406

  9. FROM THE HISTORY OF PHYSICS: Moscow State University physics alumni and the Soviet Atomic Project

    NASA Astrophysics Data System (ADS)

    Kiselev, Gennadii V.

    2005-12-01

    In this paper, two closely related themes are addressed: (1) the role that M V Lomonosov Moscow State University (MSU) played in training specialists in physics for the Soviet Atomic Project, and (2) what its alumni contributed to the development of thermonuclear weapons. In its earlier stages, the Soviet Atomic Project was in acute need of qualified personnel, without whom building nuclear and thermonuclear weapons would be an impossible task, and MSU became a key higher educational institution grappled with the training problem. The first part of the paper discusses the efforts of the leading Soviet scientists and leaders of FMD (First Main Directorate) to organize the training of specialists in nuclear physics at the MSU Physics Department and, on the other hand, to create a new Physics and Technology Department at the university. As a result, a number of Soviet Government's resolutions were prepared and issued, part of which are presented in the paper and give an idea of the large-scale challenges this sphere of education was facing at the time. Information is presented for the first time on the early MSU Physics Department graduates in the structure of matter, being employed in the FMD organizations and enterprises from 1948 to 1951. The second part discusses the contribution to the development of thermonuclear weapons by the teams of scientists led by Academicians I E Tamm, A N Tikhonov, and I M Frank, and including MSU physics alumni. The paper will be useful to anyone interested in the history of Russian physics.

  10. Computed Cerenkov luminescence yields for radionuclides used in biology and medicine

    NASA Astrophysics Data System (ADS)

    Gill, Ruby K.; Mitchell, Gregory S.; Cherry, Simon R.

    2015-06-01

    Cerenkov luminescence imaging is an emerging biomedical imaging modality that takes advantage of the optical Cerenkov photons emitted following the decay of radionuclides in dielectric media such as tissue. Cerenkov radiation potentially allows many biomedically-relevant radionuclides, including all positron-emitting radionuclides, to be imaged in vivo using sensitive CCD cameras. Cerenkov luminescence may also provide a means to deliver light deep inside tissue over a sustained period of time using targeted radiotracers. This light could be used for photoactivation, including photorelease of therapeutics, photodynamic therapy and photochemical internalization. Essential to assessing the feasibility of these concepts, and the design of instrumentation designed for detecting Cerenkov radiation, is an understanding of the light yield of different radionuclides in tissue. This is complicated by the dependence of the light yield on refractive index and the volume of the sample being interrogated. Using Monte Carlo simulations, in conjunction with step-wise use of the Frank-Tamm equation, we studied forty-seven different radionuclides and show that Cerenkov light yields in tissue can be as high as a few tens of photons per nuclear decay for a wavelength range of 400-800 nm. The dependency on refractive index and source volume is explored, and an expression for the scaling factor necessary to compute the Cerenkov yield in any arbitrary spectral band is given. This data will be of broad utility in guiding the application of Cerenkov radiation emitted from biomedical radionuclides.

  11. Analytic derivative couplings for spin-flip configuration interaction singles and spin-flip time-dependent density functional theory

    SciTech Connect

    Zhang, Xing; Herbert, John M.

    2014-08-14

    We revisit the calculation of analytic derivative couplings for configuration interaction singles (CIS), and derive and implement these couplings for its spin-flip variant for the first time. Our algorithm is closely related to the CIS analytic energy gradient algorithm and should be straightforward to implement in any quantum chemistry code that has CIS analytic energy gradients. The additional cost of evaluating the derivative couplings is small in comparison to the cost of evaluating the gradients for the two electronic states in question. Incorporation of an exchange-correlation term provides an ad hoc extension of this formalism to time-dependent density functional theory within the Tamm-Dancoff approximation, without the need to invoke quadratic response theory or evaluate third derivatives of the exchange-correlation functional. Application to several different conical intersections in ethylene demonstrates that minimum-energy crossing points along conical seams can be located at substantially reduced cost when analytic derivative couplings are employed, as compared to use of a branching-plane updating algorithm that does not require these couplings. Application to H{sub 3} near its D{sub 3h} geometry demonstrates that correct topology is obtained in the vicinity of a conical intersection involving a degenerate ground state.

  12. Nonperturbative renormalization and the electron{close_quote}s anomalous moment in large-{alpha} QED

    SciTech Connect

    Hiller, J.R.; Brodsky, S.J.

    1999-01-01

    We study the physical electron in quantum electrodynamics expanded on the light-cone Fock space in order to address two problems: (1) the physics of the electron{close_quote}s anomalous magnetic moment a{sub e} in nonperturbative QED and (2) the practical problems of ultraviolet regularization and renormalization in truncated nonperturbative light-cone Hamiltonian theory. We present results for a{sub e} computed in a light-cone gauge Fock space truncated to include one bare electron and at most two photons, i.e., up to two photons in flight. The calculational scheme uses an invariant mass cutoff, discretized light-cone quantization (DLCQ), a Tamm-Dancoff truncation of the Fock space, and a photon mass regulator. We introduce new weighting methods which greatly improve convergence to the continuum within DLCQ. Nonperturbative renormalization of the coupling and electron mass are carried out, and a limit on the magnitude of the effective physical coupling strength is computed. A large renormalized coupling strength {alpha}{sub R}=0.1 is then used to make the nonperturbative effects in the electron anomalous moment from the one-electron, two-photon Fock state sector numerically detectable. {copyright} {ital 1998} {ital The American Physical Society}

  13. Macroscopicity of quantum superpositions on a one-parameter unitary path in Hilbert space

    NASA Astrophysics Data System (ADS)

    Volkoff, T. J.; Whaley, K. B.

    2014-12-01

    We analyze quantum states formed as superpositions of an initial pure product state and its image under local unitary evolution, using two measurement-based measures of superposition size: one based on the optimal quantum binary distinguishability of the branches of the superposition and another based on the ratio of the maximal quantum Fisher information of the superposition to that of its branches, i.e., the relative metrological usefulness of the superposition. A general formula for the effective sizes of these states according to the branch-distinguishability measure is obtained and applied to superposition states of N quantum harmonic oscillators composed of Gaussian branches. Considering optimal distinguishability of pure states on a time-evolution path leads naturally to a notion of distinguishability time that generalizes the well-known orthogonalization times of Mandelstam and Tamm and Margolus and Levitin. We further show that the distinguishability time provides a compact operational expression for the superposition size measure based on the relative quantum Fisher information. By restricting the maximization procedure in the definition of this measure to an appropriate algebra of observables, we show that the superposition size of, e.g., NOON states and hierarchical cat states, can scale linearly with the number of elementary particles comprising the superposition state, implying precision scaling inversely with the total number of photons when these states are employed as probes in quantum parameter estimation of a 1-local Hamiltonian in this algebra.

  14. Application of a Boson Expansion formalism based on the Random Phase Approximation to samarium isotopes

    SciTech Connect

    Jamaluddin, M.B.

    1986-01-01

    The Boson Expansion Theory of Kishimoto and Tamura has proved to be very successful in describing quadrupole collective motions in even-even nuclei. This theory, however, involves a complicated transformation from the Tamm-Dancoff phonons to the phonons of the random Phase Approximation. In this thesis a Boson Expansion formalism, derived directly from the Random Phase Approximation and set forth by Pedracchi and Tamura, is used to derive the boson forms of the nuclear Hamiltonian and the electromagnetic transition operator. Detailed discussions of the formalism of Pedrocchi and Tamura and its extension needed to perform realistic calculations are presented. The technique used to deriving the boson forms and the formulae used in the calculations are also given a thorough treatment to demonstrate the simplicity of this approach. Finally, the theory is tested by applying it to calculate the energy levels and some electromagnetic properties of the Samarium isotopes. The results show that the present theory is capable of describing the range of behavior from a vibrational to a rotational character of the Samarium isotopes as well as the previous theory.

  15. Effect of an isotonic rehydration sports drink and exercise on urolithiasis in rats.

    PubMed

    Abreu, N P; Bergamaschi, C T; di Marco, G S; Razvickas, C V; Schor, N

    2005-04-01

    The objective of the present study was to evaluate the role of physical exercise as well as the influence of hydration with an isotonic sports drink on renal function in male Wistar rats. Four groups were studied over a period of 42 days: 1) control (N = 9); 2) physical exercise (Exe, N = 7); 3) isotonic drink (Drink, N = 8); 4) physical exercise + isotonic drink (Exe + Drink, N = 8). Physical exercise consisted of running on a motor-driven treadmill for 1 h/day, at 20 m/min, 5 days a week. The isotonic sports drink was a commercial solution used by athletes for rehydration after physical activity, 2 ml administered by gavage twice a day. Urine cultures were performed in all animals. Twenty-four-hour urine samples were collected in metabolic cages at the beginning and at the end of the protocol period. Urinary and plasma parameters (sodium, potassium, urea, creatinine, calcium) did not differ among groups. However, an amorphous material was observed in the bladders of animals in the Exe + Drink and Drink groups. Characterization of the material by Western blot revealed the presence of Tamm-Horsfall protein and angiotensin converting enzyme. Physical exercise and the isotonic drink did not change the plasma or urinary parameters measured. However, the isotonic drink induced the formation of intravesical matrix, suggesting a potential lithogenic risk. PMID:15962183

  16. Electron correlation effects on photoionization time delay in atomic Ar and Xe

    NASA Astrophysics Data System (ADS)

    Ganesan, A.; Saha, S.; Decshmukh, P. C.; Manson, S. T.; Kheifets, A. S.

    2016-05-01

    Time delay studies in photoionization processes have stimulated much interest as they provide valuable dynamical information about electron correlation and relativistic effects. In a recent work on Wigner time delay in the photoionization of noble gas atoms, it was found that correlations resulting from interchannel coupling involving shells with different principal quantum numbers have significant effects on 2s and 2p photoionization of Ne, 3s photoionization of Ar, and 3d photoionization of Kr. In the present work, photoionization time delay in inner and outer subshells of the noble gases Ar and Xe are examined by including electron correlations using different many body techniques: (i) the relativistic-random-phase approximation (RRPA), (ii) RRPA with relaxation, to include relaxation effects of the residual ion and (iii) the relativistic multiconfiguration Tamm-Dancoff (RMCTD) approximation. The (sometimes substantial) effects of the inclusion of non-RPA correlations on the photoionization Wigner time delay are reported. Work supported by DOE, Office of Chemical Sciences and DST (India).

  17. Time-dependent projected Hartree-Fock

    NASA Astrophysics Data System (ADS)

    Tsuchimochi, Takashi; Van Voorhis, Troy

    2015-03-01

    Projected Hartree-Fock (PHF) has recently emerged as an alternative approach to describing degenerate systems where static correlation is abundant, when the spin-symmetry is projected. Here, we derive a set of linearized time-dependent equations for PHF in order to be able to access excited states. The close connection of such linear-response time-dependent PHF (TDPHF) to the stability condition of a PHF wave function is discussed. Expanding this analysis also makes it possible to give analytical expressions for the projected coupling terms of Hamiltonian and overlaps between excited Slater determinants. TDPHF with spin-projection (TDSUHF) and its Tamm-Dancoff approximation are benchmarked for several electronically degenerate molecules including the dissociating H2, F2 and O3 at equilibrium, and the distorted ethylene. It is shown that they give consistently better descriptions of excited states than does time-dependent HF (TDHF). Furthermore, we demonstrate that they offer not only singly but also doubly excited states, which naturally arise upon spin-projection. We also address the thermodynamic limit of TDSUHF, using non-interacting He gas. While TDPHF singly excited states tend to converge to those of HF with the size of the system due to the lack of size-extensivity of PHF, doubly excited states remain reasonable even at the thermodynamic limit. We find that the overall performance of our method is systematically better than the regular TDHF in many cases at the same computational scaling.

  18. Double excitations and state-to-state transition dipoles in π-π∗ excited singlet states of linear polyenes: Time-dependent density-functional theory versus multiconfigurational methods

    NASA Astrophysics Data System (ADS)

    Mikhailov, Ivan A.; Tafur, Sergio; Masunov, Artëm E.

    2008-01-01

    The effect of static and dynamic electron correlation on the nature of excited states and state-to-state transition dipole moments is studied with a multideterminant wave function approach on the example of all-trans linear polyenes ( C4H6 , C6H8 , and C8H10 ). Symmetry-forbidden singlet nAg states were found to separate into three groups: purely single, mostly single, and mostly double excitations. The excited-state absorption spectrum is dominated by two bright transitions: 1Bu-2Ag and 1Bu-mAg , where mAg is the state, corresponding to two-electron excitation from the highest occupied to lowest unoccupied molecular orbital. The richness of the excited-state absorption spectra and strong mixing of the doubly excited determinants into lower- nAg states, reported previously at the complete active space self-consistent field level of theory, were found to be an artifact of the smaller active space, limited to π orbitals. When dynamic σ-π correlation is taken into account, single- and double-excited states become relatively well separated at least at the equilibrium geometry of the ground state. This electronic structure is closely reproduced within time-dependent density-functional theory (TD DFT), where double excitations appear in a second-order coupled electronic oscillator formalism and do not mix with the single excitations obtained within the linear response. An extension of TD DFT is proposed, where the Tamm-Dancoff approximation (TDA) is invoked after the linear response equations are solved (a posteriori TDA). The numerical performance of this extension is validated against multideterminant-wave-function and quadratic-response TD DFT results. It is recommended for use with a sum-over-states approach to predict the nonlinear optical properties of conjugated molecules.

  19. Acid-base buffering of soils in transitional and transitional-accumulative positions of undisturbed southern-taiga landscapes

    NASA Astrophysics Data System (ADS)

    Rusakova, E. S.; Ishkova, I. V.; Tolpeshta, I. I.; Sokolova, T. A.

    2012-05-01

    The method of continuous potentiometric titration (CPT) of soil water suspensions was used to evaluate the acid-base buffering of samples from the major genetic horizons of podzolic soils on a slope and soddy gley soils on the adjacent floodplain of a rivulet. In the soils of the slope, the buffering to acid upon titration from the pH of the initial titration point (ITP) to pH 3 in all the horizons was 1.5-2.0 times lower than that in the podzolic soils of the leveled interfluve, which could be due to the active leaching of exchangeable bases and oxalate-soluble aluminum and iron compounds with the later soil flows. In the soddy gley soils, the buffering to acid in the mineral horizons was 2-10 times higher than that in the podzolic soils. A direct dependence of the soil buffering to acid on the total content of exchangeable bases and on the content of oxalate-soluble aluminum compounds was found. A direct dependence of the buffering to basic upon titration from the ITP to pH 10 on the contents of the oxalate-soluble aluminum and organic matter was observed in the mineral horizons of all the studied soils. The soil treatment with Tamm's reagent resulted in the decrease of the buffering to acid in the soddy gley soils of the floodplain, as well as in the decrease of the buffering to basic in the soils on the slopes and in the soddy gley soils. It was also found that the redistribution of the mobile aluminum compounds between the eluvial, transitional, and transitional-accumulative positions in the undisturbed southern taiga landscapes leads to significant spatial differentiation of the acid-base buffering of the mineral soil horizons with a considerable increase in the buffer capacity of the soils within the transitional-accumulative terrain positions.

  20. Fructus Gardenia Extract ameliorates oxonate-induced hyperuricemia with renal dysfunction in mice by regulating organic ion transporters and mOIT3.

    PubMed

    Hu, Qing-Hua; Zhu, Ji-Xiao; Ji, Jing; Wei, Lin-Lin; Miao, Ming-Xing; Ji, Hui

    2013-01-01

    The potent anti-hyperuricemia activities of Fructus Gardenia Extract (FGE) have been well reported. The aim of this study was to evaluate the uricosuric and nephro-protective effects of FGE and explore its possible mechanisms of action in oxonate-induced hyperuricemic mice. FGE was orally administered to hyperuricemic and normal mice for 1 week. Serum and urinary levels of uric acid, creatinine and blood urea nitrogen (BUN), and fractional excretion of uric acid (FEUA) were measured. The mRNA and protein levels of mouse urate transporter 1 (mURAT1), glucose transporter 9 (mGLUT9), ATP-binding cassette, subfamily G, 2 (mABCG2), organic anion transporter 1 (mOAT1), mOAT3, oncoprotein induced transcript 3 (mOIT3), organic cation/carnitine transporters in the kidney were analyzed. Simultaneously, Tamm-Horsfall glycoprotein (THP) levels in urine and kidney were detected. FGE significantly reduced serum urate levels and increased urinary urate levels and FEUA in hyperuricemic mice. It could also effectively reverse oxonate-induced alterations in renal mURAT1, mGLUT9, mOAT1 and mOIT3 expressions, as well as THP levels, resulting in the enhancement of renal uric acid excretion. Moreover, FGE decreased serum creatinine and BUN levels, and up-regulated expression of organic cation/carnitine transporters, improving renal dysfunction in this model. Furthermore, FGE decreased renal mABCG2 expressions in hyperuricemic mice, contributing to its beneficial actions. However, further investigation is needed in clinical trials of FGE and its bioactive components. PMID:23899832

  1. Characterization of renal biomarkers for use in clinical trials: biomarker evaluation in healthy volunteers

    PubMed Central

    Brott, David A; Adler, Scott H; Arani, Ramin; Lovick, Susan C; Pinches, Mark; Furlong, Stephen T

    2014-01-01

    Background Several preclinical urinary biomarkers have been qualified and accepted by the health authorities (US Food and Drug Administration, European Medicines Agency, and Pharmaceuticals and Medical Devices Agency) for detecting drug-induced kidney injury during preclinical toxicologic testing. Validated human assays for many of these biomarkers have become commercially available, and this study was designed to characterize some of the novel clinical renal biomarkers. The objective of this study was to evaluate clinical renal biomarkers in a typical Phase I healthy volunteer population to determine confidence intervals (pilot reference intervals), intersubject and intrasubject variability, effects of food intake, effect of sex, and vendor assay comparisons. Methods Spot urine samples from 20 male and 19 female healthy volunteers collected on multiple days were analyzed using single analyte and multiplex assays. The following analytes were measured: α-1-microglobulin, β-2-microglobulin, calbindin, clusterin, connective tissue growth factor, creatinine, cystatin C, glutathione S-transferase-α, kidney injury marker-1, microalbumin, N-acetyl-β-(D) glucosaminidase, neutrophil gelatinase-associated lipocalin, osteopontin, Tamm-Horsfall urinary glycoprotein, tissue inhibitor of metalloproteinase 1, trefoil factor 3, and vascular endothelial growth factor. Results Confidence intervals were determined from the single analyte and multiplex assays. Intersubject and intrasubject variability ranged from 38% to 299% and from 29% to 82% for biomarker concentration, and from 24% to 331% and from 10% to 67% for biomarker concentration normalized to creatinine, respectively. There was no major effect of food intake or sex. Single analyte and multiplex assays correlated with r2≥0.700 for five of six biomarkers when evaluating biomarker concentration, but for only two biomarkers when evaluating concentration normalized to creatinine. Conclusion Confidence intervals as well as

  2. Calibration of scalar relativistic density functional theory for the calculation of sulfur K-edge X-ray absorption spectra.

    PubMed

    Debeer George, Serena; Neese, Frank

    2010-02-15

    Sulfur K-edge X-ray absorption spectroscopy has been proven to be a powerful tool for investigating the electronic structures of sulfur-containing coordination complexes. The full information content of the spectra can be developed through a combination of experiment and time-dependent density functional theory (TD-DFT). In this work, the necessary calibration is carried out for a range of contemporary functionals (BP86, PBE, OLYP, OPBE, B3LYP, PBE0, TPSSh) in a scalar relativistic (0(th) order regular approximation, ZORA) DFT framework. It is shown that with recently developed segmented all-electron scalar relativistic (SARC) basis sets one obtains results that are as good as with large, uncontracted basis sets. The errors in the calibrated transition energies are on the order of 0.1 eV. The error in calibrated intensities is slightly larger, but the calculations are still in excellent agreement with experiment. The behavior of full TD-DFT linear response versus the Tamm-Dancoff approximation has been evaluated with the result that two methods are almost indistinguishable. The inclusion of relativistic effects barely changes the results for first row transition metal complexes, however, the contributions become visible for second-row transition metals and reach a maximum (of an approximately 10% change in the calibration parameters) for third row transition metal species. The protocol developed here is approximately 10 times more efficient than the previously employed protocol, which was based on large, uncontracted basis sets. The calibration strategy followed here may be readily extended to other edges. PMID:20092349

  3. Immunolocalization of the four prostaglandin E2 receptor proteins EP1, EP2, EP3, and EP4 in human kidney.

    PubMed

    Morath, R; Klein, T; Seyberth, H W; Nüsing, R M

    1999-09-01

    Four prostaglandin E2 receptor subtypes designated EP1, EP2, EP3, and EP4 have been shown to mediate a variety of effects of prostaglandin E2 (PGE2) on glomerular hemodynamics, tubular salt and water reabsorption, and on blood vessels in the human kidney. Despite the important role of renal PGE2, the localization of PGE2 receptor proteins in the human kidney is unknown. The present study used antipeptide antibodies to the EP1 to EP4 receptor proteins for immunolocalization in human kidney tissue. Immunoblot studies using these antibodies demonstrated distinct bands in membrane fraction from human kidney. By means of immunohistochemistry, expression of the human EP1 receptor subtype protein in renal tissue was detected mainly in connecting segments, cortical and medullary collecting ducts, and in the media of arteries and afferent and efferent arterioles. The human EP2 receptor subtype protein was detectable only in the media of arteries and arterioles. The human EP3 receptor subtype protein was strongly expressed in glomeruli, Tamm-Horsfall negative late distal convoluted tubules, connecting segments, cortical and medullary collecting ducts, as well as in the media and the endothelial cells of arteries and arterioles. Staining of the human EP4 receptor subtype protein was observed in glomeruli and in the media of arteries. However, no signal of either receptor subtype was detected in the thick ascending limb, the macula densa, or in adjacent juxtaglomerular cells. These results support the concept that PGE2 modulates specific functions in different anatomical structures of the human kidney. PMID:10477136

  4. Perturbation theory in light-cone quantization

    SciTech Connect

    Langnau, A.

    1992-01-01

    A thorough investigation of light-cone properties which are characteristic for higher dimensions is very important. The easiest way of addressing these issues is by analyzing the perturbative structure of light-cone field theories first. Perturbative studies cannot be substituted for an analysis of problems related to a nonperturbative approach. However, in order to lay down groundwork for upcoming nonperturbative studies, it is indispensable to validate the renormalization methods at the perturbative level, i.e., to gain control over the perturbative treatment first. A clear understanding of divergences in perturbation theory, as well as their numerical treatment, is a necessary first step towards formulating such a program. The first objective of this dissertation is to clarify this issue, at least in second and fourth-order in perturbation theory. The work in this dissertation can provide guidance for the choice of counterterms in Discrete Light-Cone Quantization or the Tamm-Dancoff approach. A second objective of this work is the study of light-cone perturbation theory as a competitive tool for conducting perturbative Feynman diagram calculations. Feynman perturbation theory has become the most practical tool for computing cross sections in high energy physics and other physical properties of field theory. Although this standard covariant method has been applied to a great range of problems, computations beyond one-loop corrections are very difficult. Because of the algebraic complexity of the Feynman calculations in higher-order perturbation theory, it is desirable to automatize Feynman diagram calculations so that algebraic manipulation programs can carry out almost the entire calculation. This thesis presents a step in this direction. The technique we are elaborating on here is known as light-cone perturbation theory.

  5. High Sodium-Induced Oxidative Stress and Poor Anticrystallization Defense Aggravate Calcium Oxalate Crystal Formation in Rat Hyperoxaluric Kidneys.

    PubMed

    Huang, Ho-Shiang; Ma, Ming-Chieh

    2015-01-01

    Enhanced sodium excretion is associated with intrarenal oxidative stress. The present study evaluated whether oxidative stress caused by high sodium (HS) may be involved in calcium oxalate crystal formation. Male rats were fed a sodium-depleted diet. Normal-sodium and HS diets were achieved by providing drinking water containing 0.3% and 3% NaCl, respectively. Rats were fed a sodium-depleted diet with 5% hydroxyl-L-proline (HP) for 7 and 42 days to induce hyperoxaluria and/or calcium oxalate deposition. Compared to normal sodium, HS slightly increased calcium excretion despite diuresis; however, the result did not reach statistical significance. HS did not affect the hyperoxaluria, hypocalciuria or supersaturation caused by HP; however, it increased calcium oxalate crystal deposition soon after 7 days of co-treatment. Massive calcium oxalate formation and calcium crystal excretion in HS+HP rats were seen after 42 days of treatment. HP-mediated hypocitraturia was further exacerbated by HS. Moreover, HS aggravated HP-induced renal injury and tubular damage via increased apoptosis and oxidative stress. Increased urinary malondialdehyde excretion, in situ superoxide production, NAD(P)H oxidase and xanthine oxidase expression and activity, and decreased antioxidant enzyme expression or activity in the HS+HP kidney indicated exaggerated oxidative stress. Interestingly, this redox imbalance was associated with reduced renal osteopontin and Tamm-Horsfall protein expression (via increased excretion) and sodium-dependent dicarboxylate cotransporter NaDC-1 upregulation. Collectively, our results demonstrate that a HS diet induces massive crystal formation in the hyperoxaluric kidney; this is not due to increased urinary calcium excretion but is related to oxidative injury and loss of anticrystallization defense. PMID:26241473

  6. Extreme positive selection on a new highly-expressed larval glycoprotein (LGP) gene in Galaxias fishes (Osmeriformes: Galaxiidae).

    PubMed

    Wallis, Lise J; Wallis, Graham P

    2011-01-01

    We describe the intron-exon structure and DNA/protein sequences of a new larval glycoprotein (LGP) gene from nine species of galaxiid fish. The gene has a distant similarity to Danio THP (Tamm-Horsfall urinary glycoprotein; uromodulin) and cichlid SPP120 (seminal plasma glycoprotein) due to conserved features of its zona pellucida (ZP) domain, including eight highly conserved cysteines and a consensus furin cleavage site. Using a combination of 454 sequencing of cDNA and exon-primed intron-spanning sequencing of genomic DNA, we obtained full sequences of the coding region (996 bp) and its intervening sequences (1,459 bp). LGP shows an exceptionally strong signal of positive selection over the entire coding region, as evidenced by d(N)/d(S) values >1. Across nine species of Galaxias, 87/332 (26%) amino acid residues are variable, compared with 9/386 (2%) for mitochondrial cytochrome b (cytb) in the same group of species. Across 36 interspecific pairwise comparisons, genetic distances are in all cases larger for coding region than for introns, by a factor of 2.4-fold on average. Reading frame, gene structure, splice sites, and many ZP motifs are conserved across all species. Together with the fact that the gene is expressed in all species, these results argue clearly against the possibility of a pseudogene. We show by 454 sequencing and quantitative polymerase chain reaction that the transcript is abundant (ca. 0.5%) in newly hatched larvae and appears to be almost absent from a range of adult tissues. We postulate that the strong Darwinian evolution exhibited by this protein may reflect some type of immunoprotection at this vulnerable larval stage. PMID:20696791

  7. Threshold reduction by multidimensional photonic confinement in metal-organic microcavities

    NASA Astrophysics Data System (ADS)

    Mischok, Andreas; Brückner, Robert; Reinhardt, Christoph; Sudzius, Markas; Lyssenko, Vadim G.; Fröb, Hartmut; Leo, Karl

    2014-05-01

    Due to their geometry, optical microcavities allow strong confinement of light between the mirrors and promise single mode operation at lowest possible lasing thresholds. Nevertheless, such devices suffer from losses not only due to parasitic absorption of the active or mirror layers, but especially via outcoupling of leaky and waveguided modes within the active layer. In this work, we present an organic microcavity sandwiched between high quality dielectric distributed Bragg reflectors. A highly conductive silver layer of 40nm thickness is added next to the active layer, leading to the formation of Tamm-Plasmon-Polaritons (TPP), one replacing the original cavity mode and shifting its resonance to the red, another one emerging from the long-wavelength sideband and moving to the blue. To avoid parasitic absorption introduced by such contacts, the silver layer is structured on the micrometer-scale using photolithography, yielding separated areas supporting either original cavity mode or red shifted TPP-resonances. This separation leads to a strong spatial trapping of the modes to only their resonant regions on the sample and can in turn be exploited to achieve complete three-dimensional confinement of photons. In elliptic holes produced in the metal layer, we observe the formation of Mathieu-Modes, leading to a reduction of the lasing threshold by six times. Facilitating triangular cuts in the silver layer, highly confined standing modes develop in the system, allowing a precise optimization of the spatial mode extension and reducing the threshold even further down to one order of magnitude below the threshold of an unstructured organic cavity. These results show that the introduction of absorptive metals, needed for the realization of an electrically driven laser, can in turn be harnessed to improve the characteristics of the device.

  8. Microwaves in dispersive magnetic composite media (Review Article)

    NASA Astrophysics Data System (ADS)

    Tarapov, S. I.; Belozorov, D. P.

    2012-07-01

    Review discusses some special questions of physics of composite media (metamaterials), which are formed by elements made from natural materials of two kinds. The first ones are "carriers of permittivity" and are presented by plasma-like media and semiconductors. The second ones are "carriers of permeability"—they are presented by ferromagnets. Among such ferromagnets are ferrodielectrics (ferrites) and manganite-perovskite compounds. In the first chapter of the review some principal aspects of the electrodynamics of periodical structures—magnetophotonic crystals are considered. The questions of zone structure and possible violations of periodicity (Tamm states, defect mode) as well as the influence of external magnetic field on the spectral characteristics of magnetophotonic crystals are considered. The second chapter of the review is devoted to the electrodynamics of left-handed media (left-handed metamaterials). Different versions of composite left-handed media are considered. Particular attention is paid to features of electrodynamics of artificially synthesized left-handed media, the doped lanthanum manganites-perovskites, which in a certain concentrations of doping element and temperature range can serve as an example of natural left-handed media. The Appendix describes the details of experimental techniques radiophysical research. Note that the research and design of the metamaterials listed above in a range of low temperatures are particularly important. This is due to the fact that at low temperatures a main disadvantage of artificial materials mentioned above (quite large losses) becomes less noticeable. At the same time the main their advantage (namely the possibility to control their frequency dispersion) remains. Thus it seems that the most prospective areas of application and further study of the magnetic metamaterials lie at low temperatures.

  9. 4-Component relativistic calculations of L3 ionization and excitations for the isoelectronic species UO2(2+), OUN(+) and UN2.

    PubMed

    South, Christopher; Shee, Avijit; Mukherjee, Debashis; Wilson, Angela K; Saue, Trond

    2016-08-01

    We present a 4-component relativistic study of uranium 2p3/2 ionization and excitation in the isoelectronic series UO2(2+), OUN(+) and UN2. We calculate ionization energies by ΔSCF at the Hartree-Fock (HF) and Kohn-Sham (KS) level of theory. At the ΔHF level we observe a perfectly linear chemical shift of ionization energies with respect to uranium atomic charges obtained from projection analysis. We have also developed a non-canonical 2nd-order Møller-Plesset code for wave function based correlation studies. We observe the well-known failure of Koopmans' theorem for core ionization due to the dominance of orbital relaxation over electron correlation effects. More unexpectedly, we find that the correlation contribution has the same sign as the relaxation contribution and show that this is due to a strong coupling of relaxation and correlation. We simulate uranium L3 XANES spectra, dominated by 2p3/2 → U6d transitions, by restricted excitation window time-dependent density functional theory (REW-TDDFT) and the complex polarization propagator (CPP) approach and demonstrate that they give identical spectra when the same Lorentz broadening is chosen. We also simulate XANES spectra by the Hartree-Fock based static exchange (STEX) method and show how STEX excitation energies can be reproduced by time-dependent Hartree-Fock calculations within the Tamm-Dancoff approximation. We furthermore show that Koopmans' theorem provide a correct approximation of ionization energies in the linear response regime and use this observation to align REW-TDDFT and CPP spectra with STEX ones. We point out that the STEX method affords the most detailed assignment of spectra since it employs virtual orbitals optimized for the selected core ionization. The calculated XANES spectra reflect the loss of bound virtual orbitals as the molecular charge is reduced along the isoelectronic series. PMID:26878601

  10. Proteomic Analysis of Urine Exosomes Reveals Renal Tubule Response to Leptospiral Colonization in Experimentally Infected Rats

    PubMed Central

    RamachandraRao, Satish P.; Matthias, Michael A.; Mondrogon, Chanthel-Kokoy; Aghania, Eamon; Park, Cathleen; Kong, Casey; Ishaya, Michelle; Madrigal, Assael; Horng, Jennifer; Khoshaba, Roni; Bounkhoun, Anousone; De Palma, Antonella; Agresta, Anna Maria; Awdishu, Linda; Naviaux, Robert K.; Vinetz, Joseph M.; Mauri, Pierluigi

    2015-01-01

    Background Infectious Leptospira colonize the kidneys of reservoir (e.g. rats) and accidental hosts such as humans. The renal response to persistent leptospiral colonization, as measured by urinary protein biosignatures, has not been systematically studied. Urinary exosomes--bioactive membrane-bound nanovesicles--contain cell-state specific cargo that additively reflect formation all along the nephron. We hypothesized that Leptospira-infection will alter the content of urine exosomes, and further, that these Leptospira-induced alterations will hold clues to unravel novel pathways related to bacterial-host interactions. Methodology/Principal findings Exosome protein content from 24 hour urine samples of Leptospira-infected rats was compared with that of uninfected rats using SDS-PAGE and liquid chromatography/tandem mass spectrometry (LC-MS/MS). Statistical models were used to identify significantly dysregulated proteins in Leptospira-infected and uninfected rat urine exosomes. In all, 842 proteins were identified by LC-MS/MS proteomics of total rat urine and 204 proteins associated specifically with exosomes. Multivariate analysis showed that 25 proteins significantly discriminated between uninfected control and infected rats. Alanyl (membrane) aminopeptidase, also known as CD13 topped this list with the highest score, a finding we validated by Western immunoblotting. Whole urine analysis showed Tamm-Horsfall protein level reduction in the infected rat urine. Total urine and exosome proteins were significantly different in male vs. female infected rats. Conclusions We identified exosome-associated renal tubule-specific responses to Leptospira infection in a rat chronic colonization model. Quantitative differences in infected male and female rat urine exosome proteins vs. uninfected controls suggest that urine exosome analysis identifies important differences in kidney function that may be of clinical and pathological significance. PMID:25793258

  11. Hydrogen sulfide attenuates cytokine production through the modulation of chromatin remodeling

    PubMed Central

    RIOS, ESTER C.S.; SZCZESNY, BARTOSZ; SORIANO, FRANCISCO G.; OLAH, GABOR; SZABO, CSABA

    2015-01-01

    Hydrogen sulfide (H2S) is an endogenous gaseous biological mediator, which regulates, among others, the oxidative balance of cells under normal physiological conditions, as well as in various diseases. Several previous studies have reported that H2S attenuates inflammatory mediator production. In this study, we investigated the role of H2S in chromatin modulation in an in vitro model of lipopolysaccharide (LPS)-induced inflammation and evaluated its effects on inflammatory cytokine production. Tamm-Horsfall protein 1 (THP-1) differentiated macrophages were pre-treated with sodium hydrosulfide (NaHS) (an H2S donor) at 0.01, 0.1, 0.5 or 1 mM for 30 min. To stimulate cytokine production, the cells were challenged with bacterial LPS (1 μg/ml) for 1, 4, 8 or 24 h. Histone H3 acetylation was analyzed by chromatin immunoprecipitation (ChIP), cytokine production was measured by ELISA and histone deacetylase (HDAC) activity was analyzed using a standard biochemical assay. H2S inhibited the production of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) in a concentration-dependent manner; it was most effective at the two highest concentrations used. This effect was associated with a decrease in histone H3 acetylation at the IL-6 and TNF-α promoters in the cells exposed to H2S or H2S + LPS. The findings of the present study suggest that H2S suppresses histone acetylation, which, in turn, inhibits chromatin openness, leading to a decrease in the gene transcription of various pro-inflammatory cytokines. Therefore, this mechanism may contribute to the previously demonstrated anti-inflammatory effects of H2S and various H2S donors. PMID:25873160

  12. [Kidney damage in multiple myeloma and other monoclonal gammopathies].

    PubMed

    Adam, Z; Pour, L; Krejcí, M; Stĕpánková, S; Svobodová, I; Veselý, K; Hájek, R

    2008-09-01

    Multiple myeloma typically damages the skeleton in the form of osteolytic lesions or diffuse osteoporosis and causes a decrease in blood production. Renal insufficiency is diagnosed immediately at the onset of illness when establishing diagnosis in up to 20% of patients. Where patients suffer from an advanced form of the illness, it occurs in up to 40%. The predominant cause of damage to the kidneys is the monoclonal light chains. Most frequently, nephropathy is caused by the precipitation of light chains with the Tamm-Horsfall protein in the distal part of the loop of Henle and subsequent tubular ruptures and the creation of fibrous changes in the interstitium. Less frequently, there is clinically serious damage to tubular functions without indication of renal insufficiency. In some patients monoclonal immunoglobulin induces changes in the glomeruli. A rare type of damage is deposits of light chains in the form of AL-amyloid and subsequent nephritic syndrome. A very rare form is the deposition of monoclonal immunoglobulin in the form of amorphous matter (light-chain deposition disease) or in the form of crystals within tissue histiocytes (crystal storing histiocytosis). Both of these disorders cause renal insufficiency and less frequently nephritic syndrome such as AL amyloidosis. With timely and intensive treatment of multiple myeloma, which quickly suppresses the creation of light chains, a significant proportion of patients experience reparative changes and improved kidney function. The benefit of plasmapheresis for patients with severe kidney damage has not been confirmed by randomised studies. At the present time the first positive results are becoming available from tests of the use of pre-emptive haemodialysis with special columns that are permeable for light chains. The aim of the text is to provide information on the various forms of nephropathy whose closer analysis can reveal multiple myeloma and contribute to the timely diagnosis of the cause of the

  13. Theoretical and numerical assessments of spin-flip time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Li, Zhendong; Liu, Wenjian

    2012-01-01

    Spin-flip time-dependent density functional theory (SF-TD-DFT) with the full noncollinear hybrid exchange-correlation kernel and its approximate variants are critically assessed, both formally and numerically. As demonstrated by the ethylene torsion and the C2v ring-opening of oxirane, SF-TD-DFT is very useful for describing nearly degenerate situations. However, it may occasionally yield unphysical results. This stems from the noncollinear form of the generalized gradient approximation, which becomes numerically instable in the presence of spin-flip excitations from the closed- to vacant-shell orbitals of an open-shell reference. To cure this defect, a simple modification, dubbed as ALDA0, is proposed in the spirit of adiabatic local density approximation (ALDA). It is applicable to all kinds of density functionals and yields stable results without too much loss of accuracy. In particular, the combination of ALDA0 with the Tamm-Dancoff approximation is a promising tool for studying global potential energy surfaces. In addition to the kernel problem, SF-TD-DFT is also rather sensitive to the choice of reference states, as demonstrated by the spin multiplet states of closed-shell molecules of H2O, CH2O, and C2H4. Surprisingly, SF-TD-DFT with pure density functionals may also fail for valance excitations with large orbital overlaps, at variance with the spin-conserving counterpart (SC-TD-DFT). In this case, the inclusion of a large amount of Hartree-Fock exchange is mandatory for quantitative results. Nonetheless, for spatially degenerate cases such as CF, CH, and NH+, SF-TD-DFT is more advantageous than SC-TD-DFT, unless the latter is also space adapted. These findings are very instructive for future development and applications of TD-DFT.

  14. Neutrino mean free paths in cold symmetric nuclear matter

    SciTech Connect

    Cowell, S.; Pandharipande, V.R.

    2004-09-01

    The neutrino mean free paths (NMFP) for scattering and absorption in cold symmetric nuclear matter (SNM) are calculated using two-body effective interactions and one-body effective weak operators obtained from realistic models of nuclear forces using correlated basis theory. The infinite system is modeled in a box with periodic boundary conditions and the one particle-hole (p-h) response functions are calculated using the Tamm-Dancoff approximation (TDA). For the densities {rho}=(1/2), 1 (3/2){rho}{sub 0}, where {rho}{sub 0} is the equilibrium density of SNM, the strength of the response is shifted to higher energy transfers when compared to a noninteracting Fermi gas (FG). This and the weakness of effective operators compared to the bare operators, significantly reduces the cross sections, enhancing the NMFP by factors of {approx}2.5-3.5 at the densities considered. The NMFP at the equilibrium density {rho}{sub 0} are also calculated using the TDA and random phase approximation (RPA) using zero range Skyrme-like effective interactions with parameters chosen to reproduce the equation of state and spin-isospin susceptibilities of matter. Their results indicate that RPA corrections to correlated TDA may further increase the NMFP by {approx}25% to 3-4 times those in a noninteracting FG. Finally, the sums and the energy weighted sums of the Fermi and Gamow-Teller responses obtained from the correlated ground state are compared with those of the 1 p-h response functions to extract the sum and mean energies of multi p-h contributions to the weak response. The relatively large mean energy of the multi p-h excitations suggests that they may not contribute significantly to low energy NMFP.

  15. Theoretical studies on the dimerization of substituted paraphenylenediamine radical cations

    NASA Astrophysics Data System (ADS)

    Punyain, Kraiwan; Kelterer, Anne-Marie; Grampp, Günter

    2011-12-01

    Organic radical cations form dicationic dimers in solution, observed experimentally as diamagnetic species in temperature-dependent EPR and low temperature UV/Vis spectroscopy. Dimerization of paraphenylenediamine, N,N-dimethyl-paraphenylenediamine and 2,3,5,6-tetramethyl-paraphenylenediamine radical cation in ethanol/diethylether mixture was investigated theoretically according to geometry, energetics and UV/Vis spectroscopy. Density Functional Theory including dispersion correction describes stable dimers after geometry optimization with conductor-like screening model of solvation and inclusion of the counter-ion. Energy corrections were done on double-hybrid Density Functional Theory with perturbative second-order correlation (B2PLYP-D) including basis set superposition error (BSSE), and multireference Møller-Plesset second-order perturbation theory method (MRMP2) based on complete active space method (CASSCF(2,2)) single point calculation, respectively. All three dication π-dimers exhibit long multicenter π-bonds around 2.9 ± 0.1 Å with strongly interacting orbitals. Substitution with methyl groups does not influence the dimerization process substantially. Dispersion interaction and electrostatic attraction from counter-ion play an important role to stabilize the dication dimers in solution. Dispersion-corrected double hybrid functional B2PLYP-D and CASSCF(2,2) can describe the interaction energetics properly. Vertical excitations were computed with Tamm-Dancoff approximation for time-dependent Density Functional Theory (TDA-DFT) at the B3LYP level with the cc-pVTZ basis set including ethanol solvent molecules explicitly. A strong interaction of the counter-ion and the solvent ethanol with the monomeric species is observed, whereas in the dimers the strong interaction of both radical cation species is the dominating factor for the additional peak in UV/Vis spectra.

  16. Mixed time-dependent density-functional theory/classical trajectory surface hopping study of oxirane photochemistry

    NASA Astrophysics Data System (ADS)

    Tapavicza, Enrico; Tavernelli, Ivano; Rothlisberger, Ursula; Filippi, Claudia; Casida, Mark E.

    2008-09-01

    We present a mixed time-dependent density-functional theory (TDDFT)/classical trajectory surface hopping (SH) study of the photochemical ring opening in oxirane. Previous preparatory work limited to the symmetric CC ring-opening pathways of oxirane concluded that the Tamm-Dancoff approximation (TDA) is important for improving the performance of TDDFT away from the equilibrium geometry. This observation is supported by the present TDDFT TDA/SH calculations which successfully confirm the main experimentally derived Gomer-Noyes mechanism for the photochemical CO ring opening of oxirane and, in addition, provide important state-specific information not easily accessible from experiments. In particular, we find that, while one of the lowest two excited states is photochemically relatively inert, excitation into the other excited state leads predominantly to rapid ring opening, cyclic-C2H4O→C•H2CH2O•. This is followed by hopping to the electronic ground state where hot (4000K) dynamics leads to further reactions, namely, C•H2CH2O•→CH3CHO→C•H3+C•HO and CH4+CO. We note that, in the dynamics, we are not limited to following minimum energy pathways and several surface hops may actually be needed before products are finally reached. The performance of different functionals is then assessed by comparison of TDDFT and diffusion Monte Carlo potential energy curves along a typical TDDFT TDA/SH reaction path. Finally, although true (S0,S1) conical intersections are expected to be absent in adiabatic TDDFT, we show that the TDDFT TDA is able to approximate a conical intersection in this system.

  17. NR2 and P3+: Accurate, Efficient Electron-Propagator Methods for Calculating Valence, Vertical Ionization Energies of Closed-Shell Molecules.

    PubMed

    Corzo, H H; Galano, Annia; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V

    2015-08-20

    Two accurate and computationally efficient electron-propagator (EP) methods for calculating the valence, vertical ionization energies (VIEs) of closed-shell molecules have been identified through comparisons with related approximations. VIEs of a representative set of closed-shell molecules were calculated with EP methods using 10 basis sets. The most easily executed method, the diagonal, second-order (D2) EP approximation, produces results that steadily rise as basis sets are improved toward values based on extrapolated coupled-cluster singles and doubles plus perturbative triples calculations, but its mean errors remain unacceptably large. The outer valence Green function, partial third-order and renormalized partial third-order methods (P3+), which employ the diagonal self-energy approximation, produce markedly better results but have a greater tendency to overestimate VIEs with larger basis sets. The best combination of accuracy and efficiency with a diagonal self-energy matrix is the P3+ approximation, which exhibits the best trends with respect to basis-set saturation. Several renormalized methods with more flexible nondiagonal self-energies also have been examined: the two-particle, one-hole Tamm-Dancoff approximation (2ph-TDA), the third-order algebraic diagrammatic construction or ADC(3), the renormalized third-order (3+) method, and the nondiagonal second-order renormalized (NR2) approximation. Like D2, 2ph-TDA produces steady improvements with basis set augmentation, but its average errors are too large. Errors obtained with 3+ and ADC(3) are smaller on average than those of 2ph-TDA. These methods also have a greater tendency to overestimate VIEs with larger basis sets. The smallest average errors occur for the NR2 approximation; these errors decrease steadily with basis augmentations. As basis sets approach saturation, NR2 becomes the most accurate and efficient method with a nondiagonal self-energy. PMID:26226061

  18. Mixed time-dependent density-functional theory/classical trajectory surface hopping study of oxirane photochemistry

    SciTech Connect

    Tapavicza, Enrico; Tavernelli, Ivano; Rothlisberger, Ursula; Filippi, Claudia; Casida, Mark E.

    2008-09-28

    We present a mixed time-dependent density-functional theory (TDDFT)/classical trajectory surface hopping (SH) study of the photochemical ring opening in oxirane. Previous preparatory work limited to the symmetric CC ring-opening pathways of oxirane concluded that the Tamm-Dancoff approximation (TDA) is important for improving the performance of TDDFT away from the equilibrium geometry. This observation is supported by the present TDDFT TDA/SH calculations which successfully confirm the main experimentally derived Gomer-Noyes mechanism for the photochemical CO ring opening of oxirane and, in addition, provide important state-specific information not easily accessible from experiments. In particular, we find that, while one of the lowest two excited states is photochemically relatively inert, excitation into the other excited state leads predominantly to rapid ring opening, cyclic-C{sub 2}H{sub 4}O{yields}CH{sub 2}CH{sub 2}O. This is followed by hopping to the electronic ground state where hot (4000 K) dynamics leads to further reactions, namely, CH{sub 2}CH{sub 2}O{yields}CH{sub 3}CHO{yields}CH{sub 3}+CHO and CH{sub 4}+CO. We note that, in the dynamics, we are not limited to following minimum energy pathways and several surface hops may actually be needed before products are finally reached. The performance of different functionals is then assessed by comparison of TDDFT and diffusion Monte Carlo potential energy curves along a typical TDDFT TDA/SH reaction path. Finally, although true (S{sub 0},S{sub 1}) conical intersections are expected to be absent in adiabatic TDDFT, we show that the TDDFT TDA is able to approximate a conical intersection in this system.

  19. The role of retardation in the structure and linear response of finite nuclei

    SciTech Connect

    Crecca, M.A.

    1989-01-01

    Conventional random phase approximation (RPA) and Tamm-Dancoff approximation (TDA) calculations of nuclear structure and the linear response employ interactions between nucleons that are instantaneous. However, N-N interactions derived from the exchange of mesons between nucleons must depend on the space-time separation of the nucleons since the mesons travel at finite speeds. Furthermore, a quantum field theory that contains interacting meson and nucleon degrees of freedom employ the Feynman propagator, i{Delta}{sub F}(x - x{prime}), to connect the nucleon-meson vertices of Feynman diagrams. This raises the question of whether calculations done with space-time dependent interactions differ significantly from the conventional calculations that employ instantaneous forces, and what are the qualitative features of the difference. The inquiry into this question begins by generalizing the traditional RPA and TDA equations into the domain of retarded (space-time dependant) interactions. This entails establishing an integral equation (the Bethe-Salpeter equation) for the polarization propagator with the appropriate RPA or TDA kernel such that the integral equation reduces to the usual RPA or TDA matrix equation for the polarization propagator as the interaction becomes instantaneous. After establishing this generalization of the RPA and TDA, a TDA calculation is performed for an interaction arising from the exchange of a scalar meson. The results are compared with those obtained from the conventional instantaneous reduction of the scalar meson exchange interaction, the Yukawa potential. Upon comparing these results one finds that in general the nuclear structure obtained from scalar meson exchange differ little less than 10%.

  20. Self-consistent quasiparticle formulation of a multiphonon method and its application to the neutron-rich O20 nucleus

    NASA Astrophysics Data System (ADS)

    De Gregorio, G.; Knapp, F.; Lo Iudice, N.; Vesely, P.

    2016-04-01

    A Bogoliubov quasiparticle formulation of an equation-of-motion phonon method, suited for open-shell nuclei, is derived. Like its particle-hole version, it consists of deriving a set of equations of motions whose iterative solution generates an orthonormal basis of n -phonon states (n =0 ,1 ,2 ,... ), built of quasiparticle Tamm-Dancoff phonons, which simplifies the solution of the eigenvalue problem. The method is applied to the open-shell neutron-rich O20 for illustrative purposes. A Hartree-Fock-Bogoliubov canonical basis, derived from an intrinsic two-body optimized chiral Hamiltonian, is used to derive and solve the eigenvalue equations in a space encompassing a truncated two-phonon basis. The spurious admixtures induced by the violation of the particle number and the center-of-mass motion are eliminated to a large extent by a Gram-Schmidt orthogonalization procedure. The calculation takes into account the Pauli principle, is self-consistent, and is parameter free except for the energy cutoff used to truncate the two-phonon basis, which induces an increasing depression of the ground state through its strong coupling to the quasiparticle vacuum. Such a cutoff is fixed so as to reproduce the first 1- level. The two-phonon states are shown to enhance the level density of the low-energy spectrum, consistently with the data, and to induce a fragmentation of the E 1 strength which, while accounting for the very low E 1 transitions, is not sufficient to reproduce the experimental cross section in the intermediate energy region. This and other discrepancies suggest the need of including the three-phonon states. These are also expected to offset the action of the two phonons on the quasiparticle vacuum and, therefore, free the calculation from any parameter.

  1. Recent Progress in GW-based Methods for Excited-State Calculations of Reduced Dimensional Systems

    NASA Astrophysics Data System (ADS)

    da Jornada, Felipe H.

    2015-03-01

    Ab initio calculations of excited-state phenomena within the GW and GW-Bethe-Salpeter equation (GW-BSE) approaches allow one to accurately study the electronic and optical properties of various materials, including systems with reduced dimensionality. However, several challenges arise when dealing with complicated nanostructures where the electronic screening is strongly spatially and directionally dependent. In this talk, we discuss some recent developments to address these issues. First, we turn to the slow convergence of quasiparticle energies and exciton binding energies with respect to k-point sampling. This is very effectively dealt with using a new hybrid sampling scheme, which results in savings of several orders of magnitude in computation time. A new ab initio method is also developed to incorporate substrate screening into GW and GW-BSE calculations. These two methods have been applied to mono- and few-layer MoSe2, and yielded strong environmental dependent behaviors in good agreement with experiment. Other issues that arise in confined systems and materials with reduced dimensionality, such as the effect of the Tamm-Dancoff approximation to GW-BSE, and the calculation of non-radiative exciton lifetime, are also addressed. These developments have been efficiently implemented and successfully applied to real systems in an ab initio framework using the BerkeleyGW package. I would like to acknowledge collaborations with Diana Y. Qiu, Steven G. Louie, Meiyue Shao, Chao Yang, and the experimental groups of M. Crommie and F. Wang. This work was supported by Department of Energy under Contract No. DE-AC02-05CH11231 and by National Science Foundation under Grant No. DMR10-1006184.

  2. Internal photoemission from plasmonic nanoparticles: comparison between surface and volume photoelectric effects.

    PubMed

    Uskov, Alexander V; Protsenko, Igor E; Ikhsanov, Renat S; Babicheva, Viktoriia E; Zhukovsky, Sergei V; Lavrinenko, Andrei V; O'Reilly, Eoin P; Xu, Hongxing

    2014-05-01

    We study the emission of photoelectrons from plasmonic nanoparticles into a surrounding matrix. We consider two mechanisms of electron emission from the nanoparticles--surface and volume ones--and use models for these two mechanisms which allow us to obtain analytical results for the photoelectron emission rate from a nanoparticle. Calculations have been carried out for a step potential at the surface of a spherical nanoparticle, and a simple model for the hot electron cooling has been used. We highlight the effect of the discontinuity of the dielectric permittivity at the nanoparticle boundary in the surface mechanism, which leads to a substantial (by ∼5 times) increase of the internal photoelectron emission rate from a nanoparticle compared to the case when such a discontinuity is absent. For a plasmonic nanoparticle, a comparison of the two photoeffect mechanisms was undertaken for the first time which showed that the surface photoeffect can in the general case be larger than the volume one, which agrees with the results obtained for a flat metal surface first formulated by Tamm and Schubin in their pioneering development of a quantum-mechanical theory of photoeffect in 1931. In accordance with our calculations, this possible predominance of the surface effect is based on two factors: (i) effective cooling of hot carriers during their propagation from the volume of the nanoparticle to its surface in the scenario of the volume mechanism and (ii) strengthening of the surface mechanism through the effect of the discontinuity of the dielectric permittivity at the nanoparticle boundary. The latter is stronger at relatively lower photon energies and correspondingly is more substantial for internal photoemission than for an external one. We show that in the general case, it is essential to take both mechanisms into account in the development of devices based on the photoelectric effect and when considering hot electron emission from a plasmonic nanoantenna. PMID

  3. Transition matrices and orbitals from reduced density matrix theory

    SciTech Connect

    Etienne, Thibaud

    2015-06-28

    In this contribution, we report two different methodologies for characterizing the electronic structure reorganization occurring when a chromophore undergoes an electronic transition. For the first method, we start by setting the theoretical background necessary to the reinterpretation through simple tensor analysis of (i) the transition density matrix and (ii) the natural transition orbitals in the scope of reduced density matrix theory. This novel interpretation is made more clear thanks to a short compendium of the one-particle reduced density matrix theory in a Fock space. The formalism is further applied to two different classes of excited states calculation methods, both requiring a single-determinant reference, that express an excited state as a hole-particle mono-excited configurations expansion, to which particle-hole correlation is coupled (time-dependent Hartree-Fock/time-dependent density functional theory) or not (configuration interaction single/Tamm-Dancoff approximation). For the second methodology presented in this paper, we introduce a novel and complementary concept related to electronic transitions with the canonical transition density matrix and the canonical transition orbitals. Their expression actually reflects the electronic cloud polarisation in the orbital space with a decomposition based on the actual contribution of one-particle excitations from occupied canonical orbitals to virtual ones. This approach validates our novel interpretation of the transition density matrix elements in terms of the Euclidean norm of elementary transition vectors in a linear tensor space. A proper use of these new concepts leads to the conclusion that despite the different principles underlying their construction, they provide two equivalent excited states topological analyses. This connexion is evidenced through simple illustrations of (in)organic dyes electronic transitions analysis.

  4. Validation of local hybrid functionals for TDDFT calculations of electronic excitation energies

    NASA Astrophysics Data System (ADS)

    Maier, Toni M.; Bahmann, Hilke; Arbuznikov, Alexei V.; Kaupp, Martin

    2016-02-01

    -energy dependent local hybrids, differences between spin-resolved and "common" local mixing functions in local hybrids, and the effects of the Tamm-Dancoff approximation on the excitation energies are also discussed.

  5. Demonstration of the functional impact of vasopressin signaling in the thick ascending limb by a targeted transgenic rat approach.

    PubMed

    Mutig, Kerim; Borowski, Tordis; Boldt, Christin; Borschewski, Aljona; Paliege, Alexander; Popova, Elena; Bader, Michael; Bachmann, Sebastian

    2016-08-01

    The antidiuretic hormone vasopressin (AVP) regulates renal salt and water reabsorption along the distal nephron and collecting duct system. These effects are mediated by vasopressin 2 receptors (V2R) and release of intracellular Gs-mediated cAMP to activate epithelial transport proteins. Inactivating mutations in the V2R gene lead to the X-linked form of nephrogenic diabetes insipidus (NDI), which has chiefly been related with impaired aquaporin 2-mediated water reabsorption in the collecting ducts. Previous work also suggested the AVP-V2R-mediated activation of Na(+)-K(+)-2Cl(-)-cotransporters (NKCC2) along the thick ascending limb (TAL) in the context of urine concentration, but its individual contribution to NDI or, more generally, to overall renal function was unclear. We hypothesized that V2R-mediated effects in TAL essentially determine its reabsorptive function. To test this, we reevaluated V2R expression. Basolateral membranes of medullary and cortical TAL were clearly stained, whereas cells of the macula densa were unreactive. A dominant-negative, NDI-causing truncated V2R mutant (Ni3-Glu242stop) was then introduced into the rat genome under control of the Tamm-Horsfall protein promoter to cause a tissue-specific AVP-signaling defect exclusively in TAL. Resulting Ni3-V2R transgenic rats revealed decreased basolateral but increased intracellular V2R signal in TAL epithelia, suggesting impaired trafficking of the receptor. Rats displayed significant baseline polyuria, failure to concentrate the urine in response to water deprivation, and hypercalciuria. NKCC2 abundance, phosphorylation, and surface expression were markedly decreased. In summary, these data indicate that suppression of AVP-V2R signaling in TAL causes major impairment in renal fluid and electrolyte handling. Our results may have clinical implications. PMID:27306979

  6. Proteomic analysis of proteins selectively associated with hydroxyapatite, brushite, and uric acid crystals precipitated from human urine.

    PubMed

    Thurgood, Lauren A; Ryall, Rosemary L

    2010-10-01

    The aim of this study was to compare the intracrystalline protein profiles of hydroxyapatite (HA), brushite (BR), and uric acid (UA) crystals precipitated from the same urine samples. HA, BR, and UA crystals were precipitated on two different occasions from the same pooled healthy urine. Crystals were washed to remove surface-bound proteins, and their composition was confirmed using Fourier transform infrared spectroscopy (FTIR) and field emission scanning electron microscopy (FESEM) coupled with energy dispersive X-ray analysis (EDAX). SDS-PAGE was used for visual comparison of the protein content of the demineralised crystal extracts, which were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). HA comprised nanosized particles interspersed with organic material, which was absent from the BR and UA crystals. The number and type of individual proteins differed between the 3 minerals: 45 proteins were detected in the HA crystal extracts and 77 in the BR crystals, including a number of keratins, which were regarded as methodological contaminants. After excluding the keratins, 21 proteins were common to both HA and BR crystals. Seven nonkeratin proteins were identified in the UA extracts. Several proteins consistently detected in the HA and BR crystal extracts have been previously implicated in kidney stone disease, including osteopontin, prothrombin, protein S100A9 (calgranulin B), inter-α-inhibitor, α1-microglobulin bikunin (AMBP), heparan sulfate proteoglycan, and Tamm-Horsfall glycoprotein, all of which are strong calcium binders. We concluded that the association of proteins with HA, BR, and UA crystals formed in healthy urine is selective and that only a few of the numerous proteins present in healthy urine are likely to play any significant role in preventing stone pathogenesis. PMID:20795672

  7. PREFACE: Preface

    NASA Astrophysics Data System (ADS)

    2011-10-01

    The International Conference Alt100 - 'Resonances in Condensed Matter' was held in Kazan, Russian Federation, from 21-25 June, at Kazan (Volga Region) Federal University. The conference was devoted to the centenary of Professor, Corresponding member of Academy of Sciences of the USSR S A Altshuler (24.09.1911-24.01.1983), well known for his pioneer works together with E K Zavoiskii on EPR, prediction of neutron magnetic moment (with I E Tamm) and acoustic magnetic resonance. The program of the conference covered experimental and theoretical studies of (i) electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), ferromagnetic and antiferromagnetic resonances (FMR, AFMR) in condensed matter, enhanced nuclear magnetic resonance in Van-Vleck paramagnets (ENMR), optical spectroscopy of paramagnetic crystals; (ii) magnetic relaxation; (iii) bulk and local magnetic properties of transition metal oxides and intermetallic compounds; (iv) modern applications of magnetic resonance techniques and methods. The conference attracted 120 participants from 14 countries. There were 26 invited talks and 36 regular oral talks in the morning and afternoon sessions, and 70 poster presentations. A book of Abstracts is available on the conference website (http://alt100.ksu.ru). The Memorial Session involved talks from B I Kochelaev (Chairman of the Organizing Committee) and A A Manenkov and reminiscences about S A Altshuler given by A A Kaplyanskii, V A Kutuzov, Yu R Pol_skii and I N Pen_kov. The memorial talks and Kaplyanskii_ speech are presented in this volume. The papers submitted for this Proceedings were carefully considered by at least two referees, and we are very grateful to referees for their quick and very thoughtful responses. A few papers were eliminated because of referee reports. Finally 41 papers have been included. We thank the international advisory committee members very much for their recommendations of speakers for Alt100 and especially members of the

  8. A. Sakharov and Fusion Research

    NASA Astrophysics Data System (ADS)

    Coppi, Bruno

    2012-02-01

    In the landmark paper by Tamm and Sakharov [1], a controlled nuclear fusion reactor based on an axisymmetric magnetic confinement configuration whose principles remain valid to this day, was proposed. In the light of present understanding of plasma physics the virtues (e.g. that of considering the D-D reaction) and the shortcomings of this paper are pointed out. In fact, relatively recent results of theoretical plasma physics (e.g. discovery of the so called second stability region) and advances in high field magnet technology have made it possible to identify the parameters of meaningful experiments capable of exploring D-D and D-^3He burn conditions. At the same time an experimental program (IGNIR) has been undertaken through a (funded) collaboration between Italy and Russia to investigate D-T plasmas close to ignition conditions based on an advanced high field toroidal confinement configuration. A. Sakharov envisioned a bolder approach to fusion research than that advocated by some of his contemporaries. The time taken to design and decide to fabricate the first experiment capable of reaching ignition conditions is due in part to the problem of gaining an adequate understanding the expected physics of fusion burning plasmas. However, most of the relevant financial effort has gone in the pursuit of slow and indirect enterprises complying with the ``playing it safe'' tendencies of large organizations or motivated by the purpose to develop technologies or maintain a high level of expertise in plasma physics to the expected benefit of other kinds of endeavors. The creativity demonstrated by A. Sakharov in dealing with civil rights and disarmament issues is needed, while maintaining our concerns for energy and the environment on a global scale, to orient the funding for fusion research toward a direct and well based scientific effort on concepts for which a variety of developments can be envisioned. These can span from uncovering new physics relevant, for instance

  9. The influence of physico-chemical properties of soils on the bioavailability of 65Zn

    NASA Astrophysics Data System (ADS)

    Kochetkov, Ilia; Anisimov, Vyacheslav

    2014-05-01

    Stability of soils to the effects of man-made origin pollutants is determined by their buffer capaci-ty (the ability to inactivate pollutants in a soil - soil solution - plant system). Soils are character-ized by the same types of stability as the ecosystem as a whole. Increased migration activity of pollutants is a symptom of ecological trouble, due to the soil transformation in an unstable state. Thus, the problem of the stability of soil is one of the fundamental problems of modern science. The aim of the study was to estimate the buffering capacity of soil as a key factor of their ecological and geochemical stability with respect to a relatively long-lived radionuclides 65Zn (T1/2 = 224 days), representing the radiological hazard in the location of nuclear facilities. There was proposed a method for scoring the buffering capacity of soils as for 65Zn contamination. It's based on dependence between the main physico-chemical soil properties and accumulation of the radionuclide in the aboveground plant parts (barley kind of "Zazersky-85"). The role of the considered indicators of soil health in the accumulation of radiozinc by plants was defined. The essence of this technique was to assess the contribution of individual characteristics of the soil condition, which play the most important role in the regulation of mobility (and bioavailability) of radionuclides, using the method of stepwise multiple regression analysis. For this aim representative sampling was compiled (from 20 soil types and varieties belonging to different climatic zones of the European part of the Russian Federation), thus providing a wide range of variation of the studied physical and chemical parameters, and also vegetation model experiments using 65Zn were held. On the basis of the conducted statistical analysis was revealed that the dominant contribution to the variation of the effective trait (accumulation coefficient of 65Zn) make: CaCO3 content, mobile iron (Tamm extract) and pH. As a

  10. pH-induced conformational changes of membrane-bound influenza hemagglutinin and its effect on target lipid bilayers.

    PubMed Central

    Gray, C.; Tamm, L. K.

    1998-01-01

    Influenza virus hemagglutinin (HA) has served as a paradigm for both pH-dependent and -independent viral membrane fusion. Although large conformational changes were observed by X-ray crystallography when soluble fragments of HA were subjected to fusion-pH conditions, it is not clear whether the same changes occur in membrane-bound HA, what the spatial relationship is between the conformationally changed HA and the target and viral membranes, and in what way HA perturbs the target membrane at low pH. We have taken a spectroscopic approach using an array of recently developed FTIR techniques to address these questions. Difference attenuated total reflection FTIR spectroscopy was employed to reveal reversible and irreversible components of the pH-induced conformational change of the membrane-bound bromelain fragment of HA, BHA. Additional proteolytic fragments of BHA were produced which permitted a tentative assignment of the observed changes to the HA1 and HA2 subunits, respectively. The membrane-bound HA1 subunit undergoes a reversible conformational change, which most likely involves the loss of a small proportion of beta-sheet at low pH. BHA was found to undergo a partially reversible tilting motion relative to the target membrane upon exposure to pH 5, indicating a previously undescribed hinge near the anchoring point to the target membrane. Time-resolved amide H/D exchange experiments revealed a more dynamic (tertiary) structure of membrane-bound BHA and its HA2, but not its HA1, subunit. Finally BHA and, to a lesser degree, HA1 perturbed the lipid bilayer of the target membrane at the interface, as assessed by spectral changes of the lipid ester carbonyl groups. These results are discussed in the context of a complementary study of HA that was bound to viral membranes through its transmembrane peptide (Gray C, Tamm LK, 1997, Protein Sci 6:1993-2006). A distinctive role for the HA1 subunit in the conformational change of HA becomes apparent from these combined

  11. Directing fluorescence with plasmonic and photonic structures.

    PubMed

    Dutta Choudhury, Sharmistha; Badugu, Ramachandram; Lakowicz, Joseph R

    2015-08-18

    Fluorescence technology pervades all areas of chemical and biological sciences. In recent years, it is being realized that traditional fluorescence can be enriched in many ways by harnessing the power of plasmonic or photonic structures that have remarkable abilities to mold the flow of optical energy. Conventional fluorescence is omnidirectional in nature, which makes it difficult to capture the entire emission. Suitably designed emission directivity can improve collection efficiency and is desirable for many fluorescence-based applications like sensing, imaging, single molecule spectroscopy, and optical communication. By incorporating fluorophores in plasmonic or photonic substrates, it is possible to tailor the optical environment surrounding the fluorophores and to modify the spatial distribution of emission. This promising approach works on the principle of near-field interaction of fluorescence with spectrally overlapping optical modes present in the substrates. In this Account, we present our studies on directional emission with different kinds of planar metallic, dielectric, and hybrid structures. In metal-dielectric substrates, the coupling of fluorescence with surface plasmons leads to directional surface-plasmon-coupled emission with characteristic dispersion and polarization properties. In one-dimensional photonic crystals (1DPC), fluorophores can interact with Bloch surface waves, giving rise to sharply directional Bloch surface wave-coupled emission. The interaction of fluorescence with Fabry-Pérot-like modes in metal-dielectric-metal substrates and with Tamm states in plasmonic-photonic hybrid substrates provides beaming emission normal to the substrate surface. These interesting features are explained in the context of reflectivity dispersion diagrams, which provide a complete picture of the mode profiles and the corresponding coupled emission patterns. Other than planar substrates, specially fabricated plasmonic nanoantennas also have tremendous

  12. Efficient time-dependent density functional theory approximations for hybrid density functionals: analytical gradients and parallelization.

    PubMed

    Petrenko, Taras; Kossmann, Simone; Neese, Frank

    2011-02-01

    In this paper, we present the implementation of efficient approximations to time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation (TDA) for hybrid density functionals. For the calculation of the TDDFT/TDA excitation energies and analytical gradients, we combine the resolution of identity (RI-J) algorithm for the computation of the Coulomb terms and the recently introduced "chain of spheres exchange" (COSX) algorithm for the calculation of the exchange terms. It is shown that for extended basis sets, the RIJCOSX approximation leads to speedups of up to 2 orders of magnitude compared to traditional methods, as demonstrated for hydrocarbon chains. The accuracy of the adiabatic transition energies, excited state structures, and vibrational frequencies is assessed on a set of 27 excited states for 25 molecules with the configuration interaction singles and hybrid TDDFT/TDA methods using various basis sets. Compared to the canonical values, the typical error in transition energies is of the order of 0.01 eV. Similar to the ground-state results, excited state equilibrium geometries differ by less than 0.3 pm in the bond distances and 0.5° in the bond angles from the canonical values. The typical error in the calculated excited state normal coordinate displacements is of the order of 0.01, and relative error in the calculated excited state vibrational frequencies is less than 1%. The errors introduced by the RIJCOSX approximation are, thus, insignificant compared to the errors related to the approximate nature of the TDDFT methods and basis set truncation. For TDDFT/TDA energy and gradient calculations on Ag-TB2-helicate (156 atoms, 2732 basis functions), it is demonstrated that the COSX algorithm parallelizes almost perfectly (speedup ~26-29 for 30 processors). The exchange-correlation terms also parallelize well (speedup ~27-29 for 30 processors). The solution of the Z-vector equations shows a speedup of ~24 on 30 processors. The

  13. Glycoprotein 2 antibodies in Crohn's disease.

    PubMed

    Roggenbuck, Dirk; Reinhold, Dirk; Werner, Lael; Schierack, Peter; Bogdanos, Dimitrios P; Conrad, Karsten

    2013-01-01

    The pathogenesis of Crohn's disease (CrD) and ulcerative colitis (UC), the two major inflammatory bowel diseases (IBD), remains poorly understood. Autoimmunity is considered to be involved in the triggering and perpetuation of inflammatory processes leading to overt disease. Approximately 30% of CrD patients and less than 8% of UC patients show evidence of humoral autoimmunity to exocrine pancreas, detected by indirect immunofluorescence. Pancreatic autoantibodies (PAB) were described for the first time in 1984, but the autoantigenic target(s) of PABs were identified only in 2009. Utilizing immunoblotting and matrix-assisted laser desorption ionization time-of-flight mass spectrometry, the major zymogen granule membrane glycoprotein 2 (GP2) has been discovered as the main PAB autoantigen. The expression of GP2 has been demonstrated at the site of intestinal inflammation, explaining the previously unaddressed contradiction of pancreatic autoimmunity and intestinal inflammation. Recent data demonstrate GP2 to be a specific receptor on microfold (M) cells of intestinal Peyer's patches, which are considered to be the original site of inflammation in CrD. Novel ELISAs, employing recombinant GP2 as the solid phase antigen, have confirmed the presence of IgA and IgG anti-GP2 PABs in CrD patients and revealed an association of anti-GP2 IgA as well as IgG levels with a specific clinical phenotype in CrD. Also, GP2 plays an important role in modulating innate and acquired intestinal immunity. Its urinary homologue, Tamm-Horsfall protein or uromodulin, has a similar effect in the urinary tract, further indicating that GP2 is not just an epiphenomenon of intestinal destruction. This review discusses the role of anti-GP2 autoantibodies as novel CrD-specific markers, the quantification of which provides the basis for further stratification of IBD patients. Given the association with a disease phenotype and the immunomodulating properties of GP2 itself, an important role for GP2

  14. The mechanism of Vavilov-Cherenkov radiation

    NASA Astrophysics Data System (ADS)

    Kobzev, A. P.

    2010-05-01

    The mechanism of generation of Vavilov-Cherenkov radiation is discussed in this article. The developers of the theory of the Vavilov-Cherenkov effect, I.E. Tamm and I.M. Frank, attributed this effect to their discovery of a new mechanism of radiation when a charged particle moves uniformly and rectilinearly in the medium. As such a mechanism presupposes the violation of the laws of conservation of energy and momentum, they proposed the abolition of these laws to account for the Vavilov-Cherenkov radiation mechanism. This idea has received a considerably wide acceptance in the creation of other theories, for example, transition radiation theory. In this paper, the radiation mechanism for the charge constant motion is demonstrated to be incorrect, because it contradicts not only the laws of conservation of energy and momentum, but also the very definitions of uniform and rectilinear motion (Newton's First Law). A consistent explanation of the Vavilov-Cherenkov radiation microscopic mechanism that does not contradict the basic laws is proposed. It is shown that the radiation arises from the interaction of the moving charge with bound charges that are spaced fairly far away from its trajectory. The Vavilov-Cherenkov radiation mechanism bears a slowing down character, but it differs fundamentally from bremsstrahlung, primarily because the Vavilov-Cherenkov radiation onset results from a two-stage process. First, the moving particle polarizes the medium; then, the already polarized atoms radiate coherently, provided that the particle velocity exceeds the phase speed of light in the medium. If the particle velocity is less than the phase speed of light in the medium, the polarized atoms return energy to the outgoing particle. In this case, radiation is not observed. Special attention is given to the relatively constant particle velocity as the condition of the coherent composition of waves. However, its motion cannot be designated as a uniform and rectilinear one in the

  15. Failures of TDDFT in describing the lowest intramolecular charge-transfer excitation in para-nitroaniline

    NASA Astrophysics Data System (ADS)

    Eriksen, Janus J.; Sauer, Stephan P. A.; Mikkelsen, Kurt V.; Christiansen, Ove; Jensen, Hans Jørgen Aa.; Kongsted, Jacob

    2013-07-01

    We investigate the failure of time-dependent density functional theory (TDDFT) with the CAM-B3LYP exchange-correlation (xc) functional coupled to the polarisable embedding (PE) scheme (PE-CAM-B3LYP) in reproducing the solvatochromic shift of the lowest intense charge-transfer excitation in para-nitroaniline (pNA) in water by comparing with results obtained with the coupled cluster singles and doubles (CCSD) model also coupled to the polarisable embedding scheme (PE-CCSD). We determine the amount of charge separation in the ground and excited charge-transfer state with both methods by calculating the electric dipole moments in the gas phase and for 100 solvent configurations. We find that CAM-B3LYP overestimates the amount of charge separation inherent in the ground state and TDDFT/CAM-B3LYP drastically underestimates this amount in the excited charge-transfer state. As the errors in the solvatochromatic shift are found to be inverse proportional to the change in dipole moment upon excitation, we conclude that the flaws in the description of the solvatochromic shift of this excitation are related to TDDFT itself and how it responds to the solvent effects modelled by the PE scheme. We recommend therefore to benchmark results of TDDFT calculations with CAM-B3LYP for intramolecular charge-transfer excitations in molecular systems similar to pNA against higher level ab initio wave function methods, like, e.g. CCSD, prior to their use. Using the calculated change in dipole moment upon excitation as a measure for charge-transfer character, we furthermore confirm that the difference between excitation energies calculated with TDDFT and with the Tamm-Dancoff approximation (TDA) to TDDFT is indeed correlated with the charge-transfer character of a given electronic transition both in vacuo and in solution. This is supported by a corresponding correlation between the change in dipole moment and the size of the Λ index diagnostic for the investigated CT excitation.

  16. Critical Assessment of Time-Dependent Density Functional Theory for Excited States of Open-Shell Systems: II. Doublet-Quartet Transitions.

    PubMed

    Li, Zhendong; Liu, Wenjian

    2016-06-14

    Compared with closed-shell systems, open-shell systems place three additional challenges to time-dependent density functional theory (TD-DFT) for electronically excited states: (a) the spin-contamination problem is a serious issue; (b) the exchange-correlation (XC) kernel may be numerically instable; and (c) the single-determinant description of open-shell ground states readily becomes energetically instable. Confined to flip-up single excitations, the spin-contamination problem can largely be avoided by using the spin-flip TD-DFT (SF-TD-DFT) formalism, provided that a noncollinear XC kernel is employed. As for the numerical instabilities associated with such a kernel, only an ad hoc scheme has been proposed so far, viz., the ALDA0 kernel, which amounts to setting the divergent components (arising from density gradients and kinetic energy density) simply to zero. The ground-state instability problem can effectively be avoided by introducing the Tamm-Dancoff approximation (TDA) to TD-DFT. Therefore, on a general basis, the SF-TDA/ALDA0 Ansatz is so far the only promising means within the TD-DFT framework for flip-up single excitations of open-shell systems. To assess systematically the performance of SF-TDA/ALDA0, in total 61 low-lying quartet excited states of the benchmark set of 11 small radicals [J. Chem. Theory Comput. 2016, 12, 238] are investigated with various XC functionals. Taking the MRCISD+Q (multireference configuration interaction with singles and doubles plus the Davidson correction) results as benchmark, it is found that the mean absolute errors of SF-TDA/ALDA0 with the SAOP (statistical averaging of model orbital potentials), global hybrid, and range-separated hybrid functionals are in the range of 0.2-0.4 eV. This is in line not only with the typical accuracy of TD-DFT for singlet and triplet excited states of closed-shell systems but also with the gross accuracy of spin-adapted TD-DFT for spin-conserving excited states of open-shell systems. PMID

  17. Efficient time-dependent density functional theory approximations for hybrid density functionals: Analytical gradients and parallelization

    NASA Astrophysics Data System (ADS)

    Petrenko, Taras; Kossmann, Simone; Neese, Frank

    2011-02-01

    In this paper, we present the implementation of efficient approximations to time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation (TDA) for hybrid density functionals. For the calculation of the TDDFT/TDA excitation energies and analytical gradients, we combine the resolution of identity (RI-J) algorithm for the computation of the Coulomb terms and the recently introduced "chain of spheres exchange" (COSX) algorithm for the calculation of the exchange terms. It is shown that for extended basis sets, the RIJCOSX approximation leads to speedups of up to 2 orders of magnitude compared to traditional methods, as demonstrated for hydrocarbon chains. The accuracy of the adiabatic transition energies, excited state structures, and vibrational frequencies is assessed on a set of 27 excited states for 25 molecules with the configuration interaction singles and hybrid TDDFT/TDA methods using various basis sets. Compared to the canonical values, the typical error in transition energies is of the order of 0.01 eV. Similar to the ground-state results, excited state equilibrium geometries differ by less than 0.3 pm in the bond distances and 0.5° in the bond angles from the canonical values. The typical error in the calculated excited state normal coordinate displacements is of the order of 0.01, and relative error in the calculated excited state vibrational frequencies is less than 1%. The errors introduced by the RIJCOSX approximation are, thus, insignificant compared to the errors related to the approximate nature of the TDDFT methods and basis set truncation. For TDDFT/TDA energy and gradient calculations on Ag-TB2-helicate (156 atoms, 2732 basis functions), it is demonstrated that the COSX algorithm parallelizes almost perfectly (speedup ˜26-29 for 30 processors). The exchange-correlation terms also parallelize well (speedup ˜27-29 for 30 processors). The solution of the Z-vector equations shows a speedup of ˜24 on 30 processors. The

  18. The electronic states of 1,2,5-oxadiazole studied by VUV absorption spectroscopy and CI, CCSD(T) and DFT methods

    NASA Astrophysics Data System (ADS)

    Palmer, Michael H.

    2009-06-01

    The 1,2,5-oxadiazole VUV absorption spectrum in the range 5-11.5 eV, shows broad bands centred near 6.2, 7.1, 8.3, 8.8, 10.6 and 11.3 eV. Rydberg states associated with three ionisation energies (IE) were identified in the complex fine structure above 8.7 eV. Electronic vertical excitation energies for singlet and triplet valence, and Rydberg states were computed using ab initio multi-reference multi-root CI methods. There is generally a good correlation between the envelope of the theoretical intensities and the experimental spectrum. The nature of the more intense calculated Rydberg states, and positions of the main valence and Rydberg bands are discussed. The lowest triplet, singlet and Rydberg 3s excited states have equilibrium structures that are non-planar with CS symmetry, in a chair-like orientation where the O and H atoms lie out of the NCCN plane. This finding is consistent with the doubling of the low energy UV spectral lines [B.J. Forrest, A.W. Richardson, Can. J. Chem., 50 (1972) 2088]. The nearly degenerate IE of the UV-photoelectron spectrum (UV-PES, Palmer et al. 1977) makes analysis of the VUV spectrum difficult, leading to the necessity for reinvestigation. Vertical studies (IEV) using CI, Tamm-Dancoff (TDA) and Green's Function (GF) methods all gave similar results, with near degeneracy of the first 3IEV confirming the earlier study. Studies of the adiabatic IE (IEA) using CCSD(T) and B3LYP methods, showed the energy sequence 2A2 < 2B1 < 2B2, but these states are all saddle points, in contrast to the 4th state (2A1) which is a minimum. In contrast, MP2 study of the 2B2 state showed a minimum, with only two saddle points. Complete minima were found after minor twisting of the structures. The lowest energy cationic state is 2A″ (CS), which closely resembles the 2B2 state. The O-N-C-C skeleton is twisted by 8°. The corresponding 2A‧ state (CS) is effectively identical to the 2B1 state. Attempts to find minima for other symmetry states were

  19. Double-hybrid density functional theory for excited electronic states of molecules

    NASA Astrophysics Data System (ADS)

    Grimme, Stefan; Neese, Frank

    2007-10-01

    Double-hybrid density functionals are based on a mixing of standard generalized gradient approximations (GGAs) for exchange and correlation with Hartree-Fock (HF) exchange and a perturbative second-order correlation part (PT2) that is obtained from the Kohn-Sham (GGA) orbitals and eigenvalues. This virtual orbital-dependent functional (dubbed B2PLYP) contains only two empirical parameters that describe the mixture of HF and GGA exchange (ax) and of the PT2 and GGA correlation (ac), respectively. Extensive testing has recently demonstrated the outstanding accuracy of this approach for various ground state problems in general chemistry applications. The method is extended here without any further empirical adjustments to electronically excited states in the framework of time-dependent density functional theory (TD-DFT) or the closely related Tamm-Dancoff approximation (TDA-DFT). In complete analogy to the ground state treatment, a scaled second-order perturbation correction to configuration interaction with singles (CIS(D)) wave functions developed some years ago by Head-Gordon et al. [Chem. Phys. Lett. 219, 21 (1994)] is computed on the basis of density functional data and added to the TD(A)-DFT/GGA excitation energy. The method is implemented by applying the resolution of the identity approximation and the efficiency of the code is discussed. Extensive tests for a wide variety of molecules and excited states (of singlet, triplet, and doublet multiplicities) including electronic spectra are presented. In general, rather accurate excitation energies (deviations from reference data typically <0.2eV) are obtained that are mostly better than those from standard functionals. Still, systematic errors are obtained for Rydberg (too low on average by about 0.3eV) and charge-transfer transitions but due to the relatively large ax parameter (0.53), B2PLYP outperforms most other functionals in this respect. Compared to conventional HF-based CIS(D), the method is more robust in

  20. Identification and quantification of nitrogen cycling processes in cryptogamic covers

    NASA Astrophysics Data System (ADS)

    Weber, Bettina; Wu, Dianming; Lenhart, Katharina; Tamm, Alexandra; Ruckteschler, Nina; Rodríguez-Caballero, Emilio; Elbert, Wolfgang; Burrows, Susannah; Clough, Tim; Steinkamp, Jörg; Meusel, Hannah; Behrendt, Thomas; Büdel, Burkhard; Andreae, Meinrat O.; Sörgel, Matthias; Cheng, Yafang; Crutzen, Paul; Keppler, Frank; Su, Hang; Pöschl, Ulrich

    2016-04-01

    budget from natural terrestrial sources (Lenhart et al., 2015). 15N isotope labeling experiments revealed that nitrate (NO3‑) was a precursor of N2O, suggesting that N2O may be formed during denitrification. Thus, our experiments revealed that CC play a prominent role in different steps of the N cycle, being relevant in terrestrial biogeochemistry, atmospheric chemistry and air quality. Literature Elbert W, Weber B, Burrows S, Steinkamp J, Büdel B, Andreae MO, Pöschl U (2012) Contribution of cryptogamic covers to the global cycles of carbon and nitrogen. Nature Geosciences 5: 459-462. Lenhart K, Weber B, Elbert W, Steinkamp J, Clough T, Crutzen P, Pöschl U, Keppler F (2015) Nitrous oxide and methane emissions from cryptogamic covers. Global Change Biology 21(10): 3889-3900. Weber B, Wu D, Tamm A, Ruckteschler N, Rodríguez-Caballero E, Steinkamp J, Meusel H, Elbert W, Behrendt T, Sörgel M, Cheng Y, Crutzen P, Su H, Pöschl U (2015) Biological soil crusts accelerate the nitrogen cycle through large NO and HONO emissions in drylands. Proceedings of the National Academy of Sciences 112(50): 15384-15389.

  1. “The Marshall Rosenbluth International Summer School – 2007: Plasma Thermonuclear Fusion and Plasma Astrophysics – 2007”

    SciTech Connect

    Stefan, Vladislav Alexander

    2007-10-01

    plasma instabilities, together with pioneering works of A. Sakharov, I. Tamm, L. Spitzer, Jr., L. A. Artsimovich, and others, led to the design of the TOKAMAK, the principal configuration used for contemporary magnetic fusion experiments. In addition to his research achievements, he has made significant administrative contributions as a scientific advisor in the fields of energy policy and national defense. He is the founder and the first director of The Institute for Fusion Studies at Austin, Texas. M. N. Rosenbluth has been the recipient of the E. O. Lawrence Memorial Award (1964),the Albert Einstein Award (1967),the James Clerk Maxwell prize in Plasma Physics(1976),and the Enrico Fermi Award (1986). M. N. Rosenbluth had been Science Advisor for the INSTITUTE for ADVANCED PHYSICS STUDIES (presently a division of The Stefan University) since 1989. He is the editor-in-chief of the FSRC, (Frontier Science Research Conferences) Book: "NEW IDEAS in TOKAMAK CONFINEMENT" Published by the American Institute of Physics (August 1994) in the Research Trends in Physics Series founded and edited by V. Alexander Stefan in 1989. M. N. Rosenbluth was a member of the American Academy of Arts and Sciences and the National Academy of Sciences of the USA, a Professor Emeritus at the University of California, San Diego, and a Senior Scientist at General Atomics, San Diego.

  2. Frequency Standards and Metrology

    NASA Astrophysics Data System (ADS)

    Maleki, Lute

    2009-04-01

    imaging an event horizon (Invited) / S. Doeleman. Optically-pumped space cesium clock for Galileo: results of the breadboard / R. Ruffieux ... [et al.] -- pt. IV. Optical clocks I: lattice clocks. Optical lattice clock: seven years of progress and next steps (Invited) / H. Katori, M. Takamoto and T. Akatsuka. The Yb optical lattice clock (Invited) / N. D. Demke ... [et al.]. Optical Lattice clock with Sr atoms (Invited) / P. G. Westergaard ... [et al.]. Development of an optical clock based on neutral strontium atoms held in a lattice trap / E. A. Curtis ... [et al.]. Decoherence and losses by collisions in a [symbol]Sr lattice clock / J. S. R. Vellore Winfred ... [et al.]. Lattice Yb optical clock and cryogenic Cs fountain at INRIM / F. Levi ... [et al.] -- pt. V. Optical clocks II: ion clocks. [Symbol]Yb+ single-ion optical frequency standards (Invited) / Chr. Tamm ... [et al.]. An optical clock based on a single trapped [symbol]Sr+ ion (Invited) / H. S. Margolis ... [et al.]. A trapped [symbol]Yb+ ion optical frequency standard based on the [symbol] transition (Invited) / P. Gill ... [et al.]. Overview of highly accurate RF and optical frequency standards at the National Research Council of Canada (Invited) / A. A. Madej ... [et al.] -- pt. VI. Optical frequency combs. Extreme ultraviolet frequency combs for spectroscopy (Invited) / A. Ozawa ... [et al.]. Development of an optical clockwork for the single trapped strontium ion standard at 445 THz / J. E. Bernard ... [et al.]. A phase-coherent link between the visible and infrared spectral ranges using a combination of CW OPO and femtosecond laser frequency comb / E. V. Kovalchuk and A. Peters. Improvements to the robustness of a TI: sapphire-based femtosecond comb at NPL / V. Tsatourian ... [et al.] -- pt. VII. Atomic microwave standards. NIST FI and F2 (Invited) / T. P. Heavner ... [et al.]. Atomic fountains for the USNO master clock (Invited) / C. Ekstrom ... [et al.]. The transportable cesium fountain clock NIM5

  3. Frequency Standards and Metrology

    NASA Astrophysics Data System (ADS)

    Maleki, Lute

    2009-04-01

    imaging an event horizon (Invited) / S. Doeleman. Optically-pumped space cesium clock for Galileo: results of the breadboard / R. Ruffieux ... [et al.] -- pt. IV. Optical clocks I: lattice clocks. Optical lattice clock: seven years of progress and next steps (Invited) / H. Katori, M. Takamoto and T. Akatsuka. The Yb optical lattice clock (Invited) / N. D. Demke ... [et al.]. Optical Lattice clock with Sr atoms (Invited) / P. G. Westergaard ... [et al.]. Development of an optical clock based on neutral strontium atoms held in a lattice trap / E. A. Curtis ... [et al.]. Decoherence and losses by collisions in a [symbol]Sr lattice clock / J. S. R. Vellore Winfred ... [et al.]. Lattice Yb optical clock and cryogenic Cs fountain at INRIM / F. Levi ... [et al.] -- pt. V. Optical clocks II: ion clocks. [Symbol]Yb+ single-ion optical frequency standards (Invited) / Chr. Tamm ... [et al.]. An optical clock based on a single trapped [symbol]Sr+ ion (Invited) / H. S. Margolis ... [et al.]. A trapped [symbol]Yb+ ion optical frequency standard based on the [symbol] transition (Invited) / P. Gill ... [et al.]. Overview of highly accurate RF and optical frequency standards at the National Research Council of Canada (Invited) / A. A. Madej ... [et al.] -- pt. VI. Optical frequency combs. Extreme ultraviolet frequency combs for spectroscopy (Invited) / A. Ozawa ... [et al.]. Development of an optical clockwork for the single trapped strontium ion standard at 445 THz / J. E. Bernard ... [et al.]. A phase-coherent link between the visible and infrared spectral ranges using a combination of CW OPO and femtosecond laser frequency comb / E. V. Kovalchuk and A. Peters. Improvements to the robustness of a TI: sapphire-based femtosecond comb at NPL / V. Tsatourian ... [et al.] -- pt. VII. Atomic microwave standards. NIST FI and F2 (Invited) / T. P. Heavner ... [et al.]. Atomic fountains for the USNO master clock (Invited) / C. Ekstrom ... [et al.]. The transportable cesium fountain clock NIM5