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Sample records for cell linear dichroism

  1. Live cell linear dichroism imaging reveals extensive membrane ruffling within the docking structure of natural killer cell immune synapses

    DEFF Research Database (Denmark)

    Benninger, Richard K P; Vanherberghen, Bruno; Young, Stephen;

    2009-01-01

    We have applied fluorescence imaging of two-photon linear dichroism to measure the subresolution organization of the cell membrane during formation of the activating (cytolytic) natural killer (NK) cell immune synapse (IS). This approach revealed that the NK cell plasma membrane is convoluted into...... absent from the center of the mature synapse. Understanding the role of such extensive membrane ruffling in the assembly of cytolytic synapses is an intriguing new goal....

  2. X-ray linear dichroism dependence on ferroelectric polarization

    International Nuclear Information System (INIS)

    X-ray absorption spectroscopy and photoemission electron microscopy are techniques commonly used to determine the magnetic properties of thin films, crystals, and heterostructures. Recently, these methods have been used in the study of magnetoelectrics and multiferroics. The analysis of such materials has been compromised by the presence of multiple order parameters and the lack of information on how to separate these coupled properties. In this work, we shed light on the manifestation of dichroism from ferroelectric polarization and atomic structure using photoemission electron microscopy and x-ray absorption spectroscopy. Linear dichroism arising from the ferroelectric order in the PbZr0.2Ti0.8O3 thin films was studied as a function of incident x-ray polarization and geometry to unambiguously determine the angular dependence of the ferroelectric contribution to the dichroism. These measurements allow us to examine the contribution of surface charges and ferroelectric polarization as potential mechanisms for linear dichroism. The x-ray linear dichroism from ferroelectric order revealed an angular dependence based on the angle between the ferroelectric polarization direction and the x-ray polarization axis, allowing a formula for linear dichroism in ferroelectric samples to be defined. (paper)

  3. Orientational dependence of linear dichroism exemplified by dyed spherulites.

    Science.gov (United States)

    Benedict, Jason B; Freudenthal, John H; Hollis, Eva; Kahr, Bart

    2008-08-13

    D-sorbitol forms so-called spherulites from under-cooled melts. These polycrystalline formations have optically uniaxial radii. Melts pressed between glasses crystallize as plane sections of spheres. Dyes that are soluble in molten sorbitol become oriented as the crystallization front passes through the melt so as to form disks with large linear dichroism in the absorption bands of the dyes. The dyeing of spherulites is thus a general method of solute alignment. The linear optical properties of sorbitol spherulites containing the azo dye amaranth were analyzed in detail so as to correct a persistent confusion in the literature regarding the orientational dependence of linear dichroism. In cases involving thin film dichroism of multilayered samples requiring many corrections of intensity data in non-normal incidence, some authors have taken transmittance and others absorbance as having a cosine-squared angular dependence on the plane of the electric vector of linearly polarized light. Plane sections of doped spherulites present all orientations of an electric dipole oscillator in spatially localized region in normal incidence. As such, the samples described herein are ideally suited to resolving this confusion. Images of transmittance of dyed spherulites in polarized light were recorded with a CCD camera and simulated under the assumption that both absorbance and transmittance show a cosine-squared angular dependence but with respect to different angles. Transmittance with a cosine-squared dependence follows azimuthal rotations of the spherulite radii around the wave vector, while absorbance with a cosine-squared dependence follows rotations about axes perpendicular to the wave vector, natural consequences of the properties of the optical indicatrix that are often overlooked. Spherulites obviate the substantial experimental complexities that are engendered in non-normal incidence by sample reorientation. Thus, the principles of anisotropic absorption are given in a

  4. Nucleic acid vibrational circular dichroism, absorption, and linear dichroism spectra. I. A DeVoe theory approach.

    OpenAIRE

    Self, B D; Moore, D S

    1997-01-01

    Infrared (IR) vibrational circular dichroism (VCD), absorption, and linear dichroism (LD) spectra of four homopolyribonucleotides, poly(rA), poly(rG), poly(rC), and poly(rU), have been calculated, in the 1750-1550 cm-1 spectral region, using the DeVoe polarizability theory. A newly derived algorithm, which approximates the Hilbert transform of imaginaries to reals, was used in the calculations to obtain real parts of oscillator polarizabilities associated with each normal mode. The calculated...

  5. Nucleic acid vibrational circular dichroism, absorption, and linear dichroism spectra. II. A DeVoe theory approach.

    OpenAIRE

    Self, B D; Moore, D S

    1998-01-01

    The DeVoe polarizability theory is used to calculate vibrational circular dichroism (VCD) and infrared (IR) absorption spectra of four polyribonucleotides: poly(rA) x poly(rU), poly(rU) x poly(rA) x poly(rU), poly(rG) x poly(rC), and poly(rC+) x poly(rI) x poly(rC). This is the first report on the use of the DeVoe theory to calculate VCD, oriented VCD, IR absorption, and IR linear dichroism (LD) spectra of double- and triple-stranded polyribonucleotides. Results are reported for DeVoe theory ...

  6. Linear and Chiral Dichroism in the Electron Microscope

    CERN Document Server

    Schattschneider, Peter

    2012-01-01

    The growing interest in the miniaturization of magnetic storage media and the quest for novel spintronics applications rely on element specific detection of spin and orbital magnetic moments in a solid. The most sophisticated technique to reach this aim has been XMCD (X-ray magnetic circular dichroism), largely used in synchrotron beam lines. The spatial resolution limit of this technique is of the order of 20 - 50 nm. This poses a sensible limit for the study of nanostructured devices. This book describes EMCD (energy loss magnetic chiral dichroism), a phenomenon in energy loss spectroscopy d

  7. Electronic states of 1,4-bis(phenylethynyl)benzene. A synchrotron radiation linear dichroism investigation

    DEFF Research Database (Denmark)

    Nguyen, Duy Duc; Jones, Nykola C.; Hoffmann, Søren Vrønning;

    2012-01-01

    The electronic transitions of 1,4-bis(phenylethynyl)benzene (BPEB) were investigated by UV synchrotron radiation linear dichroism (SRLD) spectroscopy in the range 25,000 – 58,000 cm–1 (400 – 170 nm) on molecular samples aligned in stretched polyethylene. The investigation was supported by variable...

  8. Magnetic x-ray linear dichroism of ultrathin Fe-Ni alloy films

    Energy Technology Data Exchange (ETDEWEB)

    Schumann, F.O.; Willis, R.F. [Pennsylvania State Univ., University Park, PA (United States); Goodman, K.W. [Lawrence Berkeley National Lab., CA (United States)] [and others

    1997-04-01

    The authors have studied the magnetic structure of ultrathin Fe-Ni alloy films as a function of Fe concentration by measuring the linear dichroism of the 3p-core levels in angle-resolved photoemission spectroscopy. The alloy films, grown by molecular-beam epitaxy on Cu(001) surfaces, were fcc and approximately four monolayers thick. The intensity of the Fe dichroism varied with Fe concentration, with larger dichroisms at lower Fe concentrations. The implication of these results to an ultrathin film analogue of the bulk Invar effect in Fe-Ni alloys will be discussed. These measurements were performed at the Spectromicroscopy Facility (Beamline 7.0.1) of the Advanced Light Source.

  9. Magnetic x-ray linear dichroism in resonant and non-resonant Gd 4f photoemission

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, S.; Gammon, W.J.; Pappas, D.P. [Virginia Commonwealth Univ., Richmond, VA (United States)] [and others

    1997-04-01

    The enhancement of the magnetic linear dichroism in resonant 4f photoemission (MLDRPE) is studied from a 50 monolayer film of Gd/Y(0001). The ALS at beamline 7.0.1 provided the source of linearly polarized x-rays used in this study. The polarized light was incident at an angle of 30 degrees relative to the film plane, and the sample magnetization was perpendicular to the photon polarization. The linear dichroism of the 4f core levels is measured as the photon energy is tuned through the 4d-4f resonance. The authors find that the MLDRPE asymmetry is strongest at the resonance. Near the threshold the asymmetry has several features which are out of phase with the fine structure of the total yield.

  10. Synchrotron radiation linear dichroism (SRLD) investigation of the electronictransitions of quinizarin, chrysazin, and anthrarufin

    DEFF Research Database (Denmark)

    Nguyen, Duy Duc; Jones, Nykola C.; Hoffmann, Søren Vrønning; Spanget-Larsen, Jens

    2010-01-01

    The electronic transitions of the three , (alpha), (alphaPrime) -dihydroxy derivatives of anthraquinone, 1,4-dihydroxy-, 1,8-dihydroxy-, and 1,5-dihydroxy-9,10-anthraquinone (quinizarin, chrysazin, and anthrarufin), were investigated by synchrotron radiation linear dichroism (SRLD) spectroscopy on...... samples aligned in stretched polyethylene. With synchrotron radiation, polarization data could be determined in the UV region up to ca. 58,000cm-1 (7.2 eV), which amounts to an extension by ca. 11,000cm-1 (1.4 eV) relative to the range accessible with a conventional light source. Throughout the...

  11. Linear birefringence and dichroism measurement in oil-based Fe3O4 magnetic nanoparticles

    Science.gov (United States)

    Lin, Jing-Fung; Wang, Chia-Hung; Lee, Meng-Zhe

    2013-04-01

    To prepare dispersed Fe3O4 magnetic nanoparticles (MNPs), we adopt a co-precipitation method and consider surfactant amount, stirring speed, dispersion mode, and molar ratio of Fe3+/Fe2+. Via transmission electronic microscopy and X-ray diffractometry, we characterize the dispersibility and size of the products and determine the appropriate values of experimental parameters. The stirring speed is 1000 rpm in titration. There is simultaneous ultrasonic vibration and mechanical stirring in the titration and surface coating processes. The surfactant amount of oleic acid is 1.2 ml for molar ratios of Fe3+/Fe2+ as 1.7:1, 1.8:1, and 1.9:1. The average diameters of these Fe3O4 MNPs are 11 nm, and the ratios of saturation magnetization for these MNPs to that of bulk magnetite range from 45% to 65%, with remanent magnetization close to zero and low coercivity. Above all, the linear birefringence and dichroism measurements of the kerosene-based ferrofluid (FF) samples are investigated by a Stokes polarimeter. The influences of particle size distribution and magnetization in the birefringence and dichroism measurements of FFs are discussed.

  12. Electronic states of the fluorophore 9,10-bis(phenylethynyl)anthracene (BPEA). A synchrotron radiation linear dichroism investigation

    DEFF Research Database (Denmark)

    Thulstrup, Peter Waaben; Jones, Nykola; Hoffmann, Søren Vrønning; Spanget-Larsen, Jens

    2013-01-01

    The electronic transitions of 9,10-bis(phenylethynyl)anthracene (BPEA) were investigated by synchrotron radiation linear dichroism (SRLD) spectroscopy in the range 20000–58000 cm1 (500–170 nm) on molecular samples aligned in stretched polyethylene. The investigation was supported by variable...

  13. Effects of symmetry on circular and linear magnetic dichroism in angle-resolved photoemission spectra of Gd/Y (0001) and Fe-Ni//Cu (001)

    Energy Technology Data Exchange (ETDEWEB)

    Goodman, K.W.; Tobin, J.G.; Schumann, F.O. [Pennsylvania State Univ., University Park, PA (United States); Willis, R.F. [Pennsylvania State Univ., University Park, PA (United States); Gammon, J.W. [Virginia Commonwealth Univ., Richmond, VA (United States); Pappas, D.P. [Virginia Commonwealth Univ., Richmond, VA (United States); Kortright, J.B. [Lawrence Berkeley National Lab., CA (United States); Denlinger, J.D. [Lawrence Berkeley National Lab., CA (United States); Rotenberg, E. [Lawrence Berkeley National Lab., CA (United States); Warwick, A. [Lawrence Berkeley National Lab., CA (United States); Smith, N.V. [Lawrence Berkeley National Lab., CA (United States)

    1997-03-26

    We have observed circular and linear magnetic dichroism in angle- resolved photoemission spectra of 50-monolayer Gd film grown on Y(0001) and 6-monolayer Fe-Ni alloy films grown on Cu(001). The 4f level of Gd and the Fe 3p level of the Fe-Ni alloy were measured. A different geometry was used for the magnetic circular dichroism than was used to measure the magnetic linear dichroism. The geometries were chosen so that the shape of the magnetic circular dichroism is predicted to be equal to the shape of the magnetic linear dichroism for four-fold symmetric Fe-Ni/Cu(001) but not for three-fold symmetric Gd/Y(0001). Experimental results are presented. In this paper we examine the effect of symmetry (experimental geometry and sample geometry) on magnetic linear and circular dichroism in angle- resolved photoemission. In particular we chose separate geometries for measuring magnetic circular and magnetic linear dichroism. The geometries were chosen such that samples with four-fold symmetry about the sample normal may have magnetic circular and magnetic linear dichroism of the same shape. But samples with three-fold symmetry should not exhibit circular and magnetic linear dichroism of the same shape. The samples studied are three-fold symmetric Gd films grown on Y(0001) and four-fold symmetric Fe-Ni alloy grown on Cu(001). After presenting the methods of the experiment, we briefly review parts of a model of magnetic dichroism developed by Venus and coworkers and our specialization and extension of it, particularly for FeNi/Cu(001). We then show the results of our measurements.

  14. A new highly adaptable design of shear-flow device for orientation of macromolecules for Linear Dichroism (LD) measurement

    KAUST Repository

    Lundahl, P. Johan

    2011-01-01

    This article presents a new design of flow-orientation device for the study of bio-macromolecules, including DNA and protein complexes, as well as aggregates such as amyloid fibrils and liposome membranes, using Linear Dichroism (LD) spectroscopy. The design provides a number of technical advantages that should make the device inexpensive to manufacture, easier to use and more reliable than existing techniques. The degree of orientation achieved is of the same order of magnitude as that of the commonly used concentric cylinders Couette flow cell, however, since the device exploits a set of flat strain-free quartz plates, a number of problems associated with refraction and birefringence of light are eliminated, increasing the sensitivity and accuracy of measurement. The device provides similar shear rates to those of the Couette cell but is superior in that the shear rate is constant across the gap. Other major advantages of the design is the possibility to change parts and vary sample volume and path length easily and at a low cost. © 2011 The Royal Society of Chemistry.

  15. Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

    Science.gov (United States)

    Bertolotto, Jorge A.; Umazano, Juan P.

    2016-06-01

    In the present work we make a theoretical study of the steady state electric linear dichroism of DNA fragments in aqueous solution. The here developed theoretical approach considers a flexible bent rod model with a saturating induced dipole moment. The electric polarizability tensor of bent DNA fragments is calculated considering a phenomenological model which theoretical and experimental backgroung is presented here. The model has into account the electric polarizability longitudinal and transversal to the macroion. Molecular flexibility is described using an elastic potential. We consider DNA fragments originally bent with bending fluctuations around an average bending angle. The induced dipole moment is supposed constant once the electric field strength grows up at critical value. To calculate the reduced electric linear dichroism we determine the optical factor considering the basis of the bent DNA perpendicular to the molecular axis. The orientational distribution function has into account the anisotropic electric properties and the molecule flexibility. We applied the present theoretical background to fit electric dichroism experimental data of DNA fragments reported in the bibliography in a wide range of molecular weight and electric field. From these fits, values of DNA physical properties are estimated. We compare and discuss the results here obtained with the theoretical and experimental data presented by other authors. The original contributions of this work are: the inclusion of the transversal electric polarizability saturating with the electric field, the description of the electric properties with an electric polarizability tensor dependant on the bending angle and the use of an arc model originally bent.

  16. Linear birefringence and dichroism in citric acid coated Fe{sub 3}O{sub 4} magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jing-Fung, E-mail: jacklin@cc.feu.edu.tw [Graduate School of Computer Application Engineering, Far East University, No. 49, Zhonghua Road, Xinshi District, Tainan, Taiwan, ROC (China); Tsai, Chun-Chin [Department of Optoelectronic Engineering, Far East University, No. 49, Zhonghua Road, Xinshi District, Tainan, Taiwan, ROC (China); Lee, Meng-Zhe [Graduate School of Computer Application Engineering, Far East University, No. 49, Zhonghua Road, Xinshi District, Tainan, Taiwan, ROC (China)

    2014-12-15

    To prepare highly dispersed water-based Fe{sub 3}O{sub 4} magnetic nanoparticles (MNPs), we adopted the co-precipitation method and used citric acid (CA) as the surfactant. Via transmission electronic microscopy, dynamic light scattering, and X-ray diffractometry, we characterized the dispersibility and size of the products. Through two single-parameter experiments, including the pH value of suspension and the action of double centrifugations, the appropriate parameters' values were determined. Further, to produce CA coated MNPs with good magneto-optical properties as high retardance and low dichroism, the orthogonal design method was used to find the optimal parameters' values, including pH value of suspension after coating was 5, molar ratio of CA to Fe{sub 3}O{sub 4} MNPs was 0.06, volume of CA was 40 ml, and coating temperature was 70 °C. Above all, the linear birefringence and dichroism of the best CA coated ferrofluid we produced were measured by a Stokes polarimeter as 23.6294° and 0.3411 under 64.5 mT, respectively. Thus, the biomedical applications could be performed hereafter. - Highlights: • We examine pH changes about retardance/dichroism of citric acid coated ferrofluid. • We examine centrifugal action about dispersity of citric acid coated ferrofluid. • Dispersity of coated suspensions with different pH is investigated by DLS results. • Optimum combination and influence sequence obtained by Taguchi method is found. • Molar ratio of CA to Fe{sub 3}O{sub 4} deeply influences the retardance and dichroism of FFs.

  17. Domain imaging on multiferroic BiFeO{sub 3}(001) by linear and circular dichroism in threshold photoemission

    Energy Technology Data Exchange (ETDEWEB)

    Sander, Anke; Christl, Maik [Institute of Physics, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 3, 06120 Halle(Saale) (Germany); Chiang, Cheng-Tien [Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle(Saale) (Germany); Institute of Physics, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 3, 06120 Halle(Saale) (Germany); Alexe, Marin [Department of Physics, University of Warwick, Coventry CV4 7AL (United Kingdom); Widdra, Wolf, E-mail: wolf.widdra@physik.uni-halle.de [Institute of Physics, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 3, 06120 Halle(Saale) (Germany); Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle(Saale) (Germany)

    2015-12-14

    We demonstrate ferroelectric domain imaging at BiFeO{sub 3}(001) single crystal surfaces with laser-based threshold photoemission electron microscopy (PEEM). Work function differences and linear dichroism allow for the identification of the eight independent ferroelectric domain configurations in the PEEM images. There, the determined domain structure is consistent with piezoresponse force microscopy of the sample surface and can also be related to the circular dichroic PEEM images. Our results provide a method for efficient mapping of complex ferroelectric domains with laser-excited PEEM and may allow lab-based time-resolved studies of the domain dynamics in the future.

  18. Electronic states of model hydrocarbon chromophores investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy on aligned samples

    DEFF Research Database (Denmark)

    Nguyen, Duy Duc; Hoffmann, Søren Vrønning; Jones, Nykola;

    2010-01-01

    solvents, for example stretched polyethylene. With a traditional UV light source (deuterium lamp, Glan prism polarizer), LD spectroscopy on thin polyethylene samples can be performed in the spectral range up to 47 000 cm-1 (210 nm). But with synchrotron radiation as a source of linearly polarized UV light......, the region can be extended considerably. Previous SRLD experiments performed with the UV1 beamline at ISA (Aarhus University) obtained excellent LD spectra up to 57000 cm-1 (175 nm), thereby increasing the investigated range by no less than 10000 cm-1. In this communication, we present corresponding......Conventional UV-VIS absorption spectroscopy provides information on transition energies and intensities. Linear dichroism (LD) spectroscopy on aligned molecular samples yields additional information on transition moment directions, thereby frequently leading to resolution of otherwise overlapping...

  19. Linear birefringence and dichroism measurement in oil-based Fe{sub 3}O{sub 4} magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jing-Fung, E-mail: jacklin@cc.feu.edu.tw [Graduate School of Computer Application Engineering, Far East University, Tainan 74448, Taiwan (China); Wang, Chia-Hung [Department of Automation and Control Engineering, Far East University, Tainan 74448, Taiwan (China); Lee, Meng-Zhe [Graduate School of Computer Application Engineering, Far East University, Tainan 74448, Taiwan (China)

    2013-04-15

    To prepare dispersed Fe{sub 3}O{sub 4} magnetic nanoparticles (MNPs), we adopt a co-precipitation method and consider surfactant amount, stirring speed, dispersion mode, and molar ratio of Fe{sup 3+}/Fe{sup 2+}. Via transmission electronic microscopy and X-ray diffractometry, we characterize the dispersibility and size of the products and determine the appropriate values of experimental parameters. The stirring speed is 1000 rpm in titration. There is simultaneous ultrasonic vibration and mechanical stirring in the titration and surface coating processes. The surfactant amount of oleic acid is 1.2 ml for molar ratios of Fe{sup 3+}/Fe{sup 2+} as 1.7:1, 1.8:1, and 1.9:1. The average diameters of these Fe{sub 3}O{sub 4} MNPs are 11 nm, and the ratios of saturation magnetization for these MNPs to that of bulk magnetite range from 45% to 65%, with remanent magnetization close to zero and low coercivity. Above all, the linear birefringence and dichroism measurements of the kerosene-based ferrofluid (FF) samples are investigated by a Stokes polarimeter. The influences of particle size distribution and magnetization in the birefringence and dichroism measurements of FFs are discussed. - Highlights: ► Dispersed Fe{sub 3}O{sub 4} magnetic nanoparticles (MNPs) are produced by a co-precipitation method. ► Simultaneous ultrasonic vibration and mechanical stirring are used in titration and coating. ► Diameters of Fe{sub 3}O{sub 4} MNPs are determined as 11 nm with maximum magnetization as 54.27 emu/g. ► Birefringence and dichroism of ferrofluids are obtained by a Stokes polarimeter successfully.

  20. An analysis of the x-ray linear dichroism spectrum for NiO thin films grown on vicinal Ag(001)

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Y.Z.; Zhao, Y.; Arenholz, E.; Young, A.T.; Sinkovic, B.; Qiu, Z.Q.

    2008-05-10

    Antiferromagnetic (AFM) NiO thin films are grown epitaxially on vicinal Ag(118) substrate and investigated by x-ray linear dichroism (XLD). We find that the NiO AFM spin exhibits an in-plane spin reorientation transition from parallel to perpendicular to the step edges with increasing the NiO film thickness. In addition to the conventional L{sub 2} adsorption edge, x-ray linear dichroism (XLD) effect at the Ni L{sub 3} adsorption edge is also measured and analyzed. The result identifies a small energy shift of the L{sub 3} peak. Temperature-dependent measurement confirms that the observed XLD effect in this system at the normal incidence of the x-rays originates entirely from the NiO magnetic ordering.

  1. The vibrational structure of (E,E’)-1,4-diphenyl-1,3-butadiene. Linear dichroism FTIR spectroscopy and quantum chemical calculations

    DEFF Research Database (Denmark)

    Hansen, Bjarke Knud Vilster; Møller, Søren; Spanget-Larsen, Jens

    2006-01-01

    The title compound (DPB) was investigated by FTIR spectroscopy in liquid solutions and by FTIR linear dichroism (LD) measurements on samples aligned in stretched polyethylene. The LD data provided experimental assignments of molecular transition moment directions and vibrational symmetries for mo...... of a nearly complete assignment of the IR active fundamentals of DPB, involving reassignment of a number of transitions. In addition, previously published Raman spectra of DPB were well predicted by the B3LYP/cc-pVTZ calculations....

  2. Magneto-optical granulometry: on the determination of the statistics of magnetically induced particle chains in concentrated ferrofluids from linear dichroism experiments

    OpenAIRE

    Socoliuc, V.; Popescu, L. B.

    2014-01-01

    An analytical theoretical model for the influence of the magnetically induced nanoparticle chaining on the linear dichroism in ferrofluids was developed. The model is based on a statistical theory for magnetic nanoparticle chaining in ferrofluids. Together with appropriate experimental approach and data processing strategy, the model grounds a magneto-optical granulometry method able to determine the magnetic field dependence of the statistics of magnetically induced particle chains in concen...

  3. Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy

    KAUST Repository

    Reymer, A.

    2009-07-08

    To get mechanistic insight into the DNA strand-exchange reaction of homologous recombination, we solved a filament structure of a human Rad51 protein, combining molecular modeling with experimental data. We build our structure on reported structures for central and N-terminal parts of pure (uncomplexed) Rad51 protein by aid of linear dichroism spectroscopy, providing angular orientations of substituted tyrosine residues of Rad51-dsDNA filaments in solution. The structure, validated by comparison with an electron microscopy density map and results from mutation analysis, is proposed to represent an active solution structure of the nucleo-protein complex. An inhomogeneously stretched double-stranded DNA fitted into the filament emphasizes the strategic positioning of 2 putative DNA-binding loops in a way that allows us speculate about their possibly distinct roles in nucleo-protein filament assembly and DNA strand-exchange reaction. The model suggests that the extension of a single-stranded DNA molecule upon binding of Rad51 is ensured by intercalation of Tyr-232 of the L1 loop, which might act as a docking tool, aligning protein monomers along the DNA strand upon filament assembly. Arg-235, also sitting on L1, is in the right position to make electrostatic contact with the phosphate backbone of the other DNA strand. The L2 loop position and its more ordered compact conformation makes us propose that this loop has another role, as a binding site for an incoming double-stranded DNA. Our filament structure and spectroscopic approach open the possibility of analyzing details along the multistep path of the strand-exchange reaction.

  4. Investigation of chromophore-chromophore interaction by electro-optic measurements, linear dichroism, x-ray scattering, and density-functional calculations

    DEFF Research Database (Denmark)

    Apitz, Dirk; Bertram, R.P.; Benter, N.;

    2005-01-01

    Free-beam interferometry and angle-resolved absorption spectra are used to investigate the linear electro-optic coefficients and the linear dichroism in photoaddressable bis-azo copolymer thin films. From the first- and second order parameters deduced, the chromophore orientation distribution is ...... density-functional calculations support the picture of differently aligned bis-azo dye molecules in a trans,trans configuration. Complementary wide-angle x-ray scattering is recorded to confirm the various kinds of ordering in samples poled at different temperatures....

  5. Compact optical cell system for vacuum ultraviolet absorption and circular dichroism spectroscopy and its application to aqueous solution sample.

    Science.gov (United States)

    Tanaka, Masahito; Yagi-Watanabe, Kazutoshi; Kaneko, Fusae; Nakagawa, Kazumichi

    2008-09-01

    We have designed a compact optical cell for studying the absorption and circular dichroism (CD) of a solution sample in the vacuum ultraviolet (VUV) region using a temperature control unit. The cell size was 34 mm in diameter and 14 mm in length. Such compactness was obtained by coating the VUV scintillator onto the outside of the back window. Because this scintillator converts the transmitted VUV light to visible light, the outside of this cell is operated under atmospheric pressure. The temperature of the sample solution was maintained in the range of 5 degrees C to 80 degrees C using a temperature control unit with a Peltier thermoelectric element. Changes in the sample temperature were observed by monitoring the absorption intensity of water. Through the study of VUV-CD spectra of ammonium camphor-10-sulfonate aqueous solutions and the transmitted spectrum of an empty cell, it was concluded that this cell unit has sufficient performance for use in VUV spectroscopy. PMID:18473342

  6. Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions

    OpenAIRE

    Phelps, Carey; Lee, Wonbae; Jose, Davis; von Hippel, Peter H.; Marcus, Andrew H.

    2013-01-01

    Unique single-molecule fluorescence techniques were used to monitor DNA “breathing” at and near the junctions of model DNA replication forks on biologically relevant microsecond-to-millisecond time scales. Experiments performed in the absence and presence of helicase complexes addressed the role of these fluctuations in helicase function during DNA replication. These studies simultaneously monitored single-molecule Förster resonance energy transfer and single-molecule fluorescence linear dich...

  7. An optically transparent thin-layer electrochemical cell for the study of vibrational circular dichroism of chiral redox-active molecules.

    Science.gov (United States)

    Domingos, Sérgio R; Luyten, Henk; van Anrooij, Fred; Sanders, Hans J; Bakker, Bert H; Buma, Wybren J; Hartl, František; Woutersen, Sander

    2013-03-01

    An optically transparent thin-layer electrochemical (OTTLE) cell with a locally extended optical path has been developed in order to perform vibrational circular dichroism (VCD) spectroscopy on chiral molecules prepared in specific oxidation states by means of electrochemical reduction or oxidation. The new design of the electrochemical cell successfully addresses the technical challenges involved in achieving sufficient infrared absorption. The VCD-OTTLE cell proves to be a valuable tool for the investigation of chiral redox-active molecules. PMID:23556803

  8. An optically transparent thin-layer electrochemical cell for the study of vibrational circular dichroism of chiral redox-active molecules

    Science.gov (United States)

    Domingos, Sérgio R.; Luyten, Henk; van Anrooij, Fred; Sanders, Hans J.; Bakker, Bert H.; Buma, Wybren J.; Hartl, František; Woutersen, Sander

    2013-03-01

    An optically transparent thin-layer electrochemical (OTTLE) cell with a locally extended optical path has been developed in order to perform vibrational circular dichroism (VCD) spectroscopy on chiral molecules prepared in specific oxidation states by means of electrochemical reduction or oxidation. The new design of the electrochemical cell successfully addresses the technical challenges involved in achieving sufficient infrared absorption. The VCD-OTTLE cell proves to be a valuable tool for the investigation of chiral redox-active molecules.

  9. Toroidal circular dichroism

    Science.gov (United States)

    Raybould, T. A.; Fedotov, V. A.; Papasimakis, N.; Kuprov, I.; Youngs, I. J.; Chen, W. T.; Tsai, D. P.; Zheludev, N. I.

    2016-07-01

    We demonstrate that the induced toroidal dipole, represented by currents flowing on the surface of a torus, makes a distinct and indispensable contribution to circular dichroism. We show that toroidal circular dichroism supplements the well-known mechanism involving electric dipole and magnetic dipole transitions. We illustrate this with rigorous analysis of the experimentally measured polarization-sensitive transmission spectra of an artificial metamaterial, constructed from elements of toroidal symmetry. We argue that toroidal circular dichroism will be found in large biomolecules with elements of toroidal symmetry and should be taken into account in the interpretation of circular dichroism spectra of organics.

  10. Linear Basal Cell Carcinoma: A Case Report

    OpenAIRE

    Ichinokawa, Yuko; Ohtuki, Akiko; Hattori, Mariko; Sadamasa, Hiroko; Hiruma, Masataro; Matumoto, Toshiharu

    2011-01-01

    Basal cell carcinoma (BCC) presents with diverse clinical features, and several morphologic and histologic variants of BCC have been reported [Sexton et al.: J Am Acad Dermatol 1990;23:1118-1126]. Linear BCC was first described as a new clinical subtype in 1985 by Lewis [Int J Dematol 1985;24:124-125]. Here, we present a case of linear BCC that we recently encountered in an elderly Japanese patient, and review other cases reported in Japan.

  11. Towards an exact theory of linear absorbance and circular dichroism of pigment-protein complexes: Importance of non-secular contributions

    Energy Technology Data Exchange (ETDEWEB)

    Dinh, Thanh-Chung; Renger, Thomas, E-mail: thomas.renger@jku.at [Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz (Austria)

    2015-01-21

    A challenge for the theory of optical spectra of pigment-protein complexes is the equal strength of the pigment-pigment and the pigment-protein couplings. Treating both on an equal footing so far can only be managed by numerically costly approaches. Here, we exploit recent results on a normal mode analysis derived spectral density that revealed the dominance of the diagonal matrix elements of the exciton-vibrational coupling in the exciton state representation. We use a cumulant expansion technique that treats the diagonal parts exactly, includes an infinite summation of the off-diagonal parts in secular and Markov approximations, and provides a systematic perturbative way to include non-secular and non-Markov corrections. The theory is applied to a model dimer and to chlorophyll (Chl) a and Chl b homodimers of the reconstituted water-soluble chlorophyll-binding protein (WSCP) from cauliflower. The model calculations reveal that the non-secular/non-Markov effects redistribute oscillator strength from the strong to the weak exciton transition in absorbance and they diminish the rotational strength of the exciton transitions in circular dichroism. The magnitude of these corrections is in a few percent range of the overall signal, providing a quantitative explanation of the success of time-local convolution-less density matrix theory applied earlier. A close examination of the optical spectra of Chl a and Chl b homodimers in WSCP suggests that the opening angle between Q{sub y} transition dipole moments in Chl b homodimers is larger by about 9{sup ∘} than for Chl a homodimers for which a crystal structure of a related WSCP complex exists. It remains to be investigated whether this change is due to a different mutual geometry of the pigments or due to the different electronic structures of Chl a and Chl b.

  12. Towards an exact theory of linear absorbance and circular dichroism of pigment-protein complexes: Importance of non-secular contributions

    International Nuclear Information System (INIS)

    A challenge for the theory of optical spectra of pigment-protein complexes is the equal strength of the pigment-pigment and the pigment-protein couplings. Treating both on an equal footing so far can only be managed by numerically costly approaches. Here, we exploit recent results on a normal mode analysis derived spectral density that revealed the dominance of the diagonal matrix elements of the exciton-vibrational coupling in the exciton state representation. We use a cumulant expansion technique that treats the diagonal parts exactly, includes an infinite summation of the off-diagonal parts in secular and Markov approximations, and provides a systematic perturbative way to include non-secular and non-Markov corrections. The theory is applied to a model dimer and to chlorophyll (Chl) a and Chl b homodimers of the reconstituted water-soluble chlorophyll-binding protein (WSCP) from cauliflower. The model calculations reveal that the non-secular/non-Markov effects redistribute oscillator strength from the strong to the weak exciton transition in absorbance and they diminish the rotational strength of the exciton transitions in circular dichroism. The magnitude of these corrections is in a few percent range of the overall signal, providing a quantitative explanation of the success of time-local convolution-less density matrix theory applied earlier. A close examination of the optical spectra of Chl a and Chl b homodimers in WSCP suggests that the opening angle between Qy transition dipole moments in Chl b homodimers is larger by about 9∘ than for Chl a homodimers for which a crystal structure of a related WSCP complex exists. It remains to be investigated whether this change is due to a different mutual geometry of the pigments or due to the different electronic structures of Chl a and Chl b

  13. UV-CD12: synchrotron radiation circular dichroism beamline at ANKA

    International Nuclear Information System (INIS)

    UV-CD12 at ANKA and its current end-station are described, with a standard module for vacuum-UV synchrotron radiation circular dichroism of bio-macromolecules in the liquid state, and a unique module for macroscopically oriented lipid membranes (oriented circular dichroism). Synchrotron radiation circular dichroism (SRCD) is a rapidly growing technique for structure analysis of proteins and other chiral biomaterials. UV-CD12 is a high-flux SRCD beamline installed at the ANKA synchrotron, to which it had been transferred after the closure of the SRS Daresbury. The beamline covers an extended vacuum-UV to near-UV spectral range and has been open for users since October 2011. The current end-station allows for temperature-controlled steady-state SRCD spectroscopy, including routine automated thermal scans of microlitre volumes of water-soluble proteins down to 170 nm. It offers an excellent signal-to-noise ratio over the whole accessible spectral range. The technique of oriented circular dichroism (OCD) was recently implemented for determining the membrane alignment of α-helical peptides and proteins in macroscopically oriented lipid bilayers as mimics of cellular membranes. It offers improved spectral quality <200 nm compared with an OCD setup adapted to a bench-top instrument, and accelerated data collection by a factor of ∼3. In addition, it permits investigations of low hydrated protein films down to 130 nm using a rotatable sample cell that avoids linear dichroism artifacts

  14. UV-CD12: synchrotron radiation circular dichroism beamline at ANKA

    Energy Technology Data Exchange (ETDEWEB)

    Bürck, Jochen, E-mail: jochen.buerck@kit.edu; Roth, Siegmar; Windisch, Dirk; Wadhwani, Parvesh; Moss, David [Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe (Germany); Ulrich, Anne S., E-mail: jochen.buerck@kit.edu [Karlsruhe Institute of Technology (KIT), POB 3640, D-76021 Karlsruhe (Germany); Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe (Germany)

    2015-04-11

    UV-CD12 at ANKA and its current end-station are described, with a standard module for vacuum-UV synchrotron radiation circular dichroism of bio-macromolecules in the liquid state, and a unique module for macroscopically oriented lipid membranes (oriented circular dichroism). Synchrotron radiation circular dichroism (SRCD) is a rapidly growing technique for structure analysis of proteins and other chiral biomaterials. UV-CD12 is a high-flux SRCD beamline installed at the ANKA synchrotron, to which it had been transferred after the closure of the SRS Daresbury. The beamline covers an extended vacuum-UV to near-UV spectral range and has been open for users since October 2011. The current end-station allows for temperature-controlled steady-state SRCD spectroscopy, including routine automated thermal scans of microlitre volumes of water-soluble proteins down to 170 nm. It offers an excellent signal-to-noise ratio over the whole accessible spectral range. The technique of oriented circular dichroism (OCD) was recently implemented for determining the membrane alignment of α-helical peptides and proteins in macroscopically oriented lipid bilayers as mimics of cellular membranes. It offers improved spectral quality <200 nm compared with an OCD setup adapted to a bench-top instrument, and accelerated data collection by a factor of ∼3. In addition, it permits investigations of low hydrated protein films down to 130 nm using a rotatable sample cell that avoids linear dichroism artifacts.

  15. Non linear behaviour of cell tensegrity models

    Science.gov (United States)

    Alippi, A.; Bettucci, A.; Biagioni, A.; Conclusio, D.; D'Orazio, A.; Germano, M.; Passeri, D.

    2012-05-01

    Tensegrity models for the cytoskeleton structure of living cells is largely used nowadays for interpreting the biochemical response of living tissues to mechanical stresses. Microtubules, microfilaments and filaments are the microscopic cell counterparts of struts (microtubules) and cables (microfilaments and filaments) in the macroscopic world: the formers oppose to compression, the latters to tension, thus yielding an overall structure, light and highly deformable. Specific cell surface receptors, such as integrins, act as the coupling elements that transmit the outside mechanical stress state into the cell body. Reversible finite deformations of tensegrity structures have been widely demonstrated experimentally and in a number of living cell simulations. In the present paper, the bistability behaviour of two general models, the linear bar oscillator and the icosahedron, is studied, as they are both obtained from mathematical simulation, the former, and from larger scale experiments, the latter. The discontinuity in the frequency response of the oscillation amplitude and the lateral bending of the resonance curves are put in evidence, as it grows larger as the driving amplitude increases, respectively.

  16. Applications of X-ray magnetic dichroism in spintronics

    International Nuclear Information System (INIS)

    The advantages of X-ray magnetic circular dichroism and X-ray magnetic linear dichroism are reviewed. With some typical examples we will show that the techniques based on synchrotron facilities have many advantages, such as elemental specification, high sensitivity, nanometer space resolution, picosecond time resolution, and the capability to measure both ferromagnetic and anti-ferromagnetic properties. These techniques are thus very powerful tools in the study of spintronics and its device applications. (author)

  17. Direct surface magnetometry with photoemission magnetic x-ray dichroism

    Energy Technology Data Exchange (ETDEWEB)

    Tobin, J.G.; Goodman, K.W. [Lawrence Berkeley National Lab., CA (United States); Schumann, F.O. [Pennsylvania State Univ., University Park, PA (United States)] [and others

    1997-04-01

    Element specific surface magnetometry remains a central goal of synchrotron radiation based studies of nanomagnetic structures. One appealing possibility is the combination of x-ray absorption dichroism measurements and the theoretical framework provided by the {open_quotes}sum rules.{close_quotes} Unfortunately, sum rule analysis are hampered by several limitations including delocalization of the final state, multi-electronic phenomena and the presence of surface dipoles. An alternative experiment, Magnetic X-Ray Dichroism in Photoelectron Spectroscopy, holds out promise based upon its elemental specificity, surface sensitivity and high resolution. Computational simulations by Tamura et al. demonstrated the relationship between exchange and spin orbit splittings and experimental data of linear and circular dichroisms. Now the authors have developed an analytical framework which allows for the direct extraction of core level exchange splittings from circular and linear dichroic photoemission data. By extending a model initially proposed by Venus, it is possible to show a linear relation between normalized dichroism peaks in the experimental data and the underlying exchange splitting. Since it is reasonable to expect that exchange splittings and magnetic moments track together, this measurement thus becomes a powerful new tool for direct surface magnetometry, without recourse to time consuming and difficult spectral simulations. The theoretical derivation will be supported by high resolution linear and circular dichroism data collected at the Spectromicroscopy Facility of the Advanced Light Source.

  18. Transient vibrational circular dichroism spectrometer: technical development

    Directory of Open Access Journals (Sweden)

    Helbing J.

    2010-06-01

    Full Text Available We recently reported the first measurements of transient VCD in the C-H-stretch region following visible excitation of cobalt(--spartein complex (Co(spCl2 with picosecond time resolution [1]. This poster presents the detailed description of the setup based on the synchronization of a femtosecond laser system with a photo elastic modulator [2]. A very precise control of the probe pulse polarization is a requirement to avoid linear dichroism artefacts. This is particularly important in crossed polarizer “quasi-null” technique which can be used to significantly enhance chiral signals [3].

  19. Laser grooved buried contact cells optimised for linear concentration systems

    Energy Technology Data Exchange (ETDEWEB)

    Vivar, M.; Anton, I.; Sala, G. [Instituto de Energia Solar, UPM, Ciudad Universitaria S/N, 28040 Madrid (Spain); Morilla, C.; Fernandez, J.M. [BP Solar Espana, Pol. Ind. Tres Cantos, s/n Zona Oeste, 28760 Tres Cantos, Madrid (Spain)

    2010-02-15

    Laser grooved buried contact silicon solar cells can be optimised for use in linear concentration systems at low cost. Optimising the groove depth, the copper thickness and the finger pitch by using the Design of Experiments (DOE) experimental methodology can lead to a dramatic reduction of the cell series resistance. This type of cell can be optimised for each application in an industrial line with few changes. For the EUCLIDES III linear concentrator system, optimised cell efficiency metrics for 51 x 116 mm units are in the range of 18-19% at the 40 x concentration level. (author)

  20. Anisotropic elliptical dichroism and influence of imperfection of circular polarization upon anisotropic circular dichroism

    International Nuclear Information System (INIS)

    In spite of the importance of anisotropic circular dichroism, in practice, it is difficult to get rid of the artifacts that arise from the imperfection of the circular polarization. Undesirable linear dichroism, interference of two orthogonal polarization states, and linear birefringence prevent us from making accurate measurements. We propose a theoretical method for evaluating the contributions of the first two, which are thought to be the main artifacts when specimens are not thick enough. Using the time-dependent perturbation theory and taking into account the direction of light propagation toward an orientationally fixed molecule, we formulated the transition probability of systems perturbed by arbitrarily polarized light and the absorption difference associated with two kinds of polarized light. We also formulated, as an extension of the dissymmetry factor of circular dichroism, a newly defined dissymmetry factor associated with two arbitrary polarization states. Furthermore, we considered a mixed-state of photon ensemble in which polarization states distribute at a certain width around a certain average. Although the purity of polarization and ellipticity does not correspond immediately, by considering the mixed state it is possible to treat them consistently. We used quantum statistical mechanics to describe the absorption difference for two kinds of photon ensembles and applied the consequent formula to examine the reported experimental results of single-molecule chiroptical responses under discussion in the recent past. The artifacts are theoretically suggested to be sensitive to the incident direction of elliptically polarized light and to the oriented systems, the ellipticity, and the orientation of ellipse. The mixed state has little, if any, effect when the polarization state distribution is narrow

  1. Anisotropic elliptical dichroism and influence of imperfection of circular polarization upon anisotropic circular dichroism

    Science.gov (United States)

    Wakabayashi, Masamitsu; Yokojima, Satoshi; Fukaminato, Tuyoshi; Ohtani, Hiroyuki; Nakamura, Shinichiro

    2015-04-01

    In spite of the importance of anisotropic circular dichroism, in practice, it is difficult to get rid of the artifacts that arise from the imperfection of the circular polarization. Undesirable linear dichroism, interference of two orthogonal polarization states, and linear birefringence prevent us from making accurate measurements. We propose a theoretical method for evaluating the contributions of the first two, which are thought to be the main artifacts when specimens are not thick enough. Using the time-dependent perturbation theory and taking into account the direction of light propagation toward an orientationally fixed molecule, we formulated the transition probability of systems perturbed by arbitrarily polarized light and the absorption difference associated with two kinds of polarized light. We also formulated, as an extension of the dissymmetry factor of circular dichroism, a newly defined dissymmetry factor associated with two arbitrary polarization states. Furthermore, we considered a mixed-state of photon ensemble in which polarization states distribute at a certain width around a certain average. Although the purity of polarization and ellipticity does not correspond immediately, by considering the mixed state it is possible to treat them consistently. We used quantum statistical mechanics to describe the absorption difference for two kinds of photon ensembles and applied the consequent formula to examine the reported experimental results of single-molecule chiroptical responses under discussion in the recent past. The artifacts are theoretically suggested to be sensitive to the incident direction of elliptically polarized light and to the oriented systems, the ellipticity, and the orientation of ellipse. The mixed state has little, if any, effect when the polarization state distribution is narrow.

  2. Anisotropic elliptical dichroism and influence of imperfection of circular polarization upon anisotropic circular dichroism

    Energy Technology Data Exchange (ETDEWEB)

    Wakabayashi, Masamitsu [Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Yokojima, Satoshi, E-mail: yokojima@toyaku.ac.jp [Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachiouji-shi, Tokyo 192-0392 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Fukaminato, Tuyoshi [Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020 (Japan); PRESTO, Japan Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075 (Japan); Ohtani, Hiroyuki [Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501 (Japan); Nakamura, Shinichiro, E-mail: snakamura@riken.jp [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2015-04-21

    In spite of the importance of anisotropic circular dichroism, in practice, it is difficult to get rid of the artifacts that arise from the imperfection of the circular polarization. Undesirable linear dichroism, interference of two orthogonal polarization states, and linear birefringence prevent us from making accurate measurements. We propose a theoretical method for evaluating the contributions of the first two, which are thought to be the main artifacts when specimens are not thick enough. Using the time-dependent perturbation theory and taking into account the direction of light propagation toward an orientationally fixed molecule, we formulated the transition probability of systems perturbed by arbitrarily polarized light and the absorption difference associated with two kinds of polarized light. We also formulated, as an extension of the dissymmetry factor of circular dichroism, a newly defined dissymmetry factor associated with two arbitrary polarization states. Furthermore, we considered a mixed-state of photon ensemble in which polarization states distribute at a certain width around a certain average. Although the purity of polarization and ellipticity does not correspond immediately, by considering the mixed state it is possible to treat them consistently. We used quantum statistical mechanics to describe the absorption difference for two kinds of photon ensembles and applied the consequent formula to examine the reported experimental results of single-molecule chiroptical responses under discussion in the recent past. The artifacts are theoretically suggested to be sensitive to the incident direction of elliptically polarized light and to the oriented systems, the ellipticity, and the orientation of ellipse. The mixed state has little, if any, effect when the polarization state distribution is narrow.

  3. Controllability analysis of decentralised linear controllers for polymeric fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Serra, Maria; Aguado, Joaquin; Ansede, Xavier; Riera, Jordi [Institut de Robotica i Informatica Industrial, Universitat Politecnica de Catalunya - Consejo Superior de Investigaciones Cientificas, C. Llorens i Artigas 4, 08028 Barcelona (Spain)

    2005-10-10

    This work deals with the control of polymeric fuel cells. It includes a linear analysis of the system at different operating points, the comparison and selection of different control structures, and the validation of the controlled system by simulation. The work is based on a complex non linear model which has been linearised at several operating points. The linear analysis tools used are the Morari resiliency index, the condition number, and the relative gain array. These techniques are employed to compare the controllability of the system with different control structures and at different operating conditions. According to the results, the most promising control structures are selected and their performance with PI based diagonal controllers is evaluated through simulations with the complete non linear model. The range of operability of the examined control structures is compared. Conclusions indicate good performance of several diagonal linear controllers. However, very few have a wide operability range. (author)

  4. Correlation of magnetic dichroism in x-ray absorption and photoelectron emission using ultrathin magnetic alloy films

    Energy Technology Data Exchange (ETDEWEB)

    Tobin, J.G.; Goodman, K.W. [Lawrence Livermore National Lab., CA (United States); Mankey, G.J.; Willis, R.F. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Physics; Denlinger, J.D.; Rotenberg, E.; Warwick, A. [Lawrence Berkeley Lab., CA (United States)

    1996-04-01

    We have begun a program to characterize magnetic alloy overlays using both magnetic x-ray circular dichroism (MXCD) and magnetic x-ray linear dichroism (MXLD). This will allow a direct comparison of MXCD-absorption and MXLD-photoelectron emission. First results from the Advanced Light Source will be presented.

  5. Picosecond circular dichroism spectroscopy: experiment, theory, and applications to protein dynamics

    Science.gov (United States)

    Xie, Sunney; Simon, John D.

    1990-05-01

    An experimental technique for measuring time dependent circular dichroism signals with picosecond resolution is described. The details of the experimental apparatus are presented. Theoretical modeling of the detected signal demonstrates that the circular dichroism signal can be isolated from contributions due to pump-induced linear dichroism and linear birefringence effects. The experimental apparatus is used to examine the comformation relaxation in myoglobin following the photoelimination of CO from carbonmonoxymyoglobin. Probing the circular dichroism of the N-band of the herne at 355 nm reveals a relaxation of several hundreds of picosecond, over two orders of magnitude slower than the photo-induced bond cleavage. These results are discussed in terms of the restructuring of the protein following photodissociation.

  6. Feedback Linearized Aircraft Control Using Dynamic Cell Structure

    Science.gov (United States)

    Jorgensen, C. C.

    1998-01-01

    A Dynamic Cell Structure (DCS ) Neural Network was developed which learns a topology representing network (TRN) of F-15 aircraft aerodynamic stability and control derivatives. The network is combined with a feedback linearized tracking controller to produce a robust control architecture capable of handling multiple accident and off-nominal flight scenarios. This paper describes network and its performance for accident scenarios including differential stabilator lock, soft sensor failure, control, stability derivative variation, and turbulence.

  7. Electric dichroism transients of aqueous solutions of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Bertolotto, J A; Corral, G M; Farias de La Torre, E M; Roston, G B [Department of Physics, Faculty of Natural Sciences, National University of La Pampa, Santa Rosa, La Pampa (Argentina)

    2010-12-15

    In this work we develop a theory of reduced electric linear dichroism transients of DNA fragments in aqueous solution. The DNA fragments are modelled as rigid 'bent-rod molecules' (BRM) with the following physical parameters: electric charge, electric polarizability tensors and hydrodynamical ones, and the average transition probability tensor per molecule. In order to study the growth and decay of electric dichroism transients, the orientational distribution function of the molecules is needed. This function is obtained by solving the time-dependent Fokker-Planck equation in the presence of a low electric field E, using a perturbation method and the Fourier method with time-dependent coefficients. In our calculations the origin of the coordinate system is the mass centre of the BRM. With respect to this centre, the electric dipole moment of the molecule is zero. The developed theory adequately explains the experimental results. We show that the theoretical approach used in this work is equivalent to the one applied in the Brownian dynamics simulation work performed by Porschke and co-workers. We also analyse the effect of a possible electric dipole moment on the transients of the reduced electric linear dichroism in DNA bent fragments.

  8. Gauge-Invariant Formulation of Circular Dichroism.

    Science.gov (United States)

    Raimbault, Nathaniel; de Boeij, Paul L; Romaniello, Pina; Berger, J A

    2016-07-12

    Standard formulations of magnetic response properties, such as circular dichroism spectra, are plagued by gauge dependencies, which can lead to unphysical results. In this work, we present a general gauge-invariant and numerically efficient approach for the calculation of circular dichroism spectra from the current density. First we show that in this formulation the optical rotation tensor, the response function from which circular dichroism spectra can be obtained, is independent of the origin of the coordinate system. We then demonstrate that its trace is independent of the gauge origin of the vector potential. We also show how gauge invariance can be retained in practical calculations with finite basis sets. As an example, we explain how our method can be applied to time-dependent current-density-functional theory. Finally, we report gauge-invariant circular dichroism spectra obtained using the adiabatic local-density approximation. The circular dichroism spectra we thus obtain are in good agreement with experiment. PMID:27295541

  9. Magnetic x-ray dichroism in ultrathin epitaxial films

    Energy Technology Data Exchange (ETDEWEB)

    Tobin, J.G.; Goodman, K.W. [Lawrence Berkeley National Lab., CA (United States); Cummins, T.R. [Univ. of Missouri, Rolla, MO (United States)] [and others

    1997-04-01

    The authors have used Magnetic X-ray Linear Dichroism (MXLD) and Magnetic X-ray Circular Dichroism (MXCD) to study the magnetic properties of epitaxial overlayers in an elementally specific fashion. Both MXLD and MXCD Photoelectron Spectroscopy were performed in a high resolution mode at the Spectromicroscopy Facility of the ALS. Circular Polarization was obtained via the utilization of a novel phase retarder (soft x-ray quarter wave plate) based upon transmission through a multilayer film. The samples were low temperature Fe overlayers, magnetic alloy films of NiFe and CoNi, and Gd grown on Y. The authors results include a direct comparison of high resolution angle resolved Photoelectron Spectroscopy performed in MXLD and MXCD modes as well as structural studies with photoelectron diffraction.

  10. How pathogens use linear motifs to perturb host cell networks

    KAUST Repository

    Via, Allegra

    2015-01-01

    Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.

  11. Vacuum-ultraviolet circular dichroism spectrophotometer using synchrotron radiation

    International Nuclear Information System (INIS)

    Full text: Circular dichroism (CD) spectroscopy is powerful for analyzing the structure of optically active materials such as biopolymers. However, no commercial CD spectrophotometer is capable of measuring the CD in the vacuum ultraviolet (VUV) region below 190 nm because of technical difficulties involved in the light source, optical device, and sample cell. CD measurements extended to the VUV region can provide more detailed and new information on the structure of biopolymers based on the higher energy transition of chromophores such as hydroxyl and acetal groups. We have constructed a VUVCD spectrophotometer to measure the CD spectra of biomaterials in aqueous solutions in the 310-140 nm wavelength region under a high vacuum, using a small-scale SR source (0.7 GeV) at Hiroshima Synchrotron Radiation Center (HiSOR). All optical devices of the spectrophotometer were set up under a high vacuum (10-6 Torr), to avoid the absorption of light by air and water vapor. The SR light is separated into two orthogonal linearly polarized light beams by a linear polarizer and then modulated to circularly polarized light at 50 kHz by a photo-elastic modulator (PEM). In order to control PEM accurately and to stabilize the lock-in amplifier under a high vacuum, we used the optical servo-control system. Also, an assembled-type MgF2 cell with a temperature-control unit was constructed using a Peltier thermoelectric element. Its path length can be adjusted by various Tefron spacers in the range from 1.3 to 50 μm and its temperature can be controlled within an accuracy of ± 1 deg C in the range from -30 to 70 deg C. The performance of the spectrophotometer and MgF2 cell constructed was tested by monitoring the CD spectra of ammonium d-camphor-10-sulfonate (ACS), D- and L-isomers of amino acids. These obtained results demonstrate that the optical system and the sample cell constructed normally operate under a high vacuum to provide useful information on the structure analysis of

  12. Exciton circular dichroism in channelrhodopsin.

    Science.gov (United States)

    Pescitelli, Gennaro; Kato, Hideaki E; Oishi, Satomi; Ito, Jumpei; Maturana, Andrés Daniel; Nureki, Osamu; Woody, Robert W

    2014-10-16

    Channelrhodopsins (ChRs) are of great interest currently because of their important applications in optogenetics, the photostimulation of neurons. The absorption and circular dichroism (CD) spectra of C1C2, a chimera of ChR1 and ChR2 of Chlamydomonas reinhardtii, have been studied experimentally and theoretically. The visible absorption spectrum of C1C2 shows vibronic fine structure in the 470 nm band, consistent with the relatively nonpolar binding site. The CD spectrum has a negative band at 492 nm (Δε(max) = -6.17 M(-1) cm(-1)) and a positive band at 434 nm (Δε(max) = +6.65 M(-1) cm(-1)), indicating exciton coupling within the C1C2 dimer. Time-dependent density functional theory (TDDFT) calculations are reported for three models of the C1C2 chromophore: (1) the isolated protonated retinal Schiff base (retPSB); (2) an ion pair, including the retPSB chromophore, two carboxylate side chains (Asp 292, Glu 162), modeled by acetate, and a water molecule; and (3) a hybrid quantum mechanical/molecular mechanical (QM/MM) model depicting the binding pocket, in which the QM part consists of the same ion pair as that in (2) and the MM part consists of the protein residues surrounding the ion pair within 10 Å. For each of these models, the CD of both the monomer and the dimer was calculated with TDDFT. For the dimer, DeVoe polarizability theory and exciton calculations were also performed. The exciton calculations were supplemented by calculations of the coupling of the retinal transition with aromatic and peptide group transitions. For the dimer, all three methods and three models give a long-wavelength C2-axis-polarized band, negative in CD, and a short-wavelength band polarized perpendicular to the C2 axis with positive CD, differing in wavelength by 1-5 nm. Only the retPSB model gives an exciton couplet that agrees qualitatively with experiment. The other two models give a predominantly or solely positive band. We further analyze an N-terminal truncated mutant

  13. Determination of Myoglobin Stability by Circular Dichroism Spectroscopy: Classic and Modern Data Analysis

    Science.gov (United States)

    Mehl, Andrew F.; Crawford, Mary A.; Zhang, Lei

    2009-01-01

    Few laboratory procedures describe the use of circular dichroism (CD) at the undergraduate level. To increase the number of laboratory exercises using CD, a thermal denaturation study of myoglobin using CD is described to assess protein stability. Values obtained from a more classic linear data analysis approach are consistent with data analyzed…

  14. Years of Magnetic X-Ray Dichroism

    Science.gov (United States)

    van der Laan, Gerrit

    A historical overview of magnetic x-ray dichroism is presented. I describe the first theoretical and experimental results that have led to the development of this powerful technique for element-specific magnetometry. The theoretical progress of the sum rules is also described, starting with the spinorbit sum rule for the isotropic spectrum which led on to the spin and orbital moment sum rules for x-ray magnetic circular dichroism. The latter has been particularly useful to understand the magnetic anisotropy in thin films and multilayers. Further developments of circular dichroism in (resonant) photoemission and Auger, as well as x-ray detected optical activity, also are summarized. Currently, magnetic x-ray dichroism finds a wide application in x-ray spectroscopy and imaging for the study of magnetic materials and it is considered to be one of the most important discoveries in the field of magnetism in the last few decennia. It is hard to imagine modern research into magnetism without the aid of polarized x-rays.

  15. Nuclear spin circular dichroism in fullerenes

    Czech Academy of Sciences Publication Activity Database

    Straka, Michal

    Brno : Masaryk University Press, 2015 - (Sklenář, V.). s. 153 ISBN 978-80-210-7890-1. [EUROMAR 2015. 05.07.2015-10.07.2015, Praha] R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : nuclear spin circular dichroism * fullerenes Subject RIV: CF - Physical ; Theoretical Chemistry

  16. Vibrational circular dichroism of nucleic acids

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, Valery; Wieser, H.; Bouř, Petr

    Brescia, 2009. s. 60-60. [International Conference on Circular Dichroism /12./. Interdisciplinary Symposium on Biological Chirality /5./. 30.08.2009-04.09.2009, Brescia] Institutional research plan: CEZ:AV0Z40550506 Keywords : VCD * G-quadruplex Subject RIV: CF - Physical ; Theoretical Chemistry

  17. A Modified Bipolar Translinear Cell with Improved Linear Range and Its Applications

    Directory of Open Access Journals (Sweden)

    N. Merz

    2012-06-01

    Full Text Available This paper presents a technique to extend the linear input voltage range of a sinh mixed translinear cell proposed by Fabre [1]. This technique extends the linear operation range of the circuit by inserting common-anode-connected pairs into the mixed translinear cell. Then the relationship between the output current and the input voltage is developed to be linear. The transconductance gain can be adjusted electronically while keeping its linearity. The performance of the proposed circuit is verified by mathematical analysis and by SPICE simulations. Finally, applications of the proposed cell in a floating resistor and a CCCII for designing an instrumentation amplifier are presented.

  18. A new multichannel detector for proteomics studies and circular dichroism

    International Nuclear Information System (INIS)

    The conventional instrument for the measurement of Circular Dichroism (CD) comprises of a single anode photomultiplier tube (PMT) detector connected to a 'lock-in' amplifier. This requires the sequential scanning across the wavelength spectrum, making it a useful method for structure determination but not for time-resolved measurements and the observation of structural changes. In this paper, we report on our progress to develop a novel system based on a semiconductor linear array detector that will overcome the limitations of the conventional systems and will allow for the observation of dynamic phenomena to the time limits imposed by the technique itself, i.e. 20 μs with conventional light modulation methods. Our final aim is to develop an instrument that will enable the simultaneous measurement of both spectroscopic and time resolved CD by the realisation of energy-dispersive experiments (EDE-CD)

  19. Quantification of stromal vascular cell mechanics with a linear cell monolayer rheometer

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, Claire M., E-mail: cma9@stanford.edu; Fuller, Gerald G. [Department of Chemical Engineering, Stanford University, Stanford, California 94305 (United States); Shen, Wen-Jun; Khor, Victor K.; Kraemer, Fredric B. [Division of Endocrinology, Gerontology and Metabolism, Stanford University, Stanford, California 94305 and Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304 (United States)

    2015-01-15

    Over the past few decades researchers have developed a variety of methods for measuring the mechanical properties of whole cells, including traction force microscopy, atomic force microscopy (AFM), and single-cell tensile testing. Though each of these techniques provides insight into cell mechanics, most also involve some nonideal conditions for acquiring live cell data, such as probing only one portion of a cell at a time, or placing the cell in a nonrepresentative geometry during testing. In the present work, we describe the development of a linear cell monolayer rheometer (LCMR) and its application to measure the mechanics of a live, confluent monolayer of stromal vascular cells. In the LCMR, a monolayer of cells is contacted on both top and bottom by two collagen-coated plates and allowed to adhere. The top plate then shears the monolayer by stepping forward to induce a predetermined step strain, while a force transducer attached to the top plate collects stress information. The stress and strain data are then used to determine the maximum relaxation modulus recorded after step-strain, G{sub r}{sup 0}, referred to as the zero-time relaxation modulus of the cell monolayer. The present study validates the ability of the LCMR to quantify cell mechanics by measuring the change in G{sub r}{sup 0} of a confluent cell monolayer upon the selective inhibition of three major cytoskeletal components (actin microfilaments, vimentin intermediate filaments, and microtubules). The LCMR results indicate that both actin- and vimentin-deficient cells had ∼50% lower G{sub r}{sup 0} values than wild-type, whereas tubulin deficiency resulted in ∼100% higher G{sub r}{sup 0} values. These findings constitute the first use of a cell monolayer rheometer to quantitatively distinguish the roles of different cytoskeletal elements in maintaining cell stiffness and structure. Significantly, they are consistent with results obtained using single-cell mechanical testing methods

  20. Is cell migration or proliferation dominant in the formation of linear arrays of oligodendrocytes?

    Science.gov (United States)

    Walsh, Darragh M; Röth, Philipp T; Holmes, William R; Landman, Kerry A; Merson, Tobias D; Hughes, Barry D

    2016-10-01

    Oligodendrocytes are the myelin-producing cells of the central nervous system that are responsible for electrically insulating axons to speed the propagation of electrical impulses. A striking feature of oligodendrocyte development within white matter is that the cell bodies of many oligodendrocyte progenitor cells become organised into discrete linear arrays of three or more cells before they differentiate into myelin-producing oligodendrocytes. These linear arrays align parallel to the direction of the axons within white matter tracts and are believed to play an important role in the co-ordination of myelination. Guided by experimental data on the abundance and composition of linear arrays in the corpus callosum of the postnatal mouse brain, we construct discrete and continuous models of linear array generation to specifically investigate the relative influence of cell migration, proliferation, differentiation and death of oligodendroglia upon the genesis of linear arrays during early postnatal development. We demonstrate that only models that incorporate significant cell migration can replicate all of the experimental observations on number of arrays, number of cells in arrays and total cell count of oligodendroglia within a given area of the corpus callosum. These models are also necessary to accurately reflect experimental data on the abundance of linear arrays composed of oligodendrocytes that derive from progenitors of different clonal origins. PMID:27343034

  1. Linear Look-ahead in Conjunctive Cells: An Entorhinal Mechanism for Vector-Based Navigation

    Directory of Open Access Journals (Sweden)

    John L Kubie

    2012-04-01

    Full Text Available The crisp organization of the firing bumps of entorhinal grid cells and conjunctive cells leads to the notion that the entorhinal cortex may compute linear navigation routes. Specifically, we propose a process, termed linear look-ahead, by which a stationary animal could compute a series of locations in the direction it is facing. We speculate that this computation could be achieved through learned patterns of connection strengths among entorhinal neurons. This paper has three sections. First, we describe the minimal grid cell properties that will be built into our network. Specifically, the network relies of rigid modules of neurons, where all members have identical grid scale and orientation, but differ in spatial phase. Additionally, these neurons must be densely interconnected with synapses that are modifiable early in the animal’s life. Second, we investigate whether plasticity during short bouts of locomotion could induce patterns of connections amongst grid cells or conjunctive cells. Finally, we run a simulation to test whether the learned connection patterns can exhibit linear look-ahead. Our results are straightforward. A simulated 30-minute walk produces weak strengthening of synapses between grid cells that do not support linear look-ahead. Similar training in a conjunctive-cell module produces a small subset of very strong connections between cells. These strong pairs have three properties: The pre- and post-synaptic cells have similar heading direction. The cell pairs have neighboring grid bumps. Finally, the spatial offset of firing bumps of the cell pair is in the direction of the common heading preference. Such a module can produce strong and accurate linear look ahead starting in any location and extending in any direction. We speculate that this process may: 1. compute linear paths to goals; 2. update grid cell firing during navigation; and 3. stabilize the rigid modules of grid cells and conjunctive cells.

  2. Versatile transmission ellipsometry to study linear ferrofluid magneto-optics

    NARCIS (Netherlands)

    Kooij, E.S.; Galca, Aurelian C.; Poelsema, B.

    2006-01-01

    Linear birefringence and dichroism of magnetite ferrofluids are studied simultaneously using spectroscopic ellipsometry in transmission mode. It is shown that this versatile technique enables highly accurate characterisation of magneto-optical phenomena. Magnetic field-dependent linear birefringence

  3. Resonant second-harmonic-generation circular-dichroism microscopy reveals molecular chirality in native biological tissues

    CERN Document Server

    Chen, Mei-Yu; Kan, Che-Wei; Lin, Yen-Yin; Ye, Cin-Wei; Wu, Meng-Jer; Liu, Hsiang-Lin; Chu, Shi-Wei

    2016-01-01

    Conventional linear optical activity effects are widely used for studying chiral materials. However, poor contrast and artifacts due to sample anisotropy limit the applicability of these methods. Here we demonstrate that nonlinear second-harmonic-generation circular dichroism spectral microscopy can overcome these limits. In intact collagenous tissues, clear spectral resonance is observed with sub-micrometer spatial resolution. By performing gradual protein denaturation studies, we show that the resonant responses are dominantly due to the molecular chirality.

  4. Porphyrin Protonation Studied by Magnetic Circular Dichroism

    Czech Academy of Sciences Publication Activity Database

    Štěpánek, Petr; Andrushchenko, Valery; Ruud, K.; Bouř, Petr

    2012-01-01

    Roč. 116, č. 1 (2012), s. 778-783. ISSN 1089-5639 R&D Projects: GA ČR GAP208/11/0105; GA ČR GA203/09/2037; GA ČR GAP208/10/0559; GA MŠk(CZ) LH11033 Institutional research plan: CEZ:AV0Z40550506 Keywords : magnetic circular dichroism (MCD) * TPPS * spectra simulations * porphyrin protonation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.771, year: 2012

  5. Non-modal linear stability analysis of miscible viscous fingering in a Hele-Shaw cell

    CERN Document Server

    Hota, Tapan Kumar; Mishra, Manoranjan

    2015-01-01

    For miscible viscous fingering (VF) in a Hele-Shaw cell or in two dimensional homogeneous porous media, the transient growth of disturbances is investigated by non-modal linear stability analysis (NMA). Due to the non-autonomous nature of the linearized perturbed equations, the linear stability theory prohibits using the normal mode analysis. The linearized perturbed equations for Darcy's law coupled with a convection-diffusion equation is discretized using finite difference method. The resultant matrix valued initial value problem is then solved by fourth order Runge-Kutta method, followed by a singular value decomposition (SVD) of the propagator matrix. We demonstrate the dominant perturbation that experiences the maximum amplification within the linear regime which lead to the transient growth. This feature was previously unattained in the existing linear stability methods for miscible VF. To explore the relevance of the optimal perturbation obtained from non-modal analysis of the physical system, we perfo...

  6. Chiral Recognition of 2-Alkylalcohols with Magnetic Circular Dichroism Measurement of Porphyrin J-Aggregate on Silica Gel Plate.

    Science.gov (United States)

    Watarai, Hitoshi; Kurahashi, Yuriko

    2016-05-01

    Simple chiral recognition method of 2-alkylalcohols on a silica gel plate was proposed by using the induced circular dichroism (ICD) of J-aggregates of diprotonated tetraphenylporphyrin and magnetic circular dichroism (MCD) spectrometry. To the silica gel on a glass slide including a chiral 2-alkylalcohol and 4 M sulfuric acid, the porphyrin in toluene was added and mixed. Then, the glass slide was used for in situ MCD measurement. The observed ICD spectra could recognize well the chirality of the alcohols and the ICD intensity normalized by the MCD intensity of the J-aggregate correlated linearly to the amount of the chiral alcohols in the silica gel. PMID:27074095

  7. Circular dichroism of chiral photonic crystal liquid layers with enclosed defect inside

    Science.gov (United States)

    Gevorgyan, Ashot; Kocharian, Armen; Vardanyan, Gagik

    2015-03-01

    The photonic crystals of artificial and self-organizing structures with spatial periodic changes in dielectric and magnetic properties have attracted considerable interest recently due to unusual physical properties and wide practical applications. The chiral periodic structure in the scale of optical wavelength gives rise to strong and characteristic circular dichroism responses at visible wavelengths. Here we investigate photonic density, circular dichroism and peculiarities of absorption and emission spectra at various eigen polarizations in multilayered one-dimensional chiral soft matter with two layers of CLCs and an isotropic defect layer inside. The circular dichroism is defined by differences in light energy absorption A=1-(R + T) by the system (R and T are the reflection and transmission coefficients, respectively) and A s , r are the light absorptions, if the incident light has left and right circular polarizations, respectively. This problem can be solved by the modified Ambartsumian's layer addition method. The influence of absorption and gain on the circular dichroism, absorption and emission spectra is established in cholesteric liquid crystal (CLC) cell with an isotropic defect layer inside.

  8. Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence

    OpenAIRE

    Singh, Harinder; Ansari, Hifzur Rahman; Gajendra P. S. Raghava

    2013-01-01

    One of the major challenges in designing a peptide-based vaccine is the identification of antigenic regions in an antigen that can stimulate B-cell’s response, also called B-cell epitopes. In the past, several methods have been developed for the prediction of conformational and linear (or continuous) B-cell epitopes. However, the existing methods for predicting linear B-cell epitopes are far from perfection. In this study, an attempt has been made to develop an improved method for predicting ...

  9. Robust Linear Precoder Design for Multi-cell Downlink Transmission

    CERN Document Server

    Tajer, Ali; Wang, Xiaodong

    2010-01-01

    Coordinated information processing by the base stations of multi-cell wireless networks enhances the overall quality of communication in the network. Such coordinations for optimizing any desired network-wide quality of service (QoS) necessitate the base stations to acquire and share some channel state information (CSI). With perfect knowledge of channel states, the base stations can adjust their transmissions for achieving a network-wise QoS optimality. In practice, however, the CSI can be obtained only imperfectly. As a result, due to the uncertainties involved, the network is not guaranteed to benefit from a globally optimal QoS. Nevertheless, if the channel estimation perturbations are confined within bounded regions, the QoS measure will also lie within a bounded region. Therefore, by exploiting the notion of robustness in the worst-case sense some worst-case QoS guarantees for the network can be asserted. We adopt a popular model for noisy channel estimates that assumes that estimation noise terms lie w...

  10. PCR-based detection of a rare linear DNA in cell culture

    Directory of Open Access Journals (Sweden)

    Saveliev Sergei V.

    2002-01-01

    Full Text Available The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 107 or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

  11. Adaptive non-linear predictive control of a simulated flotation cell

    International Nuclear Information System (INIS)

    This work illustrates the non-linear modelling and control of a flotation cell using a predictive strategy. A non-linear predictive model, based on local linear models, is used to represent the predictions of the system output and to calculate the control signal. This model is directly identified, using the available input-output data, and then used to calculate the control signal. Simulated results show not only the advantages of using simple models to approximate complex phenomenological models, but also the performance of the proposed predictive control approach. (author)

  12. Design and construction of a compact end-station at NSRRC for circular-dichroism spectra in the vacuum-ultraviolet region.

    Science.gov (United States)

    Liu, Szu Heng; Lin, Yi Hung; Huang, Liang Jen; Luo, Shiang Wen; Tsai, Wan Lin; Chiang, Su Yu; Fung, Hok Sum

    2010-11-01

    A synchrotron-radiation-based circular-dichroism end-station has been implemented at beamline BL04B at the National Synchrotron Radiation Research Center (NSRRC) in Taiwan for biological research. The design and performance of this compact end-station for measuring circular-dichroism spectra in the vacuum-ultraviolet region are described. The linearly polarized light from the beamline is converted to modulated circularly polarized light with a LiF photoelastic modulator to provide a usable wavelength region of 130-330 nm. The light spot at the sample position is 5 mm × 5 mm at a slit width of 300 µm and provides a flux greater than 1 × 10(11) photons s(-1) (0.1% bandwidth)(-1). A vacuum-compatible cell made of two CaF(2) windows has a variable path length from 1.3 µm to 1 mm and a temperature range of 253-363 K. Measured CD spectra of (1S)-(+)-10-camphorsulfonic acid and proteins demonstrated the ability of this system to extend the wavelength down to 172 nm in aqueous solution and 153 nm in hexafluoro-2-propanol. PMID:20975221

  13. Linear organization of the liver cell adhesion molecule L-CAM.

    OpenAIRE

    Cunningham, B A; Leutzinger, Y; Gallin, W J; Sorkin, B C; Edelman, G M

    1984-01-01

    A linear model of the liver cell adhesion molecule L-CAM from embryonic chickens is proposed in terms of its orientation on the cell surface, the number, type, and distribution of carbohydrate moieties, and sites of phosphorylation. L-CAM is isolated from cell membranes as a glycoprotein of Mr = 124,000. A soluble fragment (Ft1) of Mr = 81,000 can be released from cells by digestion with trypsin in the presence of calcium. Radiochemical amino acid sequence analyses indicated that both polypep...

  14. Convergence of a cell-centered finite volume discretization for linear elasticity

    OpenAIRE

    Nordbotten, Jan Martin

    2015-01-01

    We show convergence of a cell-centered finite volume discretization for linear elasticity. The discretization, termed the MPSA method, was recently proposed in the context of geological applications, where cell-centered variables are often preferred. Our analysis utilizes a hybrid variational formulation, which has previously been used to analyze finite volume discretizations for the scalar diffusion equation. The current analysis deviates significantly from the previous in three respects. Fi...

  15. High-throughput linear optical stretcher for mechanical characterization of blood cells.

    Science.gov (United States)

    Roth, Kevin B; Neeves, Keith B; Squier, Jeff; Marr, David W M

    2016-04-01

    This study describes a linear optical stretcher as a high-throughput mechanical property cytometer. Custom, inexpensive, and scalable optics image a linear diode bar source into a microfluidic channel, where cells are hydrodynamically focused into the optical stretcher. Upon entering the stretching region, antipodal optical forces generated by the refraction of tightly focused laser light at the cell membrane deform each cell in flow. Each cell relaxes as it flows out of the trap and is compared to the stretched state to determine deformation. The deformation response of untreated red blood cells and neutrophils were compared to chemically treated cells. Statistically significant differences were observed between normal, diamide-treated, and glutaraldehyde-treated red blood cells, as well as between normal and cytochalasin D-treated neutrophils. Based on the behavior of the pure, untreated populations of red cells and neutrophils, a mixed population of these cells was tested and the discrete populations were identified by deformability. © 2015 International Society for Advancement of Cytometry. PMID:26565892

  16. Non-linear image blending improves visualization of head and neck primary squamous cell carcinoma compared to linear blending in dual-energy CT

    International Nuclear Information System (INIS)

    Aim: To compare non-linear and linear image-blending post-processing techniques in dual-energy CT (DECT) of primary head and neck squamous cell carcinoma (SCC) regarding subjective and objective image quality. Materials and methods: Head and neck DECT studies from 69 patients (48 male, 21 female; mean age 62.3 years) were retrospectively evaluated. All tumour lesions were histologically confirmed SCC. Linearly blended 80/140 kVp images series with varying weighting factors of 0.3 (M0.3), 0.6 and 0.8 were compared with non-linearly blended images. Attenuation of tumour lesion, various soft-tissue structures, the internal jugular vein, and image noise were measured, tumour signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were calculated. Overall image quality, delineation of tumour lesion, image sharpness, and noise level were rated individually by three radiologists using five-point Likert scales. Interobserver agreement was calculated using intraclass correlation coefficient (ICC). Results: Enhancement of tumour lesions (non-linear, 137.5 ± 20.1 HU; M0.3, 92.7 ± 14.4 HU; M0.6, 110 ± 15.4 HU; M0.8, 123 ± 18.2 HU), CNR (non-linear, 12 ± 8; M0.3, 4 ± 4.7; M0.6, 7.5 ± 5.5; M0.8, 8 ± 5.5), subjective overall image quality and tumour delineation were significantly increased (all p < 0.001) with the non-linear blending technique compared to all investigated linear blending weighting factors. Overall interobserver agreement was substantial (ICC 0.70; 95% CI: 0.66–0.73). Conclusion: Post-processing of DECT using a non-linear blending technique provides improved objective and subjective image quality of head and neck SCC compared to linearly blended images series. - Highlights: • Non-linearly blended and linearly blended images series of DECT were compared. • Non-linear blending provides superior tumor attenuation and contrast-to-noise ratio of head and neck squamous cell carcinoma. • Non-linear blending provides superior

  17. SIMULTANEOUS MEASUREMENT OF CIRCULAR DICHROISM AND FLUORESCENCE POLARIZATION ANISOTROPY.

    Energy Technology Data Exchange (ETDEWEB)

    SUTHERLAND,J.C.

    2002-01-19

    Circular dichroism and fluorescence polarization anisotropy are important tools for characterizing biomolecular systems. Both are used extensively in kinetic experiments involving stopped- or continuous flow systems as well as titrations and steady-state spectroscopy. This paper presents the theory for determining circular dichroism and fluorescence polarization anisotropy simultaneously, thus insuring the two parameters are recorded under exactly the same conditions and at exactly the same time in kinetic experiments. The approach to measuring circular dichroism is that used in almost all conventional dichrographs. Two arrangements for measuring fluorescence polarization anisotropy are described. One uses a single fluorescence detector and signal processing with a lock-in amplifier that is similar to the measurement of circular dichroism. The second approach uses classic ''T'' format detection optics, and thus can be used with conventional photon-counting detection electronics. Simple extensions permit the simultaneous measurement of the absorption and excitation intensity corrected fluorescence intensity.

  18. Electronic and vibrational circular dichroism spectra of (R)-(-)-apomorphine

    Science.gov (United States)

    Abbate, Sergio; Longhi, Giovanna; Lebon, France; Tommasini, Matteo

    2012-09-01

    Apomorphine is a chiral drug molecule; notwithstanding its extraordinary importance, little attention has been paid to the characterization of its chiroptical properties. Here we report on its electronic circular dichroism (ECD) spectra, recorded in methanol and water, and vibrational circular dichroism (VCD) in methanol and dimethyl sulfoxide (DMSO) solutions. Density functional theory (DFT) calculations have allowed us to interpret the spectra and to evaluate the role of possible conformations, charge-states and interactions with counter ions.

  19. Circular dichroism induced by Fano resonances in planar chiral oligomers

    CERN Document Server

    Hopkins, Ben; Miroshnichenko, Andrey E; Kivshar, Yuri S

    2016-01-01

    We present a general theory of circular dichroism induced in planar chiral nanostructures with rotational symmetry. It is demonstrated, analytically, that the handedness of the incident field's polarization can control whether a nanostructure induces either absorption or scattering losses, even when the total loss (extinction) is polarization-independent. We then show that this effect is a consequence of modal interference so that strong circular dichroism in absorption and scattering can be engineered by combining Fano resonances with chiral nanoparticle clusters.

  20. Circular dichroism from Fano resonances in planar chiral oligomers

    Science.gov (United States)

    Hopkins, Ben; Poddubny, Alexander N.; Miroshnichenko, Andrey E.; Kivshar, Yuri S.

    2015-05-01

    Here we present a general approach for describing the physics of Fano resonances in nanoparticle oligomers. It is shown that the interference of nonorthogonal collective eigenmodes is a sufficient condition to produce Fano resonances. We then show that such nonorthogonality between eigenmodes also permits the existence of a new form circular dichroism in the absorption and scattering cross-sections, even when circular dichroism is forbidden in the extinction cross-section.

  1. Nuclear spin circular dichroism in fullerenes: a computational study

    Czech Academy of Sciences Publication Activity Database

    Straka, Michal; Štěpánek, Petr; Coriani, S.; Vaara, J.

    2014-01-01

    Roč. 50, č. 96 (2014), s. 15228-15231. ISSN 1359-7345 R&D Projects: GA ČR(CZ) GA14-03564S Grant ostatní: GA MŠk(CZ) ED3.2.00/08.0144 Institutional support: RVO:61388963 Keywords : nuclear spin circular dichroism * fullerenes * C60 * C70 * density functional calculations * magnetic circular dichroism Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.834, year: 2014

  2. Improved method for linear B-cell epitope prediction using antigen's primary sequence.

    Directory of Open Access Journals (Sweden)

    Harinder Singh

    Full Text Available One of the major challenges in designing a peptide-based vaccine is the identification of antigenic regions in an antigen that can stimulate B-cell's response, also called B-cell epitopes. In the past, several methods have been developed for the prediction of conformational and linear (or continuous B-cell epitopes. However, the existing methods for predicting linear B-cell epitopes are far from perfection. In this study, an attempt has been made to develop an improved method for predicting linear B-cell epitopes. We have retrieved experimentally validated B-cell epitopes as well as non B-cell epitopes from Immune Epitope Database and derived two types of datasets called Lbtope_Variable and Lbtope_Fixed length datasets. The Lbtope_Variable dataset contains 14876 B-cell epitope and 23321 non-epitopes of variable length where as Lbtope_Fixed length dataset contains 12063 B-cell epitopes and 20589 non-epitopes of fixed length. We also evaluated the performance of models on above datasets after removing highly identical peptides from the datasets. In addition, we have derived third dataset Lbtope_Confirm having 1042 epitopes and 1795 non-epitopes where each epitope or non-epitope has been experimentally validated in at least two studies. A number of models have been developed to discriminate epitopes and non-epitopes using different machine-learning techniques like Support Vector Machine, and K-Nearest Neighbor. We achieved accuracy from ∼54% to 86% using diverse s features like binary profile, dipeptide composition, AAP (amino acid pair profile. In this study, for the first time experimentally validated non B-cell epitopes have been used for developing method for predicting linear B-cell epitopes. In previous studies, random peptides have been used as non B-cell epitopes. In order to provide service to scientific community, a web server LBtope has been developed for predicting and designing B-cell epitopes (http://crdd.osdd.net/raghava/lbtope/.

  3. Linear patterning of magnetically labeled Dictyostelium cells to display confined development

    Energy Technology Data Exchange (ETDEWEB)

    Frasca, Guillaume; Raynaud, Franck; Bacri, Jean-Claude; Gazeau, Florence; Wilhelm, Claire [Laboratoire Matiere et Systemes Complexes (MSC), UMR 7057 CNRS et Universite Paris-Diderot, Paris (France)], E-mail: claire.wilhelm@univ-paris-diderot.fr

    2008-05-21

    In severe nutriment conditions, the social amoeba Dictyostelium discoideum enters a particular life cycle where it forms multicellular patterns to achieve aggregation. Extensively observed from an initial dispersed state, its developmental program can usefully be studied from a confined population to implement theoretical developments regarding biological self-organization. The challenge is then to form a cell assembly of well-defined geometrical dimensions without hindering cell behavior. To achieve this goal, we imposed transient constraints by applying temporary external magnetic gradients to trap magnetically labeled cells. Deposits of various numbers of cells were geometrically characterized for different magnetic exposure conditions. We demonstrated that the cell deposit was organized as a three-dimensional (3D) structure by both stacking layers of cells and extending these layers in the substrate plane. This structure evolves during the aggregation phase, forming periodic aggregative centers along the linear initial pattern.

  4. The temperature dependence of the optical anisotropy in magnetic fluids: birefringence and dichroism

    Science.gov (United States)

    Yusuf, N. A.; Manasrah, D. A.; Abdallah, M. A.; Abu-Safia, H.; Abu-Aljarayesh, I.

    1994-11-01

    The temperature dependence of birefringence, δ, and dichroism, Δ A, in Fe 3O 4 Isopar-M based magnetic fluids have been investigated in the temperature range 100 Tm. The values of Tm and Ts are found to vary with concentration and the applied field. The results also show that δ- H2 and Δ A-H2 curves deviate from linearity. This deviation is attributed to interparticle interactions, the orientation of pre-existing clusters, and the field-induced chain formation.

  5. Non-linear elasticity of extracellular matrices enables contractile cells to communicate local position and orientation.

    Directory of Open Access Journals (Sweden)

    Jessamine P Winer

    Full Text Available Most tissue cells grown in sparse cultures on linearly elastic substrates typically display a small, round phenotype on soft substrates and become increasingly spread as the modulus of the substrate increases until their spread area reaches a maximum value. As cell density increases, individual cells retain the same stiffness-dependent differences unless they are very close or in molecular contact. On nonlinear strain-stiffening fibrin gels, the same cell types become maximally spread even when the low strain elastic modulus would predict a round morphology, and cells are influenced by the presence of neighbors hundreds of microns away. Time lapse microscopy reveals that fibroblasts and human mesenchymal stem cells on fibrin deform the substrate by several microns up to five cell lengths away from their plasma membrane through a force limited mechanism. Atomic force microscopy and rheology confirm that these strains locally and globally stiffen the gel, depending on cell density, and this effect leads to long distance cell-cell communication and alignment. Thus cells are acutely responsive to the nonlinear elasticity of their substrates and can manipulate this rheological property to induce patterning.

  6. Linear fidelity in quantification of anti-viral CD8+ T cells.

    Science.gov (United States)

    Flesch, Inge E A; Hollett, Natasha A; Wong, Yik Chun; Tscharke, David C

    2012-01-01

    Enumeration of anti-viral CD8(+) T cells to make comparisons between mice, viruses and vaccines is a frequently used approach, but controversy persists as to the most appropriate methods. Use of peptide-MHC tetramers (or variants) and intracellular staining for cytokines, in particular IFNγ, after a short ex vivo stimulation are now common, as are a variety of cytotoxicity assays, but few direct comparisons have been made. It has been argued that use of tetramers leads to the counting of non-functional T cells and that measurement of single cytokines will fail to identify cells with alternative functions. Further, the linear range of these methods has not been tested and this is required to give confidence that relative quantifications can be compared across samples. Here we show for two acute virus infections and CD8(+) T cells activated in vitro that DimerX (a tetramer variant) and intracellular staining for IFNγ, alone or in combination with CD107 to detect degranulation, gave comparable results at the peak of the response. Importantly, these methods were highly linear over nearly two orders of magnitude. In contrast, in vitro and in vivo assays for cytotoxicity were not linear, suffering from high background killing, plateaus in maximal killing and substantial underestimation of differences in magnitude of responses. PMID:22745779

  7. Linear fidelity in quantification of anti-viral CD8+ T cells.

    Directory of Open Access Journals (Sweden)

    Inge E A Flesch

    Full Text Available Enumeration of anti-viral CD8(+ T cells to make comparisons between mice, viruses and vaccines is a frequently used approach, but controversy persists as to the most appropriate methods. Use of peptide-MHC tetramers (or variants and intracellular staining for cytokines, in particular IFNγ, after a short ex vivo stimulation are now common, as are a variety of cytotoxicity assays, but few direct comparisons have been made. It has been argued that use of tetramers leads to the counting of non-functional T cells and that measurement of single cytokines will fail to identify cells with alternative functions. Further, the linear range of these methods has not been tested and this is required to give confidence that relative quantifications can be compared across samples. Here we show for two acute virus infections and CD8(+ T cells activated in vitro that DimerX (a tetramer variant and intracellular staining for IFNγ, alone or in combination with CD107 to detect degranulation, gave comparable results at the peak of the response. Importantly, these methods were highly linear over nearly two orders of magnitude. In contrast, in vitro and in vivo assays for cytotoxicity were not linear, suffering from high background killing, plateaus in maximal killing and substantial underestimation of differences in magnitude of responses.

  8. Non-linearity measurements of solar cells with an LED-based combinatorial flux addition method

    Science.gov (United States)

    Hamadani, Behrang H.; Shore, Andrew; Roller, John; Yoon, Howard W.; Campanelli, Mark

    2016-02-01

    We present a light emitting diode (LED)-based system utilizing a combinatorial flux addition method to investigate the non-linear relationship in solar cells between the output current of the cell and the incident irradiance level. The magnitude of the light flux is controlled by the supplied currents to two LEDs (or two sets of them) in a combinatorial fashion. The signals measured from the cell are arranged within a related overdetermined linear system of equations derived from an appropriately chosen Nth degree polynomial representing the relationship between the measured signals and the incident fluxes. The flux values and the polynomial coefficients are then solved for by linear least squares to obtain the best fit. The technique can be applied to any solar cell, under either monochromatic or broadband spectrum. For the unscaled solution, no reference detectors or prior calibrations of the light flux are required. However, if at least one calibrated irradiance value is known, then the entire curve can be scaled to an appropriate spectral responsivity value. Using this technique, a large number of data points can be obtained in a relatively short time scale over a large signal range.

  9. Optically-driven red blood cell rotor in linearly polarized laser tweezers

    Indian Academy of Sciences (India)

    Manas Khan; Samarendra K Mohanty; A K Sood

    2005-11-01

    We have constructed a dual trap optical tweezers set-up around an inverted microscope where both the traps can be independently controlled and manipulated in all the three dimensions. Here we report our observations on rotation of red blood cells (RBCs) in a linearly polarized optical trap. Red blood cells deform and become twisted in hypertonic phosphate buffer saline and when trapped, experience an unbalanced radiation pressure force. The torque generated from the unbalanced force causes the trapped RBC to rotate. Addition of Ca++ ions in the solution, keeping the osmolarity same, makes the cell membranes stiffer and the cells deform less. Thus the speed of rotation of the red blood cells can be controlled, as less deformation and in turn less asymmetry in shape produces less torque under the radiation pressure resulting in slower rotation at the same laser power.

  10. Microwave Quality Assurance for Single Cells of the Next Linear Collider

    International Nuclear Information System (INIS)

    The Next Linear Collider comprises about 5,000 traveling wave sections, each manufactured from about 200 precision machined cells. Each cell in a section has a different shape. Measuring the shape of a cell with sufficient accuracy takes approximately of 1/2 hour using conventional CMM techniques. This is because many points on the interior of the cell must be measured to assure the cell will be resonant at the proper monopole (accelerating) frequency and the proper dipole frequency. On the other hand these frequencies can be measured to the required accuracy of a fraction of a megahertz in a few seconds using either a modern microwave network analyzer or a specialized system designed just for measuring these cell resonances. The microwave measurement in effect does an integral over the whole surface contour to find the net error in desired frequency. In order to avoid damaging cells it is ideal to use a non-contacting RF test apparatus with non-contacting shorts and choke joints on either side of the cell. The complex geometry of the proposed damped detuned cell structures makes it difficult to obtain high Q with non-contacting shorting plates[1]. It is still possible to get sub-megahertz resolution by measuring phase rather than amplitude at resonance and using reference cavities for calibration. It is assumed that the system will be highly automated with automatic cell handling and data recording

  11. Transient expression of minimum linear gene cassettes in onion epidermal cells via direct transformation.

    Science.gov (United States)

    Cheng, Yun-Qing; Yang, Jun; Xu, Feng-Ping; An, Li-Jia; Liu, Jian-Feng; Chen, Zhi-Wen

    2009-12-01

    A new method without any special devices for direct transformation of linear gene cassettes was developed. Its feasibility was verified through 5'-fluorescent dye (fluorescein isothiocyanate, FITC)-labeled fluorescent tracing and transient expression of a gus reporter gene. Minimal linear gene cassettes, containing necessary regulation elements and a gus reporter gene, was prepared by polymerase chain reaction and dissolved in transformation buffer solution to 100 ng/mL. The basic transformation solution used was Murashige and Skoog basal salt mixture (MS) liquid medium. Hypertonic pretreatment of explants and transformation cofactors, including Ca(2+), surfactant assistants, Agrobacterium LBA4404 cell culture on transformation efficiency were evaluated. Prior to the incubation of the explants and target linear cassette in each designed transformation solution for 3 h, the onion low epidermal explants were pre-cultured in darkness at 27 degrees C for 48 h and then transferred to MS solid media for 72 h. FITC-labeled linear DNA was used to trace the delivery of DNA entry into the cell and the nuclei. By GUS staining and flow-cytometry-mediated fluorescent detection, a significant increase of the ratios of fluorescent nuclei as well as expression of the gus reporter gene was observed by each designed transformation solution. This potent and feasible method showed prospective applications in plant transgenic research. PMID:19255730

  12. Synthesis and Cell Adhesive Properties of Linear and Cyclic RGD Functionalized Polynorbornene Thin Films

    OpenAIRE

    Patel, Paresma R.; Kiser, Rosemary Conrad; Lu, Ying Y.; Fong, Eileen; Ho, Wilson C.; Tirrell, David A.; Grubbs, Robert H.

    2012-01-01

    Described herein is the efficient synthesis and evaluation of bioactive arginine-glycine-aspartic acid (RGD) functionalized polynorbornene-based materials for cell adhesion and spreading. Polynorbornenes containing either linear or cyclic RGD peptides were synthesized by ring-opening metathesis polymerization (ROMP) using the well-defined ruthenium initiator [(H_(2)IMes)(pyr)_(2)(Cl)_(2)Ru═CHPh]. The random copolymerization of three separate norbornene monomers allowed for the incorporation o...

  13. Evaluation of the effectiveness of packed red blood cell irradiation by a linear accelerator

    OpenAIRE

    Olivo, Ricardo Aparecido; da Silva, Marcus Vinícius; Garcia, Fernanda Bernadelli; Soares, Sheila; Rodrigues Junior, Virmondes; Moraes-Souza, Helio

    2015-01-01

    Irradiation of blood components with ionizing radiation generated by a specific device is recommended to prevent transfusion-associated graft-versus-host disease. However, a linear accelerator can also be used in the absence of such a device, which is the case of the blood bank facility studied herein. In order to evaluate the quality of the irradiated packed red blood cells, this study aimed to determine whether the procedure currently employed in the facility is effective in inhibiting the ...

  14. Kinetics of linear rouleaux formation studied by visual monitoring of red cell dynamic organization.

    OpenAIRE

    Barshtein, G; Wajnblum, D; Yedgar, S

    2000-01-01

    Red blood cells (RBCs) in the presence of plasma proteins or other macromolecules may form aggregates, normally in rouleaux formations, which are dispersed with increasing blood flow. Experimental observations have suggested that the spontaneous aggregation process involves the formation of linear rouleaux (FLR) followed by formation of branched rouleaux networks. Theoretical models for the spontaneous rouleaux formation were formulated, taking into consideration that FLR may involve both "po...

  15. Large Enhancement of Circular Dichroism Using an Embossed Chiral Metamaterial

    CERN Document Server

    Mousavi, S Hamed Shams; El-Sayed, Mostafa A; Eftekhar, Ali A; Adibi, Ali

    2016-01-01

    In the close vicinity of a chiral nanostructure, the circular dichroism of a biomolecule could be greatly enhanced, due to the interaction with the local superchiral fields. Modest enhancement of optical activity using a planar metamaterial, with some chiral properties, and achiral nanoparticles has been previously reported. A more substantial chirality enhancement can be achieved in the local filed of a chiral nanostructure with a three-dimensional arrangement. Using an embossed chiral nanostructure designed for chiroptical sensing, we measure the circular dichroism spectra of two biomolecules, Chlorophylls A and B, at the molecular level, using a simple polarization resolved reflection measurement. This experiment is the first realization of the on-resonance surface-enhanced circular dichroism, achieved by matching the chiral resonances of a strongly chiral metamaterial with that of a chiral molecule, resulting in an unprecedentedly large differential CD spectrum from a monolayer of a chiral material.

  16. Study of the influence of actin-binding proteins using linear analyses of cell deformability.

    Science.gov (United States)

    Plaza, Gustavo R; Uyeda, Taro Q P; Mirzaei, Zahra; Simmons, Craig A

    2015-07-21

    The actin cytoskeleton plays a key role in the deformability of the cell and in mechanosensing. Here we analyze the contributions of three major actin cross-linking proteins, myosin II, α-actinin and filamin, to cell deformability, by using micropipette aspiration of Dictyostelium cells. We examine the applicability of three simple mechanical models: for small deformation, linear viscoelasticity and drop of liquid with a tense cortex; and for large deformation, a Newtonian viscous fluid. For these models, we have derived linearized equations and we provide a novel, straightforward methodology to analyze the experiments. This methodology allowed us to differentiate the effects of the cross-linking proteins in the different regimes of deformation. Our results confirm some previous observations and suggest important relations between the molecular characteristics of the actin-binding proteins and the cell behavior: the effect of myosin is explained in terms of the relation between the lifetime of the bond to actin and the resistive force; the presence of α-actinin obstructs the deformation of the cytoskeleton, presumably mainly due to the higher molecular stiffness and to the lower dissociation rate constants; and filamin contributes critically to the global connectivity of the network, possibly by rapidly turning over cross-links during the remodeling of the cytoskeletal network, thanks to the higher rate constants, flexibility and larger size. The results suggest a sophisticated relationship between the expression levels of actin-binding proteins, deformability and mechanosensing. PMID:26059185

  17. Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.

    1999-11-13

    In this paper, we present an object-oriented three-dimensional parallel particle-in-cell code for beam dynamics simulation in linear accelerators. A two-dimensional parallel domain decomposition approach is employed within a message passing programming paradigm along with a dynamic load balancing. Implementing object-oriented software design provides the code with better maintainability, reusability, and extensibility compared with conventional structure based code. This also helps to encapsulate the details of communications syntax. Performance tests on SGI/Cray T3E-900 and SGI Origin 2000 machines show good scalability of the object-oriented code. Some important features of this code also include employing symplectic integration with linear maps of external focusing elements and using z as the independent variable, typical in accelerators. A successful application was done to simulate beam transport through three superconducting sections in the APT linac design.

  18. The Relative Biologic Effectiveness versus Linear Energy Transfer Curve as a Cell Trait

    OpenAIRE

    Quoc T. Luu; Paul DuChateau

    2013-01-01

    The magnitude of biological response varies with different radiation types. Using Linear Energy Transfer (LET) to differentiate types of incident radiation beam, the Relative Biologic Effectiveness (RBE) as a function of LET (RBE-LET) was found to have a characteristic shape with a peak around LET values 100 - 200 eV/nm. This general feature is believed to be a property of the incident beam. Our systems engineering model, however, suggests that the shape of the RBE-LET curve is a cell tr...

  19. Monitoring of Porphyrin Protonation by the Magnetic Circular Dichroism

    Czech Academy of Sciences Publication Activity Database

    Štěpánek, Petr; Bouř, Petr

    Oxford : Diamond, 2011. s. 21-21. [CD 2011. The International Conference on Chiroptical Spectroscopy /13./. 24.07.2011-28.07.2011, Oxford] Grant ostatní: 7th European Community Framework Program(XE) 230955 Institutional research plan: CEZ:AV0Z40550506 Keywords : porphyrin * magnetic circular dichroism * DFT calculation Subject RIV: CF - Physical ; Theoretical Chemistry

  20. Circular Dichroism Method for Heat Capacity Determination of Proteins

    Science.gov (United States)

    Jones, Cecil L.; Bailey, Chris; Bheemarti, Kiran Kumar

    2006-01-01

    Circular dichroism spectroscopy was used to measure the thermal unfolding of bovine pancreatic ribonuclease A (RNase A) with various concentrations of guanidine hydrochloride (GuHCl). A red shift in transition midpoint temperatures, T[subscript m], occurred with increasing concentration of the strong protein denaturant. van Hoff enthalpy changes,…

  1. Circular dichroism of graphene oxide: the chiral structure model

    Institute of Scientific and Technical Information of China (English)

    Jing CAO; Hua-Jie YIN; Rui SONG

    2013-01-01

    We have observed the circular dichroism signal of dilute graphene oxide (GO), then systematically investigated the chirality of GO and established a probable chiral unit model, This study may open up a new field for understanding the structure of GO and lay the foundation for fabrication of GO-based materials.

  2. Dichroism for Orbital Angular Momentum using Stimulated Parametric Down Conversion

    CERN Document Server

    Lowney, Joseph; Faccio, Daniele; Wright, Ewan M

    2014-01-01

    We theoretically analyze stimulated parametric down conversion as a means to produce dichroism based on the orbital angular momentum (OAM) of an incident signal field. The nonlinear interaction is shown to provide differential gain between signal states of differing OAM, the peak gain occurring at half the OAM of the pump field.

  3. Detection of magnetic circular dichroism using a transmission electron microscoe

    Czech Academy of Sciences Publication Activity Database

    Schattschneider, P.; Rubino, S.; Hébert, C.; Rusz, Ján; Kuneš, Jan; Novák, Pavel; Carlino, E.; Fabrizioli, M.; Panaccione, G.; Rossi, G.

    2006-01-01

    Roč. 441, - (2006), s. 486-488. ISSN 0028-0836 Grant ostatní: CHIRALTEM (NEST-2003-1 Adventure)(XE) STREP 508971 Institutional research plan: CEZ:AV0Z10100521 Keywords : magnetism * circular dichroism * electron microscope Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 26.681, year: 2006

  4. Vibrational circular dichroism spectroscopy study of paroxetine and femoxetine precursors

    Czech Academy of Sciences Publication Activity Database

    Urbanová, M.; Setnička, V.; Bouř, Petr; Navrátilová, H.; Volka, K.

    2002-01-01

    Roč. 67, - (2002), s. 298-301. ISSN 0006-3525 R&D Projects: GA AV ČR IAA4055104 Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.372, year: 2002

  5. Enhanced circular dichroism via slow light in dispersive structured media

    DEFF Research Database (Denmark)

    Pedersen, Jesper Goor; Mortensen, Asger

    2007-01-01

    Circular dichroism (CD) is in widespread use as a means of determining enantiomeric excess. We show how slow-light phenomena in dispersive structured media allow for a reduction in the required optical path length of an order of magnitude. The same ideas may be used to enhance the sensitivity of CD...

  6. X-ray magnetic dichroism in (Zn,Mn)O diluted magnetic semiconductors: first-principles calculations

    Energy Technology Data Exchange (ETDEWEB)

    Antonov, V. N. [Max-Planck-Institut fur Festkorperforschung, Stuttgart (Germany); Institute of Metal Physics, Kiev (Ukraine); Bekenov, L. V.; Mazur, D. V. [Institute of Metal Physics, Kiev (Ukraine); Germash, L. P. [National Technical University of Ukraine, Kiev (Ukraine)

    2012-06-15

    The electronic structure of (Zn,Mn)O diluted magnetic semiconductors was investigated theoretically from first principles by using the fully-relativistic Dirac linear muffin-tin orbital band structure method with the local spin-density approximation (LSDA) and the LSDA+U approach. The X-ray magnetic circular dichroism (XMCD) spectra at the Mn, Zn, and O K and Mn L{sub 2,3} edges were investigated theoretically from first principles. The origin of the XMCD spectra in these compounds was examined. The effect of oxygen vacancy atoms was found to be crucial for the X-ray magnetic dichroism at the Mn L{sub 2,3} edges. The calculated results are compared with available experimental data.

  7. High linear-energy-transfer radiation can overcome radioresistance of glioma stem-like cells to low linear-energy-transfer radiation

    International Nuclear Information System (INIS)

    Ionizing radiation is applied as the standard treatment for glioblastoma multiforme (GBM). However, radiotherapy remains merely palliative, not curative, because of the existence of glioma stem cells (GSCs), which are regarded as highly radioresistant to low linear-energy-transfer (LET) photons. Here we analyzed whether or not high-LET particles can overcome the radioresistance of GSCs. Glioma stem-like cells (GSLCs) were induced from the GBM cell line A172 in stem cell culture medium. The phenotypes of GSLCs and wild-type cells were confirmed using stem cell markers. These cells were irradiated with 60Co gamma rays or reactor neutron beams. Under neutron-beam irradiation, high-LET proton particles can be produced through elastic scattering or nitrogen capture reaction. Radiosensitivity was assessed by a colony-forming assay, and the DNA double-strand breaks (DSBs) were assessed by a histone gamma-H2AX focus detection assay. In stem cell culture medium, GSLCs could form neurosphere-like cells and express neural stem cell markers (Sox2 and Musashi) abundantly in comparison with their parental cells. GSLCs were significantly more radioresistant to gamma rays than their parental cells, but neutron beams overcame this resistance. There were significantly fewer gamma-H2AX foci in the A172 GSLCs 24 h after irradiation with gamma rays than in their parental cultured cells, while there was no apparent difference following neutron-beam irradiation. High-LET radiation can overcome the radioresistance of GSLCs by producing unrepairable DNA DSBs. High-LET radiation therapy might have the potential to overcome GBM's resistance to X-rays in a clinical setting. (author)

  8. Linear identification and model adjustment of a PEM fuel cell stack

    Energy Technology Data Exchange (ETDEWEB)

    Kunusch, C.; Puleston, P.F.; More, J.J. [LEICI, Departamento de Electrotecnia, Universidad Nacional de La Plata, calle 1 esq. 47 s/n, 1900 La Plata (Argentina); Consejo de Investigaciones Cientificas y Tecnicas (CONICET) (Argentina); Husar, A. [Institut de Robotica i Informatica Industrial (CSIC-UPC), c/ Llorens i Artigas 4-6, 08028 Barcelona (Spain); Mayosky, M.A. [LEICI, Departamento de Electrotecnia, Universidad Nacional de La Plata, calle 1 esq. 47 s/n, 1900 La Plata (Argentina); Comision de Investigaciones Cientificas (CIC), Provincia de Buenos Aires (Argentina)

    2008-07-15

    In the context of fuel cell stack control a mayor challenge is modeling the interdependence of various complex subsystem dynamics. In many cases, the states interaction is usually modeled through several look-up tables, decision blocks and piecewise continuous functions. Many internal variables are inaccessible for measurement and cannot be used in control algorithms. To make significant contributions in this area, it is necessary to develop reliable models for control and design purposes. In this paper, a linear model based on experimental identification of a 7-cell stack was developed. The procedure followed to obtain a linear model of the system consisted in performing spectroscopy tests of four different single-input single-output subsystems. The considered inputs for the tests were the stack current and the cathode oxygen flow rate, while the measured outputs were the stack voltage and the cathode total pressure. The resulting model can be used either for model-based control design or for on-line analysis and errors detection. (author)

  9. A nanodosimetry-based linear-quadratic model of cell survival for mixed-LET radiations

    International Nuclear Information System (INIS)

    A new nanodosimetry-based linear-quadratic (LQ) model of cell survival for mixed-LET radiations has been developed. The new model employs three physical quantities and three biological quantities. The three physical quantities are related to energy depositions at two nanometre scales, 5 nm and 25 nm. The three biological quantities are related to the lesion production and interaction probabilities and the lesion repair rate. The coefficients α and β of the LQ formula (αD + βD2) are explicitly expressed in terms of the three physical quantities and the three biological quantities. The new model is shown to be consistent with the previously published cell survival curves of V-79 cells. The advantage of this new model is that it can be conveniently adopted to estimate the iso-effect for radiotherapies that involve ionizing radiation of mixed LET. An example is given to estimate the cell survival fractions for a high-dose-rate mixed neutron and gamma-ray field from a 252Cf source

  10. A nanodosimetry-based linear-quadratic model of cell survival for mixed-LET radiations

    Science.gov (United States)

    Wang, C.-K. Chris; Zhang, Xin

    2006-12-01

    A new nanodosimetry-based linear-quadratic (LQ) model of cell survival for mixed-LET radiations has been developed. The new model employs three physical quantities and three biological quantities. The three physical quantities are related to energy depositions at two nanometre scales, 5 nm and 25 nm. The three biological quantities are related to the lesion production and interaction probabilities and the lesion repair rate. The coefficients α and β of the LQ formula (αD + βD2) are explicitly expressed in terms of the three physical quantities and the three biological quantities. The new model is shown to be consistent with the previously published cell survival curves of V-79 cells. The advantage of this new model is that it can be conveniently adopted to estimate the iso-effect for radiotherapies that involve ionizing radiation of mixed LET. An example is given to estimate the cell survival fractions for a high-dose-rate mixed neutron and gamma-ray field from a 252Cf source.

  11. A nanodosimetry-based linear-quadratic model of cell survival for mixed-LET radiations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, C-K Chris; Zhang, Xin [Nuclear/Radiological Engineering/Medical Physics Program, Neely Research Center, Georgia Institute of Technology, 900 Atlantic Drive, Atlanta, GA 30332-0425 (United States)

    2006-12-07

    A new nanodosimetry-based linear-quadratic (LQ) model of cell survival for mixed-LET radiations has been developed. The new model employs three physical quantities and three biological quantities. The three physical quantities are related to energy depositions at two nanometre scales, 5 nm and 25 nm. The three biological quantities are related to the lesion production and interaction probabilities and the lesion repair rate. The coefficients {alpha} and {beta} of the LQ formula ({alpha}D + {beta}D{sup 2}) are explicitly expressed in terms of the three physical quantities and the three biological quantities. The new model is shown to be consistent with the previously published cell survival curves of V-79 cells. The advantage of this new model is that it can be conveniently adopted to estimate the iso-effect for radiotherapies that involve ionizing radiation of mixed LET. An example is given to estimate the cell survival fractions for a high-dose-rate mixed neutron and gamma-ray field from a {sup 252}Cf source.

  12. Effect of linear alkylbenzene sulfonate (LAS) on human intestinal Caco-2 cells at non cytotoxic concentrations.

    Science.gov (United States)

    Bradai, Mohamed; Han, Junkyu; Omri, Abdelfatteh El; Funamizu, Naoyuki; Sayadi, Sami; Isoda, Hiroko

    2016-08-01

    Linear alkylbenzene sulfonate (LAS) is a cytotoxic synthetic anionic surfactant widely present in the environment due to its large-scale production and intensive use in the detergency field. In this study, we investigated the effect of LAS (CAS No. 25155-30-0) at non cytotoxic concentrations on human intestinal Caco-2 cells using different in vitro bioassays. As results, LAS increased Caco-2 cell proliferation at concentrations ranging from 1 to 15 ppm, more significantly for shorter exposure time (24 h), confirmed using flow cytometry and trypan blue exclusion methods. Moreover, proteomics analysis revealed that this effect was associated with an over-expression of elongation factor 2 and dipeptidyl peptidase 3, and a down-regulation of 14-3-3 protein theta, confirmed at mRNA level using real-time PCR. These findings suggest that LAS at non cytotoxic concentrations, similar to those observed at wastewater treatment plants outlets, increases the growth rate of colon cancer cells, raising thereby its tumor promotion effect potential. PMID:25999174

  13. Linear gyrokinetic particle-in-cell simulations of Alfven instabilities in tokamaks

    CERN Document Server

    Biancalani, A; Briguglio, S; Koenies, A; Lauber, Ph; Mishchenko, A; Poli, E; Scott, B D; Zonca, F

    2015-01-01

    The linear dynamics of Alfven modes in tokamaks is investigated here by means of the global gyrokinetic particle-in-cell code NEMORB. The model equations are shown and the local shear Alfven wave dispersion relation is derived, recovering the continuous spectrum in the incompressible ideal MHD limit. A verification and benchmark analysis is performed for continuum modes in a cylinder and for toroidicity-induced Alfven Eigenmodes. Modes in a reversed-shear equilibrium are also investigated, and the dependence of the spatial structure in the poloidal plane on the equilibrium parameters is described. In particular, a phase-shift in the poloidal angle is found to be present for modes whose frequency touches the continuum, whereas a radial symmetry is found to be characteristic of modes in the continuum gap.

  14. Analytical considerations for linear and nonlinear optimization of the TME cells. Application to the CLIC pre-damping rings

    CERN Document Server

    Fanouria, Antoniou

    2014-01-01

    The theoretical minimum emittance cells are the optimal configurations for achieving the absolute minimum emittance, if specific optics constraints are satisfied at the middle of the cell's dipole. Linear lattice design options based on an analytical approach for the theoretical minimum emittance cells are presented in this paper. In particular the parametrization of the quadrupole strengths and optics functions with respect to the emittance and drift lengths is derived. A multi-parametric space can be then created with all the cell parameters, from which one can chose any of them to be optimized. An application of this approach are finally presented for the linear and non-linear optimization of the CLIC Pre-damping rings.

  15. Electronic and vibrational circular dichroism spectra of (R)-(-)-apomorphine

    Energy Technology Data Exchange (ETDEWEB)

    Abbate, Sergio, E-mail: abbate@med.unibs.it [Dipartimento di Scienze Biomediche e Biotecnologie, Universita di Brescia, Viale Europa 11, 25123 Brescia (Italy); CNISM, Consorzio Interuniversitario Scienze Fisiche della Materia, Via della Vasca Navale 84, 00146 Roma (Italy); Longhi, Giovanna; Lebon, France [Dipartimento di Scienze Biomediche e Biotecnologie, Universita di Brescia, Viale Europa 11, 25123 Brescia (Italy); CNISM, Consorzio Interuniversitario Scienze Fisiche della Materia, Via della Vasca Navale 84, 00146 Roma (Italy); Tommasini, Matteo [Dipartimento di Chimica, Materiali e Ingegneria Chimica ' G. Natta' , Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Consorzio Interuniversitario per la Scienza e Tecnologia dei Materiali (INSTM), Unita di Ricerca del Politecnico di Milano (Dip. CMIC), Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2012-09-11

    Highlights: Black-Right-Pointing-Pointer ECD and VCD Spectra of (R)-(-)-apomorphine measured in various solvents. Black-Right-Pointing-Pointer DFT calculations allow to study the protonation state and conformations. Black-Right-Pointing-Pointer Contributions from catechol OH vibrations to the VCD spectra is studied. -- Abstract: Apomorphine is a chiral drug molecule; notwithstanding its extraordinary importance, little attention has been paid to the characterization of its chiroptical properties. Here we report on its electronic circular dichroism (ECD) spectra, recorded in methanol and water, and vibrational circular dichroism (VCD) in methanol and dimethyl sulfoxide (DMSO) solutions. Density functional theory (DFT) calculations have allowed us to interpret the spectra and to evaluate the role of possible conformations, charge-states and interactions with counter ions.

  16. On the analysis of membrane protein circular dichroism spectra

    OpenAIRE

    Sreerama, Narasimha; Woody, Robert W.

    2004-01-01

    Analysis of circular dichroism spectra of proteins provides information about protein secondary structure. Analytical methods developed for such an analysis use structures and spectra of a set of reference proteins. The reference protein sets currently in use include soluble proteins with a wide range of secondary structures, and perform quite well in analyzing CD spectra of soluble proteins. The utility of soluble protein reference sets in analyzing membrane protein CD spectra, however, has ...

  17. Amplifying vibrational circular dichroism by manipulation of the electronic manifold.

    Science.gov (United States)

    Domingos, Sérgio R; Panman, Matthijs R; Bakker, Bert H; Hartl, Frantisek; Buma, Wybren J; Woutersen, Sander

    2012-01-11

    Vibrational circular dichroism is a powerful technique to study the stereochemistry of chiral molecules, but often suffers from small signal intensities. Electrochemical modulation of the energies of the electronically excited state manifold is now demonstrated to lead to an order of magnitude enhancement of the differential absorption. Quantum-chemical calculations show that increased mixing between ground and excited states is at the origin of this amplification. PMID:22002107

  18. Mechanisms of linear energy transfer-dependent radiation resistance in myeloid leukemia cells

    Science.gov (United States)

    Haro, Kurtis John

    Ionizing radiations (IRs) of high linear energy transfer (LET), such as alpha particles, produce fundamentally different forms of DNA damage in cells than conventional low LET radiation, such as gamma rays. Alpha particle therapies have recently emerged as important potential treatments of cancer, particularly for relatively easily-accessible malignancies of the hematopoietic system. Therefore, we created stable radioresistant myeloid leukemia HL60 cell clones derived after irradiation from either gamma rays (RG) or alpha particles (RA) in order to understand whether resistance to high LET (IR) was possible and the potential differences in radioresistance that could arise from radiations of different LET. Repeated irradiations yielded radioresistant HL60 clones and, regardless of derivation, displayed similar levels of resistance to IR of either type of radiation. The resistant phenotype in each type of radioresistant clone was driven by similar, multifactorial changes that included significant reductions in apoptosis, a decreased late G2/M checkpoint accumulation that was indicative of increased genomic instability, as well as more robust repair of specific types of DNA lesions that included DNA double-strand breaks (DSBs). The relative changes in resistance to alpha particles, however, were substantially lower than the increase in resistance to gamma rays. The data suggest that these processes were interdependent, as inhibition of homology directed repair in the resistant clones sensitized them to gamma IR to a larger extent than naive HL60 cells. Finally, we identified the downregulation of iron regulatory protein 1 (IRP1) in gamma-resistant cells but not in alpha-resistant cells. Short-hairpin RNA-mediated reductions in expression of IRP1 in radiation-naive HL60 cells led to significant radioresistance to gamma rays, but not alpha particles. The IRP1-mediated radioresistance was associated with changes in iron-mediated oxidative stress that led to significant

  19. Magnetic dichroism in the one-electron atom

    International Nuclear Information System (INIS)

    The difference in absorption rate of right or left circularly polarized x-rays by magnetic materials is known as magnetic dichroism and is a well established method of investigating the magnetic properties of materials on a microscopic level. In this paper we illustrate this effect with a study of magnetic dichroism in the one-electron atom. The standard relativistic one-electron atom is solved. First-order perturbation theory is used to calculate eigenfunctions in an applied constant magnetic field. These eigenfunctions are used in a golden rule calculation of the absorption rate for right and left circularly polarized light as a function of applied field. All calculations have been done analytically. The difference in absorption rates for right and left circularly polarized light for 1s to 2p1/2 is of opposite sign to the difference for 1s to 2p3/2. We comment on the significance of these results in the interpretation of dichroism experiments on magnetic materials. (author)

  20. Magnetically induced optical activity and dichroism of gadolinium oxide nanoparticle-based ferrofluids

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Nibedita; Devi, Manasi; Mohanta, Dambarudhar [Nanoscience and Soft Matter Laboratory, Department of Physics, Tezpur University, PO Napaam, Tezpur 784 028, Assam (India); Saha, Abhijit [UGC-DAE Consortium for Scientific Research, Kolkata Centre, III/LB-8 Bidhannagar, Kolkata 700 098 (India)

    2012-02-15

    The present work reports on magnetically induced optical activity (such as Faraday rotation and linear dichroism) of pristine and gamma-irradiated gadolinium oxide (Gd{sub 2}O{sub 3}) nanoparticle-based ferrofluids. The ferrofluids were produced by dispersing N-cetyl-N,N,N-trimethyl ammonium bromide (CTAB)-coated {approx}9-nm-sized Gd{sub 2}O{sub 3} particles in a carrier fluid of ethanol. The ferrofluids were then irradiated with 1.25 MeV energetic gamma rays (dose: 868 Gy and 2.635 kGy). Irradiation-led formation of a number of point defects was revealed through high resolution electron microscopy. The interaction of light with the ionized point defects is believed to have caused substantial improvement in the magneto-optic response of irradiated magnetic fluids.

  1. Nanocomposites Polarizing by Absorption: Dichroism in the Near-Infrared Region (NIR

    Directory of Open Access Journals (Sweden)

    Lorenz Bonderer

    2014-03-01

    Full Text Available We describe the preparation of nanocomposites which exhibit dichroism in the near infrared region (NIR. These materials consist of crosslinked poly(dimethylsiloxane (PDMS and gold nanoparticles, coated with 1-dodecanethiol or tert-tetradecanethiol. The alkanethiols improve dispersibility of the gold particles, and accordingly composites were manufactured by diffusion of the particles into swollen self-supporting PDMS elastomer films. After drying, the films were exposed to solvents for one minute, stretched in wet state, dried again and annealed. This procedure led to formation of oriented linear gold particle assemblies within stretched polymer. If the aspect ratio of the particle assemblies is high, the absorption of polarized light in the NIR region is expected to depend on the angle between the polarization plane and the orientation direction of the particle assemblies, and this was observed to be the case.

  2. A novel methodology for non-linear system identification of battery cells used in non-road hybrid electric vehicles

    Science.gov (United States)

    Unger, Johannes; Hametner, Christoph; Jakubek, Stefan; Quasthoff, Marcus

    2014-12-01

    An accurate state of charge (SoC) estimation of a traction battery in hybrid electric non-road vehicles, which possess higher dynamics and power densities than on-road vehicles, requires a precise battery cell terminal voltage model. This paper presents a novel methodology for non-linear system identification of battery cells to obtain precise battery models. The methodology comprises the architecture of local model networks (LMN) and optimal model based design of experiments (DoE). Three main novelties are proposed: 1) Optimal model based DoE, which aims to high dynamically excite the battery cells at load ranges frequently used in operation. 2) The integration of corresponding inputs in the LMN to regard the non-linearities SoC, relaxation, hysteresis as well as temperature effects. 3) Enhancements to the local linear model tree (LOLIMOT) construction algorithm, to achieve a physical appropriate interpretation of the LMN. The framework is applicable for different battery cell chemistries and different temperatures, and is real time capable, which is shown on an industrial PC. The accuracy of the obtained non-linear battery model is demonstrated on cells with different chemistries and temperatures. The results show significant improvement due to optimal experiment design and integration of the battery non-linearities within the LMN structure.

  3. Electronic structure and x-ray magnetic circular dichroism in (Ge,MnTe diluted magnetic semiconductors

    Directory of Open Access Journals (Sweden)

    V.N. Antonov

    2010-01-01

    Full Text Available The electronic structure of the (Ge,MnTe diluted magnetic semiconductors was investigated theoretically from first principles, using the fully relativistic Dirac linear muffin-tin orbital (LMTO band structure method. The electronic structure is obtained with the local spin-density approximation (LSDA as well as the LSDA+U method. The x-ray magnetic circular dichroism (XMCD spectra of (Ge,MnTe DMSs at the Mn L2,3 edges are investigated theoretically from first principles. The origin of the XMCD spectra in the compound is examined. The calculated results are compared with available experimental data.

  4. Identification of critical residues of linear B cell epitope on Goodpasture autoantigen.

    Directory of Open Access Journals (Sweden)

    Xiao-yu Jia

    Full Text Available The autoantigen of anti-glomerular basement membrane (GBM disease has been identified as the non-collagenous domain 1 of α3 chain of type IV collagen, α3(IVNC1. Our previous study revealed a peptide on α3(IVNC1 as a major linear epitope for B cells and potentially nephrogenic, designated as P14 (α3129-150. This peptide has also been proven to be the epitope of auto-reactive T cells in anti-GBM patients. This study was aimed to further characterize the critical motif of P14.16 patients with anti-GBM disease and positive anti-P14 antibodies were enrolled. A set of truncated and alanine substituted peptides derived from P14 were synthesized. Circulating antibodies against the peptides were detected by enzyme linked immunosorbent assay (ELISA.We found that all sera with anti-P14 antibodies reacted with the 13-mer sequence in the C-terminus of P14 (P14c exclusively. The level of antibodies against P14 was highly correlated with the level of antibodies against P14c (r=0.970, P<0.001. P14c was the core immunogenic region and the amino acid sequence (ISLWKGFSFIMFT was highly hydrophobic. Each amino acid residue in P14c was sequentially replaced by alanine. Three residues of glycine142, phenylalanine143, and phenylalanine145 were identified crucial for antibody binding based on the remarkable decline (P<0.001 of antibody reaction after each residue replacement.We defined GFxF (α3142, 143,145 as the critical motif of P14. It may provide some clues for understanding the etiology of anti-GBM disease.

  5. An Improved Method for Predicting Linear B-cell Epitope Using Deep Maxout Networks.

    Science.gov (United States)

    Lian, Yao; Huang, Ze Chi; Ge, Meng; Pan, Xian Ming

    2015-06-01

    To establish a relation between an protein amino acid sequence and its tendencies to generate antibody response, and to investigate an improved in silico method for linear B-cell epitope (LBE) prediction. We present a sequence-based LBE predictor developed using deep maxout network (DMN) with dropout training techniques. A graphics processing unit (GPU) was used to reduce the training time of the model. A 10-fold cross-validation test on a large, non-redundant and experimentally verified dataset (Lbtope_Fixed_ non_redundant) was performed to evaluate the performance. DMN-LBE achieved an accuracy of 68.33% and an area under the receiver operating characteristic curve (AUC) of 0.743, outperforming other prediction methods in the field. A web server, DMN-LBE, of the improved prediction model has been provided for public free use. We anticipate that DMN-LBE will be beneficial to vaccine development, antibody production, disease diagnosis, and therapy. PMID:26177908

  6. Identification and automatic segmentation of multiphasic cell growth using a linear hybrid model.

    Science.gov (United States)

    Hartmann, András; Neves, Ana Rute; Lemos, João M; Vinga, Susana

    2016-09-01

    This article considers a new mathematical model for the description of multiphasic cell growth. A linear hybrid model is proposed and it is shown that the two-parameter logistic model with switching parameters can be represented by a Switched affine AutoRegressive model with eXogenous inputs (SARX). The growth phases are modeled as continuous processes, while the switches between the phases are considered to be discrete events triggering a change in growth parameters. This framework provides an easily interpretable model, because the intrinsic behavior is the same along all the phases but with a different parameterization. Another advantage of the hybrid model is that it offers a simpler alternative to recent more complex nonlinear models. The growth phases and parameters from datasets of different microorganisms exhibiting multiphasic growth behavior such as Lactococcus lactis, Streptococcus pneumoniae, and Saccharomyces cerevisiae, were inferred. The segments and parameters obtained from the growth data are close to the ones determined by the experts. The fact that the model could explain the data from three different microorganisms and experiments demonstrates the strength of this modeling approach for multiphasic growth, and presumably other processes consisting of multiple phases. PMID:27424949

  7. Kinetics of linear rouleaux formation studied by visual monitoring of red cell dynamic organization.

    Science.gov (United States)

    Barshtein, G; Wajnblum, D; Yedgar, S

    2000-05-01

    Red blood cells (RBCs) in the presence of plasma proteins or other macromolecules may form aggregates, normally in rouleaux formations, which are dispersed with increasing blood flow. Experimental observations have suggested that the spontaneous aggregation process involves the formation of linear rouleaux (FLR) followed by formation of branched rouleaux networks. Theoretical models for the spontaneous rouleaux formation were formulated, taking into consideration that FLR may involve both "polymerization," i.e., interaction between two single RBCs (e + e) and the addition of a single RBC to the end of an existing rouleau (e + r), as well as "condensation" between two rouleaux by end-to-end addition (r + r). The present study was undertaken to experimentally examine the theoretical models and their assumptions, by visual monitoring of the spontaneous FLR (from singly dispersed RBC) in plasma, in a narrow gap flow chamber. The results validate the theoretical model, showing that FLR involves both polymerization and condensation, and that the kinetic constants for the above three types of intercellular interactions are the same, i.e., k(ee) = k(er) = k(rr) = k, and for all tested hematocrits (0.625-6%) k < 0.13 +/- 0.03 s(-1). PMID:10777743

  8. Energy-dispersive phase plate for magnetic circular dichroism experiments in the X-ray range

    International Nuclear Information System (INIS)

    A 220 diamond phase plate was combined with an energy-dispersive absorption spectrometer to convert linearly polarized X-rays into circularly polarized photons and to detect circular magnetic X-ray dichroism (CMXD) from ferromagnetic samples. In these experiments, carried out at LURE, the energy-dispersive spectrometer was equipped with a bent Si (311) polychromator and vertically collimating slits accepting essentially a linearly polarized incident beam. The quarter-wave plate was operated in the Bragg geometry but well outside the range of quasi total reflection, with the consequence that the forward-diffracted beam was circularly polarized with a polarization rate approaching 80% over the whole energy bandpass of the polychromator. CMXD spectra of GdFe2 and GdCo2 intermetallic compounds were recorded at ca 7.2 keV near the Gd LIII absorption edge: they are essentially identical to the spectra commonly recorded with elliptically polarized X-ray photons collected out of the orbit plane of the storage ring. It is suggested that the energy-dispersive phase plate will be very useful to detect CMXD spectra with energy-dispersive spectrometers exploiting the well collimated linearly polarized emission of standard undulators installed on the storage rings of the third generation. (orig.)

  9. Magnetic Circular Dichroism of Porphyrin Lanthanide M3+ Complexes

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, Valery; Padula, Daniele; Zhivotova, E.; Yamamoto, S.; Bouř, Petr

    2014-01-01

    Roč. 26, č. 10 (2014), s. 655-662. ISSN 0899-0042 R&D Projects: GA ČR GA13-03978S; GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant ostatní: GA AV ČR(CZ) M200550902 Institutional support: RVO:61388963 Keywords : magnetic circular dichroism * lanthanides * porphyrin complexes * density functional theory * sum over state computations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.886, year: 2014

  10. Vibrational Circular Dichroism Studies of Biological Macromolecules and their Complexes

    Czech Academy of Sciences Publication Activity Database

    Polyanichko, A. M.; Andrushchenko, Valery; Bouř, Petr; Wieser, H.

    Hauppauge, NY : Nova Science Publishers, Inc, 2012 - (Rodgers, D.), s. 67-126 ISBN 978-1-61122-522-8 R&D Projects: GA ČR GAP208/10/0559; GA AV ČR IAA400550702 Grant ostatní: AV ČR(CZ) M200550902 Institutional research plan: CEZ:AV0Z40550506 Keywords : vibrational circular dichroism (VCD) * proteins * nucleic acids * peptides * spectra simulations Subject RIV: CF - Physical ; Theoretical Chemistry https://www.novapublishers.com/catalog/ product _info.php? product s_id=32793

  11. Plasmonic nanohelix metamaterials with tailorable giant circular dichroism

    Science.gov (United States)

    Gibbs, J. G.; Mark, A. G.; Eslami, S.; Fischer, P.

    2013-11-01

    Plasmonic nanohelix arrays are shown to interact with electromagnetic fields in ways not typically seen with ordinary matter. Chiral metamaterials (CMMs) with feature sizes small with respect to the wavelength of visible light are a promising route to experimentally achieve such phenomena as negative refraction without the need for simultaneously negative ɛ and μ. Here we not only show that giant circular dichroism in the visible is achievable with hexagonally arranged plasmonic nanohelix arrays, but that we can precisely tune the optical activity via morphology and lattice spacing. The discrete dipole approximation is implemented to support experimental data.

  12. Detecting Chiral Orbital Angular Momentum by Circular Dichroism ARPES

    OpenAIRE

    Park, Jin-Hong; Kim, Choong H.; Rhim, Jun Won; Han, Jung Hoon

    2011-01-01

    We show, by way of tight-binding and first-principles calculations, that a one-to-one correspondence between electron's crystal momentum k and non-zero orbital angular momentum (OAM) is a generic feature of surface bands. The OAM forms a chiral structure in momentum space much as its spin counterpart in Rashba model does, as a consequence of the inherent inversion symmetry breaking at the surface but not of spin-orbit interaction. Circular dichroism (CD) angle-resolved photoemission (ARPES) e...

  13. Circular dichroism in XUV + IR multiphoton ionization of atoms

    International Nuclear Information System (INIS)

    Circular dichroism (CD) is theoretically considered for two-colour multiphoton ionization of arbitrary atomic subshells. In particular, p-subshell ionization is analysed and compared with s-subshell ionization. Simple analytical expressions for the CD are obtained for both s- and p-subshell ionization. The calculations performed for Ne(2p) ionization by an extreme ultraviolet pulse in the presence of an infrared laser pulse show that the CD in this case is appreciably larger than in previously discussed s-shell ionization. It makes this case favourable for applications as a sensitive tool for measuring the helicity of short-wavelength free-electron laser beams. (paper)

  14. Circular dichroism in laser-assisted proton-hydrogen collisions

    International Nuclear Information System (INIS)

    Full text: We investigated the effects of a strong circularly polarized 1064 nm laser field on electron capture and emission in slow (keV) proton-hydrogen collisions within a reduced-dimensionality model of the scattering system in which both the motion of the active electron and the laser electric field vector are confined to the scattering plane. During the collision, the proton is assumed to move on a straight-line trajectory with impact parameter b. The rotating laser electric field breaks the azimuthal symmetry, and the projectile either follows the rotating laser field ('co-rotating' collisions) or moves against the rotating electric field ('counter-rotating' collisions). By solving the time-dependent Schroedinger equation, we examined the probabilities for electron capture and ionization as a function of laser intensity, impact parameter, and the laser phase that determines the orientation of the laser electric field with respect to the internuclear axis at the time of closest approach between target and projectile. Our results for the b-dependent ionization and capture probabilities show a strong dependence on the helicity of the circularly polarized laser light. For intensities above 2x1012 W/cm2, our model predicts a noticeable circular dichroism in the capture probability. Interestingly, this dichroism persists after averaging over . Capture and electron emission probabilities defer significantly from results for laser-unassisted collisions. Furthermore, we find evidence for a charge resonance enhanced ionization mechanism that may enable the measurement of the absolute laser phase φ. For a fixed impact parameter, the capture probability as a function of φ shows large amplitude oscillations and differs from the field-free results most strikingly at φ = 0o and 180o. It displays a strong dichroism effect, i.e., a substantial difference in the electron capture probability for co-rotating as compared to counter-rotating collisions. Ionization

  15. Stereochemical analysis of glycerophospholipids by vibrational circular dichroism.

    Science.gov (United States)

    Taniguchi, Tohru; Manai, Daisuke; Shibata, Masataka; Itabashi, Yutaka; Monde, Kenji

    2015-09-30

    The stereochemistry of glycerophospholipids (GPLs) has been of interest for its roles in the evolution of life and in their biological activity. However, because of their structural complexity, no convenient method to determine their configuration has been reported. In this work, through the first systematic application of vibrational circular dichroism (VCD) spectroscopy to various diacylated GPLs, we have revealed that their chirality can be assigned by the sign of a VCD exciton couplet generated by the interaction of two carbonyl groups. This paper also presents spectroscopic evidence for the stereochemistry of GPLs isolated from bacteria, eukaryotes, and mitochondria. PMID:26379046

  16. Angle-resolved x-ray circular and magnetic circular dichroisms: Definitions and applications

    OpenAIRE

    Tong, DSY; X Guo; Tobin, JG; Waddill, GD

    1996-01-01

    We introduce definitions of angle-resolved x-ray circular dichroism (ARXCD) and magnetic x-ray circular dichroism (ARMXCD). As defined, the much larger effect of circular dichroism (ARXCD) is separated from the smaller magnetic (ARMXCD) effect. In all materials, ARXCD is zero along mirror planes while nonzero elsewhere. ARMXCD is nonzero only in magnetic materials. The measurement and analysis of ARMXCD allow element specific surface magnetism and surface structure as well as their inter-rela...

  17. Versatile transmission ellipsometry to study linear ferrofluid magneto-optics.

    Science.gov (United States)

    Kooij, E S; Gâlcă, A C; Poelsema, B

    2006-12-01

    Linear birefringence and dichroism of magnetite ferrofluids are studied simultaneously using spectroscopic ellipsometry in transmission mode. It is shown that this versatile technique enables highly accurate characterisation of magneto-optical phenomena. Magnetic field-dependent linear birefringence and dichroism as well as the spectral dependence are shown to be in line with previous results. Despite the qualitative agreement with established models for magneto-optical phenomena, these fail to provide an accurate, quantitative description of our experimental results using the bulk dielectric function of magnetite. We discuss the results in relation to these models, and indicate how the modified dielectric function of the magnetite nanoparticles can be obtained. PMID:16997315

  18. The design and commissioning of the vacuum-ultraviolet circular dichroism facility at NSRL

    International Nuclear Information System (INIS)

    This paper describes the design and commissioning of the vacuum-ultraviolet circular dichroism facility at NSRL. At 0.5nm resolution, the normal incident beamline can provide ultraviolet and vacuum-ultraviolet radiation at fluxes higher than 1012ph/s, which is converted into the plane polarized light using a polarizer and subsequently converted into the circularly polarized light using a photoelastic modulator with a switching frequency of 50 kHz. Example spectra of (1s)-(+)-10-camphorsulphonic acid (CSA) and myoglobin are given. Normally, the measurable wavelength range is 178--300 nm. But the short wavelength limit can be shifted to 140nm by using special solvent and short light-pass sample cell. (authors)

  19. Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA.

    Science.gov (United States)

    Schinn, Song-Min; Broadbent, Andrew; Bradley, William T; Bundy, Bradley C

    2016-06-25

    A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems. PMID:27085957

  20. Pancreatic beta cell function increases in a linear dose-response manner following exercise training in adults with prediabetes

    DEFF Research Database (Denmark)

    Malin, Steven K; Solomon, Thomas; Blaszczak, Alecia;

    2013-01-01

    composition (dual-energy x-ray absorptiometry and computed tomography) were also measured before and after the intervention. Exercise dose was computed using VO2-heart rate derived linear-regression equations. Subjects expended 474.5±8.8 kcal/session (2372.5±44.1 kcal/week) during the intervention, and lost......While some studies suggest that a linear dose-response relationship exists between exercise and insulin sensitivity, the exercise dose required to enhance pancreatic beta-cell function is unknown. Thirty-five older, obese adults with prediabetes underwent a progressive 12-week supervised exercise...

  1. A new method of linear control for optimum transfer of power from a solar cell array to the distribution network

    Science.gov (United States)

    Ray, G. C.; Jha, R.

    1984-08-01

    The paper describes a new method of linear control for transfer of optimum power from a Solar Cell Array (SCA) to the distribution network. It is shown that the current corresponding to the optimum power varies almost linearly with the level of illumination. By connecting a storage battery in parallel to the SCA, the charging current to the battery is continuously adjusted by sensing the ilumination level and current simultaneously. Variation of the charging current keeps the operating point on the optimum power locus. In the ac distribution network the power is to be fed through a current-source inverter and a step up/down transformer.

  2. Flow Linear Dichroism Spectroscopic Studies of the Natural Product Curcumin and Double Stranded DNA

    DEFF Research Database (Denmark)

    Leth, Rasmus; Thulstrup, Peter Waaben

    2011-01-01

    Curcumin is a polyphenol found in the rhizomes of the plant Curcuma Longa, commonly known as turmeric. Curcumin has a bright yellow color, and in turmeric, curcumin exists along with two other curcuminoids: desmethoxy curcumin and bisdesmethoxy curcumin [1]. Curcumin has shown multiple biological...

  3. Systematic study of magnetic linear dichroism and birefringence in (Ga,Mn)As

    Czech Academy of Sciences Publication Activity Database

    Tesařová, N.; Ostatnický, T.; Novák, Vít; Olejník, Kamil; Šubrt, J.; Reichlová, Helena; Ellis, C.T.; Mukherjee, A.; Lee, J.; Sipahi, G.M.; Sinova, Jairo; Hamrle, J.; Jungwirth, Tomáš; Němec, P.; Cerne, J.; Výborný, Karel

    2014-01-01

    Roč. 89, č. 8 (2014), , "085203-1"-"085203-14". ISSN 1098-0121 R&D Projects: GA MŠk(CZ) LM2011026 EU Projects: European Commission(XE) 268066 - 0MSPIN Grant ostatní: AVČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : ferromagnetic semiconductors * magneto -optics Subject RIV: BH - Optics, Masers, Lasers Impact factor: 3.736, year: 2014

  4. Theory and experiment of linear and nonlinear optical media and waveguides with anisotropy and dichroism

    Science.gov (United States)

    Purvinis, Georgeanne M.

    Organic crystals and certain polymer films, such as ionically self-assembled monolayer (ISAM) films, are lossy and anisotropic. These materials may have a large chi(2) nonlinear response, and thus are conceivably capable of efficient second order processes. Anomalous dispersion phase-matched second harmonic generation (ADPM-SHG) in organic media is a second order wavelength conversion process that phase matches like-order modes in a waveguide (ex: TM0o → TM02o ), thus maximizing the overlap integral. Demonstration of ADPM-SHG in economical and easily fabricated polymer ISAM film is the ultimate experimental goal of this research. In order to achieve demonstration of ADPM-SHG in an ISAM film, both theoretical and material research contributions are accomplished. The predominant analysis approaches in literature are based on the finite element method, which is approximate and computationally intensive, thus prohibiting arbitrary crystallographic media orientations in devices. This restricted treatment in the literature may be insufficient with ISAM films, as SHG occurs in a spectral region of residual absorption, the film is uniaxial, and the optic axis may not be aligned the waveguide coordinate system. Thus, the theory objectives of the dissertation research are: (1) develop an exact solution for finding the polarization states in lossy anisotropic media using a new complex orthogonal similarity transformation with the complex symmetric impermeability tensor, (2) develop a rigorous transverse resonance analysis to find the eigenmodes of general lossy anisotropic planar waveguides with arbitrary principal axes orientations, and (3) integrate the results of steps 1--2 to determine the conversion efficiency of an ISAM planar waveguide using ADPM-SHG, thus illustrating the importance of the dissertation research by highlighting the errors resulting in algorithms published in other works. Experimentally, the dissertation focuses on designing anionic and cationic polymers suitable for ionic self-assembly. Multiple materials and combinations are investigated, analyzed, and characterized using ellipsometry, SEM, AFM, and Maker Fringe analysis in order to determine their ability to fabricate optical quality thin films with the required non-centrosymmetry for chi(2) nonlinear response. Demonstration of the enhanced second harmonic generation in ISAM films deposited on grating structures using the guided mode resonant effect is achieved in this dissertation.

  5. Predicting the clonogenic survival of A549 cells after modulated x-ray irradiation using the linear quadratic model

    Energy Technology Data Exchange (ETDEWEB)

    Bromley, Regina; Oliver, Lyn [Northern Sydney Cancer Centre, Radiation Oncology, Royal North Shore Hospital, Sydney, NSW 2065 (Australia); Davey, Ross; Harvie, Rozelle [Department of Medical Oncology, Bill Walsh Cancer Research Laboratories, Royal North Shore Hospital, Sydney, NSW 2065 (Australia); Baldock, Clive [Institute of Medical Physics, School of Physics, Sydney University, NSW 2006 (Australia)

    2009-01-21

    In this study we present two prediction methods, mean dose and summed dose, for predicting the number of A549 cells that will survive after modulated x-ray irradiation. The prediction methods incorporate the dose profile from the modulated x-ray fluence map applied across the cell sample and the linear quadratic (LQ) model. We investigated the clonogenic survival of A549 cells when irradiated using two different modulated x-ray fluence maps. Differences between the measured and predicted surviving fraction were observed for modulated x-ray irradiation. When the x-ray fluence map produced a steep dose gradient across the sample, fewer cells survived in the unirradiated region than expected. When the x-ray fluence map produced a less steep dose gradient across the sample, more cells survived in the unirradiated region than expected. Regardless of the steepness of the dose gradient, more cells survived in the irradiated region than expected for the reference dose range of 1-10 Gy. The change in the cell survival for the unirradiated regions of the two different dose gradients may be an important factor to consider when predicting the number of cells that will survive at the edge of modulated x-ray fields. This investigation provides an improved method of predicting cell survival for modulated x-ray radiation treatment. It highlights the limitations of the LQ model, particularly in its ability to describe the biological response of cells irradiated under these conditions.

  6. Predicting the clonogenic survival of A549 cells after modulated x-ray irradiation using the linear quadratic model

    Science.gov (United States)

    Bromley, Regina; Oliver, Lyn; Davey, Ross; Harvie, Rozelle; Baldock, Clive

    2009-01-01

    In this study we present two prediction methods, mean dose and summed dose, for predicting the number of A549 cells that will survive after modulated x-ray irradiation. The prediction methods incorporate the dose profile from the modulated x-ray fluence map applied across the cell sample and the linear quadratic (LQ) model. We investigated the clonogenic survival of A549 cells when irradiated using two different modulated x-ray fluence maps. Differences between the measured and predicted surviving fraction were observed for modulated x-ray irradiation. When the x-ray fluence map produced a steep dose gradient across the sample, fewer cells survived in the unirradiated region than expected. When the x-ray fluence map produced a less steep dose gradient across the sample, more cells survived in the unirradiated region than expected. Regardless of the steepness of the dose gradient, more cells survived in the irradiated region than expected for the reference dose range of 1-10 Gy. The change in the cell survival for the unirradiated regions of the two different dose gradients may be an important factor to consider when predicting the number of cells that will survive at the edge of modulated x-ray fields. This investigation provides an improved method of predicting cell survival for modulated x-ray radiation treatment. It highlights the limitations of the LQ model, particularly in its ability to describe the biological response of cells irradiated under these conditions.

  7. Supramolecular Chemistry: Induced Circular Dichroism to Study Host-Guest Geometry

    Science.gov (United States)

    Mendicuti, Francisco; Gonzalez-Alvarez, Maria Jose

    2010-01-01

    In this laboratory experiment, students obtain information about the structure of a host-guest complex from the interpretation of circular dichroism measurements. The value and sign of the induced circular dichroism (ICD) on an achiral chromophore guest when it complexes with a cyclodextrin can be related to the guest penetration and its…

  8. Vibrational and Electronic Circular Dichroism Monitoring of Copper(II) Coordination with a Chiral Ligand

    Czech Academy of Sciences Publication Activity Database

    Wu, T.; Zhang, X. P.; Li, C. H.; Bouř, Petr; Li, Y. Z.; You, X. Z.

    2012-01-01

    Roč. 24, č. 6 (2012), s. 451-458. ISSN 0899-0042 R&D Projects: GA ČR GAP208/11/0105 Institutional research plan: CEZ:AV0Z40550506 Keywords : circular dichroism * vibrational circular dichroism * coordination compounds * density functional theory computations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.718, year: 2012

  9. Polarimetric investigation of materials with both linear and circular anisotropy

    DEFF Research Database (Denmark)

    Naydenova, I.; Nikolova, L.; Todorov, T.; Andruzzi, F.; Hvilsted, Søren; Ramanujam, P.S.

    1997-01-01

    We investigate light propagation through materials with both linear and circular anisotropy and find the relation of the amplitude and polarization transfer functions to the four anisotropic characteristics: linear circular birefringence, and linear and circular dichroism. We determine these four...... characteristics of anisotropic samples by measuring the output intensity and polarization corresponding to different input polarization azimuths and fitting the theoretical and experimental results. In our experiments we have used films of side-chain azobenzene polyesters in which optical anisotropy had been...

  10. Optical circular dichroism of vacuum-deposited film stacks

    Science.gov (United States)

    Fan, B.; Vithana, H. K. M.; Kralik, J. C.; Faris, S. M.

    1998-02-01

    We report on optical circular dichroism of chiral multilayer SiO x films obtained by a novel vacuum deposition technique. The film layers were deposited at an oblique incidence angle to render them optically anisotropic, and were stacked such that the optic axes of the layers spiral in a helical fashion about the substrate normal. The resulting film stacks display both wavelength and polarization selectivity, in analogy with organic cholesteric liquid crystals aligned in the planar texture. Reflectance spectra of two films of opposite chirality are presented. Both film stacks are tuned to reflect in the visible and were prepared using obliquely deposited SiO x. Calculated spectra using a Berreman's 4×4 matrix approach agree well with the experimental findings. It is concluded that vacuum-deposited chiral film stacks hold promise for use as high-efficiency polarizers and other novel optical components.

  11. Structural characterization of chiral molecules using vibrational circular dichroism spectroscopy

    DEFF Research Database (Denmark)

    Lassen, Peter Rygaard

    2006-01-01

    Chiral molecules, i.e., molecules with handedness, are essential to biology, because most amino acids and sugars are chiral. A pair of molecules which are mirror images of each other have identical physical properties, but they differ in their interaction with other chiral molecules. This is the...... cornerstone of biological specificity. Chiral molecules also interact differently with different polarization states of electromagnetic radiation, because the absorption coefficient depends on the state of polarization. This is called dichroism and gives rise to several spectroscopic techniques targeting...... compounds of pharmaceutical interest. Others are transition metal complexes relevant for the search for parity-violation effects in vibrational spectroscopy (rhenium complexes), for asymmetric catalysis (Schiff-base complexes), or as model systems for metal centres in biology (Schiff-bases and heme...

  12. Calculation of magnetic circular dichroism of rare-earth elements

    International Nuclear Information System (INIS)

    We present atomic calculations for the magnetic circular dichroism (MCD) in the 4d→4f excitation region of Eu, Gd, Tb, Dy, and Ho metal. The spectral shapes at T=0 K for non-polarized, right and left circularly polarized light, and their difference spectra are given. The interference effect between the 4d→4f excitation followed by 4d-4f4f super-Coster-Kronig decay process and the 4f→εg direct excitation process, which is known as the Fano effect, is considered in the calculations. The result reproduces the overall features of recently measured experiments. It is essential to consider the Fano effect for the understanding of the heavy rare-earth 4d→4f absorption and their MCD. (author)

  13. X-ray dichroism of rare earth materials

    International Nuclear Information System (INIS)

    The theme of this thesis is the investigation of the strong polarization dependende, or dichroism, that occur in the X-ray absorption spectra of rare earth materials. The rare earth elements distinguish themselves from the other elements through the behaviour of the 4f electrons which form the valence shell. This shell lies deep inside the atom, with the result that influences from the surrounding solid are well screened off by the outer electrons, so that even in the solid the 4f shell behaves very much like a in free atom or ion, and is almost completely spherically symmetric. Perturbations from the solid environment however always disturb this symmetry to some extend, with the result that the absorption spectrum becomes dependent on the mutual orientation of the polarization vector of the radiation and the ion. Earlier the existence of a strong magnetic X-ray dichroism (MXD) in the 3d→4f transitions of rare earths. In this thesis this work is extended, to a small degree theoretically but mainly experimentally. MXD is used in experiments on bulk sample, terbium iron garnet, and on rare earth overlayers on a ferromagnetic surface, Ni(110). The results of the latter study show unequivocally the potential of the MXD technique. The second theme of the thesis concerns experimental developments in soft X-ray spectroscopy. A description is given of a double crystal monochromator beamline that was constructed by our group at LURE, France. Results of the use of an organic crystal - multilayer comination in such a monochromator is described. Also a method is described for the characterization of the resolution of soft X-ray monochromators. Finally a contribution to the characterization of the electron yield technique in the soft X-ray range is given. (author). 296 refs.; 64 figs.; 59 schemes; 9 tabs

  14. A novel T-cell-defined HLA-DR polymorphism not predicted from the linear amino acid sequence.

    Science.gov (United States)

    Termijtelen, A; van den Elsen, P; Koning, F; de Koster, S; Schroeijers, W; Vanderkerckhove, B

    1989-09-01

    Recent investigations have shown that alloreactive T cells are capable of responding to structures defined by specific linear amino acid sequences on class II molecules. In the present study we show that also a polymorphism can be recognized that is not defined by such linear amino acid sequences. Two human T-cell clones, sensitized to DRw13 haplotypes, are described. The description of clone c50 serves to exemplify the first model. This DRB1-specific clone responds to stimulator cells that carry DR molecules, different in their DRB1 first and second hypervariable regions (HV1 and HV2) but identical in their HV3 regions (i.e., DRw13,Dw18; DRw13,Dw19; DR4,Dw10; and DRw11,LDVII). The second clone, c1443, behaves nonconventionally. It responds to DRw13,Dw18; DRw13,Dw19; and DR4,Dw4 stimulator cells, although no specific amino acid sequence is shared between these specificities. The latter pattern of reactivity suggests the existence of a novel polymorphism recognized by alloreactive T cells. This particular polymorphism may also be biologically significant. PMID:2476425

  15. The influence of cell geometry on the Godunov scheme applied to the linear wave equation

    Science.gov (United States)

    Dellacherie, Stéphane; Omnes, Pascal; Rieper, Felix

    2010-08-01

    By studying the structure of the discrete kernel of the linear acoustic operator discretized with a Godunov scheme, we clearly explain why the behaviour of the Godunov scheme applied to the linear wave equation deeply depends on the space dimension and, especially, on the type of mesh. This approach allows us to explain why, in the periodic case, the Godunov scheme applied to the resolution of the compressible Euler or Navier-Stokes system is accurate at low Mach number when the mesh is triangular or tetrahedral and is not accurate when the mesh is a 2D (or 3D) cartesian mesh. This approach confirms also the fact that a Godunov scheme remains accurate when it is modified by simply centering the discretization of the pressure gradient.

  16. Applied Circular Dichroism: A Facile Spectroscopic Tool for Configurational Assignment and Determination of Enantiopurity

    Directory of Open Access Journals (Sweden)

    Macduff O. Okuom

    2015-01-01

    Full Text Available In order to determine if electronic circular dichroism (ECD is a good tool for the qualitative evaluation of absolute configuration and enantiopurity in the absence of chiral high performance liquid chromatography (HPLC, ECD studies were performed on several prescriptions and over-the-counter drugs. Cotton effects (CE were observed for both S and R isomers between 200 and 300 nm. For the drugs examined in this study, the S isomers showed a negative CE, while the R isomers displayed a positive CE. The ECD spectra of both enantiomers were nearly mirror images, with the amplitude proportional to the enantiopurity. Plotting the differential extinction coefficient (Δε versus enantiopurity at the wavelength of maximum amplitude yielded linear standard curves with coefficients of determination (R2 greater than 97% for both isomers in all cases. As expected, Equate, Advil, and Motrin, each containing a racemic mixture of ibuprofen, yielded no chiroptical signal. ECD spectra of Suphedrine and Sudafed revealed that each of them is rich in 1S,2S-pseudoephedrine, while the analysis of Equate vapor inhaler is rich in R-methamphetamine.

  17. Microwave Magnetochiral Dichroism in the Chiral-Lattice Magnet Cu_{2}OSeO_{3}.

    Science.gov (United States)

    Okamura, Y; Kagawa, F; Seki, S; Kubota, M; Kawasaki, M; Tokura, Y

    2015-05-15

    Through broadband microwave spectroscopy in Faraday geometry, we observe distinct absorption spectra accompanying magnetoelectric (ME) resonance for oppositely propagating microwaves, i.e., directional dichroism, in the multiferroic chiral-lattice magnet Cu_{2}OSeO_{3}. The magnitude of the directional dichroism critically depends on the magnetic-field direction. Such behavior is well accounted for by considering the relative direction of the oscillating electric polarizations induced via the ME effect with respect to microwave electric fields. Directional dichroism in a system with an arbitrary form of ME coupling can be also discussed in the same manner. PMID:26024193

  18. Circular and elliptical dichroism effects in two-photon disintegration of atoms and molecules

    International Nuclear Information System (INIS)

    Full text: Compact convenient for the analysis expressions for the cross sections considerably simplify studying the interaction of electromagnetic radiation with atomic systems and allow us to discover some fine effects. In the present paper on the basis of the general symmetry considerations taking only into account the dipole approximation and without any other approximations used in atomic calculations we derive the compact invariant expressions for the angular distribution of photoelectrons escaping from atoms or molecules in the process of two-photon ionization and for the angular distribution of fragments forming under two-photon two-particle dissociation of molecules. The dependence on all geometric parameters - the unit vector p determining the direction of photoelectron (photofragments in the case of dissociation) motion, k specifying the direction of propagation for the electromagnetic radiation and the unit complex vector e specifying polarization of the radiation - is completely separated in the angular distributions in the form of scalar and triple scalar products of the vectors. The information of the intrinsic structure of the atomic system is included in few constant dynamic parameters of the system that can independently be calculated using the well-known approximations. In case of atoms and optically inactive molecules the angular distributions contain the term linear in the pseudoscalar degree of circular polarization of the electromagnetic radiation ξik · (e x e*): ξaRe[k · (p x e)(p · e*)], where a is a scalar dynamic parameter of the atomic system. The term leads to the interesting effect of elliptical dichroism in the angular distribution of photoelectrons (photo-fragments of the molecule): under elliptical polarization of the radiation, 0 1ξk · p + b2ξk · p(|p · e|2 - 1/5), where b1 and b2 are the pseudoscalar dynamic parameters of the chiral molecule. The terms (2) do not vanish in case of circular polarization and, therefore

  19. TiO2 dye sensitized solar cell (DSSC): linear relationship of maximum power point and anthocyanin concentration

    Science.gov (United States)

    Ahmadian, Radin

    2010-09-01

    This study investigated the relationship of anthocyanin concentration from different organic fruit species and output voltage and current in a TiO2 dye-sensitized solar cell (DSSC) and hypothesized that fruits with greater anthocyanin concentration produce higher maximum power point (MPP) which would lead to higher current and voltage. Anthocyanin dye solution was made with crushing of a group of fresh fruits with different anthocyanin content in 2 mL of de-ionized water and filtration. Using these test fruit dyes, multiple DSSCs were assembled such that light enters through the TiO2 side of the cell. The full current-voltage (I-V) co-variations were measured using a 500 Ω potentiometer as a variable load. Point-by point current and voltage data pairs were measured at various incremental resistance values. The maximum power point (MPP) generated by the solar cell was defined as a dependent variable and the anthocyanin concentration in the fruit used in the DSSC as the independent variable. A regression model was used to investigate the linear relationship between study variables. Regression analysis showed a significant linear relationship between MPP and anthocyanin concentration with a p-value of 0.007. Fruits like blueberry and black raspberry with the highest anthocyanin content generated higher MPP. In a DSSC, a linear model may predict MPP based on the anthocyanin concentration. This model is the first step to find organic anthocyanin sources in the nature with the highest dye concentration to generate energy.

  20. Analysis of PEM fuel cell experimental data using Principal Component Analysis and Multi linear regression

    OpenAIRE

    PLACCA, L; KOUTA, R; Candusso, D.; BLACHOT, JF; CHARON, W

    2010-01-01

    Polarisation curves performed at the Fuel Cell System Laboratory (FC LAB) at Belfort on a PEM fuel cell stack using a homemade fully instrumented test bench led to more than 100 variables depending on time. Visualising and analysing all the different test variables are complex. In this work, we show how the Principal Component Analysis (PCA) method helps to explore correlations between variables and similarities between measurements at a specific sampling time (individuals). To complete this ...

  1. Non linear model for shunt current in terrestrial silicon solar cells

    Science.gov (United States)

    Cabestany, J.

    Attention is given to the failure of circuit models commonly used to determine the I(v) characteristics used in obtaining terrestrial solar cell equivalent parameters, in the case where the cell array area has a substantial metal-covered component. Two alternative methods are presently proposed for this case: an empirical approach in which a parameter is considered to be fluctuating, and an approach that includes a new exponential term in the I(v) characteristics.

  2. Optical activity and circular dichroism of plasmonic nanorod assemblies

    Science.gov (United States)

    Khosravi Khorashad, Larousse; Liu, Na; Govorov, Alexander O.

    Plasmonic circular dichroism (CD) has offered an efficient spectroscopy method for the electronic, chemical, and structural properties of different types of light active molecules in the subwavelength regime. Among the different chiral geometries of metal nanoparticles utilized by the plasmonic CD spectroscopy, gold nanorods (AuNRs) have shown strong CD signals in the visible frequency range. In this work, we theoretically study the CD signals of AuNR arrangements in order to mimic structures and chemical bonds of chiral biomolecules. In particular, our twisted three-AuNR geometries resemble a molecular structure of tartaric acid. This molecule played an important role in the discovery of chemical chirality. In our study, we show that the strength of CD signals changes dramatically by tuning the interparticle distances and angles. Since the CD signals are typically weak, we develop reliable computational approaches to calculate the plasmonic CD. Manipulating interparticle distances, size, and molecular bond angles result in full control over peak positions, handedness, and positive and negative bands which are observed in the CD spectra. This work has been supported under the grant from Volkswagen Foundation. We also acknowledge the financial support of Condensed Matter and Surface Science program of Ohio University.

  3. Heparin-induced circular dichroism of an achiral, bicyclic species.

    Science.gov (United States)

    Stanley, Floyd E; Warner, Andrew M; McWilliams, Kayla M; Stalcup, Apryll M

    2011-01-01

    Antimalarial drugs have shown potential in suppressing the role of glycosaminoglycans (GAGs) in the pathology of prion protein conformational disorders (e.g. "Mad Cow" disease) by competing for sites of electrostatic interaction. In this study, circular dichroism (CD) and UV/Visible (UV/Vis) absorption spectroscopy techniques were used to investigate the interactions between N-methyl-N'-(7-chloro-4-quinolyl)-1,3-diaminopropane (QD), an achiral, bicyclic compound similar to previously investigated antimalarial drugs, and heparin, a complex GAG that is frequently used as a clinical anticoagulant. Relatively intense heparin-induced CD features were observed for QD and were noted to be radically different from previous studies using related chiral drugs, underscoring the importance of the Pfieffer effect on this and similar heparin research. Additionally, the induced CD for QD was observed to be highly dependent upon drug concentration, heparin concentration, system pH, equilibration time, and ionic strength. These results, in connection with recent work, provide new insight into the nature of the association between GAGs and antimalarial species. PMID:21125690

  4. Applications of Circular Dichroism for Structural Analysis of Gelatin and Antimicrobial Peptides

    Directory of Open Access Journals (Sweden)

    Yoonkyung Park

    2012-03-01

    Full Text Available Circular dichroism (CD is a useful technique for monitoring changes in the conformation of antimicrobial peptides or gelatin. In this study, interactions between cationic peptides and gelatin were observed without affecting the triple helical content of the gelatin, which was more strongly affected by anionic surfactant. The peptides did not adopt a secondary structure in the presence of aqueous solution or Tween 80, but a peptide secondary structure formed upon the addition of sodium dodecyl sulfate (SDS. The peptides bound to the phosphate group of lipopolysaccharide (LPS and displayed an alpha-helical conformation while (KW4 adopted a folded conformation. Further, the peptides did not specifically interact with the fungal cell wall components of mannan or laminarin. Tryptophan blue shift assay indicated that these peptides interacted with SDS, LPS, and gelatin but not with Tween 80, mannan, or laminarin. The peptides also displayed antibacterial activity against P. aeruginosa without cytotoxicity against HaCaT cells at MIC, except for HPA3NT3-analog peptide. In this study, we used a CD spectroscopic method to demonstrate the feasibility of peptide characterization in numerous environments. The CD method can thus be used as a screening method of gelatin-peptide interactions for use in wound healing applications.

  5. A complex-polarization-propagator protocol for magneto-chiral axial dichroism and birefringence dispersion.

    Science.gov (United States)

    Cukras, Janusz; Kauczor, Joanna; Norman, Patrick; Rizzo, Antonio; Rikken, Geert L J A; Coriani, Sonia

    2016-05-21

    A computational protocol for magneto-chiral dichroism and magneto-chiral birefringence dispersion is presented within the framework of damped response theory, also known as complex polarization propagator theory, at the level of time-dependent Hartree-Fock and time-dependent density functional theory. Magneto-chiral dichroism and magneto-chiral birefringence spectra in the (resonant) frequency region below the first ionization threshold of R-methyloxirane and l-alanine are presented and compared with the corresponding results obtained for both the electronic circular dichroism and the magnetic circular dichroism. The additional information content yielded by the magneto-chiral phenomena, as well as their potential experimental detectability for the selected species, is discussed. PMID:27118603

  6. Experimental demonstration of the microscopic origin of circular dichroism in two-dimensional metamaterials

    Science.gov (United States)

    Khanikaev, A. B.; Arju, N.; Fan, Z.; Purtseladze, D.; Lu, F.; Lee, J.; Sarriugarte, P.; Schnell, M.; Hillenbrand, R.; Belkin, M. A.; Shvets, G.

    2016-01-01

    Optical activity and circular dichroism are fascinating physical phenomena originating from the interaction of light with chiral molecules or other nano objects lacking mirror symmetries in three-dimensional (3D) space. While chiral optical properties are weak in most of naturally occurring materials, they can be engineered and significantly enhanced in synthetic optical media known as chiral metamaterials, where the spatial symmetry of their building blocks is broken on a nanoscale. Although originally discovered in 3D structures, circular dichroism can also emerge in a two-dimensional (2D) metasurface. The origin of the resulting circular dichroism is rather subtle, and is related to non-radiative (Ohmic) dissipation of the constituent metamolecules. Because such dissipation occurs on a nanoscale, this effect has never been experimentally probed and visualized. Using a suite of recently developed nanoscale-measurement tools, we establish that the circular dichroism in a nanostructured metasurface occurs due to handedness-dependent Ohmic heating. PMID:27329108

  7. Circular dichroism readout of sugar recognition in the cleft of a fused-pyridine receptor

    OpenAIRE

    Tamaru, Shun-ichi; Shinkai, Seiji; Khasanov, Alisher B.; Bell, Thomas W.

    2002-01-01

    Dicarboxamide host 2 forms 1:1 complexes with n-octyl pyranosides derived from d-glucose, d-mannose, d-galactose, d-fucose, d-lyxose, and d-arabinose. Association constants (Ka) in the range of 77–940 M−1 were measured in chloroform by means of induced circular dichroism and fluorescence spectroscopy. Variations in Ka values correspond qualitatively to expected differences in hydrogen-bonding abilities of guest hydroxyl groups. Induced circular dichroism effects for...

  8. Circular dichroism of cholesteric polymers and the orbital angular momentum of light

    International Nuclear Information System (INIS)

    We explore experimentally if light's orbital angular momentum (OAM) interacts with chiral nematic polymer films. Specifically, we measure the circular dichroism of such a material using light beams with different OAM. We investigate the case of strongly focused, nonparaxial light beams, where the spatial and polarization degrees of freedom are coupled. Within the experimental accuracy, we cannot find any influence of the OAM on the circular dichroism of cholesteric polymers.

  9. A complex-polarization-propagator protocol for magneto-chiral axial dichroism and birefringence dispersion

    DEFF Research Database (Denmark)

    Cukras, Janusz; Kauczor, Joanna; Norman, Patrick;

    2016-01-01

    A computational protocol for magneto-chiral dichroism and magneto-chiral birefringence dispersion is presented within the framework of damped response theory, also known as complex polarization propagator theory, at the level of time-dependent Hartree–Fock and time-dependent density functional th...... circular dichroism. The additional information content yielded by the magneto-chiral phenomena, as well as their potential experimental detectability for the selected species, is discussed....

  10. Secondary-Structure Analysis of Denatured Proteins by Vacuum-Ultraviolet Circular Dichroism Spectroscopy

    OpenAIRE

    Matsuo, Koichi; Sakurada, Yoshie; Yonehara, Ryuta; Kataoka, Mikio; Gekko, Kunihiko

    2007-01-01

    To elucidate the structure of denatured proteins, we measured the vacuum-ultraviolet circular dichroism (VUVCD) spectra from 260 to 172 nm of three proteins (metmyoglobin, staphylococcal nuclease, and thioredoxin) in the native and the acid-, cold-, and heat-denatured states, using a synchrotron-radiation VUVCD spectrophotometer. The circular dichroism spectra of proteins fully unfolded by guanidine hydrochloride (GdnHCl) were also measured down to 197 nm for comparison. These denatured prote...

  11. Chiroptical studies on brevianamide B: vibrational and electronic circular dichroism confronted

    OpenAIRE

    Bultinck, Patrick; Cherblanc, Fanny L.; Fuchter, Matthew J.; Herrebout, Wouter A; Lo, Ya-Pei; Rzepa, Henry S; Siligardi, Giuliano; Weimar, Marko

    2015-01-01

    Chiroptical spectroscopy, such as electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) are highly sensitive techniques to probe molecular conformation, configuration, solvation and aggregation. Here we report the application of these techniques to study the fungal metabolite brevianamide B. Comparison of the experimental ECD and VCD spectra with the density functional theory (DFT) simulated counterparts establishes that VCD is the more reliable technique to assign abso...

  12. A circular dichroism sensor for Ni2+ and Co2+ based on L-cysteine capped cadmium sulfide quantum dots

    International Nuclear Information System (INIS)

    Highlights: • Demonstrated a new efficient sensor platform based quantum dots. • Used chiral quantum dots as CD sensor for the detection of heavy metal ions for the first time. • The proposed CD sensor showed highest selectivity towards Ni2+ and Co2+. • Low detection limits of 7.33 μM and 1.13 μM for Ni2+ and Co2+, respectively. • Can be used in real water samples comparing with ICP-OES. - Abstract: A new circular dichroism sensor for detecting Ni2+ and Co2+ was proposed for the first time using chiral chelating quantum dots. The detection principle was based on changing of circular dichroism signals of the chiral quantum dots when forming a chiral complex with Ni2+ or Co2+. L-Cysteine capped cadmium sulfide quantum dots (L-Cyst-CdS QDs) were proposed as a chiral probe. The CD spectrum of L-Cyst-CdS QDs was significantly changed in the presence of Ni2+ and Co2+. On the other hand, other studied cations did not alter the original CD spectrum. Moreover, when increasing the concentration of Ni2+ or Co2+, the intensity of the CD spectrum linearly increased as a function of concentration and could be useful for the quantitative analysis. The proposed CD sensor showed linear working concentration ranges of 10–60 μM and 4–80 μM with low detection limits of 7.33 μM and 1.13 μM for the detection of Ni2+ and Co2+, respectively. Parameters possibly affected the detection sensitivity such as solution pH and incubation time were studied and optimized. The proposed sensor was applied to detect Ni2+ and Co2+ in real water samples, and the results agreed well with the analysis using the standard ICP-OES

  13. Linear microrheology with optical tweezers of living cells 'is not an option'!

    Science.gov (United States)

    Tassieri, Manlio

    2015-08-01

    Optical tweezers have been successfully adopted as exceptionally sensitive transducers for microrheology studies of complex fluids. Despite the general trend, in this article I explain why a similar approach should not be adopted for microrheology studies of living cells. This conclusion is acheived on the basis of statistical mechanics principles that indicate the unsuitability of optical tweezers for such purpose. PMID:26100967

  14. Linear microrheology with optical tweezers of living cells 'is not an option'!

    OpenAIRE

    Tassieri, Manlio

    2015-01-01

    Optical tweezers have been successfully adopted as exceptionally sensitive transducers for microrheology studies of complex fluids. Despite the general trend, in this article I explain why a similar approach should not be adopted for microrheology studies of living cells. This conclusion is reached on the basis of statistical mechanics principles that indicate the unsuitability of optical tweezers for such purpose.

  15. Methanol Perturbing Modeling Cell Membranes Investigated using Linear and Nonlinear Vibrational Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    Kangzhen Tian; Hongchun Li; Shuji Ye

    2013-01-01

    Cell membranes play a crucial role in many biological functions of cells.A small change in the composition of cell membranes can strongly influence the functions of membrane-associated proteins,such as ion and water channels,and thus mediate the chemical and physical balance in cells.Such composition change could originate from the introduction of short-chain alcohols,or other anesthetics into membranes.In this work,we have applied sum frequency generation vibrational spectroscopy (SFG-VS),supplemented by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR),to investigate interaction between methanol and 1,2-dimyristoyl-d54-sn-glycero-3-phosphocholine (d54-DMPC) lipid bilayers.Lipid's hydrocarbon interior is deuterated while its head group is hydrogenated.At the same time,CH3 symmetric stretch from methanol and lipid head amine group has different frequency,thus we can distinguish the behaviors of methanol,lipid head amine group,and lipid hydrocarbon interior.Based on the spectral feature of the bending mode of the water molecules replaced by methanol,we determined that the methanol molecules are intercalated into the region between amine and phosphate groups at the lipid hydrophilic head.The dipole of CH3 groups of methanol and lipid head,and the water O-H all adopt the same orientation directions.The introduction of methanol into the lipid hydrophilic head group can strongly perturb the entire length of the alkyl chains,resulting that the signals of CD2 and CD3 groups from both leaflets can not cancel each other.

  16. Acceleration in linear growth after splenectomy for hypersplenism in homozygous sickle cell disease.

    OpenAIRE

    Singhal, A.; Thomas, P; Kearney, T; Venugopal, S.; Serjeant, G

    1995-01-01

    Chronic hypersplenism in homozygous sickle cell (SS) disease markedly increases haemolysis and the resulting erythropoietic expansion is likely to have a high metabolic cost. Splenectomy for hypersplenism in SS disease is followed by highly significant changes in haematological indices and an increase in height, but not weight, velocity. This pattern is similar to that observed in the trichuris dysentery syndrome after treatment, and differs from the increases in both height and weight veloci...

  17. Design of linear controllers applied to an ethanol steam reformer for PEM fuel cell applications

    OpenAIRE

    García, Vanesa M.; Serra, Maria; Llorca, Jordi; Riera, Jordi

    2013-01-01

    This paper focuses on the design of a controller for a low temperature ethanol steam reformer for the production of hydrogen to feed a protonic exchange membrane (PEM) fuel cell. It describes different control structures for the reformer and treats the control structure selection of this multiple input multiple output (MIMO) system. For each considered control structure, decentralised 2 × 2 controllers with proportional integral (PI) control actions in each control loop are implemented. The t...

  18. The Role of Molecular Quantum Electrodynamics in Linear Aggregations of Red Blood Cells

    OpenAIRE

    Bradonjic, K.; Swain, J. D.; Widom, A.; Srivastava, Y. N.

    2004-01-01

    Despite the fact that red blood cells carry negative charges, under certain conditions they form cylindrical stacks, or ``rouleaux''. It is shown here that a form of the Casimir effect, generalizing the more well-known van der Waals forces, can provide the necessary attractive force to balance the electrostatic repulsion. Erythrocytes in plasma are modelled as negatively charged dielectric disks in an ionic solution, allowing predictions to be made about the conditions under which rouleaux wi...

  19. The role of the magnetically induced anisotropy of the pair correlation function in the dichroism of magnetic fluids

    Energy Technology Data Exchange (ETDEWEB)

    Socoliuc, V., E-mail: vsocoliuc@acad-tim.tm.edu.ro [“Petru Poni” Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi (Romania); Laboratory of Magnetic Fluids, Center for Fundamental and Advanced Technical Research, Romanian Academy-Timisoara Branch, Bv.M. Viteazu 24, Timisoara RO-300223 (Romania); Popescu, L.B. [Institute for Space Sciences, 409 Atomistilor, Magurele 077125 (Romania)

    2013-12-15

    Experimental evidence is presented that the susceptibility for magnetically induced dichroism in concentrated magnetic fluids decays with further increasing of the magnetic nanoparticle concentration. The analysis of the predictions derived from our dichroism model, based on the pair correlation function developed by Elfimova and Ivanov (2010), showed that the observed phenomenon can be explained by the manner in which the symmetry of the pair correlation function changes with increasing magnetic field intensity and sample concentration. The increase of the dichroism with increasing concentration in diluted samples (0.2–1%) is mainly caused by the pair correlations in the first coordination layer, predominantly along the magnetic field direction. In the 1–3% concentration range, the first coordination layer becomes increasingly isotropic while pair correlations in the second coordination layer grow transversally to the magnetic field direction. Thus, with the increase of the concentration above 2%, the dichroism decreases as a combined effect of the changes in the symmetry of the pair correlations in the first and the second coordination layers. The proposed dichroism model predicts the possibility of negative magnetically induced dichroism in highly concentrated perfect colloidal dispersions of small spherical magnetic nanoparticles. - Highlights: • Experiment: the magnetically induced dichroism is inhibited in concentrated magnetic fluids. • Theory: dichroism model based on long range interparticle correlations. • The symmetry features of the pair correlation function explains the experimental findings. • The proposed dichroism model predicts the possibility of negative magnetically induced dichroism.

  20. Evaluation of the effectiveness of packed red blood cell irradiation by a linear accelerator

    OpenAIRE

    Ricardo Aparecido Olivo; Marcus Vinícius da Silva; Fernanda Bernadelli Garcia; Sheila Soares; Virmondes Rodrigues Junior; Helio Moraes-Souza

    2015-01-01

    Irradiation of blood components with ionizing radiation generated by a specific device is recommended to prevent transfusion-associated graft-versus-host disease. However, a lin- ear accelerator can also be used in the absence of such a device, which is the case of the blood bank facility studied herein. In order to evaluate the quality of the irradiated packed red blood cells, this study aimed to determine whether the procedure currently employed in the facility is effective in inhibiting the...

  1. Near-infrared dichroism of a mesogenic transition metal complex and its solubility in nematic hosts

    International Nuclear Information System (INIS)

    A transition metal complex possessing the nematic phase, bis (p-n-butylstyryl-1, 2-dithiolato) nickel, was synthesized and its optical properties and solubility in the nematic hosts K15 and MBBA were investigated. The metal complex displayed a high solubility in both host materials (up to 10% wt/wt) and a strong near-infrared absorption band centered at 860 nm. A blocking extinction of greater than OD = 3 was obtained with a 100 micron pathlength of a 0.5% wt/wt mixture of the nematic metal complex in K15, suggesting its usefulness for passive blocking of near infrared radiation. A 24 micron thick, homogeneously aligned guest-host cell containing a 1% wt/wt mixture of the metal complex in K15 possessed a contrast ratio of nearly 5:1 and a blocking extinction of OD = 3.5 at 860 nm, demonstrating for the first time the existence of near-infrared dichroism in this class of materials. The solubility and blocking extinction of the mesogenic metal complex in K15 was considerably superior to the non-mesogenic near ir laser dye bis(dimethylaminodithiobenzil) nickel in the same host. An interaction of the nematic metal complex in mixtures with MBBA which resulted in the creation of a new absorption band at 1050 nm was also observed. 21 refs., 9 figs

  2. A UV-prepared linear polymer electrolyte membrane for dye-sensitized solar cells

    International Nuclear Information System (INIS)

    The effects of LiClO4 and LiFS3SO3 on poly(glycidyl methacrylate)-based solid polymer electrolyte and its photoelectrochemical performance in a dye sensitized solar cell consisting of FTO/TiO2–dye/P(GMA)–LiClO4–EC/Pt were investigated. The electrochemical stability of films was studied by cyclic voltammetry (CV). The highest ionic conductivities obtained were 4.2×10−5 and 3.7×10−6 S cm−1 for the film containing 30 wt% LiClO4 and 25 wt% LiCF3SO3, respectively. The polymer electrolytes showed electrochemical stability windows up to 3 V and 2.8 V for LiClO4 and LiCF3SO3, respectively. The assembled dye-sensitized solar cell showed a sunlight conversion efficiency of 0.679% (Jsc=3 mA cm−2, Voc=0.48 V and FF=0.47), under light intensity of 100 mW cm−2

  3. A UV-prepared linear polymer electrolyte membrane for dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Imperiyka, M., E-mail: imperiyka@gmail.com [Faculty of Arts and Sciences, Kufra Campus, University of Benghazi, Al Kufrah (Libya); Ahmad, A.; Hanifah, S.A. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia); Polymer Research Center, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia); Bella, F. [Center for Space Human Robotics @Polito, Istituto Italiano di Tecnologia, Corso Trento 21, 10129 Torino (Italy); Department of Applied Science and Technology – DISAT, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino (Italy)

    2014-10-01

    The effects of LiClO{sub 4} and LiFS{sub 3}SO{sub 3} on poly(glycidyl methacrylate)-based solid polymer electrolyte and its photoelectrochemical performance in a dye sensitized solar cell consisting of FTO/TiO{sub 2}–dye/P(GMA)–LiClO{sub 4}–EC/Pt were investigated. The electrochemical stability of films was studied by cyclic voltammetry (CV). The highest ionic conductivities obtained were 4.2×10{sup −5} and 3.7×10{sup −6} S cm{sup −1} for the film containing 30 wt% LiClO{sub 4} and 25 wt% LiCF{sub 3}SO{sub 3}, respectively. The polymer electrolytes showed electrochemical stability windows up to 3 V and 2.8 V for LiClO{sub 4} and LiCF{sub 3}SO{sub 3}, respectively. The assembled dye-sensitized solar cell showed a sunlight conversion efficiency of 0.679% (J{sub sc}=3 mA cm{sup −2}, V{sub oc}=0.48 V and FF=0.47), under light intensity of 100 mW cm{sup −2}.

  4. Atomic force microscopy indentation and inverse analysis for non-linear viscoelastic identification of breast cancer cells.

    Science.gov (United States)

    Nguyen, Nhung; Shao, Yue; Wineman, Alan; Fu, Jianping; Waas, Anthony

    2016-07-01

    Breast cancer cells (MCF-7 and MCF-10A) are studied through indentation with spherical borosilicate glass particles in atomic force microscopy (AFM) contact mode in fluid. Their mechanical properties are obtained by analyzing the recorded reaction force-time response. The analysis is based on comparing experimental data with predictions from finite element (FE) simulation. Here, FE modeling is employed to simulate the AFM indentation experiment which is neither a displacement nor a force controlled test. This approach is expected to overcome many underlying problems of the widely used models such as Hertz contact model due to its capability to capture the contact behaviors between the spherical indentor and the cell, account for cell geometry, and incorporate with large strain theory. In this work, a non-linear viscoelastic (NLV) model in which the viscoelastic part is described by Prony series terms is used for the constitutive model of the cells. The time-dependent material parameters are extracted through an inverse analysis with the use of a surrogate model based on a Kriging estimator. The purpose is to automatically extract the NLV properties of the cells with a more efficient process compared to the iterative inverse technique that has been mostly applied in the literature. The method also allows the use of FE modeling in the analysis of a large amount of experimental data. The NLV parameters are compared between MCF-7 and MCF-10A and MCF-10A treated and untreated with the drug Cytochalasin D to examine the possibility of using relaxation properties as biomarkers for distinguishing these types of breast cancer cells. The comparisons indicate that malignant cells (MCF-7) are softer and exhibit more relaxation than benign cells (MCF-10A). Disrupting the cytoskeleton using the drug Cytochalasin D also results in a larger amount of relaxation in the cell's response. In addition, relaxation properties indicate larger differences as compared to the elastic moduli

  5. Non-linear relationship of cell hit and transformation probabilities in low dose of inhaled radon progenies

    CERN Document Server

    Balásházy, Imre; Madas, Balázs Gergely; Hofmann, Werner

    2013-01-01

    Cellular hit probabilities of alpha particles emitted by inhaled radon progenies in sensitive bronchial epithelial cell nuclei were simulated at low exposure levels to obtain useful data for the rejection or in support of the linear-non-threshold (LNT) hypothesis. In this study, local distributions of deposited inhaled radon progenies in airway bifurcation models were computed at exposure conditions, which are characteristic of homes and uranium mines. Then, maximum local deposition enhancement factors at bronchial airway bifurcations, expressed as the ratio of local to average deposition densities, were determined to characterize the inhomogeneity of deposition and to elucidate their effect on resulting hit probabilities. The results obtained suggest that in the vicinity of the carinal regions of the central airways the probability of multiple hits can be quite high even at low average doses. Assuming a uniform distribution of activity there are practically no multiple hits and the hit probability as a funct...

  6. Protecting effects specifically from low doses of ionizing radiation to mammalian cells challenge the concept of linearity

    International Nuclear Information System (INIS)

    This report examines the origin of tissue effects that may follow from different cellular responses to low-dose irradiation, using published data. Two principal categories of cellular responses are considered. One response category relates to the probability of radiation-induced DNA damage. The other category consists of low-dose induced changes in intracellular signaling that induce mechanisms of DNA damage control different from those operating at high levels of exposure. Modeled in this way, tissue is treated as a complex adaptive system. The interaction of the various cellular responses results in a net tissue dose-effect relation that is likely to deviate from linearity in the low-dose region. This suggests that the LNT hypothesis should be reexamined. The aim of this paper is to demonstrate that by use of microdosimetric concepts, the energy deposited in cell mass can be related to the occurrence of cellular responses, both damaging and defensive

  7. Protecting effects specifically from low doses of ionizing radiation to mammalian cells challenge the concept of linearity

    Energy Technology Data Exchange (ETDEWEB)

    Feinendegen, L.E. [Brookhaven National Lab., Upton, NY (United States). Medical Dept.; Bond, V.P. [Washington State Univ., Richland, WA (United States); Sondhaus, C.A. [Univ. of Arizona, Tucson, AZ (United States). Dept. of Radiology and Radiation Control Office; Altman, K.I. [Univ. of Rochester Medical Center, NY (United States). Dept. of Biochemistry and Biophysics

    1998-12-31

    This report examines the origin of tissue effects that may follow from different cellular responses to low-dose irradiation, using published data. Two principal categories of cellular responses are considered. One response category relates to the probability of radiation-induced DNA damage. The other category consists of low-dose induced changes in intracellular signaling that induce mechanisms of DNA damage control different from those operating at high levels of exposure. Modeled in this way, tissue is treated as a complex adaptive system. The interaction of the various cellular responses results in a net tissue dose-effect relation that is likely to deviate from linearity in the low-dose region. This suggests that the LNT hypothesis should be reexamined. The aim of this paper is to demonstrate that by use of microdosimetric concepts, the energy deposited in cell mass can be related to the occurrence of cellular responses, both damaging and defensive.

  8. Laser-driven electron dynamics for circular dichroism in mass spectrometry: from one-photon excitations to multiphoton ionization.

    Science.gov (United States)

    Kröner, Dominik

    2015-07-15

    The distinction of enantiomers is a key aspect of chemical analysis. In mass spectrometry the distinction of enantiomers has been achieved by ionizing the sample with circularly polarized laser pulses and comparing the ion yields for light of opposite handedness. While resonant excitation conditions are expected to be most efficient, they are not required for the detection of a circular dichroism (CD) in the ion yield. However, the prediction of the size and sign of the circular dichroism becomes challenging if non-resonant multiphoton excitations are used to ionize the sample. Employing femtosecond laser pulses to drive electron wavepacket dynamics based on ab initio calculations, we attempt to reveal underlying mechanisms that determine the CD under non-resonant excitation conditions. Simulations were done for (R)-1,2-propylene oxide, using time-dependent configuration interaction singles with perturbative doubles (TD-CIS(D)) and the aug-cc-pVTZ basis set. Interactions between the electric field and the electric dipole and quadrupole as well as between the magnetic field and the magnetic dipole were explicitly accounted for. The ion yield was determined by treating states above the ionization potential as either stationary or non-stationary with energy-dependent lifetimes based on an approved heuristic approach. The observed population dynamics do not allow for a simple interpretation, because of highly non-linear interactions. Still, the various transition pathways are governed by resonant enantiospecific n-photon excitation, with preferably high transition dipole moments, which eventually dominate the CD in the ionized population. PMID:26151731

  9. Identification of three MAPKKKs forming a linear signaling pathway leading to programmed cell death in Nicotiana benthamiana

    Directory of Open Access Journals (Sweden)

    Hashimoto Masayoshi

    2012-07-01

    MAPKKKβ kinase domain or of NbMAPKKKγ, but silencing of NbMAPKKKβ failed to suppress cell death induced by the overexpression of NbMAPKKKα or NbMAPKKKγ. Silencing of NbMAPKKKγ suppressed cell death induced by the NbMAPKKKβ kinase domain but not that induced by NbMAPKKKα. Conclusions These results demonstrate that in addition to NbMAPKKKα, NbMAPKKKβ and NbMAPKKKγ also function as positive regulators of PCD. Furthermore, these three MAPKKKs form a linear signaling pathway leading to PCD; this pathway proceeds from NbMAPKKKβ to NbMAPKKKγ to NbMAPKKKα.

  10. Synchrotron radiation circular dichroism spectroscopy study of recombinant T β4 folding

    Science.gov (United States)

    Huang, Yung-Chin; Chu, Hsueh-Liang; Chen, Peng-Jen; Chang, Chia-Ching

    Thymosin beta 4 (T β4) is a 43-amino acid small peptide, has been demonstrated that it can promote cardiac repair, wound repair, tissue protection, and involve in the proliferation of blood cell precursor stem cells of bone marrow. Moreover, T β4 has been identified as a multifunction intrinsically disordered protein, which is lacking the stable tertiary structure. Owing to the small size and disordered character, the T β4 protein degrades rapidly and the storage condition is critical. Therefore, it is not easy to reveal its folding mechanism of native T β4. However, recombinant T β4 protein (rT β4), which fused with a 5-kDa peptide in its amino-terminal, is stable and possesses identical function of T β4. Therefore, rT β4 can be used to study its folding mechanism. By using over-critical folding process, stable folding intermediates of rT β4 can be obtained. Structure analysis of folding intermediates by synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies indicate that rT β4 is a random coli major protein and its hydrophobic region becomes compact gradually. Moreover, the rT β4 folding is a two state transition. Thermal denaturation analysis indicates that rT β4 lacks stable tertiary structure. These results indicated that rT β4, similar to T β4, is an intrinsically disordered protein. Research is supported by MOST, Taiwan. MOST 103-2112-M-009-011-MY3. Corresponding author: Chia-Ching Chang; ccchang01@faculty.nctu.edu.tw.

  11. X-ray magnetic dichroism: from quantitative determination of magnetic moments to imaging of magnetization dynamics

    International Nuclear Information System (INIS)

    In this document, I use some results of my research activities of the last ten years to show the power of x-ray magnetic dichroism for determining magnetic properties of thin layers, multilayers and nano-structures. The use of sum rules for x-ray dichroism allows a quantitative determination of the spin and orbital contributions to the magnetic moment, for each element of a heterogeneous material separately. Used in a qualitative way, x-ray dichroism allows monitoring the magnetization of the different layers in a multilayer material as a function of applied field. In combination with the temporal structure of synchrotron radiation, it is possible to study fast magnetization reversal with element selectivity, which is important for devices like spin valves and magnetic tunnel junctions. Adding the spatial resolution of a photoelectron emission microscope (PEEM), it becomes possible to study all the details of the fast magnetization reversal in complex magnetic systems. (author)

  12. Extreme optical activity and circular dichroism of chiral metal hole arrays

    CERN Document Server

    Gorkunov, M V; Artemov, V V; Rogov, O Y; Yudin, S G

    2014-01-01

    We report extremely strong optical activity and circular dichroism exhibited by subwavelength arrays of four-start-screw holes fabricated with one-pass focused ion beam milling of freely suspended silver films. Having the fourth order rotational symmetry, the structures exhibit the polarization rotation up to 90 degrees and peaks of full circular dichroism and operate as circular polarizers within certain ranges of wavelengths in the visible. We discuss the observations on the basis of general principles (symmetry, reciprocity and reversibility) and conclude that the extreme optical chirality is determined by the chiral localized plasmonic resonances.

  13. Surface plasmon resonance coupled circular dichroism of DNA–gold nanorods assembly

    International Nuclear Information System (INIS)

    Linker mediated self-assembly of gold nanoparticles is emerging as an interesting strategy for construction of hybrid nanoscale systems with enhanced plasmonic circular dichroism (PCD) signals. Herein, gold nanorods were assembled via DNA linker to investigate the possibility of signal enhancement. Assemblies were characterized by UV–visible, fluorescence, dynamic light scattering and circular dichroism (CD) spectroscopy. Hybridization of complementary strands resulted in PCD signal enhancement, which was further monitored by the increase of real time PicoGreen fluorescence intensity. Impressively, such changes in the real time fluorescence and plasmonic CD responses could be used as a new detection method for ultrasensitive sensors. (paper)

  14. Origination of electron magnetic chiral dichroism in cobalt-doped ZnO dilute magnetic semiconductors

    International Nuclear Information System (INIS)

    Electron magnetic chiral dichroism (EMCD) relates the microstructure of a single nanostructure with the magnetic property, indicating that the ferromagnetism observed in cobalt-doped ZnO dilute magnetic semiconductor is intrinsic. First-principles calculations were carried out and the electronic states contributing to the spin imbalance are identified. An exact model is developed, allowing one to visualize the origination of dichroism to be the difference of transition intensity from spin-polarized 2p states to Co-3d states in cobalt-doped ZnO nanostructures.

  15. Vibrational Circular Dichroism (VCD) Reveals Subtle Conformational Aspects and Intermolecular Interactions in the Carnitine Family.

    Science.gov (United States)

    Mazzeo, Giuseppe; Abbate, Sergio; Longhi, Giovanna; Castiglioni, Ettore; Villani, Claudio

    2015-12-01

    Vibrational circular dichroism spectra (VCD) in the mid-IR region and electronic circular dichroism (ECD) spectra for three carnitine derivatives in the form of hydrochloride salts were recorded in deuterated methanol solutions. Density Functional Theory calculations help one to understand the significance of the observed VCD bands. VCD and ECD spectra are informative about the absolute configuration of the molecule, but VCD data reveal also some conformational aspects in the N,N,N-trimethyl moiety and inform us about intermolecular interactions gained from the carbonyl stretching region for the acyl substituted carnitines. PMID:26447810

  16. Prediction of the herd somatic cell count of the following month using a linear mixed effect model.

    Science.gov (United States)

    Lievaart, J J; Barkema, H W; van den Broek, J; Heesterbeek, J A P; Kremer, W D J

    2010-01-01

    An accurate prediction of the average somatic cell count (SCC) for the next month would be a valuable tool to support udder health management decisions. A linear mixed effect (LME) model was used to predict the average herd SCC (HSCC) for the following month. The LME model included data on SCC, herd characteristics, season, and management practices determined in a previous study that quantified the contribution of each factor for the HSCC. The LME model was tested on a new data set of 101 farms and included data from 3 consecutive years. The farms were split randomly in 2 groups of 50 and 51 farms. The first group of 50 farms was used to check for systematic errors in predicting monthly HSCC. An initial model was based on older data from a different part of the Netherlands and systematically overestimated HSCC in most months. Therefore, the model was adjusted for the difference in average HSCC between the 2 sets of farms (from the previous and current study) using the data from the first group of 50 farms. Subsequently, the data from the second group of 51 farms were used to independently assess this final model. A null model (no explanatory variables included) predicted 48 and 59% of the HSCC within the predetermined range of 20,000 and 30,000 cells/mL, respectively. The final LME model predicted 72 and 81% of the HSCC of the next month correctly within these 2 ranges. These outcomes indicate that the final LME model was a valid additional tool for farmers that could be useful in their short-term decisions regarding udder health management and could be included in dairy herd health programs. PMID:20059921

  17. Identification of human linear B-cell epitope sites on the envelope glycoproteins of Crimean-Congo haemorrhagic fever virus.

    Science.gov (United States)

    Goedhals, D; Paweska, J T; Burt, F J

    2015-05-01

    A peptide library was used to screen for regions containing potential linear B-cell epitope sites in the glycoproteins and nucleoprotein of Crimean-Congo haemorrhagic fever virus (CCHFV) in an enzyme-linked immunosorbent assay (ELISA). The library consisted of 156 peptides, spanning the nucleoprotein and mature GN and GC proteins in a 19-mer with 9-mer overlap format. Using pooled serum samples from convalescent patients to screen the library, six peptides were identified as potential epitope sites. Further testing of these six peptides with individual patient sera identified two of these peptides as probable epitope sites, with peptide G1451-1469 reacting to 13/15 and peptide G1613-1631 to 14/15 human sera. These peptides are situated on the GC protein at amino acid positions 1451-1469 (relative to CCHFV isolate SPU103/97) (TCTGCYACSSGISCKVRIH) and 1613-1631 (FMFGWRILFCFKCCRRTRG). Identified peptides may have application in ELISA for diagnostic or serosurveillance purposes. PMID:25185583

  18. Circular dichroism study on the diastereoselective self-assembly of bacteriochlorophyll cs

    Science.gov (United States)

    Balaban, Teodor S.; Holzwarth, Alfred R.; Schaffner, Kurt

    1995-04-01

    Circular dichroism (CD) spectra of self-assembled bacteriochlorophyll cs (BChl cs) aggregates show a pronounced dependency on the solvent, the concentration and on the stereochemistry of the 3 1-hydroxy groups. In n-hexane a psi-type CD is obtained due to the formation of nanostructural aggregates.

  19. Synthesis and structural study of sugar derivatives of oligopyrroles using circular dichroism

    Czech Academy of Sciences Publication Activity Database

    Štěpánek, P.; Kaminský, Jakub; Šimák, Ondřej; Drašar, P.

    2012-01-01

    Roč. 106, - (2012), s1354-s1354. ISSN 0009-2770. [EuCheMS Chemistry Congress /4./. 26.08.2012-30.08.2012, Prague] Institutional research plan: CEZ:AV0Z40550506 Keywords : circular dichroism * C-Glycosides * supramolecular chemistry Subject RIV: CC - Organic Chemistry

  20. Circular dichroism as a means to follow DNA gymnastics: on the shoulders of giants

    Directory of Open Access Journals (Sweden)

    H.H. Klump

    2010-01-01

    Full Text Available This is the first report of DNA stem-loops self-assembled by ‘foot-loop’ interactions into either two-dimensional strings or three-dimensional spirals, distinguished by circular dichroism spectroscopy. All subunits are linked by cooperative Watson-Crick hydrogen bonds.

  1. DNA electronic circular dichroism on the inter-base pair scale

    DEFF Research Database (Denmark)

    Di Meo, Florent; Nørby, Morten Steen; Rubio-Magnieto, Jenifer;

    2015-01-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the...

  2. Enantioselective femtosecond laser photoionization spectrometry of limonene using photoelectron circular dichroism.

    Science.gov (United States)

    Rafiee Fanood, Mohammad M; Janssen, Maurice H M; Powis, Ivan

    2015-04-14

    Limonene is ionized by circularly polarized 420 nm femtosecond laser pulses. Ion mass and photoelectron energy spectra identify the dominant (2 + 1) multiphoton ionization mechanism, aided by TDDFT calculations of the Rydberg excitations. Photoelectron circular dichroism measurements on pure enantiomers reveal a chiral asymmetry of ±4 %. PMID:25744283

  3. RNA structural forms studied by vibrational circular dichroism: Ab initio interpretation of the spectra

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, V.; Wieser, H.; Bouř, Petr

    2004-01-01

    Roč. 108, - (2004), s. 3899-3911. ISSN 1089-5647 R&D Projects: GA AV ČR IAA4055104; GA ČR GA203/01/0031 Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism * RNA Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.679, year: 2003

  4. Comparison of Vibrational Circular Dichroism Instruments: Development of a New Dispersive VCD

    Czech Academy of Sciences Publication Activity Database

    Lakhani, A.; Maloň, Petr; Keiderling, T. A.

    2009-01-01

    Roč. 63, č. 7 (2009), s. 775-785. ISSN 0003-7028 Institutional research plan: CEZ:AV0Z40550506 Keywords : vibrational circular dichroism * VCD * dispersive infrared spectroscopy * peptides Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.564, year: 2009

  5. Conformational flexibility of Corey lactone derivatives indicated by absorption and vibrational circular dichroism spectra

    Czech Academy of Sciences Publication Activity Database

    Tománková, Z.; Setnička, V.; Urbanová, M.; Matějka, P.; Král, V.; Volka, K.; Bouř, Petr

    2004-01-01

    Roč. 69, č. 1 (2004), s. 26-32. ISSN 0022-3263 R&D Projects: GA AV ČR IAA4055104; GA ČR GA203/01/0031 Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism * lactone Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.462, year: 2004

  6. Vibrational circular dichroism of nucleic acids: Combination of theory and experiment

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, Valery; Wieser, H.; Bouř, Petr

    Pisa : -, 2012. s. 46-46. [CECAM 2012. International Conference on Vibrational Optical Activity: Interplay of Theory and Experiment /3./. 23.09.2012-27.09.2012, Pisa] Institutional support: RVO:61388963 Keywords : vibrational circular dichroism * VCD spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry

  7. Oriented Circular Dichroism: A Method to Characterize Membrane-Active Peptides in Oriented Lipid Bilayers.

    Science.gov (United States)

    Bürck, Jochen; Wadhwani, Parvesh; Fanghänel, Susanne; Ulrich, Anne S

    2016-02-16

    The structures of membrane-bound polypeptides are intimately related to their functions and may change dramatically with the lipid environment. Circular dichroism (CD) is a rapid analytical method that requires relatively low amounts of material and no labeling. Conventional CD is routinely used to monitor the secondary structure of peptides and proteins in solution, for example, in the presence of ligands and other binding partners. In the case of membrane-active peptides and transmembrane proteins, these measurements can be applied to, and remain limited to, samples containing detergent micelles or small sonicated lipid vesicles. Such traditional CD analysis reveals only secondary structures. With the help of an oriented circular dichroism (OCD) setup, however, based on the preparation of macroscopically oriented lipid bilayers, it is possible to address the membrane alignment of a peptide in addition to its conformation. This approach has been mostly used for α-helical peptides so far, but other structural elements are conceivable as well. OCD analysis relies on Moffitt's theory, which predicts that the electronic transition dipole moments of the backbone amide bonds in helical polypeptides are polarized either parallel or perpendicular to the helix axis. The interaction of the electric field vector of the circularly polarized light with these transitions results in an OCD spectrum of a membrane-bound α-helical peptide, which exhibits a characteristic line shape and reflects the angle between the helix axis and the bilayer normal. For parallel alignment of a peptide helix with respect to the membrane surface (S-state), the corresponding "fingerprint" CD band around 208 nm will exhibit maximum negative amplitude. If the helix changes its alignment via an obliquely tilted (T-state) to a fully inserted transmembrane orientation (I-state), the ellipticity at 208 nm decreases and the value approaches zero due to the decreased interactions between the field and the

  8. Analysis of boundary point (break point) in Linear Delay Model for nanoscale VLSI standard cell library characterization at PVT corners

    CERN Document Server

    Agarwal, Gaurav Kumar

    2014-01-01

    In VLSI chip design flow, Static Timing Analysis (STA) is used for fast and accurate analysis of data-path delay. This process is fast because delay is picked from Look Up Tables (LUT) rather than conventional SPICE simulations. But accuracy of this method depends upon the underlying delay model with which LUT was characterized. Non Linear Delay Model (NLDM) based LUTs are quite common in industries. These LUT requires huge amount to time during characterization because of huge number of SPICE simulations done at arbitrary points. To improve this people proposed various other delay models like alpha-power and piecewise linear delay models. Bulusu et al proposed Linear Delay Model(LDM) which reduces LUT generation time to 50 percent. LDM divides delay curve w.r.t input rise time(trin) into two different region one is linear and other is non-linear. This boundary point between linear and non- linear region was called break point (trb). Linear region will be done if we simulate at only two points. This advantage...

  9. Linear gate

    International Nuclear Information System (INIS)

    A linear gate providing a variable gate duration from 0,40μsec to 4μsec was developed. The electronic circuity consists of a linear circuit and an enable circuit. The input signal can be either unipolar or bipolar. If the input signal is bipolar, the negative portion will be filtered. The operation of the linear gate is controlled by the application of a positive enable pulse. (author)

  10. Linear Accelerators

    CERN Document Server

    Vretenar, M

    2014-01-01

    The main features of radio-frequency linear accelerators are introduced, reviewing the different types of accelerating structures and presenting the main characteristics aspects of linac beam dynamics.

  11. High-dose rate intracavitary irradiation using linear source arrangement for squamous cell carcinoma of the uterine cervix

    International Nuclear Information System (INIS)

    Purpose: To evaluate the results of fractionated high-dose-rate (HDR) intracavitary irradiation using a linear source arrangement (LSA) without vaginal ovoids for patients with squamous cell carcinoma of the uterine cervix. Methods and Materials: From 1980 to 1990, 236 patients with squamous cell carcinoma received external beam therapy (EBT) followed by fractionated HDR intracavitary irradiation using LSA (HDR-LSA). The initial FIGO stage was I, II, and III for 19, 71, and 146 patients respectively. Forty Gy in 20 fractions (40 Gy/20 Fr) were delivered to the whole pelvis and additional 10 Gy/5 Fr to the center shielding field with parallel opposed ports. The HDR-LSA dose was 30 Gy/6 Fr or 35 Gy/7 Fr at Manchester's point A giving two fractions per week. During the intracavitary irradiation, patients were treated in the out-patient clinic. A vaginal plastic applicator was inserted with lubricating gel without spinal or general anesthesia and gauze packing. Results: Pelvic failure rate was 10.5% for stage I, 12.7% for stage II, and 35.6% for stage III. Cause-specific 5-year survival rates were 69.1% for stage I, 77.1 % for stage II, and 50.1 % for stage III, respectively. The low survival for stage I disease was suggested to be due to selection bias. In multivariant analyses, stage (stage I+II vs. III, p=0.0003), pre-treatment serum hemoglobin level (p=0.0021), pre-treatment serum total protein level (p=0.0028), and total treatment time (p=0.0035) were significantly associated with cause-specific survival. The rate of late severe complications was 2.1% for rectum, 1.2% for small intestine, and 1.3 % for bladder. Conclusions: The LSA-HDR method following EBT is a safe and effective technique for the majority of patients. Reproducibility of dose distribution and the easiness of the insertion for the patients are suitable for multi-fractionated schedule required in HDR treatment. The benefit of the LSA, compared to the arrangement using a tandem and ovoids, should be

  12. Analyses of genetic relationships between linear type traits, fat-to-protein ratio, milk production traits, and somatic cell count in first-parity Czech Holstein cows

    DEFF Research Database (Denmark)

    Zink, V; Zavadilová, L; Lassen, Jan;

    2014-01-01

    Genetic and phenotypic correlations between production traits, selected linear type traits, and somatic cell score were estimated. The results could be useful for breeding programs involving Czech Holstein dairy cows or other populations. A series of bivariate analyses was applied whereby (co......)variance components were estimated using average information (AI-REML) implemented via the DMU statistical package. Chosen phenotypic data included average somatic cell score per a 305-day standard first lactation as well as the production traits milk yield, fat yield, protein yield, fat percentage, and protein...... and protein yield. In total, 27 098 somatic cell score records were available. The strongest positive genetic correlation between production traits and linear type traits was estimated between udder width and fat yield (0.51 ± 0.04), while the strongest negative correlation estimated was between body...

  13. Linear colliders

    International Nuclear Information System (INIS)

    From November 28 to December 9, the Stanford Linear Accelerator Center hosted an International Workshop on Next Generation Linear Colliders. The attendance, including delegations from CERN, Frascati (Italy), KEK (Japan), Livermore (US), Novosibirsk (USSR), Drsay (France) and SLAC itself reflected the international interest in this new approach to higher energies

  14. An atomic orbital based real-time time-dependent density functional theory for computing electronic circular dichroism band spectra

    Science.gov (United States)

    Goings, Joshua J.; Li, Xiaosong

    2016-06-01

    One of the challenges of interpreting electronic circular dichroism (ECD) band spectra is that different states may have different rotatory strength signs, determined by their absolute configuration. If the states are closely spaced and opposite in sign, observed transitions may be washed out by nearby states, unlike absorption spectra where transitions are always positive additive. To accurately compute ECD bands, it is necessary to compute a large number of excited states, which may be prohibitively costly if one uses the linear-response time-dependent density functional theory (TDDFT) framework. Here we implement a real-time, atomic-orbital based TDDFT method for computing the entire ECD spectrum simultaneously. The method is advantageous for large systems with a high density of states. In contrast to previous implementations based on real-space grids, the method is variational, independent of nuclear orientation, and does not rely on pseudopotential approximations, making it suitable for computation of chiroptical properties well into the X-ray regime.

  15. Linear algebra

    CERN Document Server

    Stoll, R R

    1968-01-01

    Linear Algebra is intended to be used as a text for a one-semester course in linear algebra at the undergraduate level. The treatment of the subject will be both useful to students of mathematics and those interested primarily in applications of the theory. The major prerequisite for mastering the material is the readiness of the student to reason abstractly. Specifically, this calls for an understanding of the fact that axioms are assumptions and that theorems are logical consequences of one or more axioms. Familiarity with calculus and linear differential equations is required for understand

  16. Linear algebra

    CERN Document Server

    Liesen, Jörg

    2015-01-01

    This self-contained textbook takes a matrix-oriented approach to linear algebra and presents a complete theory, including all details and proofs, culminating in the Jordan canonical form and its proof. Throughout the development, the applicability of the results is highlighted. Additionally, the book presents special topics from applied linear algebra including matrix functions, the singular value decomposition, the Kronecker product and linear matrix equations. The matrix-oriented approach to linear algebra leads to a better intuition and a deeper understanding of the abstract concepts, and therefore simplifies their use in real world applications. Some of these applications are presented in detailed examples. In several ‘MATLAB-Minutes’ students can comprehend the concepts and results using computational experiments. Necessary basics for the use of MATLAB are presented in a short introduction. Students can also actively work with the material and practice their mathematical skills in more than 300 exerc...

  17. Electronic and vibrational circular dichroism spectra of (R)-(−)-apomorphine

    International Nuclear Information System (INIS)

    Highlights: ► ECD and VCD Spectra of (R)-(−)-apomorphine measured in various solvents. ► DFT calculations allow to study the protonation state and conformations. ► Contributions from catechol OH vibrations to the VCD spectra is studied. -- Abstract: Apomorphine is a chiral drug molecule; notwithstanding its extraordinary importance, little attention has been paid to the characterization of its chiroptical properties. Here we report on its electronic circular dichroism (ECD) spectra, recorded in methanol and water, and vibrational circular dichroism (VCD) in methanol and dimethyl sulfoxide (DMSO) solutions. Density functional theory (DFT) calculations have allowed us to interpret the spectra and to evaluate the role of possible conformations, charge-states and interactions with counter ions.

  18. Optically induced dichroism of Z2-centers in LiF : Mg, Ti (TLD-100)

    International Nuclear Information System (INIS)

    Crystals of γ-irradiated TLD-100 are bleached at 313 nm at 77 K with light polarized in one selected direction, and then with light polarized at 900 from the initial direction. Dichroism is induced in the Z2 center by bleaching with polarized light. The decrease in absorbance is always larger when measured with light polarized in the same direction as the bleaching light. There is an increase in absorbance at 313 nm after the second bleach when the measuring light is polarized perpendicular to the bleaching light. The results are observed in all four directions: [001], [010], [011], and [011]. A second defect center, which adsorbs at 313 nm, is proposed to explain the observed dichroism. (author)

  19. Circular dichroism in a three-dimensional semiconductor chiral photonic crystal

    CERN Document Server

    Takahashi, S; Ota, Y; Tatebayashi, J; Iwamoto, S; Arakawa, Y

    2014-01-01

    Circular dichroism covering the telecommunication band is experimentally demonstrated in a semiconductor-based three-dimensional chiral photonic crystal (PhC). We design a rotationally-stacked woodpile PhC structure where neighboring layers are rotated by 60 degrees and three layers construct a single helical unit. The mirror-asymmetric PhC made from GaAs with sub-micron periodicity is fabricated by a micro-manipulation technique. Due to the large contrast of refractive indices between GaAs and air, the experimentally obtained circular dichroism extends over a wide wavelength range, with the transmittance of right-handed circularly polarized incident light being 85% and that of left-handed light being 15% at a wavelength of 1300 nm. The obtained results show good agreement with numerical simulations.

  20. Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory

    OpenAIRE

    Uporov, Igor V.; Forlemu, Neville Y.; Rahul Nori; Tsvetan Aleksandrov; Sango, Boris A.; Yvonne E. Bongfen Mbote; Sandeep Pothuganti; Thomasson, Kathryn A.

    2015-01-01

    The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either...

  1. Fano resonance assisting plasmonic circular dichroism from nanorice heterodimers for extrinsic chirality

    OpenAIRE

    Li Hu; Yingzhou Huang; Liang Fang; Guo Chen; Hua Wei; Yurui Fang

    2015-01-01

    In this work, the circular dichroisms (CD) of nanorice heterodimers consisting of two parallel arranged nanorices with the same size but different materials are investigated theoretically. Symmetry-breaking is introduced by using different materials and oblique incidence to achieve strong CD at the vicinity of Fano resonance peaks. We demonstrate that all Au-Ag heterodimers exhibit multipolar Fano resonances and strong CD effect. A simple quantitative analysis shows that the structure with la...

  2. Degradation of electron-induced dichroism in glassy As2S3-Sb2S3

    Directory of Open Access Journals (Sweden)

    Balitska V. O.

    2000-12-01

    Full Text Available Experimental results on time degradation of electron-induced dichroism in vitreous chalcogenide semiconductors As2S3-Sb2S3 are discussed. The adequate model for the quantitative description of this process can be developed on the basis of monomolecular relaxation function proper to annihilation of dipol-like coordination defects created on the basis of radiation-induced broken covalent chemical bonds

  3. Degradation of electron-induced dichroism in glassy As2S3-Sb2S3

    OpenAIRE

    Balitska V. O.; Shpotyuk O. I.; Vakiv M. M.

    2000-01-01

    Experimental results on time degradation of electron-induced dichroism in vitreous chalcogenide semiconductors As2S3-Sb2S3 are discussed. The adequate model for the quantitative description of this process can be developed on the basis of monomolecular relaxation function proper to annihilation of dipol-like coordination defects created on the basis of radiation-induced broken covalent chemical bonds

  4. Achieving atomic resolution magnetic dichroism by controlling the phase symmetry of an electron probe

    OpenAIRE

    Rusz, Jan; Idrobo, Juan-Carlos; Bhowmick, Somnath

    2014-01-01

    The calculations presented here reveal that an electron probe carrying orbital angular momentum is just a particular case of a wider class of electron beams that can be used to measure electron magnetic circular dichroism (EMCD) with atomic resolution. It is possible to obtain an EMCD signal with atomic resolution by simply breaking the symmetry of the electron probe phase distribution using the aberration-corrected optics of an scanning transmission electron microscope. The required phase di...

  5. Emerging Magneto-Optic Spectroscopy: Nuclear Spin-Induced Circular Dichroism in Fullerenes

    Czech Academy of Sciences Publication Activity Database

    Štěpánek, Petr; Vaara, J.; Coriani, S.; Straka, Michal

    Opole: -, 2014. P11. [MMNB 2014. Polish-Taiwanese Conference. From Molecular Modeling to Nano- and Biotechnology. 04.09.2014-06.09.2014, Opole] R&D Projects: GA ČR(CZ) GA14-03564S; GA ČR GA13-03978S Institutional support: RVO:61388963 Keywords : nuclear spin circular dichroism * fullerene * nuclei-specific signal Subject RIV: CF - Physical ; Theoretical Chemistry

  6. Orientation of gramicidin A transmembrane channel. Infrared dichroism study of gramicidin in vesicles.

    OpenAIRE

    Nabedryk, E.; Gingold, M P; Breton, J

    1982-01-01

    Polarized infrared spectroscopy has been used to investigate the orientation of gramicidin A incorporated in dimyristoylphosphatidylcholine liposomes. Dichroism measurements of the major lipid (C = O ester, PO2-, CH2) and peptide (amide A, I, II) bands were performed on liposomes (with or without gramicidin) oriented by air-drying. The mean orientation of the lipid groups and of the pi LD helix chain in the gramicidin has been determined. It can be inferred from infrared frequencies of gramic...

  7. Circular magnetic dichroism of the Fa center adsorption in KCl doped with Li and Na

    International Nuclear Information System (INIS)

    The spin-orbit structure of FA in KCl:Li and KCl:Na have been studied by means of the magnetic circular dichroism. Due to their C4V, symmetry the FA centers have two different spin-orbit parameters, Δ* and Δ*, which only in the KCl:Li case follow the relation: Δ* F A centers have been determined using the method of moment

  8. Irreversible Denaturation of Maltodextrin Glucosidase Studied by Differential Scanning Calorimetry, Circular Dichroism, and Turbidity Measurements

    OpenAIRE

    Goyal, Megha; Chaudhuri, Tapan K; Kuwajima, Kunihiro

    2014-01-01

    Thermal denaturation of Escherichia coli maltodextrin glucosidase was studied by differential scanning calorimetry, circular dichroism (230 nm), and UV-absorption measurements (340 nm), which were respectively used to monitor heat absorption, conformational unfolding, and the production of solution turbidity. The denaturation was irreversible, and the thermal transition recorded at scan rates of 0.5–1.5 K/min was significantly scan-rate dependent, indicating that the thermal denaturation was ...

  9. Circular dichroism spectra of langasite family crystals in the range of electronic transitions of structure defects

    International Nuclear Information System (INIS)

    The absorption and circular dichroism spectra of langasite family crystals are studied. Wide bands in the range of 285-500 nm that are related to the structure lattice defects are found. For all the crystals, these bands are in approximately the same spectral region, have identical structures, and can be attributed to one type of defects formed by cation vacancies and excess oxygen atoms in the optically active positions.

  10. Levels of Supramolecular Chirality of Polyglutamine Aggregates Revealed by Vibrational Circular Dichroism

    OpenAIRE

    Kurouski, Dmitry; Kar, Karunakar; Wetzel, Ronald; Dukor, Rina K; Lednev, Igor K.; Nafie, Laurence A.

    2013-01-01

    Polyglutamine (PolyQ) aggregates are a hallmark of several severe neurodegenerative diseases, expanded CAG-repeat diseases in which inheritance of an expanded polyQ sequence above a pathological threshold is associated with a high risk of disease. Application of vibrational circular dichroism (VCD) reveals that these PolyQ fibril aggregates exhibit a chiral supramolecular organization that is distinct from the supramolecular organization of previously observed amyloid fibrils. PolyQ fibrils g...

  11. Elucidating the backbone conformation of photoswitchable foldamers using vibrational circular dichroism

    OpenAIRE

    Domingos, S.R.; Roeters, S.J.; Amirjalayer, S.; Yu, Z.L.; Hecht, S; Woutersen, S.

    2013-01-01

    The backbone conformation of amphiphilic oligo(azobenzene) foldamers is investigated using vibrational circular dichroism (VCD) spectroscopy on a mode involving the stretching of the N=N bonds in the backbone. From denaturation experiments, we find that the VCD response in the helical conformation arises mainly from through-space interaction between the N=N-stretch transition-dipole moments, so that the coupled-oscillator model can be used to predict the VCD spectrum associated with a particu...

  12. Vibrational circular dichroism of 1,1'-binaphthyl derivatives: experimental and theoretical study

    Czech Academy of Sciences Publication Activity Database

    Setnička, V.; Urbanová, M.; Bouř, Petr; Král, V.; Volka, K.

    2001-01-01

    Roč. 105, - (2001), s. 8931-8938. ISSN 1089-5639 R&D Projects: GA ČR GA203/97/P002; GA ČR GA203/01/0031; GA AV ČR IAA4055104 Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism Subject RIV: CE - Biochemistry Impact factor: 2.630, year: 2001

  13. Circular Dichroism Enhancement in Large DNA Aggregates Simulated by a generalized oscillator model

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, Valery; Bouř, Petr

    2008-01-01

    Roč. 29, č. 16 (2008), s. 2693-2703. ISSN 0192-8651 R&D Projects: GA ČR GA203/06/0420; GA ČR GA202/07/0732; GA AV ČR IAA400550702 Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA * circular dichroism * oscillator model Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.390, year: 2008

  14. A critical assessment of possible pitfalls in absolute configuration assignment using Vibrational Circular Dichroism

    OpenAIRE

    Debie, Elke

    2009-01-01

    Vibrational Circular Dichroism (VCD) is no longuer a curious novelty in the field of molecular spectroscopy as VCD spectrometers are commercially available as well as the algorithms to calculate the spectra, which are implemented in various software packages. This makes VCD routinely applicable for the determination of absolute configurations. The VCD technique is gaining interest in mainly pharmaceutical industry and the technique also has been accepted by regulatory agencies (e.g. FDA) as a...

  15. Magnetic moments in a gadolinium iron garnet studied by soft-X-ray magnetic circular dichroism

    NARCIS (Netherlands)

    Rudolf, P.; Sette, F.; Tjeng, L.H.; Meigs, G.; Chen, C.T.

    1992-01-01

    The magnetic moments of Gd and Fe in gadolinium iron garnet (Gd3Fe5O12) were probed at 77 and 300 K by soft-X-ray magnetic circular dichroism (SXMCD) measurements at the GdMa4,5 and at the FeL2,3 absorption edges. The SXMCD signal at each edge allows one to independently determine the magnetic order

  16. Optical and structural properties of plasma-treated Cordyceps bassiana spores as studied by circular dichroism, absorption, and fluorescence spectroscopy

    Science.gov (United States)

    Lee, Geon Joon; Sim, Geon Bo; Choi, Eun Ha; Kwon, Young-Wan; Kim, Jun Young; Jang, Siun; Kim, Seong Hwan

    2015-01-01

    To understand the killing mechanism of fungal spores by plasma treatment, the optical, structural, and biological properties of the insect pathogenic fungus Cordyceps bassiana spores were studied. A nonthermal atmospheric-pressure plasma jet (APPJ) was used to treat the spores in aqueous solution. Optical emission spectra of the APPJ acquired in air indicated emission peaks corresponding to hydroxyl radicals and atomic oxygen. When the APPJ entered the aqueous solution, additional reactive species were derived from the interaction of plasma radicals with the aqueous solution. Fluorescence and absorption spectroscopy confirmed the generation of hydroxyl radicals and hydrogen peroxide in the plasma-activated water (PAW). Spore counting showed that plasma treatment significantly reduced spore viability. Absorption spectroscopy, circular dichroism (CD) spectroscopy, and agarose gel electrophoresis of the DNA extracted from plasma-treated spores showed a reduction in spore DNA content. The magnitude of the dip in the CD spectrum was lower in the plasma-treated spores than in the control, indicating that plasma treatment causes structural modifications and/or damage to cellular components. Tryptophan fluorescence intensity was lower in the plasma-treated spores than in the control, suggesting that plasma treatment modified cell wall proteins. Changes in spore viability and DNA content were attributed to structural modification of the cell wall by reactive species coming from the APPJ and the PAW. Our results provided evidence that the plasma radicals and the derived reactive species play critical roles in fungal spore inactivation.

  17. Optical and structural properties of plasma-treated Cordyceps bassiana spores as studied by circular dichroism, absorption, and fluorescence spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Geon Joon, E-mail: gjlee@kw.ac.kr; Sim, Geon Bo; Choi, Eun Ha [Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul 139-701 (Korea, Republic of); Kwon, Young-Wan [KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 136-701 (Korea, Republic of); Kim, Jun Young; Jang, Siun; Kim, Seong Hwan, E-mail: piceae@naver.com [Department of Microbiology and Institute of Basic Sciences, Dankook University, Cheonan 330-714 (Korea, Republic of)

    2015-01-14

    To understand the killing mechanism of fungal spores by plasma treatment, the optical, structural, and biological properties of the insect pathogenic fungus Cordyceps bassiana spores were studied. A nonthermal atmospheric-pressure plasma jet (APPJ) was used to treat the spores in aqueous solution. Optical emission spectra of the APPJ acquired in air indicated emission peaks corresponding to hydroxyl radicals and atomic oxygen. When the APPJ entered the aqueous solution, additional reactive species were derived from the interaction of plasma radicals with the aqueous solution. Fluorescence and absorption spectroscopy confirmed the generation of hydroxyl radicals and hydrogen peroxide in the plasma-activated water (PAW). Spore counting showed that plasma treatment significantly reduced spore viability. Absorption spectroscopy, circular dichroism (CD) spectroscopy, and agarose gel electrophoresis of the DNA extracted from plasma-treated spores showed a reduction in spore DNA content. The magnitude of the dip in the CD spectrum was lower in the plasma-treated spores than in the control, indicating that plasma treatment causes structural modifications and/or damage to cellular components. Tryptophan fluorescence intensity was lower in the plasma-treated spores than in the control, suggesting that plasma treatment modified cell wall proteins. Changes in spore viability and DNA content were attributed to structural modification of the cell wall by reactive species coming from the APPJ and the PAW. Our results provided evidence that the plasma radicals and the derived reactive species play critical roles in fungal spore inactivation.

  18. Synchrotron Radiation Linear Dichroism (SRLD) and Time Dependent Density Functional Theory (TD-DFT) Calculations on Dihydroxy-Anthraquinones

    DEFF Research Database (Denmark)

    Nguyen, Duy Duc; Spanget-Larsen, Jens

    SRLD spectra of Quinizarin, Anthrarufin, and Chrysazin partially aligned in stretched polyethylene were measured at the ASTRID synchrotron UV1 beamline (ISA, Aarhus University), yielding absorbance and polarization data up to 57000 cm-1. The observed absorption bands were assigned to electronic t...... transitions predicted by TD-DFT calculations...

  19. Synchrotron Radiation Linear Dichroism (SRLD) and Time Dependent Density Functional Theory (TD-DFT) Calculations on Dihydroxy-Anthraquinones

    DEFF Research Database (Denmark)

    Nguyen, Duy Duc; Spanget-Larsen, Jens

    SRLD spectra of Quinizarin, Anthrarufin, and Chrysazin partially aligned in stretched polyethylene were measured at the ASTRID synchrotron UV1 beamline (ISA, Aarhus University), yielding absorbance and polarization data up to 57000 cm-1. The observed absorption bands were assigned to electronic t...

  20. Magnetic dichroism in angle-resolved hard x-ray photoemission from buried layers

    Science.gov (United States)

    Kozina, Xeniya; Fecher, Gerhard H.; Stryganyuk, Gregory; Ouardi, Siham; Balke, Benjamin; Felser, Claudia; Schönhense, Gerd; Ikenaga, Eiji; Sugiyama, Takeharu; Kawamura, Naomi; Suzuki, Motohiro; Taira, Tomoyuki; Uemura, Tetsuya; Yamamoto, Masafumi; Sukegawa, Hiroaki; Wang, Wenhong; Inomata, Koichiro; Kobayashi, Keisuke

    2011-08-01

    This work reports the measurement of magnetic dichroism in angular-resolved photoemission from in-plane magnetized buried thin films. The high bulk sensitivity of hard x-ray photoelectron spectroscopy (HAXPES) in combination with circularly polarized radiation enables the investigation of the magnetic properties of buried layers. HAXPES experiments with an excitation energy of 8 keV were performed on exchange-biased magnetic layers covered by thin oxide films. Two types of structures were investigated with the IrMn exchange-biasing layer either above or below the ferromagnetic layer: one with a CoFe layer on top and another with a Co2FeAl layer buried beneath the IrMn layer. A pronounced magnetic dichroism is found in the Co and Fe 2p states of both materials. The localization of the magnetic moments at the Fe site conditioning the peculiar characteristics of the Co2FeAl Heusler compound, predicted to be a half-metallic ferromagnet, is revealed from the magnetic dichroism detected in the Fe 2p states.

  1. Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures.

    Science.gov (United States)

    Gattuso, Hugo; Spinello, Angelo; Terenzi, Alessio; Assfeld, Xavier; Barone, Giampaolo; Monari, Antonio

    2016-03-31

    We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromolecular induced circular dichroism. The coupling of spectroscopy and molecular simulation allows an efficient one-to-one mapping between structures and optical properties, offering a way to disentangle the rich, yet complicated, quantity of information embedded in circular dichroism spectra. We show that our methodology is robust and efficient and allows us to take into account subtle conformational changes. As such, it could be used as an efficient tool to investigate structural modification upon DNA/drug interactions. PMID:26943487

  2. Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy - An Enhanced Method for Examining Protein Conformations and Protein Interactions

    Energy Technology Data Exchange (ETDEWEB)

    B Wallace; R Janes

    2011-12-31

    CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins, the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein-protein complex formation involving either induced-fit or rigid-body mechanisms, and protein-lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.

  3. Electronic structure and x-ray magnetic circular dichroism in YbAgCu4 and YbInCu4

    Energy Technology Data Exchange (ETDEWEB)

    Antonov, VN; Bekenov, LV; Antropov, VP

    2014-04-08

    X-ray absorption and magnetic circular dichroism spectra at the L-3 edge of Yb have been studied theoretically in the mixed-valent compounds YbAgCu4 and YbInCu4 using the fully relativistic Dirac linear muffin-tin orbital band structure method. The effect of the spin-orbit (SO) interaction and Coulomb repulsion U on the electronic structure of YbAgCu4 and YbInCu4 is examined in the frame of the local spin-density approximation (LSDA)+SO+U method. The core-hole effect in the final states as well as the effect of the electric quadrupole E-2 and magnetic dipole M-1 transitions have been investigated. The calculated results are compared with available experimental data.

  4. Electronic structure, magnetic ordering and X-ray magnetic circular dichroism in La1-xPrxCo2P2 phosphides

    Directory of Open Access Journals (Sweden)

    L.V. Bekenov

    2015-09-01

    Full Text Available The electronic structure and magnetic ordering in La1-xPrxCo2P2 (x=0, 0.25, and 1 phosphides have been studied theoretically using the fully relativistic spin-polarized Dirac linear muffin-tin orbital (LMTO band-structure method. The X-ray absorption and X-ray magnetic circular dichroism spectra at the Co L2,3 and Pr M4,5 edges have been investigated theoretically within the framework of the LSDA+U method. The core-hole effect in the final state as well as the effects of the electric quadrupole E2 and magnetic dipole M1 transitions have been investigated. Good agreement with experimental measurements has been found.

  5. Electronic structure and x-ray magnetic circular dichroism in YbAgCu4 and YbInCu4

    Energy Technology Data Exchange (ETDEWEB)

    Antonov, V N; Bekenov, L V; Antropov, V P

    2014-04-01

    X-ray absorption and magnetic circular dichroism spectra at the L3 edge of Yb have been studied theoretically in the mixed-valent compounds YbAgCu4 and YbInCu4 using the fully relativistic Dirac linear muffin-tin orbital band structure method. The effect of the spin-orbit (SO) interaction and Coulomb repulsion U on the electronic structure of YbAgCu4 and YbInCu4 is examined in the frame of the local spin-density approximation (LSDA)+SO+U method. The core-hole effect in the final states as well as the effect of the electric quadrupole E2 and magnetic dipole M1 transitions have been investigated. The calculated results are compared with available experimental data.

  6. Theoretical computations of vibrational circular dichroism (VCD) and IR spectra of oligonucleotides and comparison with experimental results

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, V.; Wieser, H.; Bouř, Petr

    Toronto, 2002. s. 77. [International Symposium on Bioorganic Chemistry /6./. 11.08.2002-14.08.2002, Toronto] Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism Subject RIV: CE - Biochemistry

  7. Comparison of Behaviour in Different Liquids and in Cells of Gold Nanorods and Spherical Nanoparticles Modified by Linear Polyethyleneimine and Bovine Serum Albumin

    Directory of Open Access Journals (Sweden)

    Inna A. Pyshnaya

    2014-01-01

    Full Text Available Gold nanorods (GNRs are considered one of the most promising forms of nanoparticles for nanobiotechnology; however, the problem of their toxicity is currently not resolved. We synthesised GNRs, modified with linear polyethyleneimine (PEI-GNRs, and examined their physicochemical and some biological properties in comparison with GNRs modified with BSA and spherical gold nanoparticles (sGNPs modified with the same agents. The influence of the buffer, cell culture media, and serum on hydrodynamic diameter and zeta potential of all GNPs was studied. Simultaneously, the size, shape, and formation of a corona were examined by transmission electron microscopy (TEM. PEI-GNRs and GNPs were nontoxic for BHK-21 and HeLa cells (MTT test. Penetration of all GNPs into BHK-21, melanoma B16, and HeLa cells was examined after 30 min, 3 h, and 24 h of incubation using TEM ultrathin sections. PEI-GNRs and PEI-sGNPs demonstrated fast and active penetration into cells by caveolin-dependent and lipid raft-mediated endocytosis and accumulated in endosomes and lysosomes. BSA-modified GNPs showed prolonged flotation and a significant delay in cell penetration. The results show that the charge of initial NPs determines penetration into cells. Thus, the designed PEI-GNRs were nontoxic and stable in cell culture media and could efficiently penetrate cells.

  8. Linear algebra

    CERN Document Server

    Edwards, Harold M

    1995-01-01

    In his new undergraduate textbook, Harold M Edwards proposes a radically new and thoroughly algorithmic approach to linear algebra Originally inspired by the constructive philosophy of mathematics championed in the 19th century by Leopold Kronecker, the approach is well suited to students in the computer-dominated late 20th century Each proof is an algorithm described in English that can be translated into the computer language the class is using and put to work solving problems and generating new examples, making the study of linear algebra a truly interactive experience Designed for a one-semester course, this text adopts an algorithmic approach to linear algebra giving the student many examples to work through and copious exercises to test their skills and extend their knowledge of the subject Students at all levels will find much interactive instruction in this text while teachers will find stimulating examples and methods of approach to the subject

  9. Linear algebra

    CERN Document Server

    Allenby, Reg

    1995-01-01

    As the basis of equations (and therefore problem-solving), linear algebra is the most widely taught sub-division of pure mathematics. Dr Allenby has used his experience of teaching linear algebra to write a lively book on the subject that includes historical information about the founders of the subject as well as giving a basic introduction to the mathematics undergraduate. The whole text has been written in a connected way with ideas introduced as they occur naturally. As with the other books in the series, there are many worked examples.Solutions to the exercises are available onlin

  10. The linear structure of β-glucan from baker's yeast and its activation of macrophage-like RAW264.7 cells.

    Science.gov (United States)

    Zheng, Xing; Zou, Siwei; Xu, Hui; Liu, Qingye; Song, Jianhui; Xu, Min; Xu, Xiaojuan; Zhang, Lina

    2016-09-01

    Yeast β-glucan has many formulations with different chemical structures, water solubility and purity. In particular, the purity of β-glucan in these formulations is variable and relatively low, contributing to different data on its biological activity. In this study, the major polysaccharide component in the crude Baker's yeast polysaccharides coded as BBG with high purity of 99% was obtained, and its chemical structure was determined to be a linear β-(1,3)-glucan. It was found that BBG interacted with complement receptor 3 (CR3) and toll-like receptor 2 (TLR2) on the surface of macrophage-like RAW264.7 cells, and initiated activation of RAW264.7 cells characterized by significant production of tumor necrosis factor-α (TNF-α) and monocyte chemoattractant protein 1 (MCP-1). Additionally, activation of the nuclear factor kappaB p65 (NF-κB p65), c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) induced by BBG, were also observed, further confirming the stimulation of RAW264.7 cells by BBG. All these findings provided important scientific evidences for better understanding the molecular mechanism of action for the linear β-(1,3)-glucan in cells. PMID:27185116

  11. Star-shaped and linear π-conjugated oligomers consisting of a tetrathienoanthracene core and multiple diketopyrrolopyrrole arms for organic solar cells

    Science.gov (United States)

    Adachi, Chihaya

    2016-01-01

    Summary Solution-processable star-shaped and linear π-conjugated oligomers consisting of an electron-donating tetrathienoanthracene (TTA) core and electron-accepting diketopyrrolopyrrole (DPP) arms, namely, TTA-DPP4 and TTA-DPP2, were designed and synthesized. Based on density functional theory calculations, the star-shaped TTA-DPP4 has a larger oscillator strength than the linear TTA-DPP2, and consequently, better photoabsorption property over a wide range of visible wavelengths. The photovoltaic properties of organic solar cells based on TTA-DPP4 and TTA-DPP2 with a fullerene derivative were evaluated by varying the thickness of the bulk heterojunction active layer. As a result of the enhanced visible absorption properties of the star-shaped π-conjugated structure, better photovoltaic performances were obtained with relatively thin active layers (40–60 nm).

  12. In silico Identification and Validation of a Linear and Naturally Immunogenic B-Cell Epitope of the Plasmodium vivax Malaria Vaccine Candidate Merozoite Surface Protein-9.

    Science.gov (United States)

    Rodrigues-da-Silva, Rodrigo Nunes; Martins da Silva, João Hermínio; Singh, Balwan; Jiang, Jianlin; Meyer, Esmeralda V S; Santos, Fátima; Banic, Dalma Maria; Moreno, Alberto; Galinski, Mary R; Oliveira-Ferreira, Joseli; Lima-Junior, Josué da Costa

    2016-01-01

    Synthetic peptide vaccines provide the advantages of safety, stability and low cost. The success of this approach is highly dependent on efficient epitope identification and synthetic strategies for efficacious delivery. In malaria, the Merozoite Surface Protein-9 of Plasmodium vivax (PvMSP9) has been considered a vaccine candidate based on the evidence that specific antibodies were able to inhibit merozoite invasion and recombinant proteins were highly immunogenic in mice and humans. However the identities of linear B-cell epitopes within PvMSP9 as targets of functional antibodies remain undefined. We used several publicly-available algorithms for in silico analyses and prediction of relevant B cell epitopes within PMSP9. We show that the tandem repeat sequence EAAPENAEPVHENA (PvMSP9E795-A808) present at the C-terminal region is a promising target for antibodies, given its high combined score to be a linear epitope and located in a putative intrinsically unstructured region of the native protein. To confirm the predictive value of the computational approach, plasma samples from 545 naturally exposed individuals were screened for IgG reactivity against the recombinant PvMSP9-RIRII729-972 and a synthetic peptide representing the predicted B cell epitope PvMSP9E795-A808. 316 individuals (58%) were responders to the full repetitive region PvMSP9-RIRII, of which 177 (56%) also presented total IgG reactivity against the synthetic peptide, confirming it validity as a B cell epitope. The reactivity indexes of anti-PvMSP9-RIRII and anti-PvMSP9E795-A808 antibodies were correlated. Interestingly, a potential role in the acquisition of protective immunity was associated with the linear epitope, since the IgG1 subclass against PvMSP9E795-A808 was the prevalent subclass and this directly correlated with time elapsed since the last malaria episode; however this was not observed in the antibody responses against the full PvMSP9-RIRII. In conclusion, our findings identified and

  13. Linear programming

    CERN Document Server

    Karloff, Howard

    1991-01-01

    To this reviewer’s knowledge, this is the first book accessible to the upper division undergraduate or beginning graduate student that surveys linear programming from the Simplex Method…via the Ellipsoid algorithm to Karmarkar’s algorithm. Moreover, its point of view is algorithmic and thus it provides both a history and a case history of work in complexity theory. The presentation is admirable; Karloff's style is informal (even humorous at times) without sacrificing anything necessary for understanding. Diagrams (including horizontal brackets that group terms) aid in providing clarity. The end-of-chapter notes are helpful...Recommended highly for acquisition, since it is not only a textbook, but can also be used for independent reading and study. —Choice Reviews The reader will be well served by reading the monograph from cover to cover. The author succeeds in providing a concise, readable, understandable introduction to modern linear programming. —Mathematics of Computing This is a textbook intend...

  14. Evidence for linear response for the induction of mutations in human cells by x-ray exposures below 10 rads.

    OpenAIRE

    Grosovsky, A J; Little, J B

    1985-01-01

    The induction of 6-thioguanine resistance (6TGR) was studied in continuous human lymphoblast cultures exposed to daily x-ray doses of 1, 2.5, 5, or 10 rads (1 rad = 0.01 gray) for periods up to 1 month. Samples were taken every 5 days for determinations of induced mutation frequency. Cells receiving daily doses of 1-10 rads showed a mutation frequency of 0.069 X 10(-6) 6TGR cell per rad, virtually identical to the value of 0.062 X 10(-6) 6TGR cell per rad determined for lymphoblasts receiving...

  15. Analyses of sub cell balance methods with linear discontinuous expansion for three dimensional discrete ordinates transport equation

    International Nuclear Information System (INIS)

    In this paper, two types of analyzes of two sub-cell balance methods (LDEM-SCB) which were implemented in the MUST (Multi-group Unstructured geometry SN Transport) code are performed for understanding of their computational characteristics. The first one is a numerical analysis to understand the convergence of the spatial differencing of the sub-cell methods which are devised to solve three-dimensional discrete ordinates transport equation with tetrahedral meshes. The second one is the well-known asymptotic analysis in the thick diffusion limit to know if the sub-cell methods have the corresponding discretization schemes of diffusion equation in this limit

  16. Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets.

    Science.gov (United States)

    Schwarz-Schilling, M; Aufinger, L; Mückl, A; Simmel, F C

    2016-04-18

    Position-dependent gene expression in gradients of morphogens is one of the key processes involved in cellular differentiation during development. Here, we study a simple artificial differentiation process, which is based on the diffusion of genetic inducers within one-dimensional arrangements of 50 μm large water-in-oil droplets. The droplets are filled with either bacteria or cell-free gene expression systems, both equipped with genetic constructs that produce inducers or respond to them via expression of a fluorescent protein. We quantitatively study the coupled diffusion-gene expression process and demonstrate that gene expression can be made position-dependent both within bacteria-containing and cell-free droplets. By generating diffusing quorum sensing signals in situ, we also establish communication between artificial cell-free sender cells and bacterial receivers, and vice versa. PMID:26778746

  17. Study on interactions between nanoparticles and DNA by synchrotron radiation circular dichroism (SRCD)

    International Nuclear Information System (INIS)

    Fullerenic derivatives have attracted considerable attention, in particular, in the field of biomedical applications. Due to the unique structure, fullerenes exhibit intriguing biological activities. In solution, fullerenic derivatives exist as nanoparticles because of the molecular interactions. But how nanoparticles act with the biological molecules, this is an important issue that direct influences any of the biomedical applications in practice. Here we investigate how nanoparticles induce the conformational transition of the protein and DNA by the synchrotron radiation circular dichroism (SRCD). Circular dichroism (CD) is now widely used to study biological systems. Its spectral studies in the far UV region (180 nm - 250 nm) can probe the secondary structures of proteins, and in the near UV region(∼250 and ∼350) can monitor the side chain tertiary structures of proteins. Using circular dichroism spectraphotometer of Beijing Synchrotron Radiation Facility (BEPC), as well as some proteins' secondary structures, we successfully obtained the information of the changes in the secondary structures of DNA after interactions with Gd doped C82(OH)x nanoparticles. The results revealed that manufactured Gd doped C82(OH)x nanoparticles induced conformational changes in proteins and DNA at a very low concentration. Furthermore, the nanoparticle-induced structural changes depend on the percentage of the secondary structures (a-helical, β-strand, β-turn, and unordered) of DNA. These observations provide us with important information that how Gd doped C82(OH)x nanoparticles act on the biological system at the molecular level, and are helpful for understanding biomedical functions as well as the nanosafety issue of these nanoparticles.

  18. X-ray magnetic circular dichroism in (Ge,Mn) compounds: Experiments and modeling

    International Nuclear Information System (INIS)

    X-ray absorption (XAS) and x-ray magnetic circular dichroism (XMCD) spectra at the L2,3 edges of Mn in (Ge,Mn) compounds have been measured and are compared to the results of first principles calculation. Early ab initio studies show that the Density Functional Theory (DFT) can very well describe the valence band electronic properties but fails to reproduce a characteristic change of sign in the L3 XMCD spectrum of Mn in Ge3Mn5, which is observed in experiments. In this work we demonstrate that this disagreement is partially related to an underestimation of the exchange splitting of Mn 2p core states within the local density approximation. It is shown that the change in sign experimentally observed is reproduced if the exchange splitting is accurately calculated within the Hartree–Fock approximation, while the final states can be still described by the DFT. This approach is further used to calculate the XMCD in different (Ge,Mn) compounds. It demonstrates that the agreement between experimental and theoretical spectra can be improved by combining state of the art calculations for the core and valence states respectively. - Highlights: • X-ray absorption and magnetic circular dichroism spectra are measured and compared to first principles calculations in (Ge,Mn) compounds. • Standard density functional theory fails in properly describing peculiar features observed in the experiment. • A new approach to calculate theoretical X-ray absorption and magnetic circular dichroism spectra is proposed. • Improved modeling of the core levels splitting using the Hartree–Fock approximation allows for a better matching with the experiment. • This new method could be generalized to any 3d metallic-like system

  19. Non-linearity of dose-effect relationship at low level exposure on the example of cytogenetic effects in plant cells

    International Nuclear Information System (INIS)

    Complete text of publication follows. There has been an increasing concern in the current scientific society and among the public about the need to protect the environment in order to maintain the ecosystem sustainability and future well-being of man. The linear non-threshold (LNT) hypothesis as the most officially acknowledged concept of biological effect of radiation fails to explain many facts on effects at low level exposures (LLE) accumulated lately. Available information on the dose-effect relationship at low doses is scarce and incomplete for non-human species despite the fact that, under conditions of increased radiation exposure, some biota species occur at a risk of higher impact than humans because of differences in ecological niches occupied. Dose-effect relationships for cytogenetic damage in the range of LLE are studied in a series os experiments with plant (Hordeum vulgare L.) meristem cells. Dose-effect dependences obtained show an obvious non-linear behavior in the LLE region. A piecewise linear model (PLM) for dose-cytogenetic effect relationship that considers an existence of dose-independent part at LLE ('plateau') is developed and specified on the data obtained. An advantage of the PLM over linear model in approximating the frequency of cytogenetic disturbances is demonstrated. From an empirical probability distribution analysis, it is shown that the increase in cytogenetic damage level is tightly connected with changes in a process of absorbed energy distribution between target volumes in terms of fraction of cells experienced a radiation hit event. An appropriateness of the LNT hypothesis to the description of cytogenetic disturbances yield in plant meristem cells in the LLE region is discussed. The results support a conclusion about indirect mechanism of mutagenesis induced by low doses. New data obtained concern a perception of fundamental mechanisms governing cell response to LLE. These findings are of general biological interest, since

  20. Identification of two linear B-cell epitopes from West Nile virus NS1 by screening a phage-displayed random peptide library

    Directory of Open Access Journals (Sweden)

    Qin Yong-Li

    2011-07-01

    Full Text Available Abstract Background The West Nile virus (WNV nonstructural protein 1 (NS1 is an important antigenic protein that elicits protective antibody responses in animals and can be used for the serological diagnosis of WNV infection. Although previous work has demonstrated the vital role of WNV NS1-specific antibody responses, the specific epitopes in the NS1 have not been identified. Results The present study describes the identification of two linear B-cell epitopes in WNV NS1 through screening a phage-displayed random 12-mer peptide library with two monoclonal antibodies (mAbs 3C7 and 4D1 that directed against the NS1. The mAbs 3C7 and 4D1 recognized phages displaying peptides with the consensus motifs LTATTEK and VVDGPETKEC, respectively. Exact sequences of both motifs were found in the NS1 (895LTATTEK901 and 925VVDGPETKEC934. Further identification of the displayed B cell epitopes were conducted using a set of truncated peptides expressed as MBP fusion proteins. The data indicated that 896TATTEK901 and925VVDGPETKEC934 are minimal determinants of the linear B cell epitopes recognized by the mAbs 3C7 and 4D1, respectively. Antibodies present in the serum of WNV-positive horses recognized the minimal linear epitopes in Western blot analysis, indicating that the two peptides are antigenic in horses during infection. Furthermore, we found that the epitope recognized by 3C7 is conserved only among WNV strains, whereas the epitope recognized by 4D1 is a common motif shared among WNV and other members of Japanese encephalitis virus (JEV serocomplex. Conclusions We identified TATTEK and VVDGPETKEC as NS1-specific linear B-cell epitopes recognized by the mAbs 3C7 and 4D1, respectively. The knowledge and reagents generated in this study may have potential applications in differential diagnosis and the development of epitope-based marker vaccines against WNV and other viruses of JEV serocomplex.

  1. Hexamminecobalt(III)-induced condensation of calf thymus DNA: circular dichroism and hydration measurements

    OpenAIRE

    Kankia, Besik I.; Buckin, Vitaly; Bloomfield, Victor A

    2001-01-01

    The interaction of hexamminecobalt(III), Co(NH3)63+, with 160 and 3000–8000 bp length calf thymus DNA has been investigated by circular dichroism, acoustic and densimetric techniques. The acoustic titration curves of 160 bp DNA revealed three stages of interaction: (i) Co(NH3)63+ binding up to the molar ratio [Co(NH3)63+]/[P] = 0.25, prior to DNA condensation; (ii) a condensation process between [Co(NH3)63+]/[P] = 0.25 and 0.30; and (iii) precipitation after [Co(NH...

  2. Magnetic circular X-ray dichroism in amorphous Fe-RE alloys

    International Nuclear Information System (INIS)

    Magnetic circular X-ray dichroism and X-ray absorption near-edge structures were measured at the rare-earth (RE) L3,2 edges in amorphous Fe-RE alloys (RE=Pr, Sm, Gd, Tb and Dy). The Gd 5d spin and orbital moments in the amorphous 80 at% Fe-Gd alloy are evaluated to be about 0.39μB and -0.02μB per atom at room temperature using the sum rules. ((orig.))

  3. High-Flux Beamline for Ultraviolet and Vacuum-Ultraviolet Circular Dichroism at NSRL

    International Nuclear Information System (INIS)

    This paper describes the commissioning and characterization of an NSRL bending magnet beamline constructed for the measurement of vacuum-ultraviolet circular dichroism on biological and other materials. The beamline provides high fluxes of ultraviolet and vacuum-ultraviolet radiation, which is converted into plane polarized light using a polarizer and subsequently converted into circularly polarized light using a photoelastic modulator with a switching frequency of 50 kHz. The beamline has the best wavelength resolution of 0.3 nm and stray light levels better than 0.03%. Example spectra of (1s)-(+)-10-camphorsulphonic acid (CSA) and myoglobin are given

  4. Computation of magnetic circular dichroism by sum-over-states summations

    Czech Academy of Sciences Publication Activity Database

    Štěpánek, Petr; Bouř, Petr

    2013-01-01

    Roč. 34, č. 18 (2013), s. 1531-1539. ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033; GA ČR GA13-03978S Grant ostatní: AV ČR(CZ) M200551205 Institutional support: RVO:61388963 Keywords : time-dependent * density functional theory * sum over states * spectroscopy * magnetic circular dichroism * origin dependence Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.601, year: 2013

  5. Imaging photoelectron circular dichroism of chiral molecules by femtosecond multiphoton coincidence detection

    Energy Technology Data Exchange (ETDEWEB)

    Lehmann, C. Stefan; Ram, N. Bhargava; Janssen, Maurice H. M., E-mail: m.h.m.janssen@vu.nl [LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam (Netherlands); Powis, Ivan [School of Chemistry, University of Nottingham, Nottingham NG7 2RD (United Kingdom)

    2013-12-21

    Here, we provide a detailed account of novel experiments employing electron-ion coincidence imaging to discriminate chiral molecules. The full three-dimensional angular scattering distribution of electrons is measured after photoexcitation with either left or right circular polarized light. The experiment is performed using a simplified photoelectron-photoion coincidence imaging setup employing only a single particle imaging detector. Results are reported applying this technique to enantiomers of the chiral molecule camphor after three-photon ionization by circularly polarized femtosecond laser pulses at 400 nm and 380 nm. The electron-ion coincidence imaging provides the photoelectron spectrum of mass-selected ions that are observed in the time-of-flight mass spectra. The coincident photoelectron spectra of the parent camphor ion and the various fragment ions are the same, so it can be concluded that fragmentation of camphor happens after ionization. We discuss the forward-backward asymmetry in the photoelectron angular distribution which is expressed in Legendre polynomials with moments up to order six. Furthermore, we present a method, similar to one-photon electron circular dichroism, to quantify the strength of the chiral electron asymmetry in a single parameter. The circular dichroism in the photoelectron angular distribution of camphor is measured to be 8% at 400 nm. The electron circular dichroism using femtosecond multiphoton excitation is of opposite sign and about 60% larger than the electron dichroism observed before in near-threshold one-photon ionization with synchrotron excitation. We interpret our multiphoton ionization as being resonant at the two-photon level with the 3s and 3p Rydberg states of camphor. Theoretical calculations are presented that model the photoelectron angular distribution from a prealigned camphor molecule using density functional theory and continuum multiple scattering X alpha photoelectron scattering calculations

  6. Beta sheets with a twist: the conformation of helical polyisocyanopeptides determined by using vibrational circular dichroism.

    Science.gov (United States)

    Schwartz, Erik; Liégeois, Vincent; Koepf, Matthieu; Bodis, Pavol; Cornelissen, Jeroen J L M; Brocorens, Patrick; Beljonne, David; Nolte, Roeland J M; Rowan, Alan E; Woutersen, Sander; Champagne, Benoît

    2013-09-23

    Detailed information on the architecture of polyisocyanopeptides based on vibrational circular dichroism (VCD) spectroscopy in combination with DFT calculations is presented. It is demonstrated that the screw sense of the helical polyisocyanides can be determined directly from the C=N-stretch vibrational region of the VCD spectrum. Analysis of the VCD signals associated with the amide I and amide II modes provides detailed information on the peptide side-chain arrangement in the polymer and indicates the presence of a helical β-sheet architecture, in which the dihedral angles are slightly different to those of natural β-sheet helices. PMID:23939984

  7. Energetics, structures, vibrational frequencies, vibrational absorption, vibrational circular dichroism and Raman intensities of Leu-enkephalin

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.

    2003-01-01

    Here we present several low energy conformers of Leu-enkephalin (LeuE) calculated with the density functional theory using the Becke 3LYP hybrid functional and the 6-31G* basis set. The structures, conformational energies, vibrational frequencies, vibrational absorption (VA) intensities......, vibrational circular dichroism (VCD) intensities and Raman scattering intensities are reported for the conformers of LeuE which are expected to be populated at room temperature. The species of LeuE-present in non-polar solvents is the neutral non-ionic species with the NH2 and CO2H groups, in contrast to the...

  8. Elliptical dichroism as an optical mechanism of planar chirality in 2D metamaterials

    CERN Document Server

    Zhukovsky, S V; Galynsky, V M

    2009-01-01

    We employ a homogenization technique based on the Lorentz electronic theory to show that planar chiral structures (PCSs) can be described by an effective dielectric tensor similar to that of biaxial elliptically dichroic crystals. Such a crystal is shown to behave like a PCS insofar as it exhibits its characteristic optical properties (co-rotating elliptical polarization eigenstates and asymmetric transmission for left/right-handed incident wave polarization). Elliptical dichroism is thus proposed as a general optical mechanism behind planar chirality in a PCS of any geometry.

  9. The connection between robustness angles and dissymmetry factors in vibrational circular dichroism spectra

    Science.gov (United States)

    Longhi, Giovanna; Tommasini, Matteo; Abbate, Sergio; Polavarapu, Prasad L.

    2015-10-01

    To analyze vibrational circular dichroism (VCD) spectra the angle between the electric and magnetic dipole transition moments was introduced as robustness index. We demonstrate that VCD for each normal mode can be made robust by a suitable translation of the coordinate system origin to a robust point. Normal modes differ in how VCD band robustness varies under translations from these respective robust points. It is shown that variation in robustness of a VCD band depends on a parameter inversely proportional to the dissymmetry factor g. Thus, robustness varies slowly for VCD bands with large dissymmetry factors and vice versa.

  10. Assignment of absolute stereostructures through quantum mechanics electronic and vibrational circular dichroism calculations.

    Science.gov (United States)

    Dai, Peng; Jiang, Nan; Tan, Ren-Xiang

    2016-01-01

    Elucidation of absolute configuration of chiral molecules including structurally complex natural products remains a challenging problem in organic chemistry. A reliable method for assigning the absolute stereostructure is to combine the experimental circular dichroism (CD) techniques such as electronic and vibrational CD (ECD and VCD), with quantum mechanics (QM) ECD and VCD calculations. The traditional QM methods as well as their continuing developments make them more applicable with accuracy. Taking some chiral natural products with diverse conformations as examples, this review describes the basic concepts and new developments of QM approaches for ECD and VCD calculations in solution and solid states. PMID:26880597

  11. Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products.

    Science.gov (United States)

    Burgueño-Tapia, Eleuterio; Joseph-Nathan, Pedro

    2015-10-01

    Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013-2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented. PMID:26669125

  12. Linear systems

    CERN Document Server

    Bourlès, Henri

    2013-01-01

    Linear systems have all the necessary elements (modeling, identification, analysis and control), from an educational point of view, to help us understand the discipline of automation and apply it efficiently. This book is progressive and organized in such a way that different levels of readership are possible. It is addressed both to beginners and those with a good understanding of automation wishing to enhance their knowledge on the subject. The theory is rigorously developed and illustrated by numerous examples which can be reproduced with the help of appropriate computation software. 60 exe

  13. Reduction of Linear Programming to Linear Approximation

    OpenAIRE

    Vaserstein, Leonid N.

    2006-01-01

    It is well known that every Chebyshev linear approximation problem can be reduced to a linear program. In this paper we show that conversely every linear program can be reduced to a Chebyshev linear approximation problem.

  14. Effects of hyperthermia on the linear and quadratic parameters of the radiation survival curve of mammalian cells: influence of thermotolerance

    International Nuclear Information System (INIS)

    The authors conclude that their results show that thermotolerance modifies the effects of heat, both its direct cytotoxicity and radiosensitization in the same way. At an equal level of cell lethality for non-tolerant and thermotolerant cells, thermal enchancement of radiation effects is the same, both with regard to TER (Dsub(o)) (Haveman et al. 1987), TER (β) and presumably TER (α). With regard to clinical implications, when hyperthermia is to be combined with interstitial low dose-rate irradiation, a substantial enhancement of the effectiveness of irradiation may be expected. (author)

  15. Circular Dichroism is Sensitive to Monovalent Cation Binding in Monensin Complexes.

    Science.gov (United States)

    Nedzhib, Ahmed; Kessler, Jiří; Bouř, Petr; Gyurcsik, Béla; Pantcheva, Ivayla

    2016-05-01

    Monensin is a natural antibiotic that exhibits high affinity to certain metal ions. In order to explore its potential in coordination chemistry, circular dichroism (CD) spectra of monensic acid A (MonH) and its derivatives containing monovalent cations (Li(+) , Na(+) , K(+) , Rb(+) , Ag(+) , and Et4 N(+) ) in methanolic solutions were measured and compared to computational models. Whereas the conventional CD spectroscopy allowed recording of the transitions down to 192 nm, synchrotron radiation circular dichroism (SRCD) revealed other bands in the 178-192 nm wavelength range. CD signs and intensities significantly varied in the studied compounds, in spite of their similar crystal structure. Computational modeling based on the Density Functional Theory (DFT) and continuum solvent model suggests that the solid state monensin structure is largely conserved in the solutions as well. Time-dependent Density Functional Theory (TDDFT) simulations did not allow band-to-band comparison with experimental spectra due to their limited precision, but indicated that the spectral changes were caused by a combination of minor conformational changes upon the monovalent cation binding and a direct involvement of the metal electrons in monensin electronic transitions. Both the experiment and simulations thus show that the CD spectra of monensin complexes are very sensitive to the captured ions and can be used for their discrimination. Chirality 28:420-428, 2016. © 2016 Wiley Periodicals, Inc. PMID:27062535

  16. A molecular dynamics and circular dichroism study of a novel synthetic antimicrobial peptide

    Science.gov (United States)

    Rodina, N. P.; Yudenko, A. N.; Terterov, I. N.; Eliseev, I. E.

    2013-08-01

    Antimicrobial peptides are a class of small, usually positively charged amphiphilic peptides that are used by the innate immune system to combat bacterial infection in multicellular eukaryotes. Antimicrobial peptides are known for their broad-spectrum antimicrobial activity and thus can be used as a basis for a development of new antibiotics against multidrug-resistant bacteria. The most challengeous task on the way to a therapeutic use of antimicrobial peptides is a rational design of new peptides with enhanced activity and reduced toxicity. Here we report a molecular dynamics and circular dichroism study of a novel synthetic antimicrobial peptide D51. This peptide was earlier designed by Loose et al. using a linguistic model of natural antimicrobial peptides. Molecular dynamics simulation of the peptide folding in explicit solvent shows fast formation of two antiparallel beta strands connected by a beta-turn that is confirmed by circular dichroism measurements. Obtained from simulation amphipatic conformation of the peptide is analysed and possible mechanism of it's interaction with bacterial membranes together with ways to enhance it's antibacterial activity are suggested.

  17. A molecular dynamics and circular dichroism study of a novel synthetic antimicrobial peptide

    International Nuclear Information System (INIS)

    Antimicrobial peptides are a class of small, usually positively charged amphiphilic peptides that are used by the innate immune system to combat bacterial infection in multicellular eukaryotes. Antimicrobial peptides are known for their broad-spectrum antimicrobial activity and thus can be used as a basis for a development of new antibiotics against multidrug-resistant bacteria. The most challengeous task on the way to a therapeutic use of antimicrobial peptides is a rational design of new peptides with enhanced activity and reduced toxicity. Here we report a molecular dynamics and circular dichroism study of a novel synthetic antimicrobial peptide D51. This peptide was earlier designed by Loose et al. using a linguistic model of natural antimicrobial peptides. Molecular dynamics simulation of the peptide folding in explicit solvent shows fast formation of two antiparallel beta strands connected by a beta-turn that is confirmed by circular dichroism measurements. Obtained from simulation amphipatic conformation of the peptide is analysed and possible mechanism of it's interaction with bacterial membranes together with ways to enhance it's antibacterial activity are suggested

  18. A Reference Database for Circular Dichroism Spectroscopy Covering Fold and Secondary Structure Space

    International Nuclear Information System (INIS)

    Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology

  19. Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    Science.gov (United States)

    Jose, K V Jovan; Beckett, Daniel; Raghavachari, Krishnan

    2015-09-01

    We present the first implementation of the vibrational circular dichroism (VCD) spectrum of large molecules through the Molecules-in-Molecules (MIM) fragment-based method. An efficient projection of the relevant higher energy derivatives from smaller fragments to the parent molecule enables the extension of the MIM method for the evaluation of VCD spectra (MIM-VCD). The overlapping primary subsystems in this work are constructed from interacting fragments using a number-based scheme and the dangling bonds are saturated with link hydrogen atoms. Independent fragment calculations are performed to evaluate the energies, Hessian matrix, atomic polar tensor (APT), and the atomic axial tensor (AAT). Subsequently, the link atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, as in the ONIOM approach. In the two-layer model, the long-range interactions between fragments are accounted for using a less computationally intensive lower level of theory. The performance of the MIM model is calibrated on the d- and l-enantiomers of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and VCD intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-VCD method is employed to predict the VCD spectra of perhydrotriphenylene and cryptophane-A, yielding spectra in agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-VCD model for exploring vibrational circular dichroism spectra of large molecules. PMID:26575919

  20. A Solid Phase Vibrational Circular Dichroism Study of Polypeptide-Surfactant Interaction.

    Science.gov (United States)

    Novotná, Pavlína; Urbanová, Marie

    2015-12-01

    We studied the interaction of poly-l-lysine (PLL) and poly-l-arginine (PLAG) with sodium dodecyl sulfate (SDS) surfactant and the interaction of poly-l-glutamic acid (PLGA) and poly-l-aspartic acid (PLAA) with tetradecyltrimethylammonium bromide (TTAB) surfactant using vibrational circular dichroism (VCD) spectroscopy in the region of C-H stretching vibration and in the Amide I region both in solution and in mulls. A chirality transfer from polypeptides to achiral surfactants was observed in the C-H stretching region, where measurements in solution were impossible. This observation was enabled by a special sample treatment technique using lyophilization and the preparation of mulls. This technique demonstrated itself as an interesting and beneficial tool for VCD measurements. In addition, we observed that SDS changed the secondary structure of PLL to the β-sheet and of PLAG to the α-helix. TTAB disrupted the PLGA and PLAA structure. These results were obtained in the mull but were confirmed by the VCD spectra measured in solution and by electronic circular dichroism. The chirality transfer from the polypeptides to SDS was caused by polypeptides ordered into a specific conformation during the interaction, while in the TTBA system it was induced primarily by the chirality of the amino acid residues. PMID:26413930

  1. Vibrational circular dichroism and chiroptical properties of chiral Ir(iii) luminescent complexes.

    Science.gov (United States)

    Mazzeo, Giuseppe; Fusè, Marco; Longhi, Giovanna; Rimoldi, Isabella; Cesarotti, Edoardo; Crispini, Alessandra; Abbate, Sergio

    2016-01-21

    The octahedral ionic Ir(iii) complex with a dual stereogenic centre of general formula Δ,Λ-(R,S)-[(ppy)2Ir(Me-Campy)]X, where ppy = 2-phenylpyridine and Me-Campy = 2-methyl-5,6,7,8-tetrahydroquinolin-8-amine, and the complex Λ-(R,S)-[(ppy)2Ir(H-Campy)]X, where ppy = 2-phenylpyridine, H-Campy = 8-amino-5,6,7,8-tetrahydroquinolines and X(-) = Cl(-) as a counterion in both cases, have been characterized by vibrational circular dichroism (VCD), which turns out to be efficacious in diastereomeric discrimination. Moreover, the single crystal X-ray structure of the complex Δ-(R)-[(ppy)2Ir(Me-Campy)]Cl is reported here. Density functional theory (DFT) calculations allow us to conclude that the most important doublet feature in the VCD spectra is associated with a clear vibrational exciton structure located on the two dissymmetrically disposed phenylpyridine ligands. The features in the VCD spectra associated with the (R) or (S)-central chirality configuration are identified and commented on. DFT calculations provide also the interpretation of electronic circular dichroism (ECD) spectra. Finally, circularly polarized luminescence (CPL) spectra are presented as an additional chiroptical characterization of these luminescent iridium complexes. PMID:26647994

  2. Radiobiologic Parameters and Local Effect Model Predictions for Head-and-Neck Squamous Cell Carcinomas Exposed to High Linear Energy Transfer Ions

    International Nuclear Information System (INIS)

    Purpose: To establish the radiobiologic parameters of head-and-neck squamous cell carcinomas (HNSCC) in response to ion irradiation with various linear energy transfer (LET) values and to evaluate the relevance of the local effect model (LEM) in HNSCC. Methods and Materials: Cell survival curves were established in radiosensitive SCC61 and radioresistant SQ20B cell lines irradiated with [33.6 and 184 keV/n] carbon, [302 keV/n] argon, and X-rays. The results of ion experiments were confronted to LEM predictions. Results: The relative biologic efficiency ranged from 1.5 to 4.2 for SCC61 and 2.1 to 2.8 for SQ20B cells. Fixing an arbitrary D0 parameter, which characterized survival to X-ray at high doses (>10 Gy), gave unsatisfying LEM predictions for both cell lines. For D0 = 10 Gy, the error on survival fraction at 2 Gy amounted to a factor of 10 for [184 keV/n] carbon in SCC61 cells. We showed that the slope (smax) of the survival curve at high doses was much more reliable than D0. Fitting smax to 2.5 Gy-1 gave better predictions for both cell lines. Nevertheless, LEM could not predict the responses to fast and slow ions with the same accuracy. Conclusions: The LEM could predict the main trends of these experimental data with correct orders of magnitude while smax was optimized. Thus the efficiency of carbon ions cannot be simply extracted from the clinical response of a patient to X-rays. LEM should help to optimize planning for hadrontherapy if a set of experimental data is available for high-LET radiations in various types of tumors

  3. The joint statistics of mildly non-linear cosmological densities and slopes in count-in-cells

    OpenAIRE

    Bernardeau, Francis; Codis, Sandrine; Pichon, Christophe

    2015-01-01

    In the context of count-in-cells statistics, the joint probability distribution of the density in two concentric spherical shells is predicted from first first principle for sigmas of the order of one. The agreement with simulation is found to be excellent. This statistics allows us to deduce the conditional one dimensional probability distribution function of the slope within under dense (resp. overdense) regions, or of the density for positive or negative slopes. The former conditional dist...

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

    Science.gov (United States)

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

    2015-06-01

    This communication describes the general characteristics of the venom from the Brazilian scorpion Tityus fasciolatus, which is an endemic species found in the central Brazil (States of Goiás and Minas Gerais), being responsible for sting accidents in this area. The soluble venom obtained from this scorpion is toxic to mice being the LD50 is 2.984 mg/kg (subcutaneally). SDS-PAGE of the soluble venom resulted in 10 fractions ranged in size from 6 to 10-80 kDa. Sheep were employed for anti-T. fasciolatus venom serum production. Western blotting analysis showed that most of these venom proteins are immunogenic. T. fasciolatus anti-venom revealed consistent cross-reactivity with venom antigens from Tityus serrulatus. Using known primers for T. serrulatus toxins, we have identified three toxins sequences from T. fasciolatus venom. Linear epitopes of these toxins were localized and fifty-five overlapping pentadecapeptides covering complete amino acid sequence of the three toxins were synthesized in cellulose membrane (spot-synthesis technique). The epitopes were located on the 3D structures and some important residues for structure/function were identified. PMID:25817000

  5. Distinct roles of Ape1 protein, an enzyme involved in DNA repair, in high or low linear energy transfer ionizing radiation-induced cell killing.

    Science.gov (United States)

    Wang, Hongyan; Wang, Xiang; Chen, Guangnan; Zhang, Xiangming; Tang, Xiaobing; Park, Dongkyoo; Cucinotta, Francis A; Yu, David S; Deng, Xingming; Dynan, William S; Doetsch, Paul W; Wang, Ya

    2014-10-31

    High linear energy transfer (LET) radiation from space heavy charged particles or a heavier ion radiotherapy machine kills more cells than low LET radiation, mainly because high LET radiation-induced DNA damage is more difficult to repair. Relative biological effectiveness (RBE) is the ratio of the effects generated by high LET radiation to low LET radiation. Previously, our group and others demonstrated that the cell-killing RBE is involved in the interference of high LET radiation with non-homologous end joining but not homologous recombination repair. This effect is attributable, in part, to the small DNA fragments (≤40 bp) directly produced by high LET radiation, the size of which prevents Ku protein from efficiently binding to the two ends of one fragment at the same time, thereby reducing non-homologous end joining efficiency. Here we demonstrate that Ape1, an enzyme required for processing apurinic/apyrimidinic (known as abasic) sites, is also involved in the generation of small DNA fragments during the repair of high LET radiation-induced base damage, which contributes to the higher RBE of high LET radiation-induced cell killing. This discovery opens a new direction to develop approaches for either protecting astronauts from exposure to space radiation or benefiting cancer patients by sensitizing tumor cells to high LET radiotherapy. PMID:25210033

  6. The role of lymphocytes, granulocytes, mast cells and their related cytokines in lesional skin of linear IgA bullous dermatosis.

    Science.gov (United States)

    Caproni, M; Rolfo, S; Bernacchi, E; Bianchi, B; Brazzini, B; Fabbri, P

    1999-06-01

    Linear IgA bullous dermatosis (LAD) is an acquired, heterogeneous, subepidermal blistering disease characterized by linear IgA deposits at the dermoepidermal basement membrane zone (BMZ), often with circulating IgA antibodies to the BMZ. The pathogenetic mechanism, possibly related to the immunophenotype of infiltrating cells, as well as the potential role of cytokines in determining bullous lesions, have not yet been elucidated. An immunohistochemical study was performed with a large panel of monoclonal antibodies [to CD3, CD4, CD8, CD25, CD1a, CD30, CD54, CD50, endothelial leucocyte adhesion molecule-1, vascular cell adhesion molecule-1, myeloperoxidase (MPO), eosinophil cationic protein EG1 and EG2, tryptase, HLA-DR, human interleukin (IL)-3, human IL-5, human IL-8, human IL-4, tumour necrosis factor (TNF)-alpha, interferon (IFN)-gamma and granulocyte/macrophage colony-stimulating factor] using the alkaline phosphatase-antialkaline phosphatase procedure on lesional and perilesional skin of nine patients (one male, eight female; age range 8 months-80 years) with clinical, histological and immunofluorescent proven LAD. The predominant infiltrating cells, distributed mostly inside and below the bullae, were neutrophils and eosinophils which showed intense activation (MPO +, EG1 +, EG2 +). The lymphocytic infiltrate, consisting principally of CD4 +, HLA-DR + and CD30 + T cells, had a predominantly perivascular distribution. Proinflammatory cytokines, such as TNF-alpha and IFN-gamma, showed a moderate focal expression on the dermal perivascular sites; IL-8 was found to have a particularly intense staining on all the epidermal cell layers and at perivascular and vascular sites. Other cytokines, such as IL-4 and IL-5, showed a prevalent intracytoplasmic staining on some cells of the dermal infiltrate (probably mastocytes and lymphocytes), and at the dermal-epidermal separation sites there was also an intense scattered distribution of IL-5. The specific tissue lesions

  7. Enantioselective semi-preparative HPLC separation of PCB metabolites and their absolute structures determined by electronic and vibrational circular dichroism

    Energy Technology Data Exchange (ETDEWEB)

    Tuan, H.P.; Larsson, C.; Huehnerfuss, H. [Hamburg Univ. (Germany). Inst. fuer Organische Chemie; Hoffmann, F.; Froeba, M. [Giessen Univ. (Germany). Inst. fuer Anorganische und Analytische Chemie; Bergmann, Aa. [Stockholm Univ. (Sweden). Dept. of Environmental Chemistry

    2004-09-15

    The present paper represents a first result of an ongoing systematic study of atropisomeric methylsulfonyl, methylthionyl, hydroxy, and methoxy metabolites of environmentally most relevant PCBs. This involves semi-preparative enantioselective HPLC separation to obtain pure atropisomers from synthesized PCB metabolite standards, their configuration estimation using the electronic circular dichroism (UV-CD) method and the determination / confirmation of these absolute configurations applying the combined vibrational circular dichroism (VCD) / ab initio approach. The following substances have been investigated: 4-HO-, 4-MeO-, 4-MeS-, 4-MeSO2-, 3-MeS- and 3-MeSO{sub 2}-CB149.

  8. Femtosecond X-ray magnetic circular dichroism absorption spectroscopy at an X-ray free electron laser.

    Science.gov (United States)

    Higley, Daniel J; Hirsch, Konstantin; Dakovski, Georgi L; Jal, Emmanuelle; Yuan, Edwin; Liu, Tianmin; Lutman, Alberto A; MacArthur, James P; Arenholz, Elke; Chen, Zhao; Coslovich, Giacomo; Denes, Peter; Granitzka, Patrick W; Hart, Philip; Hoffmann, Matthias C; Joseph, John; Le Guyader, Loïc; Mitra, Ankush; Moeller, Stefan; Ohldag, Hendrik; Seaberg, Matthew; Shafer, Padraic; Stöhr, Joachim; Tsukamoto, Arata; Nuhn, Heinz-Dieter; Reid, Alex H; Dürr, Hermann A; Schlotter, William F

    2016-03-01

    X-ray magnetic circular dichroism spectroscopy using an X-ray free electron laser is demonstrated with spectra over the Fe L(3,2)-edges. The high brightness of the X-ray free electron laser combined with high accuracy detection of incident and transmitted X-rays enables ultrafast X-ray magnetic circular dichroism studies of unprecedented sensitivity. This new capability is applied to a study of all-optical magnetic switching dynamics of Fe and Gd magnetic sublattices in a GdFeCo thin film above its magnetization compensation temperature. PMID:27036761

  9. Thermochromic properties of the ferroelectric ?-doped ?: study of the temperature-induced dichroism

    Science.gov (United States)

    Valiente, Rafael; Rodríguez, Fernando

    1999-03-01

    A new thermochromic material formed by doping 0953-8984/11/12/014/img3 into the ferroelectric 0953-8984/11/12/014/img4 crystal is presented. The change of colour from green (room temperature) to red (low temperature) under polarized light observation is accompanied by a strong temperature-induced dichroism at low temperature. The origin of these phenomena is investigated through the polarized charge transfer spectra associated with 0953-8984/11/12/014/img3 complexes formed in the title compound, and their dependence on temperature in the 10-300 K range. Attention is paid to correlating the optical spectra with the local structure around 0953-8984/11/12/014/img3. The results are compared with those obtained in the tribromide 0953-8984/11/12/014/img7 and 0953-8984/11/12/014/img8, and the tetrabromide 0953-8984/11/12/014/img9 and 0953-8984/11/12/014/img10 crystals, where 0953-8984/11/12/014/img3 forms 0953-8984/11/12/014/img12 complexes of nearly 0953-8984/11/12/014/img13 symmetry, and tetrahedral distorted 0953-8984/11/12/014/img14 complexes of 0953-8984/11/12/014/img15 symmetry, respectively. An interesting feature is the presence of a strongly polarized absorption band at 15 800 0953-8984/11/12/014/img16 in 0953-8984/11/12/014/img17, which is responsible for the observed dichroism and thermochromism. The existence of this band is associated with the formation of highly distorted 0953-8984/11/12/014/img14 complexes in the monoclinic 0953-8984/11/12/014/img19 host crystal. The enhancement of dichroism exhibited by this crystal with decreasing temperature is noteworthy. The analysis of the spectra reveals that this unusual thermal behaviour can be explained in terms of thermally activated reorientations rather than structural changes of the 0953-8984/11/12/014/img3 complex.

  10. Estimation of protein secondary structure from synchrotron radiation circular dichroism (SRCD) spectroscopy with five methods

    International Nuclear Information System (INIS)

    To study the nanosafety issues, we integrate several different techniques including nuclear techniques such as nuclear analytical method, synchrotron radiation analyses, biological techniques, and nanotechniques, etc., applying to explore interactions of nanoparticles on the protein and DNA. Circular dichroism (CD) is a measure of the difference in absorption of left- and right- polarized light as it passes through an optically active or chiral sample. Optical activity arises due to the influence of neighbouring groups on the electronic structure of a chromophore involved in an electronic transition. Electronic transitions span a large wavelength range, including the near UV (from 300 to 250 nm), the far UV (from 250 to 190 nm) and the VUV (from 190 to 178 nm). CD has found its principal application in studies of protein secondary structures (α-helical, β-strand, β-turn, and Unordered) because the shape of a CD spectrum is related to the geometry of the polypeptide backbone. The data in the region around 190 nm are potentially very valuable as they can provide information on sheet and aperiodic structures, and helix effects dominate the higher-wavelength data. Generally, conventional CD (CCD) instruments can detect transitions in the 300-200 nm, but the signals in the VUV region go beyond the CCD research. Using the synchrotron radiation circular dichroisrn (SRCD) with a vacuum environment instrument, the data in the VUV region can be obtained. Five methods (CONTINLL, SELCON3, CDSSTR, VARSLC, and K2D) based on deferent arithmetic, models and reference protein. databases are used to analyze the circular dichroism spectra. CONTINLL, SELCON3, CDSSTR, and VARSLC methods are the development of SVD algorithm in different sides; otherwise K2D is one of a few neural network programmes. In order to establish perfect experiment and data-analysis system for circular dichroism spectraphotometer of Beijing Synchrotron Radiation Facility (BEPC), comparison and estimation of

  11. The Casimir Effect in Biology: The Role of Molecular Quantum Electrodynamics in Linear Aggregations of Red Blood Cells

    International Nuclear Information System (INIS)

    Despite the fact that red blood cells carry negative charges, under certain conditions they form cylindrical stacks, or 'rouleaux'. It is shown here that a form of the Casimir effect, generalizing the more well-known van der Waals forces, can provide the necessary attractive force to balance the electrostatic repulsion. Erythrocytes in plasma are modelled as negatively charged dielectric disks in an ionic solution, allowing predictions to be made about the conditions under which rouleaux will form. The results show qualitative agreement with observations which suggest that the basic idea is worth further pursuit. In addition to revealing a mechanism which may be widespread in biology at the cellular level, it also suggest new experiments and further applications to other biological systems, colloid chemistry and nanotechnology.

  12. The Casimir Effect in Biology: The Role of Molecular Quantum Electrodynamics in Linear Aggregations of Red Blood Cells

    Energy Technology Data Exchange (ETDEWEB)

    Bradonjic, K [Physics Department, Boston University, Boston MA (United States); Swain, J D; Widom, A; Srivastava, Y N, E-mail: john.swain@cern.c [Physics Department, Northeastern University, Boston MA (United States)

    2009-04-01

    Despite the fact that red blood cells carry negative charges, under certain conditions they form cylindrical stacks, or 'rouleaux'. It is shown here that a form of the Casimir effect, generalizing the more well-known van der Waals forces, can provide the necessary attractive force to balance the electrostatic repulsion. Erythrocytes in plasma are modelled as negatively charged dielectric disks in an ionic solution, allowing predictions to be made about the conditions under which rouleaux will form. The results show qualitative agreement with observations which suggest that the basic idea is worth further pursuit. In addition to revealing a mechanism which may be widespread in biology at the cellular level, it also suggest new experiments and further applications to other biological systems, colloid chemistry and nanotechnology.

  13. The Casimir Effect in Biology: The Role of Molecular Quantum Electrodynamics in Linear Aggregations of Red Blood Cells

    Science.gov (United States)

    Bradonjić, K.; Swain, J. D.; Widom, A.; Srivastava, Y. N.

    2009-04-01

    Despite the fact that red blood cells carry negative charges, under certain conditions they form cylindrical stacks, or "rouleaux". It is shown here that a form of the Casimir effect, generalizing the more well-known van der Waals forces, can provide the necessary attractive force to balance the electrostatic repulsion. Erythrocytes in plasma are modelled as negatively charged dielectric disks in an ionic solution, allowing predictions to be made about the conditions under which rouleaux will form. The results show qualitative agreement with observations which suggest that the basic idea is worth further pursuit. In addition to revealing a mechanism which may be widespread in biology at the cellular level, it also suggest new experiments and further applications to other biological systems, colloid chemistry and nanotechnology.

  14. Excited States Calculated by Means of the Linear Muffin-Tin Orbital Method

    OpenAIRE

    Alouani, M.; Wills, J M

    1999-01-01

    The most popular electronic structure method, the linear muffin-tin orbital method (LMTO), in its full-potential (FP) and relativistic forms has been extended to calculate the spectroscopic properties of materials form first principles, i.e, optical spectra, x-ray magnetic circular dichroism (XMCD) and magneto-optical kerr effect (MOKE). The paper describes an overview of the FP-LMTO basis set and the calculation of the momentum matrix elements. Some applications concerning the computation of...

  15. Amplification of the linear and nonlinear optical response of a chiral molecular crystal.

    Science.gov (United States)

    Domingos, Sérgio R; Silva, Pedro S Pereira; Buma, Wybren Jan; Garcia, M Helena; Lopes, Nelson C; Paixão, José António; Silva, Manuela Ramos; Woutersen, Sander

    2012-04-01

    We have observed large second-order nonlinear optical and vibrational circular dichroism (VCD) responses in a charge-transfer-type L-Histidinium salt. Using X-ray Diffraction, VCD spectroscopy, and time-dependent density functional theory to characterize the compound, we employ a two-level model to explain and quantify the strongly enhanced optical signals. We find that both linear and nonlinear optical responses are greatly enhanced by a single low-lying charge-transfer state. PMID:22482566

  16. Amplification of the linear and nonlinear optical response of a chiral molecular crystal

    Science.gov (United States)

    Domingos, Sérgio R.; Silva, Pedro S. Pereira; Buma, Wybren Jan; Garcia, M. Helena; Lopes, Nelson C.; Paixão, José António; Silva, Manuela Ramos; Woutersen, Sander

    2012-04-01

    We have observed large second-order nonlinear optical and vibrational circular dichroism (VCD) responses in a charge-transfer-type L-Histidinium salt. Using X-ray Diffraction, VCD spectroscopy, and time-dependent density functional theory to characterize the compound, we employ a two-level model to explain and quantify the strongly enhanced optical signals. We find that both linear and nonlinear optical responses are greatly enhanced by a single low-lying charge-transfer state.

  17. Non-Linearity of dose-effect relationship on the example of cytogenetic effects in plant cells at low level exposure to ionising radiation

    International Nuclear Information System (INIS)

    Over several decades, modelling the effects of ionizing radiation on biological system has relied on the target principle [Timofeeff-Ressovsky et al., 1935], which assumes that cell damage or modification to genes appear as a direct consequence of the exposure of biological macromolecules to charged particles. Furthermore, it is assumed that there is no threshold for the induction of biological damage and that the effects observed are proportional to the energy absorbed. Following this principle, the average number of hits per target should increase linearly with dose, and the yield of mutations per unit of dose is assumed to be the same at both low and high doses (linearity of response). This principle has served as the scientific background for the linear no-threshold (LNT) concept that forms the basis for the radiological protection for the public and the environment [ICRP, 1990]. It follows from the LNT that there is an additional risk for human health from exposure to any radiation level, even below natural background. Since the mid 50's, however, the scientific basis for the LNT concept has been challenged as experimental data have shown that, at low doses, there was a non linear relationship in the dose response. Luchnik and Timofeeff-Ressovsky were the first who showed a non-linear response to a low dose exposure [Luchnik, 1957; Timofeeff-Ressovsky and Luchnik, 1960]. Since then, many data have been accumulated which contradict the LNT model at low doses and dose rates. However, the hit-effect paradigm has become such a strong and indissoluble fact that it has persisted even under the growing pressure of scientific evidence for phenomena at low dose exposure that can not be successfully accounted for by the LNT concept. In recent years, additional information on non-targeted effects of radiation has been accumulated following the first reports of an adaptive response in human lymphocytes [Olivieri et al., 1984] as well as bystander mutagenic effect of alpha

  18. Non-Linearity of dose-effect relationship on the example of cytogenetic effects in plant cells at low level exposure to ionising radiation

    Energy Technology Data Exchange (ETDEWEB)

    Oudalova, Alla; Geras' kin, Stanislav; Dikarev, Vladimir; Dikareva, Nina; Chernonog, Elena [Russian Institute of Agricultural Radiology and Agroecology, RIARAE, 249032 Obninsk (Russian Federation); Copplestone, David [Environment Agency, Millbank Tower, 25th. Floor, 21/24 Millbank, London, SW1P 4XL (United Kingdom); Evseeva, Tatyana [Institute of Biology, Kommunisticheskaya st., 28 Syktyvkar 167610, Komi Republic (Russian Federation)

    2006-07-01

    Over several decades, modelling the effects of ionizing radiation on biological system has relied on the target principle [Timofeeff-Ressovsky et al., 1935], which assumes that cell damage or modification to genes appear as a direct consequence of the exposure of biological macromolecules to charged particles. Furthermore, it is assumed that there is no threshold for the induction of biological damage and that the effects observed are proportional to the energy absorbed. Following this principle, the average number of hits per target should increase linearly with dose, and the yield of mutations per unit of dose is assumed to be the same at both low and high doses (linearity of response). This principle has served as the scientific background for the linear no-threshold (LNT) concept that forms the basis for the radiological protection for the public and the environment [ICRP, 1990]. It follows from the LNT that there is an additional risk for human health from exposure to any radiation level, even below natural background. Since the mid 50's, however, the scientific basis for the LNT concept has been challenged as experimental data have shown that, at low doses, there was a non linear relationship in the dose response. Luchnik and Timofeeff-Ressovsky were the first who showed a non-linear response to a low dose exposure [Luchnik, 1957; Timofeeff-Ressovsky and Luchnik, 1960]. Since then, many data have been accumulated which contradict the LNT model at low doses and dose rates. However, the hit-effect paradigm has become such a strong and indissoluble fact that it has persisted even under the growing pressure of scientific evidence for phenomena at low dose exposure that can not be successfully accounted for by the LNT concept. In recent years, additional information on non-targeted effects of radiation has been accumulated following the first reports of an adaptive response in human lymphocytes [Olivieri et al., 1984] as well as bystander mutagenic effect of

  19. Fano resonance assisting plasmonic circular dichroism from nanorice heterodimers for extrinsic chirality

    CERN Document Server

    Hu, Li; Fang, Liang; Chen, Guo; Wei, Hua; Fang, Yurui

    2015-01-01

    In this work, the circular dichroisms (CD) of nanorice heterodimers consisting of two parallel arranged nanorices with the same size but different materials are investigated theoretically. Symmetry-breaking is introduced by using different materials and oblique incidence to achieve strong CD at the vicinity of Fano resonance peaks. We demonstrate that all Au-Ag heterodimers exhibit multipolar Fano resonances and strong CD effect. A simple quantitative analysis shows that the structure with larger Fano asymmetry factor has stronger CD. The intensity and peak positions of the CD effect can be flexibly tuned in a large range by changing particle size, shape, the inter-particle distance and surroundings. Furthermore, CD spectra exhibit high sensitivity to ambient medium in visible and near infrared regions. Our results here are beneficial for the design and application of high sensitive CD sensors and other related fields.

  20. Magnetocrystalline anisotropy in FePd alloys studied using transverse X-ray magnetic circular dichroism

    International Nuclear Information System (INIS)

    The structural and magnetic properties of Fe0.5Pd0.5 alloys have been correlated using X-ray diffraction (XD), vibrating sample magnetometry (VSM) and transverse X-ray magnetic circular dichroism (TXMCD) at the Pd L2,3 edges. XD indicates that codeposition of Fe and Pd, at elevated temperatures (350 deg. C), results in a well-ordered L10 phase which exhibits perpendicular magnetic anisotropy (PMA). On the other hand, codeposition at room temperature results in a disordered phase with in-plane easy-axis of magnetization. By codepositing at intermediate temperatures, a series of alloys has been produced with varying degree of compositional order. The TXMCD results show that increased compositional ordering leads to an increased orbital moment anisotropy favouring PMA. The magnetocrystalline anisotropy energy resulting from the orbital anisotropy is compared to VSM results

  1. A study of aliphatic amino acids using simulated vibrational circular dichroism and Raman optical activity spectra

    CERN Document Server

    Ganesan, Aravindhan; Wang, Feng

    2013-01-01

    Vibrational optical activity (VOA) spectra, such as vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra, of aliphatic amino acids are simulated using density functional theory (DFT) methods in both gas phase (neutral form) and solution (zwitterionic form), together with their respective infrared (IR) and Raman spectra of the amino acids. The DFT models, which are validated by excellent agreements with the available experimental Raman and ROA spectra of alanine in solution, are employed to study other aliphatic amino acids. The inferred (IR) intensive region (below 2000 cm-1) reveals the signature of alkyl side chains, whereas the Raman intensive region (above 3000 cm-1) contains the information of the functional groups in the amino acids. Furthermore, the chiral carbons of the amino acids (except for glycine) dominate the VCD and ROA spectra in the gas phase, but the methyl group vibrations produce stronger VCD and ROA signals in solution. The C-H related asymmetric vibrations domina...

  2. Determination of the structure of Langmuir-Blodgett monolayers by infrared dichroism

    International Nuclear Information System (INIS)

    We show that the study of absorption and reflexion infrared dichroism is a suitable tool for the determination of the crystallographic structure and of the molecules orientation in Langmuir-Blodgett multilayers. Their thickness range is comprised between 30 and 2000 angstroms. We have worked up a theoretical model which allows a quantitative interpretation of the absorption of thin anisotropic crystals. Two kind of multilayers are studied: one built of a saturated aliphatic acid and the other one with an ethylenic acid. These layers are composed of adjoining crystallites which are oriented on the substrate during the transfer process. The crystallisation propagates in a direction perpendicular to the layers in the case of the saturated acid, while ethylenic acid monolayers are constituted of a superimposition of two-dimensional smectic structures. Using reflexion experiments on metallic substrates we show that the molecules in the very first layers are oriented in a direction perpendicular to the substrate. (author)

  3. Vibrational circular dichroism of tetraphenylporphyrin in peptide complexes? A computational study.

    Science.gov (United States)

    Bour, P; Záruba, K; Urbanová, M; Setnicka, V; Matejka, P; Fiedler, Z; Král, V; Volka, K

    2000-05-01

    The Raman and absorption spectra of tetraphenylporphyrin (TPP) were calculated and compared to experiment. The computation was based on the harmonic molecular force field and electric tensors obtained ab initio at the BPW91/6-31G* level. Good agreement was found between experimental and calculated frequencies and intensities. In order to estimate whether induced optical activity in chiral complexes interferes with the signal of peptide vibrations, the vibrational circular dichroism (VCD) spectra of TPP were simulated. The magnetic field perturbation theory (MFP) and the gauge-invariant atomic orbitals (GIAO) were used for the simulation. Such spectra were compared to theoretical VCD intensities of a model tripeptide as well to experimental spectra of a complex of the peptide and tetrakis(p-sulfonatophenyl)porphyrin (TSPP). No significant contribution to VCD signal from the TPP residue was found in experimental spectra. Thus, possible peptide conformational changes occurring during the complexation can be monitored directly in the amide I frequency region. PMID:10790189

  4. Circular dichroism and Raman spectroscopic study of the spider venom toxin V50F17

    Science.gov (United States)

    Alix, A. J. P.; Berjot, M.; Dauchez, M. A. M.; Dhalluin, C.; Lippens, G.

    1999-05-01

    V50F17 is a small 45 amino acid neurotoxin fractionated (F17) from the venom V50 of the spider Segestria florentina, which has eight cysteine residues constituting four disulfide bridges. Using circular dichroism data and vibrational Raman data at both pH 2.9 and 7.0 and preliminary NMR results obtained at pH 2.9, we derived structural information for this small protein. From these data, it is seen that it is possible to characterise well the local conformation of the disulfide bridges and the overall shape of the globular protein. Moreover, using optical spectroscopic data, it is shown that consequent local and/or global modifications are obtained on changing the pH. Results of the secondary structure states, the local conformations of the disulfide bridges, the exposure of side chains of residues and particularly of Tyr41 are discussed.

  5. Infrared, Raman and ultraviolet with circular dichroism analysis and theoretical calculations of tedizolid

    Science.gov (United States)

    Michalska, Katarzyna; Mizera, Mikołaj; Lewandowska, Kornelia; Cielecka-Piontek, Judyta

    2016-07-01

    Tedizolid is the newest antibacterial agent from the oxazolidinone class. For its identification, FT-IR (2000-400 cm-1) and Raman (2000-400 cm-1) analyses were proposed. Studies of the enantiomeric purity of tedizolid were conducted based on ultraviolet-circular dichroism (UV-CD) analysis. Density functional theory (DFT) with the B3LYP hybrid functional and 6-311G(2df,2pd) basis set was used for support of the analysis of the FT-IR and Raman spectra. Theoretical methods made it possible to conduct HOMO and LUMO analysis, which was used to determine the charge transfer for two tedizolid enantiomers. Molecular electrostatic potential maps were calculated with the DFT method for both tedizolid enantiomers. The relationship between the results of ab initio calculations and knowledge about the chemical-biological properties of R- and S-tedizolid enantiomers is also discussed.

  6. Angular momentum-induced circular dichroism in non-chiral nanostructures

    CERN Document Server

    Zambrana-Puyalto, Xavier; Molina-Terriza, Gabriel

    2014-01-01

    Circular dichroism (CD), i.e. the differential response of a system to left and right circularly polarized light, is one of the only techniques capable of providing morphological information of certain samples. In biology, for instance, CD spectroscopy is widely used to study the structure of proteins. More recently, it has also been used to characterize metamaterials and plasmonic structures. Typically, CD can only be observed in chiral objects. Here, we present experimental results showing that a non-chiral sample such as a sub-wavelength circular nano-aperture can produce giant CD when a vortex beam is used to excite it. These measurements can be understood by studying the symmetries of the sample and the total angular momentum that vortex beams carry. Our results show that CD can provide a wealth of information about the sample when combined with the control of the total angular momentum of the input field.

  7. Nitrogen K-edge soft X-ray natural circular dichroism of histidine thin film

    International Nuclear Information System (INIS)

    We report preliminary natural circular dichroism (NCD) spectra of amino acids, Land D-histidine, thin films in the nitrogen K-edge energy region. NCD peaks were observed at 399.9 eV and were assigned to the 1s → π* transition of the nitrogen atoms in imidazole ring. Imidazole ring is positioned at the side chain distant from the asymmetric carbon. This result suggests that NCD spectroscopy in the soft X-ray region can selectively pick up the information on local structure around specific atoms, regardless of the position of atoms in molecules. It is interesting in view of application of NCD spectroscopy in the soft X-ray region to investigation of protein structures.

  8. 5f-hybridization in URhAl studied by X-ray magnetic circular dichroism

    International Nuclear Information System (INIS)

    We report X-ray magnetic circular dichroism experiments performed at the U-M4,5 edges of an URhAl single crystal. Thanks to the sum-rules, we derive an orbital moment on the uranium atoms equal to (1.63±0.14)μB. The comparison of the shape of the M5 dichroic signal with pure J multiplet calculations shows effects due to 5f-hybridization. However, we found that the contribution of the magnetic dipole term left angle TZ right angle to the effective spin moment left angle SZeff right angle =(SZ right angle +3 left angle TZ right angle) is non negligible. These results indicate an higher localization of the 5f-orbitals with respect to other itinerant ferromagnetic actinides compounds such as UFe2 or UNi2. (orig.)

  9. Photoelectron circular dichroism of bicyclic ketones from multiphoton ionization with femtosecond laser pulses.

    Science.gov (United States)

    Lux, Christian; Wollenhaupt, Matthias; Sarpe, Cristian; Baumert, Thomas

    2015-01-12

    Photoelectron circular dichroism (PECD) is a CD effect up to the ten-percent regime and shows contributions from higher-order Legendre polynomials when multiphoton ionization is compared to single-photon ionization. We give a full account of our experimental methodology for measuring the multiphoton PECD and derive quantitative measures that we apply on camphor, fenchone and norcamphor. Different modulations and amplitudes of the contributing Legendre polynomials are observed despite the similarity in chemical structure. In addition, we study PECD for elliptically polarized light employing tomographic reconstruction methods. Intensity studies reveal dissociative ionization as the origin of the observed PECD effect, whereas ionization of the intermediate resonance is dominating the signal. As a perspective, we suggest to make use of our tomographic data as an experimental basis for a complete photoionization experiment and give a prospect of PECD as an analytic tool. PMID:25492564

  10. Feasibility of non-invasive optical blood-glucose detection using overtone circular dichroism

    CERN Document Server

    Hokr, Brett H; Meng, Zhaokai; Petrov, Georgi I; Yakovlev, Vladislav V

    2016-01-01

    Diabetes is one of the most debilitating and costly diseases currently plaguing humanity. It is a leading cause of death and dismemberment in the world, and we know how to treat it. Accurate, continuous monitoring and control of blood glucose levels via insulin treatments are widely known to mitigate the majority of detrimental effects caused by the disease. The primary limitation of continuous glucose monitoring is patient non-compliance due to the unpleasant nature of "finger-stick" testing methods. This limitation can be largely, or even completely, removed by non-invasive testing methods. In this report, we demonstrate the vibrational overtone circular dichroism properties of glucose and analyze its use as a method of non-invasive glucose monitoring, capable of assuaging this trillion dollar scourge.

  11. Spin polarization and magnetic dichroism in core-level photoemission from ferromagnets

    Energy Technology Data Exchange (ETDEWEB)

    Menchero, J G [Univ. of California, Berkeley, CA (United States). Dept. of Physics

    1997-05-01

    In this thesis we present a theoretical investigation of angle- and spin-resolved core-level photoemission from ferromagnetic Fe and Ni. We also consider magneto-dichroic effects due to reversal of the photon helicity or reversal of the sample magnetization direction. In chapter 1, we provide a brief outline of the history of photoemission, and show how it has played an important role in the development of modern physics. We then review the basic elements of the theory of core-level photoemission, and discuss the validity of the some of the commonly-used approximations. In chapter 2, we present a one-electron theory to calculate spin- and angle-resolved photoemission spectra for an arbitrary photon polarization. The Hamiltonian includes both spin-orbit and exchange interactions. As test cases for the theory, we calculate the spin polarization and magnetic dichroism for the Fe 2p core level, and find that agreement with experiment is very good.

  12. Conformational effects on the circular dichroism of Human Carbonic Anhydrase II: a multilevel computational study.

    Directory of Open Access Journals (Sweden)

    Tatyana G Karabencheva-Christova

    Full Text Available Circular Dichroism (CD spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII, with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.

  13. Elucidating the backbone conformation of photoswitchable foldamers using vibrational circular dichroism.

    Science.gov (United States)

    Domingos, Sérgio R; Roeters, Steven J; Amirjalayer, Saeed; Yu, Zhilin; Hecht, Stefan; Woutersen, Sander

    2013-10-28

    The backbone conformation of amphiphilic oligo(azobenzene) foldamers is investigated using vibrational circular dichroism (VCD) spectroscopy on a mode involving the stretching of the N=N bonds in the backbone. From denaturation experiments, we find that the VCD response in the helical conformation arises mainly from through-space interaction between the N=N-stretch transition-dipole moments, so that the coupled-oscillator model can be used to predict the VCD spectrum associated with a particular conformation. Using this approach, we elucidate the origin of the VCD signals in the folded conformation, and can assign the observed partial loss of VCD signals upon photo-induced unfolding to specific conformational changes. Our results show that the N=N-stretch VCD response provides an excellent probe of the helical conformation of the N=N bonds in this type of switchable molecular system. PMID:24018416

  14. Switchable amplification of vibrational circular dichroism as a probe of local chiral structure.

    Science.gov (United States)

    Domingos, Sérgio R; Sanders, Hans J; Hartl, František; Buma, Wybren J; Woutersen, Sander

    2014-12-15

    A new method to detect the vibrational circular dichroism (VCD) of a localized part of a chiral molecular system is reported. A local VCD amplifier was implemented, and the distance dependence of the amplification was investigated in a series of peptides. The results indicate a characteristic distance of 2.0±0.3 bonds, which suggests that the amplification is a localized phenomenon. The amplifier can be covalently coupled to a specific part of a molecule, and can be switched ON and OFF electrochemically. By subtracting the VCD spectra obtained when the amplifier is in the ON and OFF states, the VCD of the local environment of the amplifier can be separated from the total VCD spectrum. Switchable local VCD amplification thus makes it possible to "zoom in" on a specific part of a chiral molecule. PMID:25212702

  15. Light Flux Density Threshold at Which Protein Denaturation is Induced by Synchrotron Radiation Circula Dichroism Beamlines

    International Nuclear Information System (INIS)

    New high-flux synchrotron radiation circular dichroism (SRCD) beamlines are providing important information for structural biology, but can potentially cause denaturation of the protein samples under investigation. This effect has been studied at the new CD1 dedicated SRCD beamline at ISA in Denmark, where radiation-induced thermal damage effects were observed, depending not only on the radiation flux but also on the focal spot size of the light. Comparisons with similar studies at other SRCD facilities worldwide has lead to the estimation of a flux density threshold under which SRCD beamlines should be operated when samples are to be exposed to low-wavelength vacuum ultraviolet radiation for extended periods of time.

  16. Ultrafast conformational changes in biomolecules studied by time-resolved circular dichroism

    Science.gov (United States)

    Changenet-Barret, P.; Hache, F.

    2015-10-01

    Circular dichroism (CD) is known to be a very sensitive probe of molecular conformation, and it is in particular widely used in biochemistry. Measuring the CD as a function of time is therefore very appealing to access information on the dynamics of conformational changes in molecules or biomolecules. We have implemented such a time-resolved experiments in two complementary configurations: a sub-picosecond pump-probe one and a microsecond detection of CD coupled to a T-jump experiment. We present two experiments based on these techniques: the ultrafast motion of the carbonyl group in the chromophore of the Photoactive Yellow Protein after photoexcitation and the dynamics of thermal denaturation in model peptides.

  17. Dodine as a transparent protein denaturant for circular dichroism and infrared studies.

    Science.gov (United States)

    Guin, Drishti; Sye, Kori; Dave, Kapil; Gruebele, Martin

    2016-05-01

    The fungicide dodine combines the cooperative denaturation properties of guanidine with the mM denaturation activity of SDS. It was previously tested only on two small model proteins. Here we show that it can be used as a chemical denaturant for phosphoglycerate kinase (PGK), a much larger two-domain enzyme. In addition to its properties as a chemical denaturant, dodine facilitates thermal denaturation of PGK, and we show for the first time that it also facilitates pressure denaturation of a protein. Much higher quality circular dichroism and amide I' infrared spectra of PGK can be obtained in dodine than in guanidine, opening the possibility for use of dodine as a denaturant when UV or IR detection is desirable. One caution is that dodine denaturation, like other detergent-based denaturants, is less reversible than guanidine denaturation. PMID:26941080

  18. Orbital Rashba effect and its detection by circular dichroism angle-resolved photoemission spectroscopy

    Science.gov (United States)

    Park, Jin-Hong; Kim, Choong H.; Rhim, Jun-Won; Han, Jung Hoon

    2012-05-01

    We show, by way of tight-binding and first-principles calculations, that a one-to-one correspondence between an electron's crystal momentum k and nonzero orbital angular momentum (OAM) is a generic feature of surface bands. The OAM forms a chiral structure in momentum space much as its spin counterpart in Rashba model does, as a consequence of the inherent inversion symmetry breaking at the surface but not of spin-orbit interaction. This is the orbital counterpart of conventional Rashba effect and may be called the “orbital Rashba effect.” The circular dichroism (CD) angle-resolved photoemission (ARPES) method is an efficient way to detect this new order, and we derive formulas explicitly relating the CD-ARPES signal to the existence of OAM in the band structure. The cases of degenerate p- and d-orbital bands are considered.

  19. Helical Inversion of Gel Fibrils by Elongation of Perfluoroalkyl Chains as Studied by Vibrational Circular Dichroism.

    Science.gov (United States)

    Sato, Hisako; Yajima, Tomoko; Yamagishi, Akihiko

    2016-05-01

    Vibrational circular dichroism (VCD) spectroscopy was applied to gelation by a chiral low-molecular mass weight gelator, N,N'-diperfluoroalkanoyl-1,2-trans-diaminocyclohexane. Attention was focused on the winding effects of (-CF2 )n chains on the gelating ability. For this purpose, a series of gelators were synthesized with perfluoroalkyl chains of different length (n = 6-8). When gelation was studied using acetonitrile as a solvent, the fibrils took different morphologies, depending on the chain length: twisted saddle-like ribbon or helical ribbon from fibril (n = 6) and a helical ribbon from platelet (n = 8). The signs of VCD peaks assigned to the couplet of C=O stretching and to the C-F stretching were also dependent on n, indicating that a gelator molecule changed conformation on elongating perfluoroalkyl chains. A model is proposed for the aggregation modes in fibrils. Chirality 28:361-364, 2016. © 2016 Wiley Periodicals, Inc. PMID:26992437

  20. Chirality transfer from gold nanocluster to adsorbate evidenced by vibrational circular dichroism

    Science.gov (United States)

    Dolamic, Igor; Varnholt, Birte; Bürgi, Thomas

    2015-05-01

    The transfer of chirality from one set of molecules to another is fundamental for applications in chiral technology and has likely played a crucial role for establishing homochirality on earth. Here we show that an intrinsically chiral gold cluster can transfer its handedness to an achiral molecule adsorbed on its surface. Solutions of chiral Au38(2-PET)24 (2-PET=2-phenylethylthiolate) cluster enantiomers show strong vibrational circular dichroism (VCD) signals in vibrations of the achiral adsorbate. Density functional theory (DFT) calculations reveal that 2-PET molecules adopt a chiral conformation. Chirality transfer from the cluster to the achiral adsorbate is responsible for the preference of one of the two mirror images. Intermolecular interactions between the adsorbed molecules on the crowded cluster surface seem to play a dominant role for the phenomena. Such chirality transfer from metals to adsorbates likely plays an important role in heterogeneous enantioselective catalysis.

  1. Enhanced sensitivity to conformation in various proteins. Vibrational circular dichroism results

    International Nuclear Information System (INIS)

    Vibrational circular dichroism (VCD) spectra of several globular proteins dissolved in D2O are presented and compared to conventional UV-CD results. It can be seen that, for the alpha, beta, and alpha + beta categories of Levitt and Chothia, VCD evidences much larger band shape variations, including sign alteration, than does UV-CD. A direct parallel is seen between the VCD of the alpha-helix found in model polypeptides and the amide I' VCD of myoglobin. Since all structural aspects of the protein contribute to the VCD on a roughly equal footing, a similar correlation of the chymotrypsin amide I' VCD with that of beta-sheet models is not as clear. In addition, the VCD of random-coil-type proteins is found to be clearly related to VCD results from random-coil polypeptides. Finally, simulations are presented to postulate the expected VCD for protein structures having conformations that lie between the limiting cases discussed here

  2. Multiple linear B-cell epitopes of classical swine fever virus glycoprotein E2 expressed in E.coli as multiple epitope vaccine induces a protective immune response

    Directory of Open Access Journals (Sweden)

    Wei Jian-Chao

    2011-07-01

    Full Text Available Abstract Classical swine fever is a highly contagious disease of swine caused by classical swine fever virus, an OIE list A pathogen. Epitope-based vaccines is one of the current focuses in the development of new vaccines against classical swine fever virus (CSFV. Two B-cell linear epitopes rE2-ba from the E2 glycoprotein of CSFV, rE2-a (CFRREKPFPHRMDCVTTTVENED, aa844-865 and rE2-b (CKEDYRYAISSTNEIGLLGAGGLT, aa693-716, were constructed and heterologously expressed in Escherichia coli as multiple epitope vaccine. Fifteen 6-week-old specified-pathogen-free (SPF piglets were intramuscularly immunized with epitopes twice at 2-week intervals. All epitope-vaccinated pigs could mount an anamnestic response after booster vaccination with neutralizing antibody titers ranging from 1:16 to 1:256. At this time, the pigs were subjected to challenge infection with a dose of 1 × 106 TCID50 virulent CSFV strain. After challenge infection, all of the rE2-ba-immunized pigs were alive and without symptoms or signs of CSF. In contrast, the control pigs continuously exhibited signs of CSF and had to be euthanized because of severe clinical symptoms at 5 days post challenge infection. The data from in vivo experiments shown that the multiple epitope rE2-ba shown a greater protection (similar to that of HCLV vaccine than that of mono-epitope peptide(rE2-a or rE2-b. Therefore, The results demonstrated that this multiple epitope peptide expressed in a prokaryotic system can be used as a potential DIVA (differentiating infected from vaccinated animals vaccine. The E.coli-expressed E2 multiple B-cell linear epitopes retains correct immunogenicity and is able to induce a protective immune response against CSFV infection.

  3. Recent Theoretical and Experimental Advances in the Electronic Circular Dichroisms of Planar Chiral Cyclophanes

    Science.gov (United States)

    Mori, Tadashi; Inoue, Yoshihisa

    The chiroptical properties, such as electronic and vibrational circular dichroism and optical rotation, of planar chiral cyclophanes have attracted much attention in recent years. Although the chemistry of cyclophanes has been extensively explored for more than 60 years, the studies on chiral cyclophanes are rather limited. Experimentally, the use of chiral stationary phases in HPLC becomes more popular and facilitates the enantiomer separation of chiral cyclophanes of interest. Almost all chiral cyclophanes can be readily separated, in analytical and preparative scales, most typically on a Daicel OD type column, which is based on cellulose tris(3,5-dimethylphenylcarbamate). The CD spectra of chiral cyclophanes are unique in their fairly large, significantly coupled Cotton effects observed in all the 1 B b, 1 L a, and 1 L b band regions. Theoretically, the time-dependent density functional theory, or TD-DFT, method becomes a cost-efficient, yet accurate, theoretical method to reproduce the electronic circular dichroisms and the absorption spectra of a variety of cyclophanes. The direct comparison of the experimental CD spectra with the theoretical ones readily leads to the unambiguous assignment of the absolute configuration of cyclophanes. In addition, the analysis of configuration interaction and molecular orbitals allows detailed interpretation of the electronic transitions and Cotton effects in the UV and CD spectra. Through the study of the CD spectra of chiral cyclophanes as model systems, the effects of intra- and intermolecular interactions on the chiroptical properties of molecules can be explored, and the results thus obtained are valuable in comprehensively elucidating the structure-chiroptical property relationship. In this review the recent progress in experimental and theoretical investigations of the electronic CD spectra of chiral cyclophanes is discussed.

  4. A circular dichroism sensor for Ni{sup 2+} and Co{sup 2+} based on L-cysteine capped cadmium sulfide quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Tedsana, Wimonsiri [Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002 (Thailand); Tuntulani, Thawatchai [Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330 (Thailand); Ngeontae, Wittaya, E-mail: wittayange@kku.ac.th [Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002 (Thailand)

    2015-03-31

    Highlights: • Demonstrated a new efficient sensor platform based quantum dots. • Used chiral quantum dots as CD sensor for the detection of heavy metal ions for the first time. • The proposed CD sensor showed highest selectivity towards Ni{sup 2+} and Co{sup 2+}. • Low detection limits of 7.33 μM and 1.13 μM for Ni{sup 2+} and Co{sup 2+}, respectively. • Can be used in real water samples comparing with ICP-OES. - Abstract: A new circular dichroism sensor for detecting Ni{sup 2+} and Co{sup 2+} was proposed for the first time using chiral chelating quantum dots. The detection principle was based on changing of circular dichroism signals of the chiral quantum dots when forming a chiral complex with Ni{sup 2+} or Co{sup 2+}. L-Cysteine capped cadmium sulfide quantum dots (L-Cyst-CdS QDs) were proposed as a chiral probe. The CD spectrum of L-Cyst-CdS QDs was significantly changed in the presence of Ni{sup 2+} and Co{sup 2+}. On the other hand, other studied cations did not alter the original CD spectrum. Moreover, when increasing the concentration of Ni{sup 2+} or Co{sup 2+}, the intensity of the CD spectrum linearly increased as a function of concentration and could be useful for the quantitative analysis. The proposed CD sensor showed linear working concentration ranges of 10–60 μM and 4–80 μM with low detection limits of 7.33 μM and 1.13 μM for the detection of Ni{sup 2+} and Co{sup 2+}, respectively. Parameters possibly affected the detection sensitivity such as solution pH and incubation time were studied and optimized. The proposed sensor was applied to detect Ni{sup 2+} and Co{sup 2+} in real water samples, and the results agreed well with the analysis using the standard ICP-OES.

  5. 4-Arylflavan-3-ols as Proanthocyanidin Models: Absolute Configuration via Density Functional Calculation of Electronic Circular Dichroism

    Science.gov (United States)

    Density functional theory/B3LYP has been employed to optimize the conformations of selected 4-arylflavan-3-ols and their phenolic methyl ether 3-O-acetates. The electronic circular dichroism spectra of the major conformers have been calculated using time-dependent density functional theory to valida...

  6. Synthesis and vibrational circular dichroism of enantiopure chiral oxorhenium(V) complexes containing the hydrotris(1-pyrazolyl)borate ligand

    DEFF Research Database (Denmark)

    Lassen, Peter Rygaard

    2006-01-01

    The infrared and vibrational circular dichroism (VCD) spectra of six chiral oxorhenium(V) complexes, bearing a hydrotris(1-pyrazolyl)borate (Tp) ligand, have been investigated. These complexes are promising candidates for observation of parity violation (symmetry breaking due to the weak nuclear ...

  7. Theoretical computations of vibrational circular dichroism (VCD) and IR spectra of oligonucleotides and comparison with experimental results

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, V.; Wieser, H.; Bouř, Petr

    Lille : Université des Sciences et Technologies de Lille, 2002. s. 112. [European Congress on Molecular Spectroscopy /26./. 01.09.2002-06.09.2002, Villeneuve d'Ascq] Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism Subject RIV: CF - Physical ; Theoretical Chemistry

  8. (3 R ,4 S )-4-(4-fluorophenyl)-3-hydroxymethyl-1-methylpiperidine: conformation and structure monitoring by vibrational circular dichroism

    Czech Academy of Sciences Publication Activity Database

    Bouř, Petr; Navrátilová, H.; Setnička, V.; Urbanová, M.; Volka, K.

    2002-01-01

    Roč. 67, č. 1 (2002), s. 161-168. ISSN 0022-3263 R&D Projects: GA AV ČR IAA4055104; GA ČR GA203/01/0031 Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.217, year: 2002

  9. Hydrogen bonding to carbonyl oxygen of nitrogen-pyramidalized amide - detection of pyramidalization direction preference by vibrational circular dichroism spectroscopy.

    Science.gov (United States)

    Wang, Siyuan; Taniguchi, Tohru; Monde, Kenji; Kawahata, Masatoshi; Yamaguchi, Kentaro; Otani, Yuko; Ohwada, Tomohiko

    2016-03-01

    Nitrogen-pyramidalization of amide increases electron density on nitrogen and decreases that on carbonyl oxygen. We identified hydrogen-bonding to carbonyl of nitrogen-pyramidalized bicyclic β-proline derivatives by crystallography, and by NMR and vibrational circular dichroism (VCD) spectroscopy in solution. Such hydrogen-bonding can switch the preferred nitrogen-pyramidalization direction, as detected by VCD spectroscopy. PMID:26889607

  10. B-Z conformational transition of DNA monitored by vibrational circular dichroism. Ab initio interpretation of the experiment

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, V.; Wieser, H.; Bouř, Petr

    2002-01-01

    Roč. 106, - (2002), s. 12623-12634. ISSN 1089-5647 R&D Projects: GA ČR GA203/01/0031; GA AV ČR IAA4055104 Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.611, year: 2002

  11. Vibrational circular dichroism spectroscopy as a tool to study DNA structural changes: Experimental and computional approaches (Lecture)

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, Valery; Wieser, H.; Bouř, Petr

    Kharkiv : Institute of Radiophysics and Electronics NASU, 2007, 28/145. [Kharkiv Young Scientist Conference on Radiophysics and Electronics /7./. Kharkiv (UA), 12.12.2007-14.12.2007] Institutional research plan: CEZ:AV0Z40550506 Keywords : vibrational circular dichroism * DNA * RNA Subject RIV: CF - Physical ; Theoretical Chemistry www.ire.kharkov.ua/ysc

  12. TD-DFT Modeling of the Circular Dichroism for a Tryptophan Zipper Peptide with Coupled Aromatic Residues

    Czech Academy of Sciences Publication Activity Database

    Roy, A.; Bouř, Petr; Keiderling, T. A.

    2009-01-01

    Roč. 21, S1 (2009), E163-E171. ISSN 0899-0042 R&D Projects: GA ČR GA202/07/0732; GA AV ČR IAA400550702 Institutional research plan: CEZ:AV0Z40550506 Keywords : tryptophan * circular dichroism * TDDFT Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.677, year: 2009

  13. Effects of fluorination on iridium(III) complex phosphorescence: magnetic circular dichroism and relativistic time-dependent density functional theory.

    Science.gov (United States)

    Smith, A R G; Riley, M J; Burn, P L; Gentle, I R; Lo, S-C; Powell, B J

    2012-03-01

    We use a combination of low temperature, high field magnetic circular dichroism, absorption, and emission spectroscopy with relativistic time-dependent density functional calculations to reveal a subtle interplay between the effects of chemical substitution and spin-orbit coupling (SOC) in a family of iridium(III) complexes. Fluorination at the ortho and para positions of the phenyl group of fac-tris(1-methyl-5-phenyl-3-n-propyl-[1,2,4]triazolyl)iridium(III) cause changes that are independent of whether the other position is fluorinated or protonated. This is demonstrated by a simple linear relationship found for a range of measured and calculated properties of these complexes. Further, we show that the phosphorescent radiative rate, k(r), is determined by the degree to which SOC is able to hybridize T(1) to S(3) and that k(r) is proportional to the inverse fourth power of the energy gap between these excitations. We show that fluorination in the para position leads to a much larger increase of the energy gap than fluorination at the ortho position. Theory is used to trace this back to the fact that fluorination at the para position increases the difference in electron density between the phenyl and triazolyl groups, which distorts the complex further from octahedral symmetry, and increases the energy separation between the highest occupied molecular orbital (HOMO) and the HOMO-1. This provides a new design criterion for phosphorescent iridium(III) complexes for organic optoelectronic applications. In contrast, the nonradiative rate is greatly enhanced by fluorination at the ortho position. This may be connected to a significant redistribution of spectral weight. We also show that the lowest energy excitation, 1A, has almost no oscillator strength; therefore, the second lowest excitation, 2E, is the dominant emissive state at room temperature. Nevertheless the mirror image rule between absorption and emission is obeyed, as 2E is responsible for both absorption and

  14. Fine level epitope mapping and conservation analysis of two novel linear B-cell epitopes of the avian infectious bronchitis coronavirus nucleocapsid protein.

    Science.gov (United States)

    Han, Zongxi; Zhao, Fei; Shao, Yuhao; Liu, Xiaoli; Kong, Xiangang; Song, Yang; Liu, Shengwang

    2013-01-01

    The nucleocapsid (N) protein of the infectious bronchitis virus (IBV) may play an essential role in the replication and translation of viral RNA. The N protein can also induce high titers of cross-reactive antibodies and cell-mediated immunity, which protects chickens from acute infection. In this study, we generated two monoclonal antibodies (mAbs), designated as 6D10 and 4F10, which were directed against the N protein of IBV using the whole viral particles as immunogens. Both of the mAbs do not cross react with Newcastle disease virus (NDV), infectious laryngotracheitis virus (ILTV) and subtype H9 avian influenza virus (AIV). After screening a phage display peptide library and peptide scanning, we identified two linear B-cell epitopes that were recognized by the mAbs 6D10 and 4F10, which corresponded to the amino acid sequences (242)FGPRTK(247) and (195)DLIARAAKI(203), respectively, in the IBV N protein. Alignments of amino acid sequences from a large number of IBV isolates indicated that the two epitopes, especially (242)FGPRTK(247), were well conserved among IBV strains. This conclusion was further confirmed by the relationships of 18 heterologous sequences to the 2 mAbs. The novel mAbs and the epitopes identified will be useful for developing diagnostic assays for IBV infections. PMID:23123213

  15. Regulation of ATM in DNA double strand break repair accounts for the radiosensitivity in human cells exposed to high linear energy transfer ionizing radiation

    Energy Technology Data Exchange (ETDEWEB)

    Xue Lian, E-mail: xuelian@suda.edu.cn [School of Radiation Medicine and Public Health, Medical College of Soochow University, No. 199, Ren' ai Road, Suzhou 215123 (China); Yu Dong, E-mail: ydong@ncc.go.jp [Tumor Endocrinology Project, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Furusawa, Yoshiya; Okayasu, Ryuichi [Heavy-Ion Radiobiology Research Group, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba-shi 263-8555 (Japan); Tong Jian; Cao Jianping; Fan Saijun [School of Radiation Medicine and Public Health, Medical College of Soochow University, No. 199, Ren' ai Road, Suzhou 215123 (China)

    2009-11-02

    High linear energy transfer (LET) radiation shows different biological effects from low-LET radiation. The complex nature of high LET radiation-induced damage, especially the clustered DNA damage, brings about slow repair of DNA double strand breaks (DSBs), which finally lead to higher lethality and chromosome aberration. Ionizing radiation (IR) induced DNA DSBs are repaired by both non-homologous end-joining (NHEJ) and homologous recombination repair (HRR) pathways in mammalian cells. The novel function of ataxia telangiectasia-mutated (ATM) protein is its involvement in the DSB repair of slow kinetics for 'dirty' breaks rejoining by NHEJ, this suggests that ATM may play a more important role in high LET radiation-induced DNA damage. We show here that KU55933, an ATM inhibitor could distinctly lower the clonogenic survival in normal human skin fibroblast cells exposed to carbon ion radiation and dramatically impair the normal process for DSB repair. We also implicated the involvement of ATM in the two pathways of DNA DSB repair, with DNA-PKcs and Rad51 as the representative proteins. The phosphorylation of DNA-PKcs at Thr-2609 with both immunoblotting and immunofluorescent staining indicated an ATM-dependent change, while for Rad51, KU55933 pretreatment could postpone the formation of nuclear Rad51 foci. Interestingly, we also found that pretreatment with chloroquine, an ATM stimulator could protect cells from carbon ion radiation only at lower doses. For doses over 1 Gy, protection was no longer observed. There was a dose-dependent increase for ATM kinase activity, with saturation at about 1 Gy. Chloroquine pretreatment prior to 1 Gy of carbon ion radiation did not enhance the autophosphorylation of ATM at serine 1981. The function of ATM in G2/M checkpoint arrest facilitated DSB repair in high-LET irradiation. Our results provide a possible mechanism for the direct involvement of ATM in DSB repair by high-LET irradiation.

  16. Linear Algebra and Smarandache Linear Algebra

    OpenAIRE

    Vasantha, Kandasamy

    2003-01-01

    The present book, on Smarandache linear algebra, not only studies the Smarandache analogues of linear algebra and its applications, it also aims to bridge the need for new research topics pertaining to linear algebra, purely in the algebraic sense. We have introduced Smarandache semilinear algebra, Smarandache bilinear algebra and Smarandache anti-linear algebra and their fuzzy equivalents. Moreover, in this book, we have brought out the study of linear algebra and ve...

  17. Mulliken population analysis of X-ray magnetic circular dichroism in uranium monochalcogenides. Examination of sum rules by fully relativistic full-potential LCAO method

    International Nuclear Information System (INIS)

    We study the X-ray magnetic circular dichroism (XMCD) spectra at the U M4,5 and N4,5 edges of uranium monochalcogenides, UX where X=S, Se, and Te, examining the applicability of the XMCD sum rules to UX by the fully relativistic full-potential linear-combination-of-atomic-orbitals (LCAO) method based on the density functional theory. To extract the transitions relevant to the sum-rule analysis, we employ the Mulliken population analysis (MPA). Using the MPA, the orbital sum rule is found to be valid to 10-20% for the M4,5 edges and valid to 5-15% for the N4,5 edges. On the other hand, the spin sum rule is found to be valid to 10-20% for the M4,5 edges whereas valid to 30-35% for the N4,5 edges. Furthermore, it is found that the calculated XMCD spectra are consistent with a recent experimental observation that the intensity of the N4,5 XMCD signal is comparable to that of the M4,5 XMCD signal although contradicting a previous theoretical prediction that the XMCD intensity at the N4,5 edges is one order of magnitude smaller than that at the M4,5 edges. (author)

  18. Energetics, structures, vibrational frequencies, vibrational absorption, vibrational circular dichroism and Raman intensities of Leu-enkephalin

    International Nuclear Information System (INIS)

    Here we present several low energy conformers of Leu-enkephalin (LeuE) calculated with the density functional theory using the Becke 3LYP hybrid functional and the 6-31G* basis set. The structures, conformational energies, vibrational frequencies, vibrational absorption (VA) intensities, vibrational circular dichroism (VCD) intensities and Raman scattering intensities are reported for the conformers of LeuE which are expected to be populated at room temperature. The species of LeuE present in non-polar solvents is the neutral non-ionic species with the NH2 and CO2H groups, in contrast to the zwitterionic neutral species with the NH3+ and CO2- groups which predominates in aqueous solution and in the crystal. All of our attempts to find the zwitterionic species in the isolated state failed, with the result that a hydrogen atom from the positively charged N-terminus ammonium group transferred either to one of the oxygens of the carboxylate group of the C-terminus or to the oxygen of the amide group of one of the other residues. Hence we conclude that the zwitterionic species of LeuE is not stable in the isolated state. Spectral simulations of the species expected to be found in the isolated state can be compared to the measured VA, VCD and Raman spectra of LeuE in non-polar solvents to identify which conformer or conformers of LeuE are present in these media. Characteristic features in the VCD spectra are more sensitive to conformational changes than those in either the VA or Raman spectra, similar to the characteristic features in electronic circular dichroism spectra with respect to those in the UV-vis electronic absorption spectra. Finally, we have also attempted to stabilize the zwitterionic species by treating the aqueous environment by using a continuum solvent approach, the Onsager model. Here we found that the zwitterionic species is now stable. The neutral species in an aqueous environment was also modelled by the continuum solvent approaches to determine the

  19. Electronic Circular Dichroism of [16]Helicene With Simplified TD-DFT: Beyond the Single Structure Approach.

    Science.gov (United States)

    Bannwarth, Christoph; Seibert, Jakob; Grimme, Stefan

    2016-05-01

    The electronic circular dichroism (ECD) spectrum of the recently synthesized [16]helicene and a derivative comprising two triisopropylsilyloxy protection groups was computed by means of the very efficient simplified time-dependent density functional theory (sTD-DFT) approach. Different from many previous ECD studies of helicenes, nonequilibrium structure effects were accounted for by computing ECD spectra on "snapshots" obtained from a molecular dynamics (MD) simulation including solvent molecules. The trajectories are based on a molecule specific classical potential as obtained from the recently developed quantum chemically derived force field (QMDFF) scheme. The reduced computational cost in the MD simulation due to the use of the QMDFF (compared to ab-initio MD) as well as the sTD-DFT approach make realistic spectral simulations feasible for these compounds that comprise more than 100 atoms. While the ECD spectra of [16]helicene and its derivative computed vertically on the respective gas phase, equilibrium geometries show noticeable differences, these are "washed" out when nonequilibrium structures are taken into account. The computed spectra with two recommended density functionals (ωB97X and BHLYP) and extended basis sets compare very well with the experimental one. In addition we provide an estimate for the missing absolute intensities of the latter. The approach presented here could also be used in future studies to capture nonequilibrium effects, but also to systematically average ECD spectra over different conformations in more flexible molecules. Chirality 28:365-369, 2016. © 2016 Wiley Periodicals, Inc. PMID:27071653

  20. Binding of anti-prion agents to glycosaminoglycans: Evidence from electronic absorption and circular dichroism spectroscopy

    International Nuclear Information System (INIS)

    The polyanionic glycosaminoglycans (GAGs) are intimately involved in the pathogenesis of protein conformational disorders such as amyloidosis and prion diseases. Several cationic agents are known to exhibit anti-prion activity but their mechanism of action is poorly understood. In this study, UV absorption and circular dichroism (CD) spectroscopic techniques were used to investigate the interaction between heparin and chondroitin-6-sulfate and anti-prion drugs including acridine, quinoline, and phenothiazine derivatives. UV band hypochromism of (±)-quinacrine, (±)-primaquine, tacrine, quinidine, chlorpromazine, and induced CD spectra of (±)-quinacrine upon addition of GAGs provided evidence for the GAG binding of these compounds. The association constants (∼106-107 M-1) estimated from the UV titration curves show high-affinity drug-heparin interactions. Ionic strength-dependence of the absorption spectra suggested that the interaction between GAGs and the cationic drugs is principally electrostatic in nature. Drug binding differences of heparin and chondroitin-6-sulfate were attributed to their different negative charge density. These results call the attention to the alteration of GAG-prion/GAG-amyloid interactions by which these compounds might exert their anti-prion/anti-amyloidogenic activities

  1. Band modification in (Ga, Mn)As evidenced by new measurement scheme - photoresistance magnetic circular dichroism

    Science.gov (United States)

    Huang, X. J.; Wang, L. G.; Chen, L.; Zhao, J. H.; Zheng, H. Z.

    2012-11-01

    A new scheme for measuring magneto-optical (MO) effect is developed in the present work, called photoresistance magnetic circular dichroism (PR-MCD). It detects the differential photoresistance of materials between two circularly polarized excitations. That allows us to detect the MO effect induced mainly by interband transitions, as evidenced by the appearance of a clear long wavelength cutoff at 840 nm in PR-MCD spectrum. Our results provide unambiguous evidence that the host semiconductor band structure of (Ga, Mn)As is indeed modified by the strong exchange interactions. It is also found that the interband-induced MO effect decays rather fast with increasing temperatures as compared to MO effects observed in conventional MCD measurements. Moreover, our PR-MCD measurements show interesting feature of diluted magnetic semiconductor Ga1- x Mn x As of a high mole fraction x. PR-MCD signal persists in a reentrant insulating phase at temperatures blow half of Curie temperature (~80 K), and disappears right above it. Such an intrigue feature might be self-consistently explained by recent theory, developed for diluted magnetic semiconductors in the strong correlation regime.

  2. Circular dichroism spectroscopy of complexes of semiconductor quantum dots with chlorin e6

    Science.gov (United States)

    Kundelev, Evgeny V.; Orlova, Anna O.; Maslov, Vladimir G.; Baranov, Alexsander V.; Fedorov, Anatoly V.

    2016-04-01

    Experimental investigation of circular dichroism (CD) spectra of complexes based on ZnS:Mn/ZnS and CdSe/ZnS QDs and chlorin e6 (Ce6) molecules in aqua solutions at different pH level, in methanol and in DMSO were carried out. The changes in CD spectra of Ce6 upon its bonding in complex with semiconductor QDs were analyzed. Application of CD spectroscopy allowed to obtain the CD spectrum of luminescent Ce6 dimer for the first time, and to discover a nonluminescent Ce6 aggregate, preliminary identified as a "tetramer", dissymmetry factor of which is 40 times larger than that for its monomer. The analysis of obtained data showed that in complexes with QDs Ce6 can be either in the monomeric form or in the form of non-luminescent tetramer. The interaction of relatively unstable luminescent Ce6 dimerwith QDs leads to its partial monomerization and formation complexes with chlorin e6 in monomeric form.

  3. Magnetic circular dichroism spectroscopy of weakly exchange coupled transition metal dimers: A model study

    DEFF Research Database (Denmark)

    Piligkos, S.; Slep, L.D.; Weyhermuller, T.;

    2009-01-01

    A detailed study of the magnetic circular dichroism (MCD) spectra of weakly exchange coupled transition metal heterodimers is reported. The systems consist of three isostructural complexes of the type [LM(III)(PyA)(3)M(II)](ClO4)(2) where L represents 1,4,7-trimethyl-1,4,7-triazacyclonanane and Py......A- is the monoanion of pyridine-2-aldoxime. The trivalent metal ion M(III) is either diamagnetic Ga(III) or paramagnetic Cr(III) (S-Cr = 3/2). The divalent metal ion M(II) is either diamagnetic Zn(II) or paramagnetic Ni(II) (S-Ni = 1). The three systems 1 (CrZn), 2 (GaNi) and 3 (CrNi) have been...... structurally and magnetically characterized through magnetic susceptibility measurements. For I the zero-field splitting is D = 0.6 cm(-1) while for 2 the value D = 3.5 cm(-1) was found. These values have been fixed in analyzing 3 which was found to be characterized by an antiferromagnetic interaction Of J(CrNi...

  4. Solvent-induced conformational changes in cyclic peptides: a vibrational circular dichroism study.

    Science.gov (United States)

    Merten, Christian; Li, Fee; Bravo-Rodriguez, Kenny; Sanchez-Garcia, Elsa; Xu, Yunjie; Sander, Wolfram

    2014-03-28

    The three-dimensional structure of a peptide is strongly influenced by its solvent environment. In the present study, we study three cyclic tetrapeptides which serve as model peptides for β-turns. They are of the general structure cyclo(Boc-Cys-Pro-X-Cys-OMe) with the amino acid X being either glycine (1), or L- or D-leucine (L- or D-2). Using vibrational circular dichroism (VCD) spectroscopy, we confirm previous NMR results which showed that D-2 adopts predominantly a βII turn structure in apolar and polar solvents. Our results for L-2 indicate a preference for a βI structure over βII. With increasing solvent polarity, the preference for 1 is shifted from βII towards βI. This conformational change goes along with the breaking of an intramolecular hydrogen bond which stabilizes the βII conformation. Instead, a hydrogen bond with a solvent molecule can stabilize the βI turn conformation. PMID:24513908

  5. pH titration monitored by quantum cascade laser-based vibrational circular dichroism.

    Science.gov (United States)

    Rüther, Anja; Pfeifer, Marcel; Lórenz-Fonfría, Víctor A; Lüdeke, Steffen

    2014-04-10

    Vibrational circular dichroism (VCD) spectra of aqueous solutions of proline were recorded in the course of titrations from basic to acidic pH using a spectrometer equipped with a quantum cascade laser (QCL) as an infrared light source in the spectral range from 1320 to 1220 cm(-1). The pH-dependent spectra were analyzed by singular value decomposition and global fitting of a two-pK Henderson-Hasselbalch model. The analysis delivered relative fractions of the three different protonation species. Their agreement with the relative fractions obtained from performing the same analysis on pH-dependent Fourier transform infrared (FT-IR) and QCL-IR spectra validates the quantitative results from QCL-VCD. Global fitting of the pH-dependent VCD spectra of L-proline allowed for extraction of pure spectra corresponding to anionic, zwitterionic, and cationic L-proline. From a static experiment, only pure spectra of the zwitterion would be accessible in a straightforward way. A comparison to VCD spectra calculated for all three species led to assignment of vibrational modes that are characteristic for the respective protonation states. The study demonstrates the applicability of QCL-VCD both for quantitative evaluation and for qualitative interpretation of dynamic processes in aqueous solutions. PMID:24655319

  6. Circular dichroism measured on single chlorosomal light-harvesting complexes of green photosynthetic bacteria

    KAUST Repository

    Furumaki, Shu

    2012-12-06

    We report results on circular dichroism (CD) measured on single immobilized chlorosomes of a triple mutant of green sulfur bacterium Chlorobaculum tepidum. The CD signal is measured by monitoring chlorosomal bacteriochlorphyll c fluorescence excited by alternate left and right circularly polarized laser light with a fixed wavelength of 733 nm. The excitation wavelength is close to a maximum of the negative CD signal of a bulk solution of the same chlorosomes. The average CD dissymmetry parameter obtained from an ensemble of individual chlorosomes was gs = -0.025, with an intrinsic standard deviation (due to variations between individual chlorosomes) of 0.006. The dissymmetry value is about 2.5 times larger than that obtained at the same wavelength in the bulk solution. The difference can be satisfactorily explained by taking into account the orientation factor in the single-chlorosome experiments. The observed distribution of the dissymmetry parameter reflects the well-ordered nature of the mutant chlorosomes. © 2012 American Chemical Society.

  7. Magnetic properties of Fe nanoclusters on Cu(111) studied with X-ray magnetic circular dichroism

    Energy Technology Data Exchange (ETDEWEB)

    Fauth, Kai [Physikalisches Institut, Universitaet Wuerzburg (Germany); MPI for Metals Research, Stuttgart (Germany); Ballentine, Greg E. [MPI for Metals Research, Stuttgart (Germany); Praetorius, Christian [Physikalisches Institut, Universitaet Wuerzburg (Germany); Kleibert, Armin; Wilken, Norman; Voitkans, Andris; Meiwes-Broer, Karl-Heinz [Institute of Physics, University of Rostock (Germany)

    2010-05-15

    The magnetisation and magnetic response of Fe nanoclusters are studied by temperature and density dependent in situ X-ray magnetic circular dichroism after deposition onto Cu(111). The nanoclusters possess enhanced spin magnetic moments at low temperature, whereas no enhancement is found for the orbital moments. The analysis of magnetisation curves and the temperature dependent remnant magnetisation reveals that the individual magnetic anisotropy energies are distributed over a wide range of values, ranging from below to far above the value of bulk {alpha}-Fe. As a result, ferromagnetic response is obtained at ambient temperature, even though the nanocluster densities range well below percolation threshold. At higher cluster densities agglomeration and substrate mediated interaction increase the mean blocking temperature in the particle ensemble. The observed macroscopic magnetic in-plane anisotropy derives from the average dipolar interactions between the nanoclusters. Single particle properties, substrate mediated coupling and dipolar interactions thus independently contribute to magnetic characteristics on equal footing. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  8. Origin-independent two-photon circular dichroism calculations in coupled cluster theory.

    Science.gov (United States)

    Friese, Daniel H; Hättig, Christof; Rizzo, Antonio

    2016-05-21

    We present the first origin-independent approach for the treatment of two-photon circular dichroism (TPCD) using coupled cluster methods. The approach is assessed concerning its behavior on the choice of the basis set and different coupled cluster methods. We also provide a comparison of results from CC2 with those from density functional theory using the CAM-B3LYP functional. Concerning the basis set we note that in most cases an augmented triple zeta basis or a doubly augmented double zeta basis is needed for reasonably converged results. In the comparison of different coupled cluster methods results from CCSD, CC3 and CC2 have been found to be quite similar in most cases, while CCS results differ remarkably from the results at the higher levels. However, this proof-of-principle study also shows that further benchmarking of DFT and CC2 against accurate coupled cluster reference values (e.g. CCSD or CC3) is needed. PMID:27140590

  9. Can circular dichroism in core-level photoemission provide a spectral fingerprint of adsorbed chiral molecules?

    Energy Technology Data Exchange (ETDEWEB)

    Allegretti, F [Physics Department, University of Warwick, Coventry CV4 7AL (United Kingdom); Polcik, M [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D 14195 Berlin (Germany); Sayago, D I [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D 14195 Berlin (Germany); Demirors, F [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D 14195 Berlin (Germany); O' Brien, S [Physics Department, University of Warwick, Coventry CV4 7AL (United Kingdom); Nisbet, G [Centre for Applied Catalysis, Department of Chemical and Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH (United Kingdom); Lamont, C L A [Centre for Applied Catalysis, Department of Chemical and Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH (United Kingdom); Woodruff, D P [Physics Department, University of Warwick, Coventry CV4 7AL (United Kingdom)

    2005-04-01

    The results of experimental measurements and theoretical simulations of circular dichroism in the angular distribution (CDAD) of photoemission from atomic core levels of each of the enantiomers of a chiral molecule, alanine, adsorbed on Cu(1 1 0) are presented. Measurements in, and out of, substrate mirror planes allow one to distinguish the CDAD due to the chirality of the sample from that due to a chiral experimental geometry. For these studies of oriented chiral molecules, the CDAD is seen not only in photoemission from the molecular chiral centre, but also from other atoms which have chiral geometries as a result of the adsorption. The magnitude of the CDAD due to the sample chirality differs for different adsorption phases of alanine, and for different emission angles and energies, but is generally small compared with CDAD out of the substrate mirror planes which is largely unrelated to the molecular chirality. While similar measurements of other molecules may reveal larger CDAD due to molecular chirality, the fact that the results for one chiral molecule show weak effects means that such CDAD is unlikely to provide a simple and routine general spectral fingerprint of adsorbed molecular chirality.

  10. Plasmon-Mediated Two-Photon Photoluminescence-Detected Circular Dichroism in Gold Nanosphere Assemblies.

    Science.gov (United States)

    Jarrett, Jeremy W; Zhao, Tian; Johnson, Jeffrey S; Liu, Xiaoying; Nealey, Paul F; Vaia, Richard A; Knappenberger, Kenneth L

    2016-03-01

    We report plasmon-mediated two-photon photoluminescence (TPPL)-detected circular dichroism (CD) from colloidal metal nanoparticle assemblies. Two classes of solid gold nanosphere (SGN) dimers-heterodimers and homodimers-were examined using polarization-resolved TPPL, second harmonic generation (SHG), and one-photon photoluminescence (OPPL). Unambiguous CD was detected in both the TPPL and SHG signals, and the magnitudes of the CD responses in these measurements showed agreement for individual nanostructures. Heterodimers gave larger CD responses (average TPPL-CDR = 0.62 ± 0.33; average SHG-CDR = 0.51 ± 0.21) than homodimers (average TPPL-CDR = 0.19 ± 0.04; average SHG-CDR = 0.18 ± 0.06). OPPL-CD was not detected for either structure. Analysis of dimer emission properties suggested the CD responses were determined by properties of the one-photon-resonant mode excited by the laser. Average TPPL signals were (4.3 ± 0.6)× larger than those for SHG. Because signal amplitude is a primary determinant for spatial accuracies and precisions obtained from optical microscopy, CD contrast generated from plasmon-mediated TPPL, which we report for the first time, can extend the suite of super-resolution imaging techniques. PMID:26854357

  11. A study of aliphatic amino acids using simulated vibrational circular dichroism and Raman optical activity spectra*

    Science.gov (United States)

    Ganesan, Aravindhan; Brunger, Michael J.; Wang, Feng

    2013-11-01

    Vibrational optical activity (VOA) spectra, such as vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra, of aliphatic amino acids are simulated using density functional theory (DFT) methods in both gas phase (neutral form) and solution (zwitterionic form), together with their respective infrared (IR) and Raman spectra of the amino acids. The DFT models, which are validated by excellent agreements with the available experimental Raman and ROA spectra of alanine in solution, are employed to study other aliphatic amino acids. The inferred (IR) intensive region (below 2000 cm-1) reveals the signature of alkyl side chains, whereas the Raman intensive region (above 3000 cm-1) contains the information of the functional groups in the amino acids. Furthermore, the chiral carbons of the amino acids (except for glycine) dominate the VCD and ROA spectra in the gas phase, but the methyl group vibrations produce stronger VCD and ROA signals in solution. The C-H related asymmetric vibrations dominate the VOA spectra (i.e., VCD and ROA) > 3000 cm-1 reflecting the side chain structures of the amino acids. Finally the carboxyl and the C(2)H modes of aliphatic amino acids, together with the side chain vibrations, are very active in the VCD/IR and ROA/Raman spectra, which makes such the vibrational spectroscopic methods a very attractive means to study biomolecules.

  12. Circular dichroism in valence photoelectron spectroscopy of free unoriented chiral molecules: Camphor and bromocamphor

    International Nuclear Information System (INIS)

    The circular dichroism in the photoelectron angular distribution was investigated for valence photoionization of randomly oriented pure enantiomers of camphor and bromocamphor molecules using circularly polarized light in the vacuum ultraviolet. The forward-backward electron emission spectra were recorded simultaneously with two spectrometers at several opposite angles relative to the propagation direction of the photon beam and compared for each of the two substances. Measurements were also carried out for reversed light helicity and opposite molecular handedness. For the left- and right-handed enantiomers of both molecules we observed asymmetries of comparable magnitude up to several percent. The measured asymmetry parameters vary strongly for different orbital binding energies and also for the selected photon energies in the valence region. The results for both molecules are compared. They suggest a strong influence of the final states on the asymmetry, depending on the chiral geometry of the molecular electronic structure, as well as a significant dependence on the initial states involved. They also confirm theoretical predictions describing the effect in pure electric-dipole approximation

  13. A new soft X-ray magnetic circular dichroism facility at the BSRF beamline 4B7B

    CERN Document Server

    Guo, Zhi-Ying; Xing, Hai-Ying; Tang, Kun; Xui, Wei; Chen, Dong-liang; Cui, Ming-Qi; Zhao, YI-Dong

    2014-01-01

    X-ray magnetic circular dichroism (XMCD) has become an important and powerful tool because it allows the study of material properties in combination with elemental specificity, chemical state specificity, and magnetic specificity. A new soft X-ray magnetic circular dichroism apparatus has been developed at the Beijing Synchrotron Radiation Facility (BSRF). The apparatus combines three experimental conditions: ultra-high-vacuum environment, moderate magnetic fields and in-situ sample preparation to measure the absorption signal. We designed a C type dipole electromagnet that provides magnetic fields up to 0.5T in parallel (or anti-parallel) direction relative to the incoming X-ray beam. The performances of the electromagnet are measured and the results show good agreement with the simulation ones. Following film grown in situ by evaporation methods, XMCD measurements are performed. Combined polarization corrections, the magnetic moments of the Fe and Co films determined by sum rules are consistent with other t...

  14. Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Matei, Iulia; Ionescu, Sorana [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania); Hillebrand, Mihaela, E-mail: mihh@gw-chimie.math.unibuc.ro [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania)

    2011-08-15

    The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 10{sup 5} M{sup -1} was evidenced. Foerster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes in the CD band of HSA indicate a decrease in the {alpha}-helix content upon binding. An induced CD signal for bound fisetin was observed and rationalized in terms of density functional theory calculations. - Highlights: > Fisetin-BSA system was studied by fluorescence spectroscopy. > Binding parameters, association constant and number of sites were estimated. > Binding site of fisetin was identified by competitive experiments. > Conformational changes in HSA and fisetin were evidenced by circular dichroism. > TDDFT calculated CD spectra supported the experimental data.

  15. X-ray magnetic circular dichroism at the U M4,5 absorption edges of UFe2

    International Nuclear Information System (INIS)

    We present an x-ray magnetic circular dichroism study performed at the U M4,5 edges on UFe2, a ferromagnet with almost itinerant 5f electrons. The analysis of the branching ratio of the U M4,5 edges confirms the fact that the occupation number of the 5f states in UFe2 is lower than in other compounds where the f electrons are more localized. Magnetic circular dichroism effects are observed consistently with the presence of an orbital 5f magnetic moment which aligns parallel to the total magnetic moment. In agreement with a polarized neutron study, we find a nearly perfect cancellation of the U-5f spin and orbital magnetic moments, which results in a vanishing small total U-5f magnetic moment. Results are discussed in comparison with atomic multiplet calculations. copyright 1997 The American Physical Society

  16. Detailed structural study of β-artemether: Density functional theory (DFT) calculations of Infrared, Raman spectroscopy, and vibrational circular dichroism

    Science.gov (United States)

    Wang, Zhiqiang; Chen, Jianchao; Li, Linwei; Zhou, Zhixu; Geng, Yiding; Sun, Tiemin

    2015-10-01

    In this study, the experimental and theoretical studies on the structure of β-artemether are presented. The optimized molecular structure, Mulliken atomic charges, vibrational spectra (IR, Raman and vibrational circular dichroism), and molecular electrostatic potential have been calculated by density functional theory (DFT) using B3LYP method with the 6-311++G (2d, p) basis set. Reliable vibrational assignments for Artemether have been made on the basis of potential energy distribution (PED). The vibrational circular dichroism (VCD) has been explored by ab initio calculations, and then was used to compare with the experimental VCD. The consistence between them confirmed the absolute configuration of Artemether. In addition, HOMO-LUMO of the title compound as well as thermo-dynamical parameters has illustrated the stability of β-artemether.

  17. Elucidating the Structure of Chiral Molecules by using Amplified Vibrational Circular Dichroism: From Theory to Experimental Realization.

    Science.gov (United States)

    Domingos, Sérgio R; Hartl, František; Buma, Wybren Jan; Woutersen, Sander

    2015-11-16

    Recent experimental observations of enhanced vibrational circular dichroism (VCD) in molecular systems with low-lying electronically excited states suggest interesting new applications of VCD spectroscopy. The theory describing VCD enhancement through vibronic coupling schemes was derived by Nafie in 1983, but only recently experimental evidence of VCD amplification has demonstrated the extent to which this effect can be exploited as a structure elucidation tool to probe local structure. In this Concept paper, we give an overview of the physics behind vibrational circular dichroism, in particular the equations governing the VCD amplification effect, and review the latest experimental developments with a prospective view on the application of amplified VCD to locally probe biomolecular structure. PMID:26289778

  18. Raman, SERS, and induced circular dichroism techniques as a probe of pharmaceuticals in their interactions with the human serum albumin and p-glycoprotein

    Science.gov (United States)

    Fleury, Fabrice; Ianoul, Anatoli I.; Baggetto, Loris; Jardillier, Jean-Claude; Alix, Alain J.; Nabiev, Igor R.

    1999-04-01

    Camptothecin (CPT) derivatives are the well known inhibitors of the human DNA topoisomerase (topo) I. Two of them, irinotecan and topotecan, are just in the clinics; 9-amino- CPT is on the stage II of clinical trials, and the active search for new derivatives is now in progress. Stability of the CPT derivatives on their way to the target and resistance of cancer cells to these drugs present the crucial problem of the chemotherapy. Human serum albumin (HSA) is the mediator of transport and metabolism of numerous pharmaceuticals in the blood and P-glycoprotein (P- gp) plays a crucial role of the mediator of the multidrug resistance (MDR) of the cancer cells. This paper present the result of analysis of molecular interactions of some drugs of CPT family with the HSA and P-gp. Induced circular dichroism (CD) and Raman techniques have been applied for monitoring molecular interaction of drugs with HSA as well as to identify the conformational transition of the protein induced by the drug binding. Drug molecular determinants responsible for interaction have been identified and their binding sites within the HSA have been localized. New cancer cells lines exhibiting an extremely high level of MDR resistance have been established and were shown to contain the P-gp overproduced in the quantities of 35 percent from the all membrane proteins. The membrane fractions of these cells with the controls presented by the membranes of the parental membrane proteins. The membrane fractions of these cells with the controls presented by the membranes of the parental sensitive cells may be used as a model system for spectroscopic analysis of the specific pharmaceuticals/P-gp interactions.

  19. Feedback control system for soft X-ray magnetic circular dichroism experimental station based on LabVIEW

    International Nuclear Information System (INIS)

    A feedback control system was developed for soft X-ray magnetic circular dichroism experimental station based on LabVIEW. By implementing the system, the stability of current through the sample was improved to provide a good criterion for absorption spectrum analysis. The friendly user interface, flexible interface instruction and strong data storage function are also important for National Synchrotron Radiation Laboratory which is open to users from all over the country. (authors)

  20. Computational Study of the Structure, the Flexibility, and the Electronic Circular Dichroism of Staurosporine - a Powerful Protein Kinase Inhibitor

    Science.gov (United States)

    Karabencheva-Christova, Tatyana G.; Singh, Warispreet; Christov, Christo Z.

    2014-07-01

    Staurosporine (STU) is a microbial alkaloid which is an universal kinase inhibitor. In order to understand its mechanism of action it is important to explore its structure-properties relationships. In this paper we provide the results of a computational study of the structure, the chiroptical properties, the conformational flexibility of STU as well as the correlation between the electronic circular dichroism (ECD) spectra and the structure of its complex with anaplastic lymphoma kinase.

  1. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    OpenAIRE

    Lees Jonathan G; Janes Robert W

    2008-01-01

    Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction method...

  2. Protein-containing PEGylated cubosomic particles: freeze-fracture electron microscopy and synchrotron radiation circular dichroism study

    Czech Academy of Sciences Publication Activity Database

    Angelov, Borislav; Angelova, A.; Papahadjopoulos-Sternberg, B.; Hoffmann, S. V.; Nicolas, V.; Lesieur, S.

    2012-01-01

    Roč. 116, č. 26 (2012), s. 7676-7686. ISSN 1520-6106 R&D Projects: GA ČR GAP208/10/1600 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : freeze-fracture electron microscopy * synchrotron radiation circular dichroism * SAXS Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.607, year: 2012

  3. Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution

    OpenAIRE

    Silva, R. A. G. D.; Kubelka, Jan; Bour, Petr; Decatur, Sean M.; Keiderling, Timothy A.

    2000-01-01

    Understanding the detailed mechanism of protein folding requires dynamic, site-specific stereochemical information. The short time response of vibrational spectroscopies allows evaluation of the distribution of populations in rapid equilibrium as the peptide unfolds. Spectral shifts associated with isotopic labels along with local stereochemical sensitivity of vibrational circular dichroism (VCD) allow determination of the segment sequence of unfolding. For a series of alanine-rich peptides t...

  4. Standing wave linear accelerator

    International Nuclear Information System (INIS)

    Consideration is being given to standing wave linear accelerator containing generator, phase shifter, two accelerating resonator sections, charged particle injector and waveguide bridge. Its first arm is oined up with generator via the phase shifter, the second and the third ones-with accelerating sections and the fourth one - with HF-power absorber. HF-power absorber represents a section of circular diaphragmatic wavequide with transformer with input wave and intrawaveguide output load located between injector and the first accelerating section. The section possesses holes in side walls lying on accelerator axis. The distances between centers of the last cell of the fast accelerating section and the first cell of the second accelerating sectiOn equal (2n+3)lambda/4, where n=1, 2, 3..., lambda - wave length of generator. The suggested system enables to improve by one order spectral characteristics of accelerators as compared to the prototype in which magnetrons are used as generator

  5. Linear electrochemical gel actuators

    Science.gov (United States)

    Goswami, Shailesh; McAdam, C. John; Hanton, Lyall R.; Moratti, Stephen C.

    2012-04-01

    By using electroactive monomers it is possible to produce gels that respond to oxidation or reduction by swelling and deswelling in the presence of solvent. By the inclusion of an appropriate biasing element such as a spring, it is possible to produce linear, reversible actuation. The process can be driven electrochemically in a standard cell, with driving voltages under +/- 1 V. For many systems, the intrinsic conductivity of the gel, leading to poor or no performance. This can be overcome by blending conductive carbon nanotubes at 1% concentration, which give reasonable conductivity without affecting mechanical performance. Extensions of up to 40% are possible, against an external pressure of 30 kPa. The process is slow, taking up to 160 minutes per cycle due to slow ionic diffusion. The electrochemical cell can be cycled many times without degradation.

  6. Magnetic Circular Dichroism in Resonant Raman Scattering in the Perpendicular Geometry at the L edge of 3d Transition Metal Systems

    International Nuclear Information System (INIS)

    We measured circular dichroism in resonant x-ray scattering 3dn→2p53dn+1→3s13dn+1 with incidence perpendicular to the magnetization where the absorption dichroism vanishes. The advantages of photon scattering over other techniques make it possible to study a wide range of materials. The Ni L3 dichroism in NiFe2O 4 is (28±5)% in agreement with a localized model. In the metal Co the dichroism is reduced to (10.4±1)% (L3) and (6.8±1.5)% (7.5 eV above L3 ), indicating a large sensitivity to the nature of the valence states despite the fact that this spectroscopy is based on inner shell transitions. copyright 1999 The American Physical Society

  7. Purification, structure-function analysis, and molecular characterization of novel linear peptides from scorpion Opisthacanthus madagascariensis.

    Science.gov (United States)

    Dai, Li; Corzo, Gerardo; Naoki, Hideo; Andriantsiferana, Marta; Nakajima, Terumi

    2002-05-24

    In the previous report [Biochem. Biophys. Res. Commun. 286 (2001) 820], we described a novel short linear peptide, IsCT, with cytolytic activity isolated from the venom of scorpion Opisthacanthus madagascariensis. From the same scorpion venom, we further purified and characterized three short linear peptides named IsCT2, IsCTf, and IsCT2f that shared high homology with IsCT, while with different C-terminal areas between IsCT/IsCT2 and IsCTf/IsCT2f. Structure-activity relationship was analyzed by performing vivo and vitro assays and circular dichroism spectroscopy. Like IsCT, IsCT2 showed broad activity spectra against microbes (Gram positive and negative bacteria as well as fungi) and relatively weak hemolytic activity against sheep red blood cells. It adopts an amphipathic alpha-helical structure in aqueous TFE and is able to disrupt the artificial membrane. However, the other two peptides IsCTf and IsCT2f showed no activity in antimicrobial or hemolytic assay. Furthermore, IsCTf and IsCT2f cannot form amphipathic alpha-helix while demonstrating random coil structure in aqueous TFE, which might result in their lost cytolytic activity. IsCTf and IsCT2f both exist in the crude venom and are proved to be enzymatic products from IsCT and IsCT2. Whether they have some other biological activity is still unclear. In addition, we got the cDNAs encoding the precursors of IsCT and IsCT2. Besides the signal peptide, they still contain an unusual acidic pro-peptide at the C-terminal that was quite different from other known precursors of scorpion venom peptides. The novel structure and biological activity of these peptides proposed them to be a new class in scorpion venom. PMID:12054688

  8. Origin-Independent Sum Over States Simulations of Magnetic and Electronic Circular Dichroism Spectra via the Localized Orbital/Local Origin Method

    Czech Academy of Sciences Publication Activity Database

    Štěpánek, Petr; Bouř, Petr

    2015-01-01

    Roč. 36, č. 10 (2015), s. 723-730. ISSN 0192-8651 R&D Projects: GA ČR GA13-03978S; GA ČR GAP208/11/0105 Grant ostatní: GA AV ČR(CZ) M200551205 Institutional support: RVO:61388963 Keywords : density functional theory * electronic circular dichroism * magnetic circular dichroism * origin-dependence Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014

  9. DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental-Theoretical Case Study of the AT Homo-Oligonucleotide.

    Science.gov (United States)

    Di Meo, Florent; Pedersen, Morten N; Rubio-Magnieto, Jenifer; Surin, Mathieu; Linares, Mathieu; Norman, Patrick

    2015-02-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment. PMID:26261947

  10. Linear Accelerator (LINAC)

    Science.gov (United States)

    ... News Physician Resources Professions Site Index A-Z Linear Accelerator A linear accelerator (LINAC) customizes high energy x-rays to ... ensured? What is this equipment used for? A linear accelerator (LINAC) is the device most commonly used ...

  11. Linearly constrained minimax optimization

    DEFF Research Database (Denmark)

    Madsen, Kaj; Schjær-Jacobsen, Hans

    1978-01-01

    We present an algorithm for nonlinear minimax optimization subject to linear equality and inequality constraints which requires first order partial derivatives. The algorithm is based on successive linear approximations to the functions defining the problem. The resulting linear subproblems are...

  12. Identification of three PPV1 VP2 protein-specific B cell linear epitopes using monoclonal antibodies against baculovirus-expressed recombinant VP2 protein.

    Science.gov (United States)

    Sun, Jianhui; Huang, Liping; Wei, Yanwu; Wang, Yiping; Chen, Dongjie; Du, Wenjuan; Wu, Hongli; Feng, Li; Liu, Changming

    2015-11-01

    Porcine parvovirus type 1 (PPV1) is a major causative agent of embryonic and fetal death in swine. The PPV1 VP2 protein is closely associated with viral immunogenicity for eliciting neutralizing antibodies, but its antigenic structures have been largely unknown. We generated three monoclonal antibodies (MAbs) against baculovirus-expressed recombinant PPV1 VP2 protein. A PEPSCAN analysis identified the minimal B cell linear epitopes of PPV1 VP2 based on these MAbs. Three core epitopes, (228)QQITDA(233), (284)RSLGLPPK(291), and (344)FEYSNGGPFLTPI(356), were defined and mapped onto three-dimensional models of the PPV1 virion and VP2 monomer. The epitope (228)QQITDA(233) is exposed on the virion surface, and the other two are located inside the protein. An alignment of the PPV1 VP2 amino acid sequences showed that (284)RSLGLPPK(291) and (344)FEYSNGGPFLTPI(356) are absolutely conserved, whereas (228)QQITDA(233) has a single substitution at residue 233 in some (S → A or T). We developed a VP2 epitope-based indirect enzyme-linked immunosorbent assay (iELISA) to test for anti-PPV1 antibodies. In a comparative analysis with an immunoperoxidase monolayer assay using 135 guinea pig sera, the VP2-epitope-based iELISA had a concordance rate of 85.19 %, sensitivity of 83.33 %, and specificity of 85.47 %. MAb 8H6 was used to monitor VP2 during the PPV1 replication cycle in vitro with an indirect immunofluorescence assay, which indicated that newly encapsulated virions are released from the nucleus at 24 h postinfection and the PPV1 replication cycle takes less than 24 h. This study provides valuable information clarifying the antigenic structure of PPV1 VP2 and lays the foundations for PPV1 serodiagnosis and antigen detection. PMID:26153140

  13. Mechanisms of Cell Killing Response from Low Linear Energy Transfer (LET) Radiation Originating from 177Lu Radioimmunotherapy Targeting Disseminated Intraperitoneal Tumor Xenografts

    Science.gov (United States)

    Yong, Kwon Joong; Milenic, Diane E.; Baidoo, Kwamena E.; Brechbiel, Martin W.

    2016-01-01

    Radiolabeled antibodies (mAbs) provide efficient tools for cancer therapy. The combination of low energy β−-emissions (500 keVmax; 130 keVave) along with a γ-emission for imaging makes 177Lu (T1/2 = 6.7 day) a suitable radionuclide for radioimmunotherapy (RIT) of tumor burdens possibly too large to treat with α-particle radiation. RIT with 177Lu-trastuzumab has proven to be effective for treatment of disseminated HER2 positive peritoneal disease in a pre-clinical model. To elucidate mechanisms originating from this RIT therapy at the molecular level, tumor bearing mice (LS-174T intraperitoneal xenografts) were treated with 177Lu-trastuzumab comparatively to animals treated with a non-specific control, 177Lu-HuIgG, and then to prior published results obtained using 212Pb-trastuzumab, an α-particle RIT agent. 177Lu-trastuzumab induced cell death via DNA double strand breaks (DSB), caspase-3 apoptosis, and interfered with DNA-PK expression, which is associated with the repair of DNA non-homologous end joining damage. This contrasts to prior results, wherein 212Pb-trastuzumab was found to down-regulate RAD51, which is involved with homologous recombination DNA damage repair. 177Lu-trastuzumab therapy was associated with significant chromosomal disruption and up-regulation of genes in the apoptotic process. These results suggest an inhibition of the repair mechanism specific to the type of radiation damage being inflicted by either high or low linear energy transfer radiation. Understanding the mechanisms of action of β−- and α-particle RIT comparatively through an in vivo tumor environment offers real information suitable to enhance combination therapy regimens involving α- and β−-particle RIT for the management of intraperitoneal disease. PMID:27196891

  14. X-ray magnetic circular dichroism strongly influenced by non-magnetic cover layers

    Energy Technology Data Exchange (ETDEWEB)

    Zafar, K.; Audehm, P.; Schütz, G. [Max-Planck-Institute for Intelligent Systems (Former Metals Research), Stuttgart 70569 (Germany); Goering, E., E-mail: goering@is.mpg.de [Max-Planck-Institute for Intelligent Systems (Former Metals Research), Stuttgart 70569 (Germany); Pathak, M.; Chetry, K.B.; LeClair, P.R.; Gupta, A. [MINT Center, University of Alabama, Tuscaloosa, AL 35487 (United States)

    2013-12-15

    Highlights: •Energy filtering gives much larger sampling depth and escape length as expected. •XMCD sum rules could be dramatically altered by this effect. •Strong enhanced effective escape length for buried layers. •A “universal curve” model gives semi quantitative understanding. •Buried layers are more sensitive to self-absorption phenomena. -- Abstract: Total electron yield (TEY) is the dominating measurement mode in soft X-ray absorption spectroscopy (XAS), where the sampling depth is generally assumed to be quite small and constant, and the related self-absorption or saturation phenomena are about to be negligible at normal incidence conditions. From the OK edge to CrL{sub 2,3} edge XAS ratio we determined a strong change in the effective electron escape length between an uncovered and a RuO{sub 2} covered CrO{sub 2} sample. This effect has been explained by a simple electron energy filtering model, providing a semi quantitative description. In addition, this simple model can quantitatively describe the unexpected reduced and positive CrL{sub 2,3} X-ray magnetic circular dichroism (XMCD) signal of a RuO{sub 2}/CrO{sub 2} bilayer, while previous results have identified a clear negative Cr magnetization at the RuO{sub 2}/CrO{sub 2} interface. In our case this escape length enhancement has strong impact on the XMCD sum rule results and in general it provides much deeper sampling depth, but also larger self-absorption or saturation effects.

  15. Circular dichroism and polarized fluorescence characteristics of blue-green algal allophycocyanins

    Energy Technology Data Exchange (ETDEWEB)

    Canaani, O.D.; Gantt, E.

    1980-06-24

    Allophycocyanin, the terminal pigment in the phycobiliprotein transfer sequence, isolated from dissociated phycobilisomes of Nostoc sp., was fractionated on calcium phosphate columns into four spectral forms: APC I, II, III, and B. These forms had distinctive isoelectric points of 5.15, 4.68, 4.82, and 4.98, respectively. The APC forms differed in their secondary structure as suggested by the varying percentages of their ..cap alpha.. helix and ..beta..-pleated sheets. APC II and III are short-emitting forms with a fluorescence maximum at 660 nm, while APC I and B are long-emitting forms with a maximum at 681 nm. The maximum of APC I and B at -196/sup 0/C in 0.1 M phosphate and 20% glycerol shifted to 688 nm. Fluorescence polarization spectra suggest that there are at least two groups of chromophores responsible for the absorption of APC I and similarly of APC B. In APC II and III, the fluorescence was mostly depolarized. Circular dichroism revealed extensive positive and negative ellipticity band multiplicities in the chromophore absorption region of APC I and B, but not in APC II and III. Two main CD extrema in APC B, a negative band and a positive band, are probably the result of exciton coupling of phycocyanobilin chromophores absorbing at longer wavelength. In APC I three different peaks are revealed in the absorption spectrum and four ellipticity bands in the CD spectrum at -196/sup 0/C. These can best be explained as being due to the combined interactions of the chromophore with the protein and exciton coupling between chromophores.

  16. The secondary structure of echistatin from 1H-NMR, circular-dichroism and Raman spectroscopy.

    Science.gov (United States)

    Saudek, V; Atkinson, R A; Lepage, P; Pelton, J T

    1991-12-01

    Detailed biophysical studies have been carried out on echistatin, a member of the disintegrin family of small, cysteine-rich, RGD-containing proteins, isolated from the venom of the saw-scaled viper Echis carinatus. Analysis of circular-dichroism spectra indicates that, at 20 degrees C, echistatin contains no alpha-helix but contains mostly beta-turns and beta-sheet. Two isobestic points are observed as the temperature is raised, the conformational changes associated with that observed between 40 degrees C and 72 degrees C being irreversible. Raman spectra also indicate considerable beta-turn and beta-sheet (20%) structure and an absence of alpha-helical structure. Three of the four disulphide bridges are shown to be in an all-gauche conformation, while the fourth adopts a trans-gauche-gauche conformation. The 1H-NMR spectrum of echistatin has been almost fully assigned. A single conformation was observed at 27 degrees C with the four proline residues adopting only the trans conformation. A large number of backbone amide protons were found to exchange slowly, but no segments of the backbone were found to be in either alpha-helical or beta-sheet conformation. A number of turns could be characterised. An irregular beta-hairpin contains the RGD sequence in a mobile loop at its tip. Two of the four disulphide cross-links have been identified from the NMR spectra. The data presented in this paper will serve to define the structure of echistatin more closely in subsequent studies. PMID:1761037

  17. Foundations of linear and generalized linear models

    CERN Document Server

    Agresti, Alan

    2015-01-01

    A valuable overview of the most important ideas and results in statistical analysis Written by a highly-experienced author, Foundations of Linear and Generalized Linear Models is a clear and comprehensive guide to the key concepts and results of linear statistical models. The book presents a broad, in-depth overview of the most commonly used statistical models by discussing the theory underlying the models, R software applications, and examples with crafted models to elucidate key ideas and promote practical model building. The book begins by illustrating the fundamentals of linear models,

  18. Linear side chains in benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c] pyrrole-4,6-dione polymers direct self-assembly and solar cell performance

    KAUST Repository

    Cabanetos, Clement

    2013-03-27

    While varying the size and branching of solubilizing side chains in π-conjugated polymers impacts their self-assembling properties in thin-film devices, these structural changes remain difficult to anticipate. This report emphasizes the determining role that linear side-chain substituents play in poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers for bulk heterojunction (BHJ) solar cell applications. We show that replacing branched side chains by linear ones in the BDT motifs induces a critical change in polymer self-assembly and backbone orientation in thin films that correlates with a dramatic drop in solar cell efficiency. In contrast, we show that for polymers with branched alkyl-substituted BDT motifs, controlling the number of aliphatic carbons in the linear N-alkyl-substituted TPD motifs is a major contributor to improved material performance. With this approach, PBDTTPD polymers were found to reach power conversion efficiencies of 8.5% and open-circuit voltages of 0.97 V in BHJ devices with PC71BM, making PBDTTPD one of the best polymer donors for use in the high-band-gap cell of tandem solar cells. © 2013 American Chemical Society.

  19. The experimental investigation of linear expansion coefficient measurement of car fuel supplying cell parts%轿车供油单元零件线膨胀系数测定试验研究

    Institute of Scientific and Technical Information of China (English)

    麻文焱; 杨延俊; 潘发明

    2009-01-01

    详细研究了电阻应变计法测量材料线膨胀系数的原理,结合轿车供油单元零件线膨胀系数测定试验,具体阐述了试验步骤及方法.结果表明应用电阻应变计法测试材料线膨胀系数是一种既简单实用又经济的测试技术.%This article studies the principle of measuring coefficient of linear expansion by using resistance strain gauge and discusses the experimental steps and methods combining with the determination test of linear expansion coefficient of car fuel supply cell parts. The result shows it is a practical and economical testing technique to measure linear expansion coefficients of materials by resistance strain gauge.

  20. Radiotherapy treatment planning linear-quadratic radiobiology

    CERN Document Server

    Chapman, J Donald

    2015-01-01

    Understand Quantitative Radiobiology from a Radiation Biophysics PerspectiveIn the field of radiobiology, the linear-quadratic (LQ) equation has become the standard for defining radiation-induced cell killing. Radiotherapy Treatment Planning: Linear-Quadratic Radiobiology describes tumor cell inactivation from a radiation physics perspective and offers appropriate LQ parameters for modeling tumor and normal tissue responses.Explore the Latest Cell Killing Numbers for Defining Iso-Effective Cancer TreatmentsThe book compil

  1. Modulation of the multilamellar membrane organization and of the chiral macrodomains in the diatom Phaeodactylum tricornutum revealed by small-angle neutron scattering and circular dichroism spectroscopy.

    Science.gov (United States)

    Nagy, Gergely; Szabó, Milán; Unnep, Renáta; Káli, György; Miloslavina, Yuliya; Lambrev, Petar H; Zsiros, Ottó; Porcar, Lionel; Timmins, Peter; Rosta, László; Garab, Győző

    2012-03-01

    Diatoms possess effective photoprotection mechanisms, which may involve reorganizations in the photosynthetic machinery. We have shown earlier, by using circular dichroism (CD) spectroscopy, that in Phaeodactylum tricornutum the pigment-protein complexes are arranged into chiral macrodomains, which have been proposed to be associated with the multilamellar organization of the thylakoid membranes and shown to be capable of undergoing light-induced reversible reorganizations (Szabó et al. Photosynth Res 95:237, 2008). Recently, by using small-angle neutron scattering (SANS) on the same algal cells we have determined the repeat distances and revealed reversible light-induced reorganizations in the lamellar order of thylakoids (Nagy et al. Biochem J 436:225, 2011). In this study, we show that in moderately heat-treated samples, the weakening of the lamellar order is accompanied by the diminishment of the psi-type CD signal associated with the long-range chiral order of the chromophores (psi, polymer or salt-induced). Further, we show that the light-induced reversible increase in the psi-type CD is associated with swelling in the membrane system, with magnitudes larger in high light than in low light. In contrast, shrinkage of the membrane system, induced by sorbitol, brings about a decrease in the psi-type CD signal; this shrinkage also diminishes the non-photochemical quenching capability of the cells. These data shed light on the origin of the psi-type CD signal, and confirm that both CD spectroscopy and SANS provide valuable information on the macro-organization of the thylakoid membranes and their dynamic properties; these parameters are evidently of interest with regard to the photoprotection in whole algal cells. PMID:21986933

  2. Expedient synthesis of novel pregnane-NSAIDs prodrugs, XRD, stereochemistry of their C-20 derivatives by circular dichroism, conformational analysis, their DFT and TD-DFT studies

    Science.gov (United States)

    Singh, Ranvijay Pratap; Sharma, Sonia; Kant, Rajni; Amandeep; Singh, Praveer; Sethi, Arun

    2016-02-01

    Four novel pregnane-NSAIDs prodrugs 3β-(2-(6-methoxynaphthalene-2yl) propionoxy)-16α-methoxy-pregn-5-ene-20-one (3), 16α-methoxy-pregn-5-ene-20-one-3yl-2(4-iso butyl phenyl) propanoate (4), 3β-(2-(6-methoxynaphthalene-2yl) propionoxy) 20-hydroxy-16α-methoxy-pregn-5-ene (5) and 20-hydroxy-16α-methoxy-pregn-5-ene-20-one-3yl-2(4-iso butyl phenyl) propanoate (6) have been synthesized. They were analyzed experimentally by spectroscopic techniques like 1H, 13C NMR, FT-IR, UV-visible spectroscopy, mass spectrometry and correlated by theoretical calculations. The structure and conformations of 3 was established by single crystal X-ray diffraction, which crystallized in orthorhombic form having P212121 space group. Absolute configuration of C-20 hydroxy derivatives 5 and 6 was established by circular dichroism (CD) analysis. Conformational analysis of 5 was carried out to determine the most stable conformation. The electronic properties, such as frontier orbitals, band gap energies, oscillator strength and wavelength have been calculated using time dependent density functional theory (TD-DFT). The vibrational wavenumbers have been calculated using DFT method and assigned with the help of potential energy distribution (PED). Global and local reactivity descriptors have been computed to predict reactivity and reactive sites in the molecule. First hyperpolarizability (β0) of synthesized compounds has been computed to evaluate non-linear optical (NLO) response. Molecular electrostatic potential (MEP) for synthesized compounds have also been determined to check their electrophilic or nucleophilic reactivity as well as reaction path.

  3. Magnetic Circular Dichroism spectroscopy in epitaxial La0.7Sr0.3MnO3 thin films

    OpenAIRE

    Nath, T. K.; Neal, J. R.; G A Gehring

    2008-01-01

    Magneto optic measurements are a very powerful tool for investigating the polarization of a conduction band as a function of temperature and are used here to study the polarization of the mobile electrons in 50nm LSMO (x=0.3) strained thin films grown epitaxially on single crystalline (001) LaAlO3 (LAO) and (001) lattice matched substrate (LSAT). The magnetic circular dichroism (MCD) has been investigated in magnetic fields up to 0.5 T and over a temperature range (10 to 450 K). The MCD spect...

  4. STUDY ON MAGNETIC FIELD-INDUCED ORIENTATION OF A CHIRAL SIDE-CHAIN LIQUID CRYSTAL POLYACRYLATE USING INFRARED DICHROISM

    Institute of Scientific and Technical Information of China (English)

    HE Liu; JIN Shunzi; ZHANG Shufan; QI Zongneng; WANG Fosong

    1996-01-01

    Magnetic field-induced orientation of a chiral side chain liquid crystalline polyacrylate (P-11) was studied by using IR dichroism. For the investigated P-11, it has been shown that the magnetic alignment takes place over the entire temperature range between its melting point and clearing point and the orientation level is strongly temperature-dependent, the development with time of the magnetic orientation follows an exponential-type relation,and the smectic phase state influences the thermal relaxation process in the absence of the magnetic field.

  5. Magnetic exchange coupling in 3d-4f molecular nanomagnets investigated by X-ray magnetic circular dichroism

    International Nuclear Information System (INIS)

    Full text: Single-molecule magnets are exchange-coupled spin clusters showing slow relaxation of magnetization. In recent years, efforts have been intensified to increase the magnetization reversal barrier and thus enhance relaxation times by combining rare earth ions with transition-metal ions. Rare-earth ions exhibit very large magnetic anisotropies due to their strong spin-orbit coupling and their mostly unquenched orbital momentum. In this contribution we use X-ray magnetic circular dichroism to observe element-specific magnetization curves. In conjunction with SQUID magnetization and susceptibility measurements, we are able to obtain information about the magnetic coupling between 3d and 4f ions. (author)

  6. X-ray magnetic circular dichroism study of Re 5d magnetism in Sr2CrReO6

    OpenAIRE

    Majewski, P.; Gepraegs, S.; Sanganas, O.; Opel, M.; Gross, R.; Wilhelm, F; Rogalev, A.; Alff, L.

    2006-01-01

    We have measured Re 5d spin and orbital magnetic moments in the ferrimagnetic double perovskite Sr2CrReO6 by X-ray magnetic circular dichroism at the L_{2,3} edges. In fair agreement with recent band-structure calculations [Vaitheeswaran et. al., Ref 1], at the Re site a large 5d spin magnetic moment of -0.68 mu_B and a considerable orbital moment of +0.25 mu_B have been detected. We found that the Curie temperature of the double perovskites A2BB'O6 scales with the spin magnetic moment of the...

  7. Helical nature of poly(dI-dC).poly(dI-dC). Vibrational circular dichroism results.

    OpenAIRE

    Wang, L.; Keiderling, T A

    1993-01-01

    Poly(dI-dC).poly(dI-dC) was studied using vibrational circular dichroism and IR spectroscopy in both the base deformation C = O and symmetric PO2- stretching regions. VCD spectra of this duplex under low salt conditions are consistent with its having a B-form structure. Addition of 5 M NaCl leads to relatively uniform VCD intensity loss which is consistent with loss of helical structure rather than formation of an intermediate state between the B and Z forms. This duplex polymer under high sa...

  8. Vibrational circular dichroism of A-, B-, and Z-form nucleic acids in the PO2-stretching region.

    OpenAIRE

    Wang, L.; Yang, L; Keiderling, T A

    1994-01-01

    Vibrational circular dichroism (VCD) spectra were measured for H2O solutions of several natural and model DNAs (single and double strands, oligomers and polymers) in the B-form, poly(dG-dC)-poly(dG-dC) in the Z-form, and various duplex RNAs in an A-form over the PO2-stretching region. Only the symmetric PO2 stretch at approximately 1075 cm-1 yields a significant intensity VCD signal. Differences of the PO2-stretching VCD spectra found for these conformational types are consistent with the spe...

  9. Switched linear encoding with rectified linear autoencoders

    OpenAIRE

    Johnson, Leif; Corcoran, Craig

    2013-01-01

    Several recent results in machine learning have established formal connections between autoencoders---artificial neural network models that attempt to reproduce their inputs---and other coding models like sparse coding and K-means. This paper explores in depth an autoencoder model that is constructed using rectified linear activations on its hidden units. Our analysis builds on recent results to further unify the world of sparse linear coding models. We provide an intuitive interpretation of ...

  10. Linear integrated circuits

    Science.gov (United States)

    Young, T.

    This book is intended to be used as a textbook in a one-semester course at a variety of levels. Because of self-study features incorporated, it may also be used by practicing electronic engineers as a formal and thorough introduction to the subject. The distinction between linear and digital integrated circuits is discussed, taking into account digital and linear signal characteristics, linear and digital integrated circuit characteristics, the definitions for linear and digital circuits, applications of digital and linear integrated circuits, aspects of fabrication, packaging, and classification and numbering. Operational amplifiers are considered along with linear integrated circuit (LIC) power requirements and power supplies, voltage and current regulators, linear amplifiers, linear integrated circuit oscillators, wave-shaping circuits, active filters, DA and AD converters, demodulators, comparators, instrument amplifiers, current difference amplifiers, analog circuits and devices, and aspects of troubleshooting.

  11. A linear programming manual

    Science.gov (United States)

    Tuey, R. C.

    1972-01-01

    Computer solutions of linear programming problems are outlined. Information covers vector spaces, convex sets, and matrix algebra elements for solving simultaneous linear equations. Dual problems, reduced cost analysis, ranges, and error analysis are illustrated.

  12. Linear regression analysis

    OpenAIRE

    Kılıç, Selim

    2013-01-01

    Linear regression is an approach to modeling the association between a numeric dependent variable y and one or more independent variables denoted X. The case of one explanatory variable in regression model is called simple linear regression. For more than one explanatory variable, then the model is called multiple linear regression. The dependent variable should be a numeric variable in linear regression. It is recommended at least 10 times as many cases as the number of independent variables...

  13. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    Directory of Open Access Journals (Sweden)

    Lees Jonathan G

    2008-01-01

    Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  14. Optimized Spiral Metal-Gallium-Nitride Nanowire Cavity for Ultra-High Circular Dichroism Ultraviolet Lasing at Room Temperature

    Science.gov (United States)

    Liao, Wei-Chun; Liao, Shu-Wei; Chen, Kuo-Ju; Hsiao, Yu-Hao; Chang, Shu-Wei; Kuo, Hao-Chung; Shih, Min-Hsiung

    2016-05-01

    Circularly polarized laser sources with small footprints and high efficiencies can possess advanced functionalities in optical communication and biophotonic integrated systems. However, the conventional lasers with additional circular-polarization converters are bulky and hardly compatible with nanophotonic circuits, and most active chiral plasmonic nanostructures nowadays exhibit broadband emission and low circular dichroism. In this work, with spirals of gallium nitride (GaN) nanowires (NWRs) covered by a metal layer, we demonstrated an ultrasmall semiconductor laser capable of emitting circularly-polarized photons. The left- and right-hand spiral metal nanowire cavities with varied periods were designed at ultraviolet wavelengths to achieve the high quality factor circular dichroism metastructures. The dissymmetry factors characterizing the degrees of circular polarizations of the left- and right-hand chiral lasers were 1.4 and ‑1.6 (±2 if perfectly circular polarized), respectively. The results show that the chiral cavities with only 5 spiral periods can achieve lasing signals with the high degrees of circular polarizations.

  15. A computational protocol for the study of circularly polarized phosphorescence and circular dichroism in spin-forbidden absorption.

    Science.gov (United States)

    Kamiński, Maciej; Cukras, Janusz; Pecul, Magdalena; Rizzo, Antonio; Coriani, Sonia

    2015-07-15

    We present a computational methodology to calculate the intensity of circular dichroism (CD) in spin-forbidden absorption and of circularly polarized phosphorescence (CPP) signals, a manifestation of the optical activity of the triplet-singlet transitions in chiral compounds. The protocol is based on the response function formalism and is implemented at the level of time-dependent density functional theory. It has been employed to calculate the spin-forbidden circular dichroism and circularly polarized phosphorescence signals of valence n → π* and n ← π* transitions, respectively, in several chiral enones and diketones. Basis set effects in the length and velocity gauge formulations have been explored, and the accuracy achieved when employing approximate (mean-field and effective nuclear charge) spin-orbit operators has been investigated. CPP is shown to be a sensitive probe of the triplet excited state structure. In many cases the sign of the spin-forbidden CD and CPP signals are opposite. For the β,γ-enones under investigation, where there are two minima on the lowest triplet excited state potential energy surface, each minimum exhibits a CPP signal of a different sign. PMID:26126575

  16. Lineare Algebra I & II

    OpenAIRE

    Greuel, Gert-Martin

    2000-01-01

    Inhalte der Grundvorlesungen Lineare Algebra I und II im Winter- und Sommersemester 1999/2000: Gruppen, Ringe, Körper, Vektorräume, lineare Abbildungen, Determinanten, lineare Gleichungssysteme, Polynomring, Eigenwerte, Jordansche Normalform, endlich-dimensionale Hilberträume, Hauptachsentransformation, multilineare Algebra, Dualraum, Tensorprodukt, äußeres Produkt, Einführung in Singular.

  17. Linear-Algebra Programs

    Science.gov (United States)

    Lawson, C. L.; Krogh, F. T.; Gold, S. S.; Kincaid, D. R.; Sullivan, J.; Williams, E.; Hanson, R. J.; Haskell, K.; Dongarra, J.; Moler, C. B.

    1982-01-01

    The Basic Linear Algebra Subprograms (BLAS) library is a collection of 38 FORTRAN-callable routines for performing basic operations of numerical linear algebra. BLAS library is portable and efficient source of basic operations for designers of programs involving linear algebriac computations. BLAS library is supplied in portable FORTRAN and Assembler code versions for IBM 370, UNIVAC 1100 and CDC 6000 series computers.

  18. Absorption Linear Dichroism Measured Directly on a Single Light-Harvesting System: The Role of Disorder in Chlorosomes of Green Photosynthetic Bacteria

    Czech Academy of Sciences Publication Activity Database

    Furumaki, S.; Vácha, František; Habuchi, S.; Tsukatani, Y.; Bryant, D.A.; Vácha, M.

    2011-01-01

    Roč. 133, č. 17 (2011), s. 6703-6710. ISSN 0002-7863 R&D Projects: GA ČR GA206/09/0375 Institutional research plan: CEZ:AV0Z50510513 Keywords : CHLOROBIUM-TEPIDUM * BACTERIOCHLOROPHYLL-C * SUPRAMOLECULAR ORGANIZATION Subject RIV: EF - Botanics Impact factor: 9.907, year: 2011

  19. 太阳能电池最大功率跟踪的线性近似法分析%Experimental Analysis of Solar Cell Maximum Power Point Tracking Based on Linear Approximation Method

    Institute of Scientific and Technical Information of China (English)

    袁银梅

    2011-01-01

    The linear approximation method is one of solar cell maximum power point tracking methods.Based on this method, the experiment is carried out.On three kinds of solar cells ( mono - crystalline silicon, polycrystalline silicon and amorphous silicon), the variations of the optimum working voltage Um , the optimum working current Im and the maximum output power Pm with light intensity are inspected.The results show that in the case of the same kind of solar cell, with light intensity changes, Um is essentially unchanged; Im and Pm are both linear with light intensity.With the same light intensity and at the optimum working point, parameters of mono - crystalline silicon cell are maximum, followed by polycrystalline silicon cell's, and those of amorphous silicon cell are minimum.%对太阳能电池最大功率的跟踪方法——线性近似法进行了实验分析,考察单晶硅、多晶硅、非晶硅三种材料的太阳能电池最佳工作电压Um、最佳工作电流,Im和最大输出功率Pm随光照强度的变化情况.结果发现:对同一种太阳能电池,光照强度改变时,Um可以认为基本不变;Im和Pm与光照强度均呈线性关系.同一光照强度下,单晶硅电池最佳工作点参数最大,多晶硅电池次之,非晶硅电池数值最小.

  20. Controlled cobalt doping in the spinel structure of magnetosome magnetite: new evidences from element- and site-specific X-ray magnetic circular dichroism analyses.

    Science.gov (United States)

    Li, Jinhua; Menguy, Nicolas; Arrio, Marie-Anne; Sainctavit, Philippe; Juhin, Amélie; Wang, Yinzhao; Chen, Haitao; Bunau, Oana; Otero, Edwige; Ohresser, Philippe; Pan, Yongxin

    2016-08-01

    The biomineralization of magnetite nanocrystals (called magnetosomes) by magnetotactic bacteria (MTB) has attracted intense interest in biology, geology and materials science due to the precise morphology of the particles, the chain-like assembly and their unique magnetic properties. Great efforts have been recently made in producing transition metal-doped magnetosomes with modified magnetic properties for a range of applications. Despite some successful outcomes, the coordination chemistry and magnetism of such metal-doped magnetosomes still remain largely unknown. Here, we present new evidences from X-ray magnetic circular dichroism (XMCD) for element- and site-specific magnetic analyses that cobalt is incorporated in the spinel structure of the magnetosomes within Magnetospirillum magneticum AMB-1 through the replacement of Fe(2+) ions by Co(2+) ions in octahedral (Oh) sites of magnetite. Both XMCD at Fe and Co L2,3 edges, and energy-dispersive X-ray spectroscopy on transmission electron microscopy analyses reveal a heterogeneous distribution of cobalt occurring either in different particles or inside individual particles. Compared with non-doped one, cobalt-doped magnetosome sample has lower Verwey transition temperature and larger magnetic coercivity, related to the amount of doped cobalt. This study also demonstrates that the addition of trace cobalt in the growth medium can significantly improve both the cell growth and the magnetosome formation within M. magneticum AMB-1. Together with the cobalt occupancy within the spinel structure of magnetosomes, this study indicates that MTB may provide a promising biomimetic system for producing chains of metal-doped single-domain magnetite with an appropriate tuning of the magnetic properties for technological and biomedical applications. PMID:27512138

  1. Basic linear algebra

    CERN Document Server

    Blyth, T S

    2002-01-01

    Basic Linear Algebra is a text for first year students leading from concrete examples to abstract theorems, via tutorial-type exercises. More exercises (of the kind a student may expect in examination papers) are grouped at the end of each section. The book covers the most important basics of any first course on linear algebra, explaining the algebra of matrices with applications to analytic geometry, systems of linear equations, difference equations and complex numbers. Linear equations are treated via Hermite normal forms which provides a successful and concrete explanation of the notion of linear independence. Another important highlight is the connection between linear mappings and matrices leading to the change of basis theorem which opens the door to the notion of similarity. This new and revised edition features additional exercises and coverage of Cramer's rule (omitted from the first edition). However, it is the new, extra chapter on computer assistance that will be of particular interest to readers:...

  2. Linear collider: a preview

    Energy Technology Data Exchange (ETDEWEB)

    Wiedemann, H.

    1981-11-01

    Since no linear colliders have been built yet it is difficult to know at what energy the linear cost scaling of linear colliders drops below the quadratic scaling of storage rings. There is, however, no doubt that a linear collider facility for a center of mass energy above say 500 GeV is significantly cheaper than an equivalent storage ring. In order to make the linear collider principle feasible at very high energies a number of problems have to be solved. There are two kinds of problems: one which is related to the feasibility of the principle and the other kind of problems is associated with minimizing the cost of constructing and operating such a facility. This lecture series describes the problems and possible solutions. Since the real test of a principle requires the construction of a prototype I will in the last chapter describe the SLC project at the Stanford Linear Accelerator Center.

  3. Linearity in Process Languages

    DEFF Research Database (Denmark)

    Nygaard, Mikkel; Winskel, Glynn

    2002-01-01

    The meaning and mathematical consequences of linearity (managing without a presumed ability to copy) are studied for a path-based model of processes which is also a model of affine-linear logic. This connection yields an affine-linear language for processes, automatically respecting open-map bisi......The meaning and mathematical consequences of linearity (managing without a presumed ability to copy) are studied for a path-based model of processes which is also a model of affine-linear logic. This connection yields an affine-linear language for processes, automatically respecting open......-map bisimulation, in which a range of process operations can be expressed. An operational semantics is provided for the tensor fragment of the language. Different ways to make assemblies of processes lead to different choices of exponential, some of which respect bisimulation....

  4. Adding linear orders

    CERN Document Server

    Shelah, Saharon

    2011-01-01

    We address the following question: Can we expand an NIP theory by adding a linear order such that the expansion is still NIP? Easily, if acl(A)=A for all A, then this is true. Otherwise, we give counterexamples. More precisely, there is a totally categorical theory for which every expansion by a linear order has IP. There is also an \\omega-stable NDOP theory for which every expansion by a linear order interprets bounded arithmetic.

  5. Efficient Non Linear Loudspeakers

    DEFF Research Database (Denmark)

    Petersen, Bo R.; Agerkvist, Finn T.

    2006-01-01

    Loudspeakers have traditionally been designed to be as linear as possible. However, as techniques for compensating non linearities are emerging, it becomes possible to use other design criteria. This paper present and examines a new idea for improving the efficiency of loudspeakers at high levels...... by changing the voice coil layout. This deliberate non-linear design has the benefit that a smaller amplifier can be used, which has the benefit of reducing system cost as well as reducing power consumption....

  6. Deep Linear Discriminant Analysis

    OpenAIRE

    Dorfer, Matthias; Kelz, Rainer; WIDMER, Gerhard

    2015-01-01

    We introduce Deep Linear Discriminant Analysis (DeepLDA) which learns linearly separable latent representations in an end-to-end fashion. Classic LDA extracts features which preserve class separability and is used for dimensionality reduction for many classification problems. The central idea of this paper is to put LDA on top of a deep neural network. This can be seen as a non-linear extension of classic LDA. Instead of maximizing the likelihood of target labels for individual samples, we pr...

  7. Magnetism of unconventional nanoscaled materials. An X-ray circular dichroism and muon spin rotation study

    International Nuclear Information System (INIS)

    The physical properties of nanoparticles deviate strongly from its bulk counterparts. In particular, the magnetic properties change strongly due to an elevated number of surface compared to bulk atoms. As a consequence the orbital magnetic moment in nanoparticles as well as the magnetic anisotropy is enhanced. Therefore, such nanoparticles have great potential in e.g. next generation high density data storage devices. A promising way to realize such devices is to deposit nanoparticles on graphene. Depending on the preparation conditions the templated growth of nanocluster arrays with different particle size and shape is possible. Since graphene possesses outstanding properties as well it is congruous to combine the advantages of both systems and to investigate its principle properties in more detail. Thus, one part of this work is dedicated to the size and shape dependence of electronic and magnetic properties of Ni nanoclusters on graphene. The magnetic properties were investigated using X-ray Magnetic Circular Dichroism (XMCD). From the corresponding absorption spectra, the electronic structure and the nanoparticle substrate interaction could be determined. Two sets of nanoparticles were investigated, with triangular and spherical shape. For each set the size was varied. Nonmagnetic absorption spectra indicate a strong interaction between the Ni nanoclusters and the graphene substrate. The integrated absorption signal which is a measure of the number of unoccupied states in the Ni d shell decreases strongly with decreasing cluster size. This means an enhanced occupancy of the Ni d states, most likely caused by charge transfer at the Ni nanocluster/graphene interface. As a consequence the magnetic moment was much smaller than expected for nanoclusters for all samples investigated. The smallest value obtained was only 50% of the respective bulk magnetic moment. The magnetic moment increases disproportionally and converges towards bulk properties above 2 ML. No

  8. Magnetism of unconventional nanoscaled materials. An X-ray circular dichroism and muon spin rotation study

    Energy Technology Data Exchange (ETDEWEB)

    Tietze, Thomas Hermann

    2014-12-15

    The physical properties of nanoparticles deviate strongly from its bulk counterparts. In particular, the magnetic properties change strongly due to an elevated number of surface compared to bulk atoms. As a consequence the orbital magnetic moment in nanoparticles as well as the magnetic anisotropy is enhanced. Therefore, such nanoparticles have great potential in e.g. next generation high density data storage devices. A promising way to realize such devices is to deposit nanoparticles on graphene. Depending on the preparation conditions the templated growth of nanocluster arrays with different particle size and shape is possible. Since graphene possesses outstanding properties as well it is congruous to combine the advantages of both systems and to investigate its principle properties in more detail. Thus, one part of this work is dedicated to the size and shape dependence of electronic and magnetic properties of Ni nanoclusters on graphene. The magnetic properties were investigated using X-ray Magnetic Circular Dichroism (XMCD). From the corresponding absorption spectra, the electronic structure and the nanoparticle substrate interaction could be determined. Two sets of nanoparticles were investigated, with triangular and spherical shape. For each set the size was varied. Nonmagnetic absorption spectra indicate a strong interaction between the Ni nanoclusters and the graphene substrate. The integrated absorption signal which is a measure of the number of unoccupied states in the Ni d shell decreases strongly with decreasing cluster size. This means an enhanced occupancy of the Ni d states, most likely caused by charge transfer at the Ni nanocluster/graphene interface. As a consequence the magnetic moment was much smaller than expected for nanoclusters for all samples investigated. The smallest value obtained was only 50% of the respective bulk magnetic moment. The magnetic moment increases disproportionally and converges towards bulk properties above 2 ML. No

  9. Linear models with R

    CERN Document Server

    Faraway, Julian J

    2014-01-01

    A Hands-On Way to Learning Data AnalysisPart of the core of statistics, linear models are used to make predictions and explain the relationship between the response and the predictors. Understanding linear models is crucial to a broader competence in the practice of statistics. Linear Models with R, Second Edition explains how to use linear models in physical science, engineering, social science, and business applications. The book incorporates several improvements that reflect how the world of R has greatly expanded since the publication of the first edition.New to the Second EditionReorganiz

  10. Linear integrated circuits

    CERN Document Server

    Carr, Joseph

    1996-01-01

    The linear IC market is large and growing, as is the demand for well trained technicians and engineers who understand how these devices work and how to apply them. Linear Integrated Circuits provides in-depth coverage of the devices and their operation, but not at the expense of practical applications in which linear devices figure prominently. This book is written for a wide readership from FE and first degree students, to hobbyists and professionals.Chapter 1 offers a general introduction that will provide students with the foundations of linear IC technology. From chapter 2 onwa

  11. Generalized Linear Orthomorphisms

    Directory of Open Access Journals (Sweden)

    Haiqing Han

    2013-05-01

    Full Text Available In this study, we generalize the conception of orthomorphisms and obtain a counting formula on the generalized linear orthomorphisms over the Galois field with the arbitrary prime number p as the characteristic. Thus the partial generation algorithm of generalized linear orthomorphisms is achieved. The counting formula of the linear orthomorphisms over the finite field with characteristic 2 is the special case in our results. Furthermore, the generalized linear orthomorphisms generated and discussed in this study can gain the maximum branch number when they are designed as P-permutations.

  12. Linear Motor Free Piston Compressor

    Science.gov (United States)

    Bloomfield, David P.

    1995-02-01

    A Linear Motor Free Piston Compressor (LMFPC), a free piston pressure recovery system for fuel cell powerplants was developed. The LMFPC consists of a reciprocating compressor and a reciprocating expander which are separated by a piston. In the past energy efficient turbochargers have been used for pressure large (over 50 kW) fuel cell powerplants by recovering pressure energy from the powerplant exhaust. A free piston compressor allows pressurizing 3 - 5 kW sized fuel cell powerplants. The motivation for pressurizing PEM fuel cell powerplants is to improve fuel cell performance. Pressurization of direct methanol fuel cells will be required if PEM membranes are to be used Direct methanol oxidation anode catalysts require high temperatures to operate at reasonable power densities. The elevated temperatures above 80 C will cause high water loss from conventional PEM membranes unless pressurization is employed. Because pressurization is an energy intensive process, recovery of the pressure energy is required to permit high efficiency in fuel cell powerplants. A complete LMFPC which can pressurize a 3 kW fuel cell stack was built. This unit is one of several that were constructed during the course of the program.

  13. Mechanical design and analysis of an eight-pole superconducting vector magnet for soft x-ray magnetic dichroism measurements

    Energy Technology Data Exchange (ETDEWEB)

    Arbelaez, D.; Black, A.; Prestemon, S.O.; Wang, S.; Chen, J.; Arenholz, E.

    2010-01-13

    An eight-pole superconducting magnet is being developed for soft x-ray magnetic dichroism (XMD) experiments at the Advanced Light Source, Lawrence Berkley National Laboratory (LBNL). Eight conical Nb{sub 3}Sn coils with Holmium poles are arranged in octahedral symmetry to form four dipole pairs that provide magnetic fields of up to 5 T in any direction relative to the incoming x-ray beam. The dimensions of the magnet yoke as well as pole taper, diameter, and length were optimized for maximum peak field in the magnet center using the software package TOSCA. The structural analysis of the magnet is performed using ANSYS with the coil properties derived using a numerical homogenization scheme. It is found that the use of orthotropic material properties for the coil has an important influence in the design of the magnet.

  14. X-ray absorption and magnetic circular dichroism studies of Co2FeAl in magnetic tunnel junctions

    Energy Technology Data Exchange (ETDEWEB)

    Ebke, D.; Kugler, Z.; Thomas, P.; Schebaum, O.; Schafers, M.; Nissen, D.; Schmalhorst, J.; Hutten, A.; Arenholz, E.; Thomas, A.

    2010-01-11

    The bulk magnetic moment and the element specific magnetic moment of Co{sub 2}FeAl thin films were examined as a function of annealing temperature by alternating gradient magnetometer (AGM) and X-ray absorption spectroscopy (XAS)/X-ray magnetic circular dichroism (XMCD), respectively. A high magnetic moment can be achieved for all annealing temperatures and the predicted bulk and interface magnetic moment of about 5 {tilde A}{sub B} are reached via heating. We will also present tunnel magnetoresistance (TMR) values of up to 153% at room temperature and 260% at 13 K for MgO based magnetic tunnel junctions (MTJs) with Co{sub 2}FeAl and Co-Fe electrodes.

  15. Energy-loss magnetic chiral dichroism study of epitaxial MnAs film on GaAs(001)

    International Nuclear Information System (INIS)

    The room-temperature ferromagnetic behavior of MnAs/GaAs(001) thin film has been locally explored by Transmission Electron Microscope (TEM). We first differentiated hexagonal α-MnAs and quasi-hexagonal β-MnAs which are very similar in atomic structure by electron diffraction. Local magnetic moment information of the identified α-MnAs was extracted from manganese-L2,3 edges using Energy-loss Magnetic Circular Dichroism technique and the ratio of orbital to spin magnetic moment was measured. In this experiment, atomic structure identification, chemical analysis, and magnetic moment measurement were simultaneously achieved at high spatial resolution in TEM, thus providing a potential method for in-situ study of local properties of multiphase magnetic materials

  16. X-ray magnetic circular dichroism and small angle neutron scattering study of thiol capped gold nanoparticles.

    Energy Technology Data Exchange (ETDEWEB)

    de la Venta, J.; Bouzas, V.; Pucci, A.; Laguna-Marco, M. A.; Haskel, D.; Pinel, E. F.; te Velthuis, S. G. E.; Hoffmann, A.; Lal, J.; Bleuel, M.; Ruggeri, G.; de Julian, C.; Garcia, M. A.; Univ. Complutense de Madrid; Inst. de Magnetismo Aplicado UCM; Univ. Pisa; Univ. di Padova

    2009-11-01

    X-ray magnetic circular dichroism (XMCD) and Small Angle Neutron Scattering (SANS) measurements were performed on thiol capped Au nanoparticles (NPs) embedded into polyethylene. An XMCD signal of 0.8 {center_dot} 10{sup -4} was found at the Au L{sub 3} edge of thiol capped Au NPs embedded in a polyethylene matrix for which Superconducting Quantum Interference Device (SQUID) magnetometry yielded a saturation magnetization, M{sub s}, of 0.06 emu/g{sub Au}. SANS measurements showed that the 3.2 nm average-diameter nanoparticles are 28% polydispersed, but no detectable SANS magnetic signal was found with the resolution and sensitivity accessible with the neutron experiment. A comparison with previous experiments carried out on Au NPs and multilayers, yield to different values between XMCD signals and magnetization measured by SQUID magnetometer. We discuss the origin of those differences.

  17. X-ray magnetic circular dichroism and small angle neutron scattering studies of thiol capped gold nanoparticles.

    Energy Technology Data Exchange (ETDEWEB)

    de la Venta, J.; Bouzas, V.; Pucci, A.; Laguna-Marco, M. A.; Haskel, D.; te Velthuis, S. G. E; Hoffmann, A.; Lal, J.; Bleuel, M.; Ruggeri, G.; de Julian Fernandez, C.; Garcia, M. A.; Univ.Complutense de Madrid; Inst. de Magnetismo Aplicado; Univ. of Pisa; Lab. di Magnetismo Molecolare

    2009-01-01

    X-ray magnetic circular dichroism (XMCD) and Small Angle Neutron Scattering (SANS) measurements were performed on thiol capped Au nanoparticles (NPs) embedded into polyethylene. An XMCD signal of 0.8 {center_dot} 10{sup -4} was found at the Au L{sub 3} edge of thiol capped Au NPs embedded in a polyethylene matrix for which Superconducting Quantum Interference Device (SQUID) magnetometry yielded a saturation magnetization, M{sub s}, of 0.06 emu/g{sub Au}. SANS measurements showed that the 3.2 nm average-diameter nanoparticles are 28% polydispersed, but no detectable SANS magnetic signal was found with the resolution and sensitivity accessible with the neutron experiment. A comparison with previous experiments carried out on Au NPs and multilayers, yield to different values between XMCD signals and magnetization measured by SQUID magnetometer. We discuss the origin of those differences.

  18. A QM/MM-MD study on protein electronic properties: Circular dichroism spectra of oxytocin and insulin

    International Nuclear Information System (INIS)

    A QM/MM (quantum-mechanical/molecular-mechanical) molecular-dynamics approach based on the generalized hybrid-orbital (GHO) method, in conjunction with the second-order perturbation (MP2) theory and the second-order approximate coupled-cluster (CC2) model, is employed to calculate electronic property accounting for a protein environment. Circular dichroism (CD) spectra originating from chiral disulfide bridges of oxytocin and insulin at room temperature are computed. It is shown that the sampling of thermal fluctuation of molecular geometries facilitated by the GHO-MD method plays an important role in the obtained spectra. It is demonstrated that, while the protein environments in an oxytocin molecule have significant electrostatic influence on its chiral center, it is compensated by solvent induced charges. This gives a reasonable explanation to experimental observations. GHO-MD simulations starting from different experimental structures of insulin indicate that existence of the disulfide bridges with negative dihedral angles is crucial.

  19. TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids

    DEFF Research Database (Denmark)

    Fahleson, Tobias; Kauczor, Joanna; Norman, Patrick;

    2015-01-01

    We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200–300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM–B3LYP functionals. Solvent...... effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines...... and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general...

  20. Development of a depth-resolved x-ray magnetic circular dichroism: application to Fe/Cu(100) ultrathin films

    International Nuclear Information System (INIS)

    A depth-resolved technique is applied in the x-ray magnetic circular dichroism (XMCD) method by controlling the probing depth of the electron yield XMCD spectra. The usefulness of this technique is demonstrated for the study of magnetic structures of 4 and 8 ML Fe films grown on Cu(100), which are known to exhibit peculiar magnetic depth profiles. It was directly shown that the 4 ML film is uniformly magnetized, while the magnetic moment is localized at the surface in the case of the 8 ML film. The XMCD spectrum for each layer of the 4 ML film was separately extracted. All the extracted spectra were almost identical to each other, confirming the ferromagnetic coupling over the whole film. As for the 8 ML film, it was suggested that the surface two layers are ferromagnetically coupled, while the inner layers are in a spin density wave state with a wavenumber q=2π/2.4d

  1. A computational protocol for the study of circularly polarized phosphorescence and circular dichroism in spin-forbidden absorption

    DEFF Research Database (Denmark)

    Kaminski, Maciej; Cukras, Janusz; Pecul, Magdalena;

    2015-01-01

    We present a computational methodology to calculate the intensity of circular dichroism (CD) in spinforbidden absorption and of circularly polarized phosphorescence (CPP) signals, a manifestation of the optical activity of the triplet–singlet transitions in chiral compounds. The protocol is based...... chiral enones and diketones. Basis set effects in the length and velocity gauge formulations have been explored, and the accuracy achieved when employing approximate (mean-field and effective nuclear charge) spin–orbit operators has been investigated. CPP is shown to be a sensitive probe of the triplet...... excited state structure. In many cases the sign of the spin-forbidden CD and CPP signals are opposite. For the b,g-enones under investigation, where there are two minima on the lowest triplet excited state potential energy surface, each minimum exhibits a CPP signal of a different sign....

  2. Gigantic transverse x-ray magnetic circular dichroism in ultrathin Co in Au/Co/Au(001)

    International Nuclear Information System (INIS)

    Transverse-geometry x-ray magnetic circular dichroism (TXMCD) measurements on Au/Co-staircase/Au(001) reveal the orbital origin of intrinsic in-plane magnetic anisotropy A gigantic TXMCD was successfully observed at the Co L3,2 edges for Co thickness (tC0) in the 2-monolayer regime. A TXMCD-sum-rule analysis shows a remarkable enhancement of an orbital-moment anisotropy (Δmorb) and of an in-plane magnetic dipole moment (m||T). Both Δmorb and m||T exhibit close similarity in tCo dependence, reflecting the in-plane magnetic anisotropy These observations evidence that extremely strong, intrinsic, in-plane magnetic anisotropy originates from the anisotropic orbital part of the wave function, dominating the dipole-dipole-interaction-derived, extrinsic, in-plane magnetic anisotropy.

  3. Chemistry of porphyrin-appended cellulose strands with a helical structure: spectroscopy, electrochemistry, and in situ circular dichroism spectroelectrochemistry.

    Science.gov (United States)

    Redl, F X; Lutz, M; Daub, J

    2001-12-17

    Around 100 porphyrin units have been selectively linked at C(6)-O to a cellulose (Avicel). The properties of the metal-free and zincated porphyrin-celluloses 2 and Zn-2 have been determined by optical and electrochemical methods. Circular dichroism indicates a helical arrangement of the porphyrin units and reveals intra-chain coupling reminiscent, in the broadest sense, of strands of nucleic acids. Cyclic voltammetry and spectroelectrochemistry have been used to characterize the radical ions and dianions. The electrochromism of the oxidation of cellulose 2 to porphyrin radical cations of 2 has been employed for both molecular switching and the transduction of an electrochemical input into chiroptical signal expression. PMID:11822435

  4. Local X-ray magnetic circular dichroism study of Fe/Cu(111) using a tunneling smart tip.

    Science.gov (United States)

    DiLullo, Andrew; Shirato, Nozomi; Cummings, Marvin; Kersell, Heath; Chang, Hao; Rosenmann, Daniel; Miller, Dean; Freeland, John W; Hla, Saw Wai; Rose, Volker

    2016-03-01

    Localized spectroscopy with simultaneous topographic, elemental and magnetic information is presented. A synchrotron X-ray scanning tunneling microscope has been employed for the local study of the X-ray magnetic circular dichroism at the Fe L2,3-edges of a thin iron film grown on Cu(111). Polarization-dependent X-ray absorption spectra have been obtained through a tunneling smart tip that serves as a photoelectron detector. In contrast to conventional spin-polarized scanning tunneling microscopy, X-ray excitations provide magnetic contrast even with a non-magnetic tip. Intensity variations in the photoexcited tip current point to chemical variations within a single magnetic Fe domain. PMID:26917146

  5. Theoretical description of circular dichroism in photoelectron angular distributions of randomly oriented chiral molecules after multi-photon photoionization

    CERN Document Server

    Goetz, R E; Nikoobakht, B; Berger, R; Koch, C P

    2016-01-01

    Photoelectron circular dichroism refers to the forward/backward asymmetry in the photoelectron angular distribution with respect to the propagation axis of circularly polarized light. It has recently been demonstrated in femtosecond multi-photon photoionization experiments with randomly oriented camphor and fenchone molecules [C. Lux et al., Angew. Chem. Int. Ed. 51, 5001 (2012);C. S. Lehmann et al., J. Chem. Phys. 139, 234307 (2013)]. A theoretical framework describing this process as (2+1) resonantly enhanced multi-photon ionization is constructed, which consists of two-photon photoselection from randomly oriented molecules and successive one-photon ionisation of the photoselected molecules. It combines perturbation theory for the light-matter interaction with ab initio calculations for the two-photon absorption and a single-center expansion of the photoelectron wavefunction in terms of hydrogenic continuum functions. It is verified that the model correctly reproduces the basic symmetry behavior expected un...

  6. Soft x-ray circular dichroism and scattering using a modulated elliptically polarizing wiggler and double synchronous detection

    Energy Technology Data Exchange (ETDEWEB)

    Sutherland, J.C.; Polewski, K.; Monteleone, D.C. [and others

    1998-01-23

    We have constructed an experimental station (beamline) at the National Synchrotron Light Source to measure circular dichroism (CD) using soft x-rays (250 {le} hv {le} 900 eV) from a time modulated elliptically polarizing wiggler. The polarization of the soft x-ray beam switches periodically between two opposite polarizations, hence permitting the use of phase-sensitive (lock-in) detection. While the wiggler can be modulated at frequencies up to 100 Hz, switching transients limit the actual practical frequency to {approx}25 Hz. With analog detection, switching transients are blocked by a chopper synchronized to the frequency and phase of the wiggler. The CD is obtained from the ratio of the signal recovered at the frequency of polarization modulation, f, to the average beam intensity, which is recovered by synchronous detection at frequency 2f.

  7. A QM/MM-MD study on protein electronic properties: Circular dichroism spectra of oxytocin and insulin

    Energy Technology Data Exchange (ETDEWEB)

    Kitagawa, Yuya [Graduate School of System Informatics, Kobe University, Kobe 657-8501 (Japan); CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012 (Japan); Akinaga, Yoshinobu [RIKEN Advanced Institute for Computational Science, Kobe 650-0047 (Japan); Kawashima, Yukio [Department of Chemistry, Graduate School of Sciences, Kyushu University, Fukuoka 812-8581 (Japan); Institute of Advanced Research, Kyushu University, Fukuoka 812-8581 (Japan); Jung, Jaewoon [RIKEN Advanced Institute for Computational Science, Kobe 650-0047 (Japan); Ten-no, Seiichiro, E-mail: tenno@cs.kobe-u.ac.jp [Graduate School of System Informatics, Kobe University, Kobe 657-8501 (Japan); CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012 (Japan)

    2012-06-05

    A QM/MM (quantum-mechanical/molecular-mechanical) molecular-dynamics approach based on the generalized hybrid-orbital (GHO) method, in conjunction with the second-order perturbation (MP2) theory and the second-order approximate coupled-cluster (CC2) model, is employed to calculate electronic property accounting for a protein environment. Circular dichroism (CD) spectra originating from chiral disulfide bridges of oxytocin and insulin at room temperature are computed. It is shown that the sampling of thermal fluctuation of molecular geometries facilitated by the GHO-MD method plays an important role in the obtained spectra. It is demonstrated that, while the protein environments in an oxytocin molecule have significant electrostatic influence on its chiral center, it is compensated by solvent induced charges. This gives a reasonable explanation to experimental observations. GHO-MD simulations starting from different experimental structures of insulin indicate that existence of the disulfide bridges with negative dihedral angles is crucial.

  8. Toroidal Interaction and Propeller Chirality of Hexaarylbenzenes. Dynamic Domino Inversion Revealed by Combined Experimental and Theoretical Circular Dichroism Studies.

    Science.gov (United States)

    Kosaka, Tomoyo; Inoue, Yoshihisa; Mori, Tadashi

    2016-03-01

    Hexaarylbenzenes (HABs) have greatly attracted much attention due to their unique propeller-shaped structure and potential application in materials science, such as liquid crystals, molecular capsules/rotors, redox materials, nonlinear optical materials, as well as molecular wires. Less attention has however been paid to their propeller chirality. By introducing small point-chiral group(s) at the periphery of HABs, propeller chirality was effectively induced, provoking strong Cotton effects in the circular dichroism (CD) spectrum. Temperature and solvent polarity manipulate the dynamics of propeller inversion in solution. As such, whizzing toroids become more substantial in polar solvents and at an elevated temperature, where radial aromatic rings (propeller blades) prefer orthogonal alignment against the central benzene ring (C6 core), maximizing toroidal interactions. PMID:26882341

  9. Thermolysis of (1R,2R)-1,2-dideuteriocyclobutane. An application of vibrational circular dichroism to kinetic analysis

    International Nuclear Information System (INIS)

    The relative rates of geometric isomerization to racemization have been studied for the title compound by using a combination of infrared (IR) and vibrational circular dichroism (VCD) spectroscopies, respectively. The results are interpreted with a kinetic and mechanistic scheme which parallels that used by Berson, Pedersen, and Carpenter on a similar study of chiral cyclopropane-d2 thermolysis. Relative rates of isomerization to stereomutation of 1.5 +/- 0.4 were obtained which can be interpreted to be consistent with a mechanism best described by random methylene rotation in tetramethylene-d2. This is the first application of VCD to kinetic analysis, and the advantages of IR techniques over the more usually employed UV spectroscopies to this type of basic mechanistic problem are illustrated

  10. First principles structures and circular dichroism spectra for the close-packed and the 7/2 motif of collagen

    CERN Document Server

    Jalkanen, Karl J; Knapp-Mohammady, Michaela; Bohr, Jakob

    2012-01-01

    The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the close-packed motif is shown to be stable. For the case of the 7/2 motif a similar stability exists. The electronic circular dichroism of the close-packed model has a significant negative bias and a large signal. An interesting feature of the close-packed structure is the existence of a central channel. Simulations show that, if hydrogen atoms are placed in the cavity, a chain of molecular hydrogens is formed suggesting a possible biological function for molecular hydrogen.

  11. Simulations of Vibrational Circular Dichroism (VCD) and IR absorption spectra of several nucleic acid octamers. Comparison of calculated and experimental spectra

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, V.; Bouř, Petr; Wieser, H.

    Lugano : ETH, 2002. s. PC443. [WAT '02. World Congress of Theoretically Oriented Chemists /6./. 04.08.2002-09.08.2002, Lugano] Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism Subject RIV: CF - Physical ; Theoretical Chemistry

  12. Vibrational circular dichroism (VCD) and IR spectroscopic study of DNA structural changes induced by metal ions and drugs. Experimental results and theoretical simulations

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, V.; Sande van de, J. H.; Bouř, Petr; Wieser, H.

    Lille : Université des Sciences et Technologies de Lille, 2002. s. 13. [European Congress on Molecular Spectroscopy /26./. 01.09.2002-06.09.2002, Villeneuve d'Ascq] Institutional research plan: CEZ:AV0Z4055905 Keywords : vibrational circular dichroism Subject RIV: CF - Physical ; Theoretical Chemistry

  13. Curcumin Regulates Low-Linear Energy Transfer γ-Radiation-Induced NFκB-Dependent Telomerase Activity in Human Neuroblastoma Cells

    International Nuclear Information System (INIS)

    Purpose: We recently reported that curcumin attenuates ionizing radiation (IR)-induced survival signaling and proliferation in human neuroblastoma cells. Also, in the endothelial system, we have demonstrated that NFκB regulates IR-induced telomerase activity (TA). Accordingly, we investigated the effect of curcumin in inhibiting IR-induced NFκB-dependent hTERT transcription, TA, and cell survival in neuroblastoma cells. Methods and Materials: SK-N-MC or SH-SY5Y cells exposed to IR and treated with curcumin (10-100 nM) with or without IR were harvested after 1 h through 24 h. NFκB-dependent regulation was investigated either by luciferase reporter assays using pNFκB-, pGL3-354-, pGL3-347-, or pUSE-IκBα-Luc, p50/p65, or RelA siRNA-transfected cells. NFκB activity was analyzed using an electrophoretic mobility shift assay and hTERT expression using the quantitative polymerase chain reaction. TA was determined using the telomerase repeat amplification protocol assay and cell survival using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltertrazolium bromide and clonogenic assay. Results: Curcumin profoundly inhibited IR-induced NFκB. Consequently, curcumin significantly inhibited IR-induced TA and hTERT mRNA at all points investigated. Furthermore, IR-induced TA is regulated at the transcriptional level by triggering telomerase reverse transcriptase (TERT) promoter activation. Moreover, NFκB becomes functionally activated after IR and mediates TA upregulation by binding to the κB-binding region in the promoter region of the TERT gene. Consistently, elimination of the NFκB-recognition site on the telomerase promoter or inhibition of NFκB by the IκBα mutant compromises IR-induced telomerase promoter activation. Significantly, curcumin inhibited IR-induced TERT transcription. Consequently, curcumin inhibited hTERT mRNA and TA in NFκB overexpressed cells. Furthermore, curcumin enhanced the IR-induced inhibition of cell survival. Conclusions: These results

  14. Handbook on linear motor application

    International Nuclear Information System (INIS)

    This book guides the application for Linear motor. It lists classification and speciality of Linear Motor, terms of linear-induction motor, principle of the Motor, types on one-side linear-induction motor, bilateral linear-induction motor, linear-DC Motor on basic of the motor, linear-DC Motor for moving-coil type, linear-DC motor for permanent-magnet moving type, linear-DC motor for electricity non-utility type, linear-pulse motor for variable motor, linear-pulse motor for permanent magneto type, linear-vibration actuator, linear-vibration actuator for moving-coil type, linear synchronous motor, linear electromagnetic motor, linear electromagnetic solenoid, technical organization and magnetic levitation and linear motor and sensor.

  15. Linear Equations: Equivalence = Success

    Science.gov (United States)

    Baratta, Wendy

    2011-01-01

    The ability to solve linear equations sets students up for success in many areas of mathematics and other disciplines requiring formula manipulations. There are many reasons why solving linear equations is a challenging skill for students to master. One major barrier for students is the inability to interpret the equals sign as anything other than…

  16. Racetrack linear accelerators

    International Nuclear Information System (INIS)

    An improved recirculating electron beam linear accelerator of the racetrack type is described. The system comprises a beam path of four straight legs with four Pretzel bending magnets at the end of each leg to direct the beam into the next leg of the beam path. At least one of the beam path legs includes a linear accelerator. (UK)

  17. Duality in linear programming

    OpenAIRE

    Albici, Mihaela; Teselios, Delia; Prundeanu, Raluca; Popa, Ionela

    2010-01-01

    Any linear programming problem marked as P and called ”primal” can be seen in connection with another linear programming problem marked as D and called ”dual”. The economic interpretation of the dual model brings about new information when analyzing such phenomena and when substantiating decision making

  18. Efficient Non Linear Loudspeakers

    DEFF Research Database (Denmark)

    Petersen, Bo R.; Agerkvist, Finn T.

    2006-01-01

    Loudspeakers have traditionally been designed to be as linear as possible. However, as techniques for compensating non linearities are emerging, it becomes possible to use other design criteria. This paper present and examines a new idea for improving the efficiency of loudspeakers at high levels...

  19. Linear models: permutation methods

    Science.gov (United States)

    Cade, B.S.

    2005-01-01

    Permutation tests (see Permutation Based Inference) for the linear model have applications in behavioral studies when traditional parametric assumptions about the error term in a linear model are not tenable. Improved validity of Type I error rates can be achieved with properly constructed permutation tests. Perhaps more importantly, increased statistical power, improved robustness to effects of outliers, and detection of alternative distributional differences can be achieved by coupling permutation inference with alternative linear model estimators. For example, it is well-known that estimates of the mean in linear model are extremely sensitive to even a single outlying value of the dependent variable compared to estimates of the median [7, 19]. Traditionally, linear modeling focused on estimating changes in the center of distributions (means or medians). However, quantile regression allows distributional changes to be estimated in all or any selected part of a distribution or responses, providing a more complete statistical picture that has relevance to many biological questions [6]...

  20. Semidefinite linear complementarity problems

    International Nuclear Information System (INIS)

    Semidefinite linear complementarity problems arise by discretization of variational inequalities describing e.g. elastic contact problems, free boundary value problems etc. In the present paper linear complementarity problems are introduced and the theory as well as the numerical treatment of them are described. In the special case of semidefinite linear complementarity problems a numerical method is presented which combines the advantages of elimination and iteration methods without suffering from their drawbacks. This new method has very attractive properties since it has a high degree of invariance with respect to the representation of the set of all feasible solutions of a linear complementarity problem by linear inequalities. By means of some practical applications the properties of the new method are demonstrated. (orig.)

  1. Linear algebra done right

    CERN Document Server

    Axler, Sheldon

    2015-01-01

    This best-selling textbook for a second course in linear algebra is aimed at undergrad math majors and graduate students. The novel approach taken here banishes determinants to the end of the book. The text focuses on the central goal of linear algebra: understanding the structure of linear operators on finite-dimensional vector spaces. The author has taken unusual care to motivate concepts and to simplify proofs. A variety of interesting exercises in each chapter helps students understand and manipulate the objects of linear algebra. The third edition contains major improvements and revisions throughout the book. More than 300 new exercises have been added since the previous edition. Many new examples have been added to illustrate the key ideas of linear algebra. New topics covered in the book include product spaces, quotient spaces, and dual spaces. Beautiful new formatting creates pages with an unusually pleasant appearance in both print and electronic versions. No prerequisites are assumed other than the ...

  2. Photosensitized damage inflicted on plasma membranes of live cells by an extracellular generator of singlet oxygen--a linear dependence of a lethal dose on light intensity.

    Science.gov (United States)

    Zarębski, Mirosław; Kordon, Magdalena; Dobrucki, Jurek W

    2014-01-01

    We describe a study of the influence of a dose rate, i.e. light intensity or photon flux, on the efficiency of induction of a loss of integrity of plasma membranes of live cells in culture. The influence of a photon flux on the size of the light dose, which was capable of causing lethal effects, was measured in an experimental system where singlet oxygen was generated exclusively outside of live cells by ruthenium(II) phenantroline complex. Instantaneous, sensitive detection of a loss of integrity of a plasma membrane was achieved by fluorescence confocal imaging of the entry of this complex into a cell interior. We demonstrate that the size of the lethal dose of light is directly proportional to the intensity of the exciting light. Thus, the probability of a photon of the exciting light inflicting photosensitized damage on plasma membranes diminishes with increasing density of the incident photons. PMID:24279807

  3. In vitro screening for synergism of high-linear energy transfer Bi-213-radiotherapy with other therapeutic agents for the treatment of B-Cell chronic lymphocytic leukemia

    NARCIS (Netherlands)

    Vandenbulcke, Katia; Thierens, Hubert; De Vos, Filip; Philippe, Jan; Offner, Fritz; Janssens, Ann; Apostolidis, Christos; Morgenstern, Alfred; Bacher, Klaus; de Gelder, Virginie; Dierckx, Rudi A.; Slegers, Guido

    2006-01-01

    Background: External beam radiotherapy and beta-radioimmunotherapy (RIT) are effective treatments for lymphoid malignancies. The development of RIT with alpha-emitters is attractive, owing to the high (LET) nature and short path length of alpha particles allowing for higher tumor cell kill and lower

  4. Applied linear regression

    CERN Document Server

    Weisberg, Sanford

    2005-01-01

    Master linear regression techniques with a new edition of a classic text Reviews of the Second Edition: ""I found it enjoyable reading and so full of interesting material that even the well-informed reader will probably find something new . . . a necessity for all of those who do linear regression."" -Technometrics, February 1987 ""Overall, I feel that the book is a valuable addition to the now considerable list of texts on applied linear regression. It should be a strong contender as the leading text for a first serious course in regression analysis."" -American Scientist, May-June 1987

  5. Linear Network Fractional Routing

    Directory of Open Access Journals (Sweden)

    S.ASOKAN,

    2011-07-01

    Full Text Available A Network is a finite directed acyclic graph with source messages from a fixed alphabet and message demands at sink nodes. Linear Programming is an algorithm design method. It can be used whenthe solution to a problem can be viewed as the result of a sequence of decisions. The Linear Programming model for the network problem where in every variable has a value one or zero. The problem is todetermine a method of transmitting the messages through the network such that all sink demands are satisfied. We will prove fractional routing capacity for some solvable network using Linear Programmingmodel.

  6. Applied linear regression

    CERN Document Server

    Weisberg, Sanford

    2013-01-01

    Praise for the Third Edition ""...this is an excellent book which could easily be used as a course text...""-International Statistical Institute The Fourth Edition of Applied Linear Regression provides a thorough update of the basic theory and methodology of linear regression modeling. Demonstrating the practical applications of linear regression analysis techniques, the Fourth Edition uses interesting, real-world exercises and examples. Stressing central concepts such as model building, understanding parameters, assessing fit and reliability, and drawing conclusions, the new edition illus

  7. Elements of linear space

    CERN Document Server

    Amir-Moez, A R; Sneddon, I N

    1962-01-01

    Elements of Linear Space is a detailed treatment of the elements of linear spaces, including real spaces with no more than three dimensions and complex n-dimensional spaces. The geometry of conic sections and quadric surfaces is considered, along with algebraic structures, especially vector spaces and transformations. Problems drawn from various branches of geometry are given.Comprised of 12 chapters, this volume begins with an introduction to real Euclidean space, followed by a discussion on linear transformations and matrices. The addition and multiplication of transformations and matrices a

  8. Matrices and linear algebra

    CERN Document Server

    Schneider, Hans

    1989-01-01

    Linear algebra is one of the central disciplines in mathematics. A student of pure mathematics must know linear algebra if he is to continue with modern algebra or functional analysis. Much of the mathematics now taught to engineers and physicists requires it.This well-known and highly regarded text makes the subject accessible to undergraduates with little mathematical experience. Written mainly for students in physics, engineering, economics, and other fields outside mathematics, the book gives the theory of matrices and applications to systems of linear equations, as well as many related t

  9. X-ray magnetic dichroism: from quantitative determination of magnetic moments to imaging of magnetization dynamics; Dichroisme magnetique des rayons X: de la determination quantitative des moments magnetiques a l'imagerie de la dynamique de l'aimantation

    Energy Technology Data Exchange (ETDEWEB)

    Vogel, J

    2006-03-15

    In this document, I use some results of my research activities of the last ten years to show the power of x-ray magnetic dichroism for determining magnetic properties of thin layers, multilayers and nano-structures. The use of sum rules for x-ray dichroism allows a quantitative determination of the spin and orbital contributions to the magnetic moment, for each element of a heterogeneous material separately. Used in a qualitative way, x-ray dichroism allows monitoring the magnetization of the different layers in a multilayer material as a function of applied field. In combination with the temporal structure of synchrotron radiation, it is possible to study fast magnetization reversal with element selectivity, which is important for devices like spin valves and magnetic tunnel junctions. Adding the spatial resolution of a photoelectron emission microscope (PEEM), it becomes possible to study all the details of the fast magnetization reversal in complex magnetic systems. (author)

  10. Unsupervised Linear Discriminant Analysis

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    An algorithm for unsupervised linear discriminant analysis was presented. Optimal unsupervised discriminant vectors are obtained through maximizing covariance of all samples and minimizing covariance of local k-nearest neighbor samples. The experimental results show our algorithm is effective.

  11. Linear Integer Arithmetic Revisited

    OpenAIRE

    Bromberger, M.; Sturm, T.; Weidenbach, C.

    2015-01-01

    We consider feasibility of linear integer programs in the context of verification systems such as SMT solvers or theorem provers. Although satisfiability of linear integer programs is decidable, many state-of-the-art solvers neglect termination in favor of efficiency. It is challenging to design a solver that is both terminating and practically efficient. Recent work by Jovanovic and de Moura constitutes an important step into this direction. Their algorithm CUTSAT is sound, but does not term...

  12. Linear system theory

    Science.gov (United States)

    Callier, Frank M.; Desoer, Charles A.

    1991-01-01

    The aim of this book is to provide a systematic and rigorous access to the main topics of linear state-space system theory in both the continuous-time case and the discrete-time case; and the I/O description of linear systems. The main thrusts of the work are the analysis of system descriptions and derivations of their properties, LQ-optimal control, state feedback and state estimation, and MIMO unity-feedback systems.

  13. Dimension of linear models

    DEFF Research Database (Denmark)

    Høskuldsson, Agnar

    1996-01-01

    Determination of the proper dimension of a given linear model is one of the most important tasks in the applied modeling work. We consider here eight criteria that can be used to determine the dimension of the model, or equivalently, the number of components to use in the model. Four of these...... the basic problems in determining the dimension of linear models. Then each of the eight measures are treated. The results are illustrated by examples....

  14. Online Sparse Linear Regression

    OpenAIRE

    Foster, Dean; Kale, Satyen; Karloff, Howard

    2016-01-01

    We consider the online sparse linear regression problem, which is the problem of sequentially making predictions observing only a limited number of features in each round, to minimize regret with respect to the best sparse linear regressor, where prediction accuracy is measured by square loss. We give an inefficient algorithm that obtains regret bounded by $\\tilde{O}(\\sqrt{T})$ after $T$ prediction rounds. We complement this result by showing that no algorithm running in polynomial time per i...

  15. Elementary linear algebra

    CERN Document Server

    Andrilli, Stephen

    2010-01-01

    Elementary Linear Algebra develops and explains in careful detail the computational techniques and fundamental theoretical results central to a first course in linear algebra. This highly acclaimed text focuses on developing the abstract thinking essential for further mathematical study. The authors give early, intensive attention to the skills necessary to make students comfortable with mathematical proofs. The text builds a gradual and smooth transition from computational results to general theory of abstract vector spaces. It also provides flexbile coverage of practical applications, expl

  16. Systematized linear epidermolytic hyperkeratosis

    OpenAIRE

    Kumar, Piyush; Kumar, Rajesh; Mandal, Rajesh Kumar; Hassan, Shahid

    2014-01-01

    A 5-year-old boy presented with widespread asymptomatic hyperpigmented verrucous plaques since 3 months of age. The lesions were distributed in a linear manner along Blaschko's lines on trunk and extremities and were accentuated in flexures and around joints. There was no history of blistering or redness and no other family member was affected. Ichthyosis hystrix (of Curth and Macklin) and generalized linear/mosaic epidermolytic hyperkeratosis (EHK) were considered in the differential diagnos...

  17. Preconditioning Parametrized Linear Systems

    OpenAIRE

    Grim-McNally, Arielle; de Sturler, Eric; Gugercin, Serkan

    2016-01-01

    Preconditioners are generally essential for fast convergence in the iterative solution of linear systems of equations. However, the computation of a good preconditioner can be expensive. So, while solving a sequence of many linear systems, it is advantageous to recycle preconditioners, that is, update a previous preconditioner and reuse the updated version. In this paper, we introduce a simple and effective method for doing this. Although our approach can be used for matrices changing slowly ...

  18. A non-linear detection of phospho-histone H2AX in EA.hy926 endothelial cells following low-dose X-irradiation is modulated by reactive oxygen species

    International Nuclear Information System (INIS)

    A discontinuous dose response relationship is a major characteristic of the anti-inflammatory effects of low-dose X-irradiation therapy. Although recent data indicate an involvement of a variety of molecular mechanisms in these characteristics, the impact of reactive oxygen species (ROS) production to give rise or contribute to these phenomena in endothelial cells (EC) remains elusive. HUVEC derived immortalized EA.hy926 cells were stimulated by tumor necrosis factor-α (TNF-α, 20 ng/ml) 4 h before irradiation with doses ranging from 0.3 to 1 Gy. To analyse DNA repair capacity, phospho-histone H2AX foci were assayed at 1 h, 4 h and 24 h after irradiation. ROS production and superoxide dismutase (SOD) activity were analysed by fluorometric 2′,7′-dichlorodihydrofluorescein-diacetate (H2DCFDA) and colorimetric assays. A functional impact of ROS on γH2AX production was analysed by treatment with the scavenger N-acetyl-L-cysteine (NAC). Irrespective of stimulation by TNF-α, EA.hy926 cells revealed a linear dose response characteristic of γH2AX foci detection at 1 h and 4 h after irradiation. By contrast, we observed a discontinuity in residual γH2AX foci detection at 24 h after irradiation with locally elevated values following a 0.5 Gy exposure that was abolished by inhibition of ROS by NAC. Moreover, SOD protein expression was significantly decreased at doses of 0.5 Gy and 0.7 Gy concomitant with a reduced SOD activity. These data implicate a non-linear regulation of ROS production and SOD activity in EA.hy926 EC following irradiation with doses < 1 Gy that may contribute to a discontinuous dose-response relationship of residual γH2AX foci detection

  19. Parallel beam dynamics simulation of linear accelerators

    OpenAIRE

    Qiang, Ji; Ryne, Robert D.

    2002-01-01

    In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity b...

  20. Non-Markovian Quantum State Diffusion for Temperature-Dependent Linear Spectra of Light Harvesting Aggregates

    CERN Document Server

    Ritschel, Gerhard; Möbius, Sebastian; Strunz, Walter T; Eisfeld, Alexander

    2014-01-01

    Non-Markovian Quantum State Diffusion (NMQSD) has turned out to be an effective method to calculate excitonic properties of aggregates composed of organic chromophores, taking into account the strong coupling of electronic transitions to vibrational modes of the chromophores. In this paper we show how to calculate linear optical spectra at finite temperatures in an efficient way. To this end we map a finite temperature environment to the zero temperature case using the so-called thermofield method. The zero temperature case equations can then be solved efficiently by standard integrators. As an example we calculate absorption and circular dichroism spectra of a linear aggregate. The formalism developed can be applied to calculate arbitrary correlation functions.

  1. Further linear algebra

    CERN Document Server

    Blyth, T S

    2002-01-01

    Most of the introductory courses on linear algebra develop the basic theory of finite­ dimensional vector spaces, and in so doing relate the notion of a linear mapping to that of a matrix. Generally speaking, such courses culminate in the diagonalisation of certain matrices and the application of this process to various situations. Such is the case, for example, in our previous SUMS volume Basic Linear Algebra. The present text is a continuation of that volume, and has the objective of introducing the reader to more advanced properties of vector spaces and linear mappings, and consequently of matrices. For readers who are not familiar with the contents of Basic Linear Algebra we provide an introductory chapter that consists of a compact summary of the prerequisites for the present volume. In order to consolidate the student's understanding we have included a large num­ ber of illustrative and worked examples, as well as many exercises that are strategi­ cally placed throughout the text. Solutions to the ex...

  2. Classifications of Linear Controlled Systems

    OpenAIRE

    Li, Jing

    2008-01-01

    This paper is devoted to a study of linear, differential and topological classifications for linear controlled systems governed by ordinary differential equations. The necessary and sufficient conditions for the linear and topological equivalence are given. It is also shown that the differential equivalence is the same as the linear equivalence for the linear controlled systems.

  3. Co K-edge magnetic circular dichroism across the spin state transition in LaCoO3 single crystal

    Science.gov (United States)

    Efimov, V.; Ignatov, A.; Troyanchuk, I. O.; Sikolenko, V. V.; Rogalev, A.; Wilhelm, F.; Efimova, E.; Tiutiunnikov, S. I.; Karpinsky, D.; Kriventsov, V.; Yakimchuk, E.; Molodtsov, S.; Sainctavit, P.; Prabhakaran, D.

    2016-05-01

    We report on Co K-edge x-ray magnetic circular dichroism (XMCD) measurements of LaCoO3 single crystal in temperature range from 5 to 300 K and external magnetic field of 17 T. The response consists of pre-edge (at 7712 eV) and bi-polar peak (up at 7727, down at 7731 eV) with amplitudes, respectively, less than 10-3 and 10-2 of the Co K-edge jump. Using the sum rule the orbital magnetic moment of 4p Co is evaluated. Its temperature dependence reaches a maximum of (2.7 ± 0.9) x10-3 μB at 120 K, following the trend for the total magnetic moment on the Co obtained from the superconducting quantum interference device measurements. However, on warming from 25 to 120 K, the orbital magnetic moment of the 4p Co doubles while total magnetic moment of Co increases 10 times. First principle calculations are in order to relate the Co K-edge XMCD results to the orbital and spin moment of 3d Co.

  4. Enhanced biocatalysis mechanism under microwave irradiation in isoquercitrin production revealed by circular dichroism and surface plasmon resonance spectroscopy.

    Science.gov (United States)

    Gong, An; Zhu, Dan; Mei, Yi-Yuan; Xu, Xiao-Hui; Wu, Fu-An; Wang, Jun

    2016-04-01

    An efficient and rapid process for isoquercitrin production by hesperidinase-catalyzed hydrolysis of rutin was successfully developed under microwave irradiation detecting the affinity by circular dichroism (CD) and surface plasmon resonance (SPR) spectroscopy. A maximum isoquercitrin yield of 91.5±2.7% was obtained in 10min with the conditions of 10g/L hesperidinase, 2g/L rutin, 30°C and microwave power density 88.9W/L. Enzymatic reaction rate and Vm/Km in the microwave reactor were 6.34-fold higher than in a continuous flow microreactor and 1.24-fold higher than in a biphasic system. CD and SPR analysis results also showed that hesperidinase has a better selectivity and affinity (3.3-fold than in a batch reactor) to generate isoquercitrin under microwave irradiation. Microwave irradiation greatly improved the reaction efficiency and productivity, leading to a more positive economical assessment. The binding affinity indicates the presence of strong multivalent interactions between rutin and hesperidinase under microwave irradiation. PMID:26803794

  5. Soft X-ray magnetic dichroism of (Ca,Sr)RuO{sub 3}: Evidence for strain-dependent magnetism

    Energy Technology Data Exchange (ETDEWEB)

    Assmann, Andrea; Uebe, Stephan; Wissinger, Markus; Loehneysen, Hilbert von [Karlsruhe Institute of Technology, Institut fuer Festkoerperphysik (Germany); Karlsruhe Institute of Technology, Physikalisches Institut (Germany); Merz, Michael; Fuchs, Dirk; Nagel, Peter; Schuppler, Stefan [Karlsruhe Institute of Technology, Institut fuer Festkoerperphysik (Germany)

    2010-07-01

    The 4d transition metal oxide Ca{sub 1-x}Sr{sub x}RuO{sub 3} exhibits ferromagnetic order in the doping range 0.4dichroism at the Ru M{sub 2,3} and O K edges. It turns out that at 20 K, the magnetic moments strongly depend on the strain: while the spin moment of samples on LSAT almost vanishes, a distinct moment is found for (Ca,Sr)RuO{sub 3} films deposited on STO and DSO. Furthermore, a significant magnetic anisotropy is observed, with the spin moments mainly oriented perpendicular to the substrate plane. Implications are discussed.

  6. X-ray magnetic circular dichroism study of epitaxial magnetite ultrathin film on MgO(100)

    Energy Technology Data Exchange (ETDEWEB)

    Liu, W. Q.; Xu, Y. B., E-mail: yongbing.xu@york.ac.uk, E-mail: rzhang@nju.edu.cn [York-Nanjing International Center for Spintronics (YNICS), School of Electronics Science and Engineering, Nanjing University, Nanjing 210093 (China); Spintronics and Nanodevice Laboratory, Department of Electronics, University of York, York YO10 5DD (United Kingdom); Song, M. Y.; Lin, J. G. [Center for Condensed Matter Sciences, National Taiwan University, Taipei 106, Taiwan (China); Maltby, N. J.; Li, S. P. [Spintronics and Nanodevice Laboratory, Department of Electronics, University of York, York YO10 5DD (United Kingdom); Samant, M. G.; Parkin, S. S. P. [IBM Research Division, Almaden Research Center, San Jose, California 95120 (United States); Bencok, P.; Steadman, Paul; Dobrynin, Alexey [Diamond Light Source, Didcot OX11 0DE (United Kingdom); Zhang, R., E-mail: yongbing.xu@york.ac.uk, E-mail: rzhang@nju.edu.cn [York-Nanjing International Center for Spintronics (YNICS), School of Electronics Science and Engineering, Nanjing University, Nanjing 210093 (China)

    2015-05-07

    The spin and orbital magnetic moments of the Fe{sub 3}O{sub 4} epitaxial ultrathin film synthesized by plasma assisted simultaneous oxidization on MgO(100) have been studied with X-ray magnetic circular dichroism. The ultrathin film retains a rather large total magnetic moment, i.e., (2.73 ± 0.15) μ{sub B}/f.u., which is ∼70% of that for the bulk-like Fe{sub 3}O{sub 4}. A significant unquenched orbital moment up to 0.54 ± 0.05 μ{sub B}/f.u. was observed, which could come from the symmetry breaking at the Fe{sub 3}O{sub 4}/MgO interface. Such sizable orbital moment will add capacities to the Fe{sub 3}O{sub 4}-based spintronics devices in the magnetization reversal by the electric field.

  7. Vibronic Coupling Explains the Different Shape of Electronic Circular Dichroism and of Circularly Polarized Luminescence Spectra of Hexahelicenes.

    Science.gov (United States)

    Liu, Yanli; Cerezo, Javier; Mazzeo, Giuseppe; Lin, Na; Zhao, Xian; Longhi, Giovanna; Abbate, Sergio; Santoro, Fabrizio

    2016-06-14

    We present the simulation of the absorption (ABS), electronic circular dichroism (ECD), emission (EMI), and circularly polarized luminescence (CPL) spectra for the weak electronic transition between the ground (S0) and the lowest excited state (S1) of hexahelicene, 2-methylhexahelicene, 2-bromohexahelicene, and 5-azahexahelicene. Vibronic contributions have been computed at zero Kelvin and at room temperature in harmonic approximation including Duschinsky effects and accounting for both Franck-Condon and Herzberg-Teller contributions. Our results nicely capture the effects of the different substituents on the experimental spectra. They also show that HT effects dominate the shape of ECD and CPL spectra where they even induce changes of signs; HT effects are also relevant in ABS and EMI, tuning the relative intensities of the different vibronic bands. HT effects are the main reason for the differences in the line shapes of ABS and ECD and of EMI and CPL spectra and for the mirror-symmetry breaking between ABS and EMI and between ECD and CPL spectra. In order to check the robustness of our results, given also that few examples of calculations of vibronic CPL spectra exist, we adopted both adiabatic and vertical approaches to define the model potential energy surfaces of the (S0) and the (S1) states; moreover we expanded the electric and magnetic dipole transition moments around both the S0 and S1 equilibrium geometries. PMID:27120334

  8. UV and VUV spectrum of matrix-isolated In: an investigation by absorption, magnetic circular dichroism and emission yield spectroscopy

    Science.gov (United States)

    Schroeder, W.; Rotermund, H.-H.; Wiggenhauser, H.; Schrittenlacher, W.; Hormes, J.; Krebs, W.; Laaser, W.

    1986-05-01

    The electronic absorption spectra of In atoms isolated in neon, argon, krypton and xenon matrices have been measured in the energy range between 2.5 and 9.0 eV. This region includes the 5s 25p → 5s 26s and 5s 25p → 5s 25d resonance transitions, higher members of the corresponding s- and d-Rydberg series and the inner shell 5s 25p → 5s5p 2 transitions. A correlation of the absorption spectra with results obtained from magnetic circular dichroism and fluorescence measurements has made it possible to provide a detailed assignment of most of the features in the spectra in spite of the complexities associated with their behavior. For example, the transition to 5s 26s could not be detected in any of the matrices and the 5s 25d configuration was found to be strongly quenched in intensity as compared to the other transitions. In contrast, several Rydberg transitions could be observed for In in Ne. These were satisfactorily interpreted within the Frenkel formalism. Some of these observations have been rationalized by assuming that the average radius of the wavefunction for the excited state is the dominant parameter for the matrix interaction.

  9. Circular Dichroism in Mass Spectrometry: Quantum Chemical Investigations for the Differences between (R)-3-Methylcyclopentanone and Its Cation.

    Science.gov (United States)

    Kröner, Dominik; Gaebel, Tina

    2015-08-27

    In mass spectrometry enantiomers can be distinguished by multiphoton ionization employing circular polarized laser pulses. The circular dichroism (CD) is detected from the normalized difference in the ion yield after excitation with light of opposite handedness. While there are cases in which fragment and parent ions exhibit the same sign of the CD in the ion yield, several experiments show that they might also differ in sign and magnitude. Supported by experimental observations it has been proposed that the parent ion, once it has been formed, is further excited by the laser, which may result in a change of the CD in the ion yield of the formed fragments compared to the parent ion. To gain a deeper insight in possible excitation pathways we calculated and compared the electronic CD absorption spectra of neutral and cationic (R)-3-methylcyclopentanone, applying density functional theory. In addition, electron wavepacket dynamics were used to compare the CD of one- and two-photon transitions. Our results support the proposed subsequent excitation of the parent ion as a possible origin of the difference of the CD in the ion yield between parent ion and fragments. PMID:26214257

  10. Studying the magnetic anisotropy in CuFeO2 by x-ray magnetic circular dichroism

    International Nuclear Information System (INIS)

    Full text: The compound CuFeO2 has a delafossite structure where triangular layers of magnetic Fe3+ are separated by non-magnetic Cu1+ and O2- layers. CuFeO2 orders in a collinear four sublattice structure below TN2=11K. Moreover, associated with TN2 is a first order structural transition from hexagonal to orthorhombic. The explanation for the collinear magnetic structure remains unclear for CuFeO2, since it requires a 2D Ising model type, which is difficult to conciliate with the spherical Fe3+ ion. However, structural distortions around the Fe3+ ion and/or charge transfer could lead to a non-zero orbital magnetic moment. This might explain the puzzling strong magnetic anisotropy in CuFeO2. We present x-ray magnetic circular dichroism (XMCD) data extracting separately the orbital and spin moments of the Fe3+ ions. These results are discussed in the context to the observed magnetic anisotropy. (author)

  11. Dependence of magnetic circular dichroism on doping and temperature in In1-xMnxAs epitaxial films

    Science.gov (United States)

    Chiu, P. T.; Wessels, B. W.

    2007-10-01

    To elucidate the nature of the exchange interactions in ferromagnetic In1-xMnxAs , the composition and temperature dependencies of the magnetic circular dichroism (MCD) spectrum were investigated. The spectrum is comprised of both a broad transition from 1.6to3.0eV and a negative peak between 2.68 and 2.8eV associated with L -point sp-d transitions. The spectral response of the MCD is strongly temperature dependent. The magnitude of the negative peak and magnetization increases significantly with decreasing temperature for Tconstant over the same temperature range. The difference in the temperature dependence of the two negative background and peak corroborates previous assertions that the two features are due to two distinct transitions. For a series of films ranging from x=0.020to0.063 , the magnitude of the MCD peak and background exhibits a superlinear dependence on Mn concentration at room temperature. The superlinear dependence is attributed to the formation of atomic scale, tetrahedrally coordinated MnAs clusters.

  12. Comparative Analysis of IR and Vibrational Circular Dichroism Spectra for a Series of Camphor-Related Molecules

    Science.gov (United States)

    Abbate, Sergio; Burgi, Luigi Filippo; Gangemi, Fabrizio; Gangemi, Roberto; Lebon, France; Longhi, Giovanna; Pultz, Vaughan M.; Lightner, David A.

    2009-09-01

    The absorption spectra and vibrational circular dichroism (VCD) spectra in the mid-IR range 1600-950 cm-1 of 10 camphor-related compounds have been recorded and compared to DFT calculated spectra at the B3PW91/TZ2P level and have been examined together with the corresponding data of the parent molecules. The rigidity of the bridged structure common to all compounds investigated permits (a) identification of three spectroscopic regions in the mid-IR range that can be "used" separately by the interested stereochemist for structural diagnosis and assignment of some major characteristics of the VCD spectra in these regions to what we call "skeletal chiral sense" and (b) recognition of possible conformers for flexible substituent groups, when present. VCD spectra of the 10 molecules have been recorded and analyzed also in the CH-stretching region, 3100-2800 cm-1. Here, we have been able to identify and characterize features of vibrational excitons by comparison of data within the 10-molecule class. To find a theoretical justification of result (a), we have examined the potential energy distribution of the normal modes in the mid-IR range, the partitioning of the calculated rotational strengths in terms of contributions from all couples of internal coordinates, the angle formed by the two vectors, the electric dipole transition moment and the magnetic dipole transition moment, and finally the overlap of normal modes of different molecules. A discussion is provided as to the usability of the introduced algorithms.

  13. Time-Resolved X-Ray Magnetic Circular Dichroism - A Selective Probe of Magnetization Dynamics on Nanosecond Timescales

    Science.gov (United States)

    Pizzini, Stefania; Vogel, Jan; Bonfim, Marlio; Fontaine, Alain

    Many synchrotron radiation techniques have been developed in the last 15 years for studying the magnetic properties of thin-film materials. The most attractive properties of synchrotron radiation are its energy tunability and its time structure. The first property allows measurements in resonant conditions at an absorption edge of each of the magnetic elements constituting the probed sample, and the latter allows time-resolved measurements on subnanosecond timescales. In this review, we introduce some of the synchrotron-based techniques used for magnetic investigations. We then describe in detail X-ray magnetic circular dichroism (XMCD) and how time-resolved XMCD studies can be carried out in the pump-probe mode. Finally, we illustrate some applications to magnetization reversal dynamics in spin valves and tunnel junctions, using fast magnetic field pulses applied along the easy magnetization axis of the samples. Thanks to the element-selectivity of X-ray absorption spectroscopy, the magnetization dynamics of the soft (Permalloy) and the hard (cobalt) layers can be studied independently. In the case of spin valves, this allowed us to show that two magnetic layers that are strongly coupled in a static regime can become uncoupled on nanosecond timescales.Present address: Universidade Federal do Paraná, Centro Politécnico CP 19011, Curitiba - PR CEP 81531-990, Brazil

  14. Silica as a Matrix for Encapsulating Proteins: Surface Effects on Protein Structure Assessed by Circular Dichroism Spectroscopy

    Directory of Open Access Journals (Sweden)

    Genet H. Zemede

    2012-08-01

    Full Text Available The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition of a secondary solute or modification of the silica surface leads to an increase in structure. Refinement of the glass surface by addition of a monosubstituted alkoxysilane during sol-gel processing is shown to be a valuable tool for testing the effects of surface chemistry on protein structure. Because silica entrapment prevents protein aggregation by isolating individual protein molecules in the pores of the glass material, one may monitor aggregation-prone polypeptides under solvent conditions that are prohibited in solution, as demonstrated with polyglutamine and a disease-related variant of superoxide dismutase.

  15. IR and Vibrational Circular Dichroism Spectroscopy of Matrine- and Artemisinin-Type Herbal Products: Stereochemical Characterization and Solvent Effects.

    Science.gov (United States)

    Zhang, Yuefei; Poopari, M Reza; Cai, Xiaoli; Savin, Aliaksandr; Dezhahang, Zahra; Cheramy, Joseph; Xu, Yunjie

    2016-04-22

    Five Chinese herbal medicines--matrine, oxymatrine, sophoridine, artemisinin, and dihydroartemisinin--were investigated using vibrational circular dichroism (VCD) experiments and density functional theory calculations to extract their stereochemical information. The three matrine-type alkaloids are available from the dry roots of Sophora flavescens and have long been used in various traditional Chinese herbal medicines to combat diseases such as cancer and cardiac arrhythmia. Artemisinin and the related dihydroartemisinin, discovered in 1979 by Professor Youyou Tu, a 2015 Nobel laureate in medicine, are effective drugs for the treatment of malaria. The VCD measurements were carried out in CDCl3 and DMSO-d6, two solvents with different dielectric constants and hydrogen-bonding characteristics. A "clusters-in-a-liquid" approach was used to model both explicit and implicit solvent effects. The studies show that effectively accounting for solvent effects is critical to using IR and VCD spectroscopy to provide unique spectroscopic features to differentiate the potential stereoisomers of these Chinese herbal medicines. PMID:27070079

  16. X-ray magnetic circular dichroism and reflection anisotropy spectroscopy Kerr effect studies of capped magnetic nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Cunniffe, J. P.; McNally, D.E.; Liberati, M.; Arenholz, E.; McGuinness, C.; McGilp, J. F.

    2010-03-02

    Aligned Co wires grown on Pt(997) under ultra-high vacuum conditions have been capped successfully by the epitaxial growth of Au monolayers (ML) at room temperature. The samples were kept under vacuum except when transferring between apparatus or when making some of the measurements. No degradation of the Co wires was detected during the measurements. The magneto-optic response of the system was measured using X-ray magnetic circular dichroism (XMCD) at the Co L{sub 2,3} edge and reflection anisotropy spectroscopy (RAS) at near normal incidence, which is sensitive to the normal component of the out-of-plane magnetization via the Kerr effect (MOKE). Capping the wires significantly impacts their magnetic properties. Comparison of the magneto-optic response of the system at X-ray and optical energies reveals small differences that are attributed to the induced moment in the Pt substrate and Au capping layer not picked up by the element specific XMCD measurements. The sensitivity of RAS-MOKE is sufficient to allow the determination of the easy axis direction of the capped wires to within a few degrees. The results for a 6-atom-wide Co wire sample, capped with 6 ML of Au, are consistent with the capped wires possessing perpendicular magnetization.

  17. Exciton circular dichroism couplet arising from nitrile-derivatized aromatic residues as a structural probe of proteins.

    Science.gov (United States)

    Mukherjee, Debopreeti; Gai, Feng

    2016-08-15

    Exciton coupling between two chromophores can produce a circular dichroism (CD) couplet that depends on their separation distance, among other factors. Therefore, exciton CD signals arising from aromatic sidechains, especially those of tryptophan (Trp), have been used in various protein conformational studies. However, the long-wavelength component of the commonly used CD couplet produced by a pair of Trp residues is typically located around 230 nm, thereby overlapping significantly with the protein backbone CD signal. This overlap often prevents a direct and quantitative assessment of the Trp CD couplet in question without further spectral analysis. Here, we show that this inconvenience can be alleviated by using a derivative of Trp, 5-cyanotryptophan (TrpCN), as the chromophore. Specifically, through studying a series of peptides that fold into either α-helical or ß-hairpin conformations, we demonstrate that in comparison with the Trp CD couplet, that arising from two TrpCN residues not only is significantly red-shifted but also becomes more intense due to the larger extinction coefficient of the underlying electronic transition. In addition, we show that a pair of p-cyanophenylalanines (PheCN) or a PheCN-TrpCN pair can also produce a distinct exciton CD couplet that can be useful in monitoring conformational changes in proteins. PMID:27251434

  18. Determination of the Absolute Configurations Using Exciton Chirality Method for Vibrational Circular Dichroism: Right Answers for the Wrong Reasons?

    Science.gov (United States)

    Covington, Cody L; Nicu, Valentin P; Polavarapu, Prasad L

    2015-10-22

    Quantum chemical (QC) predictions of vibrational circular dichroism (VCD) spectra for the keto form of 3-benzoylcamphor and conformationally flexible diacetates of spiroindicumide A and B are presented. The exciton chirality (EC) model has been briefly reviewed, and a procedure to evaluate the relevance of the EC model has been presented. The QC results are compared with literature experimental VCD spectra as well as with those obtained using the EC model for VCD. These comparisons reveal that the EC contributions to bisignate VCD couplets associated with the C═O stretching vibrations of benzoylcamphor, spiroindicumide A diacetate, and spiroindicumide B diacetate are only ∼30%, ∼3%, and ∼15%, respectively. With such meager EC contributions, the correct absolute configurations (ACs) suggested in the literature for spiroindicumide A diacetate and spiroindicumide B diacetate molecules using the EC concepts can be considered fortuitous. The possibilities for obtaining wrong AC predictions using the EC concepts for VCD are identified, and guidelines for the future use of this model are presented. PMID:26401833

  19. Dimethyl Sulfoxide Induced Destabilization and Disassembly of Various Structural Variants of Insulin Fibrils Monitored by Vibrational Circular Dichroism.

    Science.gov (United States)

    Zhang, Ge; Babenko, Viktoria; Dzwolak, Wojciech; Keiderling, Timothy A

    2015-12-15

    Dimethyl sulfoxide (DMSO) induced destabilization of insulin fibrils has been previously studied by Fourier transform infrared spectroscopy and interpreted in terms of secondary structural changes. The variation of this process for fibrils with different types of higher-order morphological structures remained unclear. Here, we utilize vibrational circular dichroism (VCD), which has been reported to provide a useful biophysical probe of the supramolecular chirality of amyloid fibrils, to characterize changes in the macroscopic chirality following DMSO-induced disassembly for two types of insulin fibrils formed under different conditions, at different reduced pH values with and without added salt and agitation. We confirm that very high concentrations of DMSO can disaggregate both types of insulin fibrils, which initially maintained a β-sheet conformation and eventually changed their secondary structure to a disordered form. The two types responded to varying concentrations of DMSO, and disaggregation followed different mechanisms. Interconversion of specific insulin fibril morphological types also occurred during the destabilization process as monitored by VCD. With transmission electron microscopy, we were able to correlate the changes in VCD sign patterns to alteration of morphology of the insulin fibrils. PMID:26582046

  20. Interplay of Exciton Coupling and Large-Amplitude Motions in the Vibrational Circular Dichroism Spectrum of Dehydroquinidine.

    Science.gov (United States)

    Nicu, Valentin P; Domingos, Sérgio R; Strudwick, Benjamin H; Brouwer, Albert M; Buma, Wybren J

    2016-01-11

    A detailed analysis of the computed structure, energies, vibrational absorption (VA) and circular dichroism (VCD) spectra of 30 low-energy conformers of dehydroquinidine reveals the existence of families of pseudo-conformers, the structures of which differ mostly in the orientation of a single O-H bond. The pseudo-conformers in a family are separated by very small energy barriers (i.e., 1.0 kcal mol(-1) or smaller) and have very different VCD spectra. First, we demonstrate the unreliable character of the Boltzmann factors predicted with DFT. Then, we show that the large differences observed between the VCD spectra of the pseudo-conformers in a family are caused by large-amplitude motions involving the O-H bond, which trigger the appearance/disappearance of strong VCD exciton-coupling bands in the fingerprint region. This interplay between exciton coupling and large-amplitude-motion phenomena demonstrates that when dealing with flexible molecules with polar bonds, vibrational averaging of VCD spectra should not be neglected. In this regard, the dehydroquinidine molecule considered here is expected to be a typical example and not the exception to the rule. PMID:26611817

  1. Resonant photoemission and magnetic x-ray circular dichroism in the M shell of ultrathin films of Fe

    International Nuclear Information System (INIS)

    Using magnetic ultra thin films (2--4 ml) of Fe on Cu(001) and bulk-like Fe, the Fe3p and Fe3s core states have been investigated with resonant photoemission and core-level photoemission, including, magnetic x-ray circular dichroism (MXCD) experiments. The resonant photoemission experiment has been done in fine steps over a wide photon energy range (hν = 695 eV - 715 eV), to probe the parentage of various spectral structures. The onset of secondary channels at the L3(hν = 707 eV) and L2(hν = 72O eV) edges will be analyzed in light of results from bulk Ni. The MXCD photoelectron spectroscopy of the Fe3p exhibits a 0.2 eV shift with circular polarization variation. The previously observed split peak structure in the Fe3s will be discussed with regard to the new resonant photoemission results. The resonant photoemission results will also be put into the context of our MXCD absorption results for monolayer and multilayers of Fe

  2. Tunable chirality and circular dichroism of a topological insulator with C2v symmetry as a function of Rashba and Dresselhaus parameters

    Science.gov (United States)

    Sengupta, Parijat; Bellotti, Enrico

    2016-01-01

    Polarization-sensitive devices rely on meta-materials to exhibit varying degrees of absorption of light of a given handedness. The chiral surface states of a topological insulator selectively absorb right- and left-circularly polarized light in the vicinity of the Dirac cone reaching its maximum of unity at the Γ point. In this letter, we show that a band gap open topological insulator with C2v symmetry, which is represented through a combination of Rashba and Dresselhaus Hamiltonians, alters the preferential absorption of left- and right-circularly polarized light allowing a smooth variation of the circular dichroism. This variation in circular dichroism, in a range of positive and negative values, is shown to be a function of the Rashba and Dresselhaus coupling parameters.

  3. Multi-frame acquisition scheme for efficient energy-dispersive X-ray magnetic circular dichroism in pulsed high magnetic fields at the Fe K-edge

    International Nuclear Information System (INIS)

    A multi-frame acquisition scheme for efficient energy-dispersive X-ray magnetic circular dichroism at the Fe K-edge is presented. Using a fast silicon strip detector, a multi-frame acquisition scheme was implemented to perform energy-dispersive X-ray magnetic circular dichroism at the iron K-edge in pulsed high magnetic fields. The acquisition scheme makes use of the entire field pulse. The quality of the signal obtained from samples of ferrimagnetic erbium iron garnet allows for quantitative evaluation of the signal amplitude. Below the compensation point, two successive field-induced phase transitions and the reversal of the net magnetization of the iron sublattices in the intermediate phase were observed

  4. Advanced linear algebra

    CERN Document Server

    Cooperstein, Bruce

    2015-01-01

    Advanced Linear Algebra, Second Edition takes a gentle approach that starts with familiar concepts and then gradually builds to deeper results. Each section begins with an outline of previously introduced concepts and results necessary for mastering the new material. By reviewing what students need to know before moving forward, the text builds a solid foundation upon which to progress. The new edition of this successful text focuses on vector spaces and the maps between them that preserve their structure (linear transformations). Designed for advanced undergraduate and beginning graduate stud

  5. Linear Equations in Primes

    OpenAIRE

    Green, Ben; Tao, Terence

    2006-01-01

    Consider a system \\Psi of non-constant affine-linear forms \\psi_1,...,\\psi_t: Z^d -> Z, no two of which are linearly dependent. Let N be a large integer, and let K be a convex subset of [-N,N]^d. A famous and difficult open conjecture of Hardy and Littlewood predicts an asymptotic, as N -> \\infty, for the number of integer points n in K for which the integers \\psi_1(n),...,\\psi_t(n) are simultaneously prime. This implies many other well-known conjectures, such as the Hardy-Littlewood prime tu...

  6. Structured Stochastic Linear Bandits

    OpenAIRE

    Johnson, Nicholas; Sivakumar, Vidyashankar; Banerjee, Arindam

    2016-01-01

    The stochastic linear bandit problem proceeds in rounds where at each round the algorithm selects a vector from a decision set after which it receives a noisy linear loss parameterized by an unknown vector. The goal in such a problem is to minimize the (pseudo) regret which is the difference between the total expected loss of the algorithm and the total expected loss of the best fixed vector in hindsight. In this paper, we consider settings where the unknown parameter has structure, e.g., spa...

  7. Handbook of linear algebra

    CERN Document Server

    Hogben, Leslie

    2013-01-01

    With a substantial amount of new material, the Handbook of Linear Algebra, Second Edition provides comprehensive coverage of linear algebra concepts, applications, and computational software packages in an easy-to-use format. It guides you from the very elementary aspects of the subject to the frontiers of current research. Along with revisions and updates throughout, the second edition of this bestseller includes 20 new chapters.New to the Second EditionSeparate chapters on Schur complements, additional types of canonical forms, tensors, matrix polynomials, matrix equations, special types of

  8. Linear quantum feedback networks

    Science.gov (United States)

    Gough, J. E.; Gohm, R.; Yanagisawa, M.

    2008-12-01

    The mathematical theory of quantum feedback networks has recently been developed [J. Gough and M. R. James, e-print arXiv:0804.3442v2] for general open quantum dynamical systems interacting with bosonic input fields. In this article we show, for the special case of linear dynamical Markovian systems with instantaneous feedback connections, that the transfer functions can be deduced and agree with the algebraic rules obtained in the nonlinear case. Using these rules, we derive the transfer functions for linear quantum systems in series, in cascade, and in feedback arrangements mediated by beam splitter devices.

  9. Linear Logical Voting Protocols

    DEFF Research Database (Denmark)

    DeYoung, Henry; Schürmann, Carsten

    2012-01-01

    Current approaches to electronic implementations of voting protocols involve translating legal text to source code of an imperative programming language. Because the gap between legal text and source code is very large, it is difficult to trust that the program meets its legal specification....... In response, we promote linear logic as a high-level language for both specifying and implementing voting protocols. Our linear logical specifications of the single-winner first-past-the-post (SW- FPTP) and single transferable vote (STV) protocols demonstrate that this approach leads to concise...

  10. Applicability of the linear-quadratic formalism for modeling local tumor control probability in high dose per fraction stereotactic body radiotherapy for early stage non-small cell lung cancer

    International Nuclear Information System (INIS)

    Background and purpose: To compare the linear-quadratic (LQ) and the LQ-L formalism (linear cell survival curve beyond a threshold dose dT) for modeling local tumor control probability (TCP) in stereotactic body radiotherapy (SBRT) for stage I non-small cell lung cancer (NSCLC). Materials and methods: This study is based on 395 patients from 13 German and Austrian centers treated with SBRT for stage I NSCLC. The median number of SBRT fractions was 3 (range 1–8) and median single fraction dose was 12.5 Gy (2.9–33 Gy); dose was prescribed to the median 65% PTV encompassing isodose (60–100%). Assuming an α/β-value of 10 Gy, we modeled TCP as a sigmoid-shaped function of the biologically effective dose (BED). Models were compared using maximum likelihood ratio tests as well as Bayes factors (BFs). Results: There was strong evidence for a dose–response relationship in the total patient cohort (BFs > 20), which was lacking in single-fraction SBRT (BFs T) at 11 Gy (68% CI 8–14 Gy) or 22 Gy (14–42 Gy), respectively. However, the fit of the LQ-L models was not significantly better than a fit without the dT parameter (p = 0.07, BF = 2.1 and p = 0.86, BF = 0.8, respectively). Generally, isocentric doses resulted in much better dose–response relationships than PTV encompassing doses (BFs > 20). Conclusion: Our data suggest accurate modeling of local tumor control in fractionated SBRT for stage I NSCLC with the traditional LQ formalism

  11. Linear Epidermal Nevus of the Oral Cavity: A Rare Diagnosis

    OpenAIRE

    Mariana Dutra de Cássia Ferreira Santos; Alexandre Scalli Mathias Duarte; Guilherme Machado de Carvalho; Alexandre Caixeta Guimarães; Carlos Eduardo Monteiro Zappelini; Ana Cristina Coelho Dal Rio; Maria Elvira Pizzigatti Corrêa; Albina Messias de Almeida Milani Altemani; Ester Maria Danielli Nicola

    2012-01-01

    Linear epidermal nevus is an uncommon diagnosis of benign lesions of the oral cavity. It is characterized by a congenital malformation arising from the ectoderm cells, which are arranged according to a typical linear configuration known as Blaschko’s lines. We report a case of linear epidermal nevus of oral cavity in a 51-year-old lady or woman. The linear epidermal nevus of the oral cavity, although rare, can be considered a differential diagnosis of oral papillomatosis (OP). The histopathol...

  12. A vibrational circular dichroism implementation within a Slater-type-orbital based density functional framework and its application to hexa- and hepta-helicenes

    OpenAIRE

    Baerends, Evert; Neugebauer, Johannes; Nicu, Valentin; Wolff, Stephen

    2008-01-01

    We describe the implementation of the rotational strengths for vibrational circular dichroism (VCD) in the Slater-type orbital based Amsterdam Density Functional (ADF) package. We show that our implementation, which makes use of analytical derivative techniques and London atomic orbitals, yields origin independent rotational strengths. The basis set dependence in the particular case of Slater-type basis functions is also discussed. It turns out that the triple zeta STO basis sets with one set...

  13. Tight beta-turns in peptides. DFT-based study of infrared absorption and vibrational circular dichroism for various conformers including solvent effects

    Czech Academy of Sciences Publication Activity Database

    Kim, J.; Kapitán, Josef; Lakhani, A.; Bouř, Petr; Keiderling, T. A.

    2008-01-01

    Roč. 119, 1/3 (2008), s. 81-97. ISSN 1432-881X R&D Projects: GA ČR GA203/06/0420 Grant ostatní: NSF(US) CHE03-16014 Institutional research plan: CEZ:AV0Z40550506 Keywords : peptide beta-turn * density functional theory * infrared absorption * vibrational circular dichroism Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.370, year: 2008

  14. Conformational studies of the smallest structural motifs of DNA detectable via vibrational circular dichroism: cytidylyl-(3'-5')-guanosine and guanylyl-(3'-5')-cytidine.

    OpenAIRE

    Birke, S S; Diem, M.

    1995-01-01

    The infrared absorption and vibrational circular dichroism (VCD) spectra of buffered aqueous solutions of cytidylyl-(3'-5')-guanosine (5'(CG)3') and guanylyl-(3'-5')-cytidine (5'(GC)3') are reported. Under low ionic strength conditions, these dinucleotides exhibit VCD features that can be predicted qualitatively from structural data of (CG)2 and (GC)2 sequences of poly(dG-dC).poly(dG-dC), using the exciton model for infrared VCD intensities.

  15. Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets.

    Directory of Open Access Journals (Sweden)

    Wensheng Zhang

    Full Text Available Single-nucleotide polymorphisms (SNPs contribute to the between-individual expression variation of many genes. A regulatory (trait-associated SNP is usually located near or within a (host gene, possibly influencing the gene's transcription or/and post-transcriptional modification. But its targets may also include genes that are physically farther away from it. A heuristic explanation of such multiple-target interferences is that the host gene transfers the SNP genotypic effects to the distant gene(s by a transcriptional or signaling cascade. These connections between the host genes (regulators and the distant genes (targets make the genetic analysis of gene expression traits a promising approach for identifying unknown regulatory relationships. In this study, through a mixed model analysis of multi-source digital expression profiling for 140 human lymphocyte cell lines (LCLs and the genotypes distributed by the international HapMap project, we identified 45 thousands of potential SNP-induced regulatory relationships among genes (the significance level for the underlying associations between expression traits and SNP genotypes was set at FDR < 0.01. We grouped the identified relationships into four classes (paradigms according to the two different mechanisms by which the regulatory SNPs affect their cis- and trans- regulated genes, modifying mRNA level or altering transcript splicing patterns. We further organized the relationships in each class into a set of network modules with the cis- regulated genes as hubs. We found that the target genes in a network module were often characterized by significant functional similarity, and the distributions of the target genes in three out of the four networks roughly resemble a power-law, a typical pattern of gene networks obtained from mutation experiments. By two case studies, we also demonstrated that significant biological insights can be inferred from the identified network modules.

  16. Linear Mappings of Quaternion Algebra

    OpenAIRE

    Kleyn, Aleks

    2011-01-01

    In the paper I considered linear and antilinear automorphisms of quaternion algebra. I proved the theorem that there is unique expansion of R-linear mapping of quaternion algebra relative to the given set of linear and antilinear automorphisms.

  17. Non linear viscoelastic models

    DEFF Research Database (Denmark)

    Agerkvist, Finn T.

    2011-01-01

    Viscoelastic eects are often present in loudspeaker suspensions, this can be seen in the displacement transfer function which often shows a frequency dependent value below the resonance frequency. In this paper nonlinear versions of the standard linear solid model (SLS) are investigated. The...

  18. On Solving Linear Recurrences

    Science.gov (United States)

    Dobbs, David E.

    2013-01-01

    A direct method is given for solving first-order linear recurrences with constant coefficients. The limiting value of that solution is studied as "n to infinity." This classroom note could serve as enrichment material for the typical introductory course on discrete mathematics that follows a calculus course.

  19. Linear quantum measurements

    OpenAIRE

    Averin, D. V.

    2003-01-01

    Linear response theory describes quantum measurement with an arbitrary detector weakly coupled to a measured system. This description produces generic quantitative relation characterizing the detector that is analogous to the fluctuation-dissipation theorem for equilibrium systems. The detector characteristic obtained in this way shows how efficient the trade-off is between the back-action dephasing and information acquisition by the detector.

  20. Non-linear magnetization dynamics probed with X-rays: 1. Broken cylindrical symmetry of uniform modes

    Science.gov (United States)

    Goulon, J.; Brouder, Ch.; Rogalev, A.; Goujon, G.; Wilhelm, F.

    2014-10-01

    We discuss how X-ray magnetic circular dichroism (XMCD) and X-ray magnetic linear dichroism (XMLD) may complement each other to probe the nonlinear nature of the resonant precession of either spin or orbital magnetization components in aligned ferro-, ferri- or even antiferro-magnets. The Landau-Lifshitz-Gilbert (LLG) equation is solved in a rotating frame locked to the microwave pump field, while treating as time-dependent perturbations the terms which, in the formulation of the free energy density, break down the cylindrical symmetry of precession. Concretely, we analyze the time-oscillating deviations of the magnetization from the steady-state solutions of the LLG equation hereafter called SS-modes. At any perturbation order, one may derive magnetic dipole components which oscillate at harmonic frequencies of the pump frequency and could be probed with XMCD. Under bichromatic pumping, frequency mixing arises from a time-dependent Zeeman coupling between two rotating frames locked to each individual pump field. Similarly, we expect magnetic quadrupole components to oscillate at the same frequencies. For consistency, their derivation requires a perturbation calculation up to second order. The latter time-reversal even, rank-2 magnetic tensor components can be probed only with XMLD. Beyond the (reciprocal) linear dichroism classically measured in ferri- or antiferromagnetic samples, a non-reciprocal XMLD signal is to be expected when space parity is lost. Nonlinear effects strongly depend upon the relative orientations of the external bias field and of the pump field with respect to the symmetry axes of the magnetic system. This holds true for the foldover lineshape distortions, harmonic generation, frequency mixing or multiquanta excitations.