Sample records for excited dimers bound

  1. Vison excitations in near-critical quantum dimer models (United States)

    Strübi, G.; Ivanov, D. A.


    We study vison excitations in a quantum dimer model interpolating between the Rokhsar-Kivelson models on the square and triangular lattices. In the square-lattice case, the model is known to be critical and characterized by U(1) topological quantum numbers. Introducing diagonal dimers brings the model to a Z2 resonating-valence-bond phase. We study variationally the emergence of vison excitations at low concentration of diagonal dimers, close to the critical point. We find that, in this regime, vison excitations are large in size and their structure resembles vortices in type-II superconductors.

  2. Plasmon excitations in the dimers formed by atom chains (United States)

    Xue, Hong-jie; Hao, Da-peng; Zhang, Ming; Wang, Xiao-mei


    Based on the linear response theory in the random-phase approximation and the free-electron gas model, we study the plasmon excitations in the dimers formed by atom chains. With the help of energy absorption spectrum and charge distribution, the evolutions of longitudinal and transverse plasmon, and the effect of the system parameters such as size, atomic separation and electron filling on plasmon are obtained. In addition, the dipole, quadrupole, end and central plasmon are observed.

  3. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface. (United States)

    Buryak, Ilya; Vigasin, Andrey A


    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  4. Effects of excited state mixing on transient absorption spectra in dimers Application to photosynthetic light-harvesting complex II

    CERN Document Server

    Valkunas, L; Trinkunas, G; Müller, M G; Holzwarth, A R


    The excited state mixing effect is taken into account considering the difference spectra of dimers. Both the degenerate (homo) dimer as well as the nondegenerate (hetero) dimer are considered. Due to the higher excited state mixing with the two-exciton states in the homodimer, the excited state absorption (or the difference spectrum) can be strongly affected in comparison with the results obtained in the Heitler-London approximation. The difference spectrum of the heterodimer is influenced by two resonance effects (i) mixing of the ground state optical transitions of both monomers in the dimer and (ii) mixing of the excited state absorption of the excited monomer with the ground state optical transition in the nonexcited monomer. These effects have been tested by simulating the difference absorption spectra of the light-harvesting complex of photosystem II (LHC II) experimentally obtained with the 60 fs excitation pulses at zero delay times and various excitation wavelengths. The pairs of coupled chlorophylls...

  5. Multipole plasmon excitations of C{sub 60} dimers

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    Moradi, Afshin, E-mail: [Department of Engineering Physics, Kermanshah University of Technology, Kermanshah, Iran and Department of Nano Sciences, Institute for Studies in Theoretical Physics and Mathematics (IPM), Tehran (Iran, Islamic Republic of)


    We study the multipole plasmon mode frequencies of a pair of C{sub 60} molecules by means of the linearized hydrodynamic theory for electronic excitations on the each C{sub 60} surface. We apply the two-center spherical coordinate system for mathematical convenience and find an explicit form of the surface plasmon energies. Numerical result shows when approaching the two C{sub 60} molecules, the coupling between the bare plasmon modes leads to the appearance of additional modes having energies that are different from those of the isolated C{sub 60} molecules.

  6. Local excitations in thin metal films bounded by topological insulators

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    Granada E, J.C., E-mail:; Rojas, D.F.


    Electromagnetic excitations arising in a metal slab surrounded by an insulator with a non-trivial topology associated to time reversal symmetry (topological insulator) are described. It is shown that the topological term induces modifications to the dispersion relations of bounding and antibounding surface modes in the long wavelength non-retarded limit which depend on the square of the topological term. In particular, it is shown that a backward wave arises with a group velocity undergoing a relative change which is independent of the film thickness. It is shown that the rotation of the polarization plane induced by the non-trivial topology is a linear function of the topological term for all slab thickness.

  7. Separation and analysis techniques for bound and unbound alkyl ketene dimer (AKD in paper: A review

    Directory of Open Access Journals (Sweden)

    Sunil Kumar


    Full Text Available Alkyl ketene dimer (AKD is the reactive synthetic sizing agent that is used in alkaline or neutral papermaking conditions to provide certain level of hydrophobicity to the paper and board. The sizing mechanism of AKD involves its reaction with the hydroxyl groups on cellulose. However, all of AKD does not chemically react with fibers; some of it may undergo hydrolysis in water to form unstable β-keto acids, which decarboxylate to the corresponding ketone. This portion of AKD remains non-reacted (unbound and adsorbs onto fibers. The sizing effect depends mainly on the quantity of chemically reacted (bound AKD in paper, while the role of unbound forms, that is ketone and oligomer, is still not clear. Both bound and unbound portions of AKD have their own effect on paper. It is important to know the proportion of bound and unbound form of AKD in paper. The different techniques have been adopted for the separation and analysis of bound and unbound AKD present in paper. The aim of this paper is to review and summarize the various techniques provided by the researchers to separate the different forms of AKD and highlight the most important aspects for their separation.

  8. The reaction dynamics of alkali dimer molecules and electronically excited alkali atoms with simple molecules

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Hongtao [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry


    This dissertation presents the results from the crossed molecular beam studies on the dynamics of bimolecular collisions in the gas phase. The primary subjects include the interactions of alkali dimer molecules with simple molecules, and the inelastic scattering of electronically excited alkali atoms with O2. The reaction of the sodium dimers with oxygen molecules is described in Chapter 2. Two reaction pathways were observed for this four-center molecule-molecule reaction, i.e. the formations of NaO2 + Na and NaO + NaO. NaO2 products exhibit a very anisotropic angular distribution, indicating a direct spectator stripping mechanism for this reaction channel. The NaO formation follows the bond breaking of O2, which is likely a result of a charge transfer from Na2 to the excited state orbital of O2-. The scattering of sodium dimers from ammonium and methanol produced novel molecules, NaNH3 and Na(CH3OH), respectively. These experimental observations, as well as the discussions on the reaction dynamics and the chemical bonding within these molecules, will be presented in Chapter 3. The lower limits for the bond dissociation energies of these molecules are also obtained. Finally, Chapter 4 describes the energy transfer between oxygen molecules and electronically excited sodium atoms.

  9. Experimental Observation of Strongly Bound Dimers of Sulfuric Acid: Application to Nucleation in the Atmosphere

    DEFF Research Database (Denmark)

    Petaja, Tuukka; Sipila, Mikko; Paasonen, Pauli


    Sulfuric acid is a key compound in atmospheric nucleation. Here we report on the observation of a close-to-collision-limited sulfuric acid dimer formation in atmospherically relevant laboratory conditions in the absence of measurable quantities of ammonia or organics. The observed dimer formation...... compound(s) with (a) concentration(s) high enough to prevent the dimer evaporation. Such a stabilizing compound should be abundant enough in any natural environment and would therefore not limit the formation of sulfuric acid dimers in the atmosphere....

  10. A kinetic study on decomposition of proton-bound dimer using data obtained by ion mobility spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Jazan, Elham, E-mail:; Ghazali Khoob, Abdolhosein S.


    Graphical abstract: - Highlights: • The capability of corona discharge-IMS for easy study of kinetic properties was confirmed. • An equation for measuring the rate constant of the proton-bound dimer decomposition reaction was derived. • The effects of temperatures and sample concentration were investigated for monomer–dimer tail. - Abstract: In this study, an equation for measuring the rate constant of the proton-bound dimer decomposition reaction was derived using the data obtained by ion mobility spectrometry (IMS) technique. The ion mobility spectra of cyclohexanone (as the test compound) were obtained at various temperatures and different electric fields. The applied electric field for each temperature was varied between 375 and 500 V cm{sup −1} and the rate constant values of 188.24, 180.54, 280.64, 288.34 and 379.60 s{sup −1} were obtained at different temperatures of 463, 468, 473, 478 and 483 K, respectively. Subsequently, the activation energy and pre-exponential factor were calculated to be 69.5 kJ mol{sup −1} and 1.2 × 10{sup 10} s{sup −1}, respectively. In addition, the standard enthalpy changes were calculated for the dimer decomposition reaction of cyclohexanone at the above-mentioned temperatures.

  11. Triplet excited fluoroquinolones as mediators for thymine cyclobutane dimer formation in DNA. (United States)

    Lhiaubet-Vallet, Virginie; Cuquerella, M Consuelo; Castell, Jose V; Bosca, Francisco; Miranda, Miguel A


    A series of fluoroquinolones (FQs), including enoxacin (ENX), pefloxacin (PFX), norfloxacin (NFX), its N(4')-acetyl derivative (ANFX), ofloxacin (OFX), and rufloxacin (RFX) have been investigated to determine their potential as DNA photosensitizers via thymine cyclobutane dimer (TT) formation in DNA. At fluoroquinolone concentrations and light doses insufficient to produce direct single strand breaks, ENX, PFX, and NFX were able to produce TT dimers in DNA, revealed by enzymatic treatment with T4 endonuclease V. By contrast, ANFX, OFX, and RFX were inefficient in this assay. The absolute values of the triplet energies of ENX, PFX, NFX, ANFX, OFX, and RFX were estimated by means of laser flash photolysis, using flurbiprofen, 4-biphenylcarboxylic acid, and naproxen as energy acceptors. They were found to be 273, 269, 269, 265, 262, and 253 kJ/mol, respectively. Other triplet excited state properties of the FQs, including quantum yields and lifetimes, were also studied. All the results indicate that the threshold ET value required for a given compound to become a potential DNA photosensitizer via TT formation is in the range defined by the triplet energies of NFX and ANFX (265-269 kJ/mol). This provides the basis for an alert rule: any chemical (drugs, cosmetics, pesticides, etc.) with higher ET has to be considered with regard to its potential photogenotoxicity.

  12. Chirped-frequency excitation of gravitationally bound ultracold neutrons (United States)

    Manfredi, Giovanni; Morandi, Omar; Friedland, Lazar; Jenke, Tobias; Abele, Hartmut


    Ultracold neutrons confined in the Earth's gravitational field display quantized energy levels that have been observed for over a decade. In recent resonance spectroscopy experiments [T. Jenke et al., Nat. Phys. 7, 468 (2011), 10.1038/nphys1970], the transition between two such gravitational quantum states was driven by the mechanical oscillation of the plates that confine the neutrons. Here we show that by applying a sinusoidal modulation with slowly varying frequency (chirp), the neutrons can be brought to higher excited states by climbing the energy levels one by one. The proposed experiment should make it possible to observe the quantum-classical transition that occurs at high neutron energies. Furthermore, it provides a technique to realize superpositions of gravitational quantum states, to be used for precision tests of gravity at short distances.

  13. Electronic excited states responsible for dimer formation upon UV absorption directly by thymine strands: joint experimental and theoretical study. (United States)

    Banyasz, Akos; Douki, Thierry; Improta, Roberto; Gustavsson, Thomas; Onidas, Delphine; Vayá, Ignacio; Perron, Marion; Markovitsi, Dimitra


    The study addresses interconnected issues related to two major types of cycloadditions between adjacent thymines in DNA leading to cyclobutane dimers (TTs) and (6-4) adducts. Experimental results are obtained for the single strand (dT)(20) by steady-state and time-resolved optical spectroscopy, as well as by HPLC coupled to mass spectrometry. Calculations are carried out for the dinucleoside monophosphate in water using the TD-M052X method and including the polarizable continuum model; the reliability of TD-M052X is checked against CASPT2 calculations regarding the behavior of two stacked thymines in the gas phase. It is shown that irradiation at the main absorption band leads to cyclobutane dimers (TTs) and (6-4) adducts via different electronic excited states. TTs are formed via (1)ππ* excitons; [2 + 2] dimerization proceeds along a barrierless path, in line with the constant quantum yield (0.05) with the irradiation wavelength, the contribution of the (3)ππ* state to this reaction being less than 10%. The formation of oxetane, the reaction intermediate leading to (6-4) adducts, occurs via charge transfer excited states involving two stacked thymines, whose fingerprint is detected in the fluorescence spectra; it involves an energy barrier explaining the important decrease in the quantum yield of (6-4) adducts with the irradiation wavelength.

  14. Photoassociation spectra and the validity of the dipole approximation for weakly bound dimers (United States)

    Cocks, Daniel G.; Whittingham, Ian B.


    Photoassociation (PA) of ultracold metastable helium to the 2s2p manifold is theoretically investigated using a nonperturbative close-coupled treatment in which the laser coupling is evaluated without assuming the dipole approximation. The results are compared with our previous study [D. G. Cocks and I. B. Whittingham, Phys. Rev. A 80, 023417 (2009)], which makes use of the dipole approximation. The approximation is found to strongly affect the PA spectra because the photoassociated levels are weakly bound, and a similar impact is predicted to occur in other systems of a weakly bound nature. The inclusion of the approximation does not affect the resonance positions or widths; however, significant differences are observed in the background of the spectra and the maximum laser intensity at which resonances are discernible. Couplings not satisfying the dipole selection rule |J-1|⩽J'⩽|J+1| do not lead to observable resonances.

  15. Excitation of surface modes by electron beam in semi-bounded quantum plasma

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    Mohamed, B. F., E-mail: [Plasma Physics Department, N.R.C., Atomic Energy Authority, Cairo (Egypt); Elbasha, N. M. [Physics Department, Faculty of Science, Ain-Shams University, Cairo (Egypt)


    The excitation of the TM surface modes due to the interaction of electron beam with a semi-bounded quantum magnetized plasma is investigated. The generated current and the perturbed densities of the electron beam and plasma are obtained. The wave equation that describes the excited fields has been solved to obtain the dispersion relation for these modes. It is found that the quantum effects play important role for frequencies less and bigger than plasma frequency such that the phase velocity of modes increases with increasing the quantum effects compared to the classical case. It has also been displayed that in the absence of external magnetic field, the surface modes appear in the all regions of the wavelength while they have been only excited for high wavenumber in the presence of the magnetic field. Besides, it has been shown that the dispersion curves of the modes depend essentially on the density ratio of beam and plasma.

  16. Engineering elliptical spin-excitations by complex anisotropy fields in Fe adatoms and dimers on Cu(111) (United States)

    Guimarães, Filipe S. M.; dos Santos Dias, Manuel; Schweflinghaus, Benedikt; Lounis, Samir


    We investigate the dynamics of Fe adatoms and dimers deposited on the Cu(111) metallic surface in the presence of spin-orbit coupling, within time-dependent density functional theory. The ab initio results provide material-dependent parameters that can be used in semiclassical approaches, which are used for insightful interpretations of the excitation modes. By manipulating the surroundings of the magnetic elements, we show that elliptical precessional motion may be induced through the modification of the magnetic anisotropy energy. We also demonstrate how different kinds of spin precession are realized, considering the symmetry of the magnetic anisotropy energy, the ferro- or antiferromagnetic nature of the exchange coupling between the impurities, and the strength of the magnetic damping. In particular, the normal modes of a dimer depend on the initial magnetic configuration, changing drastically by going from a ferromagnetic metastable state to the antiferromagnetic ground state. By taking into account the effect of the damping into their resonant frequencies, we reveal that an important contribution arises for strongly biaxial systems and specially for the antiferromagnetic dimers with large exchange couplings. Counterintuitively, our results indicate that the magnetic damping influences the quantum fluctuations by decreasing the zero-point energy of the system.

  17. Role of nuclear couplings in the inelastic excitation of weakly-bound neutron-rich nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Dasso, C.H. [Niels Bohr Institute, Copenhagen (Denmark); Lenzi, S.M.; Vitturi, A. [Universita di Padova (Italy)


    Much effort is presently devoted to the study of nuclear systems far from the stability line. Particular emphasis has been placed in light systems such as {sup 11}Li, {sup 8}B and others, where the very small binding energy of the last particles causes their density distribution to extend considerably outside of the remaining nuclear core. Some of the properties associated with this feature are expected to characterize also heavier systems in the vicinity of the proton or neutron drip lines. It is by now well established that low-lying concentrations of multipole strength arise from pure configurations in which a peculiar matching between the wavelength of the continuum wavefunction of the particles and the range of the weakly-bound hole states occurs. To this end the authors consider the break-up of a weakly-bound system in a heavy-ion collision and focus attention in the inelastic excitation of the low-lying part of the continuum. They make use of the fact that previous investigations have shown that the multipole response in this region is not of a collective nature and describe their excited states as pure particle-hole configurations. Since the relevant parameter determining the strength distributions is the binding energy of the last bound orbital they find it most convenient to use single-particle wavefunctions generated by a sperical square-well potential with characteristic nuclear dimensions and whose depth has been adjusted to give rise to a situation in which the last occupied neutron orbital is loosely-bound. Spin-orbit couplings are, for the present purpose, ignored. The results of this investigation clearly indicate that nuclear couplings have the predominant role in causing projectile dissociation in many circumstances, even at bombarding energies remarkably below the Coulomb barrier.

  18. Chirped-Pulse Fourier-Transform Microwave Spectroscopy of the Prototypical C-H\\cdotsπ Interaction: the BENZENE\\cdotsACETYLENE Weakly Bound Dimer (United States)

    Ulrich, Nathan; Seifert, Nathan A.; Dorris, Rachel E.; Peebles, Rebecca A.; Peebles, Sean A.; Pate, Brooks


    The rotational spectrum of the CH\\cdotsπ bonded complex between benzene and acetylene has been measured in the 6-20 GHz range using chirped-pulse Fourier-transform microwave spectroscopy. The spectra for the normal isotopologue, three unique 13C substituted species, and the d_1-benzene\\cdotsHCCH species have allowed determination of the dimer structure. The spectrum is that of a symmetric top, with effective C6v symmetry, and a CH\\cdotsπ distance of 2.4921(1) Å. The dipole moment has been measured using the Stark effect, and is 0.438(11) D. In addition to the ground state spectrum, three additional sets of transitions corresponding to similar rotational constants have been observed, likely due to excitation of the three low energy intermolecular vibrational modes of the dimer. Analysis of these excited state transitions is in progress. Comparison of the binding energy and structure of the benzene\\cdotsHCCH dimer with other H\\cdotsπ complexes will be presented.

  19. Functional four-base A/T gap core sequence CATTAG of P53 response elements specifically bound tetrameric P53 differently than two-base A/T gap core sequence CATG bound both dimeric and tetrameric P53. (United States)

    Cai, Bi-He; Chen, Jang-Yi; Lu, Mei-Hua; Chang, Li-Tze; Lin, Hwang-Chi; Chang, Yu-Ming; Chao, Chung-Faye


    The consensus sequence of p53 is repeated half sites of PuPuPuC(A/T)(A/T)GPyPyPy. GtAGCAttAGCCCAGACATGTCC is a 14-3-3sigma promoter p53 regulation site; the first core sequence is CAttAG, and the second is CATG. Both mutants GtAGgAttAGCCCAGACATGTCC and GtAGCAttAGCCCAGACATcTCC can be activated by p53 as a 1.5-fold half site. The original p53 regulated site on the 14-3-3sigma promoter is a whole site, and CATTAG is a functional core sequence. The p53-binding affinity and the activity of CATTAG were lower than for the mutant CATATG core sequence. Wild-type p53 acts as a tetramer to bind to the whole site; however, it also can bind to a half site by one of its dimers. Wild-type p53 can only bind to a half site with core sequence CATG but not to CATATG. The 1.5-fold half site or whole site with core sequence CATATG can be bound by wild-type p53. A p53 mutant, A344, forms dimeric p53; it can only bind to CATG, and not to CATATG. Therefore, tetrameric and dimeric p53 can bind to a two-base A/T gap core sequence, but only tetrameric p53 can bind to a four-base A/T gap core sequence.

  20. Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state. (United States)

    Padariya, Monikaben; Kalathiya, Umesh


    Human immunodeficiency virus type 1 protease is a viral-encoded enzyme and it is essential for replication and assembly of the virus. Inactivation of HIV-1 protease causes production of immature, noninfectious viral particles and thus HIV-1 protease is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different ligands (COM5 - designed in our previous study, and Darunavir) and made effort to understand dynamics behaviour of our designed compound COM5. An apo form of HIV-1 protease as monomer and dimer form was also studied in order to analyze response of protein to the ligand. MD results suggest that presence of ligand in hinders the stability of HIV-1 protease and one monomer from dimer systems is dominant on other monomer in terms of interaction made with ligands. We were able to trace functional residues as well as continuous motion of opening and closing (clapping) of flap region in HIV-1 protease (apo form) during entire 1000 ns of MD simulation. COM5 showed almost similar behaviour towards HIV-1 protease enzyme as Darunavir and propose as promising lead compound for the development of new inhibitor for HIV-1 protease.

  1. Fragmentation, auto-modification and post ionisation proton bound dimer ion formation: the differential mobility spectrometry of low molecular weight alcohols. (United States)

    Ruszkiewicz, D M; Thomas, C L P; Eiceman, G A


    Differential mobility spectrometry (DMS) is currently being used for environmental monitoring of space craft atmospheres and has been proposed for the rapid assessment of patients at accident and emergency receptions. Three studies investigated hitherto undescribed complexity in the DMS spectra of methanol, ethanol, propan-1-ol and butan-1-ol product ions formed from a (63)Ni ionisation source. 54 000 DMS spectra obtained over a concentration range of 0.01 mg m(-3)(g) to 1.80 g m(-3)(g) revealed the phenomenon of auto-modification of the product ions. This occurred when the neutral vapour concentration exceeded the level required to induce a neutral-ion collision during the low field portion of the dispersion field waveform. Further, post-ionisation cluster-ion formation or protonated monomer/proton bound dimer inter-conversion within the ion-filter was indicated by apparent shifts in the values of the protonated monomer compensation field maximum; indicative of post-ionisation conversion of the protonated monomer to a proton-bound dimer. APCI-DMS-quadrupole mass spectrometry studies enabled the ion dissociation products from dispersion-field heating to be monitored and product ion fragmentation relationships to be proposed. Methanol was not observed to dissociate, while propan-1-ol and butan-1-ol underwent dissociation reactions consistent with dehydration processes that led ultimately to the generation of what is tentatively assigned as a cyclo-C3H3(+) ion (m/z 39) and hydrated protons. Studies of the interaction of ion filter temperature with dispersion-field heating of product ions isolated dissociation/fragmentation product ions that have not been previously described in DMS. The implications of these combined findings with regard to data sharing and data interpretation were highlighted.

  2. Crystal Structure of the Dimeric Oct6 (Pou3fl) POU Domain Bound to Palindromic MORE DNA

    Energy Technology Data Exchange (ETDEWEB)

    R Jauch; S Choo; C Ng; P Kolatkar


    POU domains (named after their identification in Pit1, Oct1 unc86) are found in around 15 transcription factors encoded in mammalian genomes many of which feature prominently as key regulators at development bifurcations. For example, the POU III class Octamer binding protein 6 (Oct6) is expressed in embryonic stem cells and during neural development and drives the differentia5tion of myelinated cells in the central and peripheral nervous system. Defects in oct6 expression levels are linked to neurological disorders such as schizophrenia. POU proteins contain a bi-partite DNA binding domain that assembles on various DNA motifs with differentially configured subdomains. Intriguingly, alternative configurations of POU domains on different DNA sites were shown to affect the subsequent recruitment of transcriptional coactivators. Namely, binding of Oct1 to a Palindromic Oct-factor Recognition Element (PORE) was shown to facilitate the recruitment of the OBF1 coactivator whereas More of PORE (MORE) bound Oct1 does not. Moreover, Pit1 was shown to recruit the corepressor N-CoR only when bound to a variant MORE motif with a 2 bp half-site spacing. Therefore, POU proteins are seen as a paradigm for DNA induced allosteric effects on transcription factors modulating their regulatory potential. However, a big unresolved conundrum for the POU class and for most if not all other transcription factor classes is how highly similar proteins regulate different sets of genes causing fundamentally different biological responses. Ultimately, there must be subtle features enabling those factors to engage in contrasting molecular interactions in the cell. Thus, the dissection of the molecular details of the transcription-DNA recognition in general, and the formation of multimeric regulatory complexes, in particular, is highly desirable. To contribute to these efforts they solved the 2.05 {angstrom} crystal structure of Oct6 bound as a symmetrical homodimer to palindromic MORE DNA.

  3. Optimal Bounded Control for Stationary Response of Strongly Nonlinear Oscillators under Combined Harmonic and Wide-Band Noise Excitations

    Directory of Open Access Journals (Sweden)

    Yongjun Wu


    Full Text Available We study the stochastic optimal bounded control for minimizing the stationary response of strongly nonlinear oscillators under combined harmonic and wide-band noise excitations. The stochastic averaging method and the dynamical programming principle are combined to obtain the fully averaged Itô stochastic differential equations which describe the original controlled strongly nonlinear system approximately. The stationary joint probability density of the amplitude and phase difference of the optimally controlled systems is obtained from solving the corresponding reduced Fokker-Planck-Kolmogorov (FPK equation. An example is given to illustrate the proposed procedure, and the theoretical results are verified by Monte Carlo simulation.

  4. Ultrafast dynamics of near-field enhancements at an off-resonance nano-dimer via femtosecond laser excitations (United States)

    Du, GuangQing; Yang, Qing; Chen, Feng; Bian, Hao; Wu, Yanmin; Lu, Yu; Farooq, Umar; Hou, Xun


    Giant electric-field enhancements localized on nano-antennas are important for the optical near-field applications in fields such as super-resolution imaging, near-field optical tweezers, and photothermal therapy. Physically, the field enhancement requires plasmon resonance with respect to structure matching. We report a tunable near-field effect, including localized electric-field enhancement and resistive heating at an off-resonance Au nano-sphere dimer via femtosecond laser irradiation. The near field was strongly modified (up to 81 times) with respect to time evolution at a laser fluence of 0.1 \\text{J/cm}2 . The results are explained as thermal dynamics manipulation of the Au nano-sphere dimer plasmon resonances. This study provides a new alternative route to tailoring the near-field enhancement for wide applications in nano-antennas.

  5. Collision-induced dissociation of HS-(HCN): unsymmetrical hydrogen bonding in a proton-bound dimer anion. (United States)

    Akin, F Ahu; Ervin, Kent M


    The energy-resolved competitive collision-induced dissociation of the proton-bound complex [HS.H.CN](-) is studied in a guided ion beam tandem mass spectrometer. H(2)S and HCN have nearly identical gas-phase acidities, and therefore, the HS(-) + HCN and the CN(-) + H(2)S product channels exhibit nearly the same threshold energies, as expected. However, the HS(-) + HCN channel has a cross section up to a factor of 50 larger than CN(-) + H(2)S at higher energies. The cross sections are modeled using RRKM theory and phase space theory. The complex dissociates to HS(-)+ HCN via a loose transition state, and it dissociates to CN(-) + H(2)S via a tight transition state. Theoretical calculations show that the proton-transfer potential energy surface has a single minimum and that the hydrogen bonding in the complex is strongly unsymmetrical, with an ion-molecule complex of the form HS(-)..HCN rather than CN(-)..H(2)S or an intermediate structure. The requirement for proton transfer before dissociation and curvature along the reaction path impedes the CN(-) + H(2)S product channel.

  6. Antenna organization in green photosynthetic bacteria. 2. Excitation transfer in detached and membrane-bound chlorosomes from Chloroflexus aurantiacus

    Energy Technology Data Exchange (ETDEWEB)

    Brune, D.C.; King, G.H.; Infosino, A.; Steiner, T.; Thewalt, M.L.W.; Blankenship, R.E.


    The photosynthetic antenna of Chloroflexus aurantiacus includes bacteriochlorophyll (BChl) c/sub 740/ and BChl a/sub 292/, both of which occur in chlorosomes, and B808-866 (containing BChl a/sub 808/ and BChl a/sub 866/), which is membrane-located (subscripts refer to near-infrared absorption maxima in vivo). BChl a/sub 792/ is thought to mediate excitation transfer from BChl c/sub 740/ to BChl a/sub 808/. Lifetimes of fluorescence from BChl c/sub 792/ and BChl a/sub 792/ were measured in isolated and membrane-bound chlorosomes in order to study energy transfer from these pigments. In both preparations, the lifetime of BChl c/sub 740/ fluorescence was at or below the instrumental limit of temporal resolution (about 30-50 ps), implying extremely fast excitation transfer from this pigment. Attempts to disrupt excitation transfer from BChl c/sub 740/, either by conversion of part of this pigment to a monomeric form absorbing at 671 nm or by partial destruction of BChl a/sub 792/ by oxidation with K/sub 3/Fe(CN)/sub 6/, had no discernible effects on the lifetime of BChl c/sub 740/ fluorescence. Most of the fluorescence from BChl a/sub 792/ decayed with a lifetime of 93 +/- 21 ps in membrane-attached chlorosomes and 155 +/- 22 ps in isolated chlorosomes at room temperature. Assuming that the only difference between these preparations is the occurrence of excitation transfer from BChl a/sub 792/ to B808-866, a 41% efficiency was calculated for this process. These results imply either that BChl a/sub 792/ is not an obligatory intermediate in energy transfer from BChl c/sub 7/$/sub 0/ to B808-866 or (more probably) that chlorosome isolation introduces new processes for quenching fluorescence from BChl a/sub 792/.

  7. Stepwise vs concerted excited state tautomerization of 2-hydroxypyridine: Ammonia dimer wire mediated hydrogen/proton transfer

    Energy Technology Data Exchange (ETDEWEB)

    Esboui, Mounir, E-mail: [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications, Département de Physique, Faculté des Sciences de Tunis, 2092 Tunis (Tunisia); Technical and Vocational Training Corporation, Hail College of Technology, P.O. Box 1960, Hail 81441 (Saudi Arabia)


    The stepwise and concerted excited state intermolecular proton transfer (PT) and hydrogen transfer (HT) reactions in 2-hydroxypyridine-(NH{sub 3}){sub 2} complex in the gas phase under Cs symmetry constraint and without any symmetry constraints were performed using quantum chemical calculations. It shows that upon excitation, the hydrogen bonded in 2HP-(NH{sub 3}){sub 2} cluster facilitates the releasing of both hydrogen and proton transfer reactions along ammonia wire leading to the formation of the 2-pyridone tautomer. For the stepwise mechanism, it has been found that the proton and the hydrogen may transfer consecutively. These processes are distinguished from each other through charge translocation analysis and the coupling between the motion of the proton and the electron density distribution along ammonia wire. For the complex under Cs symmetry, the excited state HT occurs on the A″({sup 1}πσ{sup ∗}) and A′({sup 1}nσ{sup ∗}) states over two accessible energy barriers along reaction coordinates, and excited state PT proceeds mainly through the A′({sup 1}ππ{sup ∗}) and A″({sup 1}nπ{sup ∗}) potential energy surfaces. For the unconstrained complex, potential energy profiles show two {sup 1}ππ{sup ∗}-{sup 1}πσ{sup ∗} conical intersections along enol → keto reaction path indicating that proton and H atom are localized, respectively, on the first and second ammonia of the wire. Moreover, the concerted excited state PT is competitive to take place with the stepwise process, because it proceeds over low barriers of 0.14 eV and 0.11 eV with respect to the Franck-Condon excitation of enol tautomer, respectively, under Cs symmetry and without any symmetry constraints. These barriers can be probably overcome through tunneling effect.

  8. Thymine dimer repair by electron transfer from photo-excited 2',3',5'-tri-O-acetyl-8-oxo-7,8-dihydroguanosine or 2',3',5'-tri-O-acetyl-ribosyluric acid - a theoretical study (United States)

    Marchaj, Marzena; Sieradzan, Iwona; Anusiewicz, Iwona; Skurski, Piotr; Simons, Jack


    Electronic structure calculations are combined with published experimental data from another laboratory to interpret trends in the rates of thymine dimer repair induced by photo-exciting the title molecules or their deprotonated derivatives. Opening of the thymine dimer's cyclobutane ring is believed to be initiated by electron transfer from the photo-excited molecule and to then pass over thermally accessible energy barriers. Therefore, the repair rates are determined by rates of accessing activation barriers connecting the photo-excited state to the electron-transferred state. These barriers are shown to depend on the electronic excitation energy and electron-binding energy of the donor and the electron affinity of the thymine dimer acceptor. For neutral donors, the barriers also depend on the distance between the donor and the thymine dimer through a screened Coulomb interaction between the donor cation and acceptor anion. For the deprotonated (anionic) donors, this Coulomb-derived distance dependence is absent. For both neutral and anionic donors, the range for electron transfer is spatially limited by the strength of the electronic couplings. The model put forth here rationalizes why anionic donors can be expected to perform better than neutrals and offers a framework for designing electron transfer agents optimal for a given electron acceptor.

  9. Investigations of the potential functions of weakly bound diatomic molecules and laser-assisted excitive Penning ionization

    Energy Technology Data Exchange (ETDEWEB)

    Goble, J.H. Jr.


    Three variations on the Dunham series expansion function of the potential of a diatomic molecule are compared. The differences among these expansions lie in the choice of the expansion variable, lambda. The functional form of these variables are lambda/sub s/ = l-r/sub e//r for the Simon-Parr-Finlan version, lambda/sub T/ - 1-(r/sub e//r)/sup p/ for that of Thakkar, and lambda/sub H/ = 1-exp(-rho(r/r/sub e/-1) for that of Huffaker. A wide selection of molecular systems are examined. It is found that, for potentials in excess of thirty kcal/mole, the Huffaker expansion provides the best description of the three, extrapolating at large internuclear separation to a value within 10% of the true dissociation energy. For potentials that result from the interaction of excited states, all series expansions show poor behavior away from the equilibrium internuclear separation of the molecule. The series representation of the potentials of weakly bound molecules are examined in more detail. The ground states of BeAr/sup +/, HeNe/sup +/, NaAr, and Ar/sub 2/ and the excited states of HeNe+, NaNe, and NaAr are best described by the Thakkar expansion. Finally, the observation of laser-assisted excitive Penning ionization in a flowing afterglow is reported. The reaction Ar(/sup 3/P/sub 2/) + Ca + h nu ..-->.. Ar + Ca/sup +/(5p /sup 2/P/sub J/) + e/sup -/ occurs when the photon energy, h nu, is approximately equal to the energy difference between the metastable argon and one of the fine structure levels of the ion's doublet. By monitoring the cascade fluorescence of the above reaction and comparing it to the flourescence from the field-free process Ar(/sup 3/P/sub 2/) + Ca ..-->.. Ar + Ca/sup +/(4p /sup 2/P/sub J/) + e/sup -/ a surprisingly large cross section of 6.7 x 10/sup 3/ A/sup 2/ is estimated.

  10. Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif (United States)

    Yang, Bo; Wu, R. R.; Rodgers, M. T.


    (CCG)n•(CGG)n trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C+•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.

  11. Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif. (United States)

    Yang, Bo; Wu, R R; Rodgers, M T


    (CCG)(n)•(CGG)(n) trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)(n)•(CGG)(n) repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C(+)•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.

  12. The effect of excitation and preparation pulses on nonslice selective 2D UTE bicomponent analysis of bound and free water in cortical bone at 3T

    Energy Technology Data Exchange (ETDEWEB)

    Li, Shihong [Department of Radiology, University of California, San Diego, California 92103-8226 (United States); Department of Radiology, Hua Dong Hospital, Fudan University, Shanghai 200040 (China); Yancheng Medical College, Jiangsu (China); The First People' s Hospital of Yancheng City, Jiangsu 224005 (China); Chang, Eric Y.; Chung, Christine B. [VA San Diego Healthcare System, San Diego, California 92161 and Department of Radiology, University of California, San Diego, California 92103-8226 (United States); Bae, Won C.; Du, Jiang, E-mail: [Department of Radiology, University of California, San Diego, California 92103-8226 (United States); Hua, Yanqing [Department of Radiology, Hua Dong Hospital, Fudan University, Shanghai 200040 (China); Zhou, Yi [The First People' s Hospital of Yancheng City, Jiangsu 224005 (China)


    Purpose: The purpose of this study was to investigate the effect of excitation, fat saturation, long T2 saturation, and adiabatic inversion pulses on ultrashort echo time (UTE) imaging with bicomponent analysis of bound and free water in cortical bone for potential applications in osteoporosis. Methods: Six bovine cortical bones and six human tibial midshaft samples were harvested for this study. Each bone sample was imaged with eight sequences using 2D UTE imaging at 3T with half and hard excitation pulses, without and with fat saturation, long T2 saturation, and adiabatic inversion recovery (IR) preparation pulses. Single- and bicomponent signal models were utilized to calculate the T2{sup *}s and/or relative fractions of short and long T2{sup *}s. Results: For all bone samples UTE T2{sup *} signal decay showed bicomponent behavior. A higher short T2{sup *} fraction was observed on UTE images with hard pulse excitation compared with half pulse excitation (75.6% vs 68.8% in bovine bone, 79.9% vs 73.2% in human bone). Fat saturation pulses slightly reduced the short T2{sup *} fraction relative to regular UTE sequences (5.0% and 2.0% reduction, respectively, with half and hard excitation pulses for bovine bone, 6.3% and 8.2% reduction, respectively, with half and hard excitation pulses for human bone). Long T2 saturation pulses significantly reduced the long T2{sup *} fraction relative to regular UTE sequence (18.9% and 17.2% reduction, respectively, with half and hard excitation pulses for bovine bone, 26.4% and 27.7% reduction, respectively, with half and hard excitation pulses for human bone). With IR-UTE preparation the long T2{sup *} components were significantly reduced relative to regular UTE sequence (75.3% and 66.4% reduction, respectively, with half and hard excitation pulses for bovine bone, 87.7% and 90.3% reduction, respectively, with half and hard excitation pulses for human bone). Conclusions: Bound and free water T2{sup *}s and relative fractions can

  13. The Noble Gas Dimers as a Probe of the Energetic Contributions of Dispersion and Short-Range Electron Correlation in Weakly-Bound Systems


    Housden, Michael Philip; Pyper, Nicholas Charles


    Abstract The binding of the noble gas dimers is examined using a theory in which the Hartree-Fock interaction energy is augmented with both a short-range correlation term derived from the theory of a uniform electron-gas plus a dispersion energy damped according to the theory of Jabobi and Csanak. The good agreement between the predicted and experimental binding energies and equilibrium inter-nuclear separations confirms that this approach captures the essential physics of the int...

  14. Wave-packet dynamics in alkaline dimers. Investigation and control through coherent excitation with fs-pulses; Wellenpaketdynamik in Alkali-Dimeren. Untersuchung und Steuerung durch kohaerente Anregung mit fs-Pulsen

    Energy Technology Data Exchange (ETDEWEB)

    Sauer, F.N.B.


    During my PhD thesis I investigated alkaline dimers with coherent control in a molecular beam as well as with pump-probe spectroscopy in a magneto-optical trap (MOT). The aim of the coherent control experiments were the isotope selective ionization with phase- and amplitude-shaped fs-pulses. Chapter 4 described the gained results of isotope selective ionization of NaK and KRb in a molecular beam by using different pulse formers. For the NaK dimer was the reached optimization factor R{sub Ph} and {sub Ampl}{sup 770}=R{sub max}/R{sub min}=25 between maximization and minimization of the isotopomer ratio ({sup 23}Na{sup 39}K){sup +}/({sup 23}Na{sup 41}K){sup +} with phase and amplitude modulation of the fs-pulse with a central wavelength of {lambda}=770 nm. From the electronic ground-state X(1){sup 1}{sigma}{sup +};{nu}''=0 transfers a one-photon-excitation population in the first excited A(2) {sup 1}{sigma}{sup +} state. The coherent control experiment on KRb was used to maximize and minimize the isotopomer ratio ({sup 124}KRb){sup +}/({sup 126}KRb){sup +}. It was the first coherent control experiment with a spectral resolution of 1.84 cm{sup -1}/Pixel. For the phase and amplitude optimization was the received optimization factor between minimization and maximization of the isotopomer ratio R{sub Ph} and {sub Ampl}=R{sub max}/R{sub min}=7 at a central wavelength of 840 nm. The results showed a stepwise excitation process from the electronic ground-state in the first excited (2){sup 1}{sigma}{sup +} state with a further excitation, that is possible over three resonant energy potential curves into the ionic ground-state. In the second part of my thesis I realized pump-probe spectroscopy of Rb{sub 2} dimers in a dark SPOT. (orig.)

  15. Photochemistry of alkyl halide dimers (United States)

    Fan, Y. B.; Randall, K. L.; Donaldson, D. J.


    Dimers and other small clusters of CH3I, C2H5I, i- and n-C3H7I, HI, CF3I, CH3Br, and C2H5Br formed in a supersonic expansion are irradiated at 248 and 193 nm and the halogen molecule product probed via laser induced fluorescence spectroscopy. Both dimers and larger clusters of RI (R=H, alkyl) excited at each wavelength yield I2 in its ground electronic state with very little internal energy. Clusters of CF3I and those containing alkyl bromides do not give halogen molecule products after excitation at either wavelength. A model for the dynamics in the dimer excited state which explains these results is presented.

  16. Transient dimers of allergens.

    Directory of Open Access Journals (Sweden)

    Juha Rouvinen

    Full Text Available BACKGROUND: Allergen-mediated cross-linking of IgE antibodies bound to the FcepsilonRI receptors on the mast cell surface is the key feature of the type I allergy. If an allergen is a homodimer, its allergenicity is enhanced because it would only need one type of antibody, instead of two, for cross-linking. METHODOLOGY/PRINCIPAL FINDINGS: An analysis of 55 crystal structures of allergens showed that 80% of them exist in symmetric dimers or oligomers in crystals. The majority are transient dimers that are formed at high protein concentrations that are reached in cells by colocalization. Native mass spectrometric analysis showed that native allergens do indeed form transient dimers in solution, while hypoallergenic variants of them exist almost solely in the monomeric form. We created a monomeric Bos d 5 allergen and show that it has a reduced capability to induce histamine release. CONCLUSIONS/SIGNIFICANCE: The results suggest that dimerization would be a very common and essential feature for allergens. Thus, the preparation of purely monomeric variants of allergens could open up novel possibilities for specific immunotherapy.

  17. Van der Waals universality in homonuclear atom-dimer elastic collisions

    CERN Document Server

    Giannakeas, P


    The universal aspects of atom-dimer elastic collisions are investigated within the framework of Faddeev equations. The two-body interactions between the neutral atoms are approximated by the separable potential approach. Our analysis considers a pure van der Waals potential tail as well as soft-core van der Waals interactions permitting us in this manner to address the universally general features of atom-dimer resonant spectra. In particular, we show that the atom-dimer resonances are solely associated with the {\\it excited} Efimov states. Furthermore, the positions of the corresponding resonances for a soft-core potentials with more than 5 bound states are in good agreement with the corresponding results from an infinitely deep pure van der Waals tail potential.

  18. Parametric sensitivity analysis for the helium dimers on a model potential

    Directory of Open Access Journals (Sweden)

    Nelson Henrique Teixeira Lemes


    Full Text Available Potential parameters sensitivity analysis for helium unlike molecules, HeNe, HeAr, HeKr and HeXe is the subject of this work. Number of bound states these rare gas dimers can support, for different angular momentum, will be presented and discussed. The variable phase method, together with the Levinson's theorem, is used to explore the quantum scattering process at very low collision energy using the Tang and Toennies potential. These diatomic dimers can support a bound state even for relative angular momentum equal to five, as in HeXe. Vibrational excited states, with zero angular momentum, are also possible for HeKr and HeXe. Results from sensitive analysis will give acceptable order of magnitude on potentials parameters.

  19. A glycophorin A-like framework for the dimerization of photosynthetic core complexes. (United States)

    Hsin, Jen; Chipot, Christophe; Schulten, Klaus


    The core complex in photosynthetic bacteria plays a central role in photosynthesis. This molecular assembly is composed of two protein complexes, viz., the light-harvesting complex I (LH1), which absorbs sunlight by means of the protein-bound bacteriochlorophylls, and the reaction center (RC), which uses the light-excitation energy absorbed by the LH complexes to produce a transmembrane (TM) charge gradient, subsequently employed for energy conversion. In Rhodobacter (Rba.) sphaeroides, the core complex contains, in addition, two copies of the single TM alpha-helix protein, PufX, and forms a (RC-LH1-PufX)(2) dimer. To this date, no high-resolution structure has been reported for the entire core complex. In particular, the location of PufX within the (RC-LH1-PufX)(2) dimer is still the subject of much debate. Here, one of the proposed locations for PufX, requiring its dimerization, is examined. The PufX-dimer model on the basis of the glycophorin A (GpA) dimer was constructed, and its robustness was probed through a series of molecular dynamics (MD) simulations. The free-energy change due to the replacement of Gly35 by valine was also determined to assess whether this mutation is responsible for distinct PufX oligomerization states in different Rba. species. The present study shows that PufX helices form a stable GpA-like dimer with a helix-helix crossing angle that could constitute the molecular basis of the reported highly bent and V-shaped structure of the Rba. sphaeroides core complex dimer.

  20. Resonant Auger decay driving intermolecular Coulombic decay in molecular dimers. (United States)

    Trinter, F; Schöffler, M S; Kim, H-K; Sturm, F P; Cole, K; Neumann, N; Vredenborg, A; Williams, J; Bocharova, I; Guillemin, R; Simon, M; Belkacem, A; Landers, A L; Weber, Th; Schmidt-Böcking, H; Dörner, R; Jahnke, T


    In 1997, it was predicted that an electronically excited atom or molecule placed in a loosely bound chemical system (such as a hydrogen-bonded or van-der-Waals-bonded cluster) could efficiently decay by transferring its excess energy to a neighbouring species that would then emit a low-energy electron. This intermolecular Coulombic decay (ICD) process has since been shown to be a common phenomenon, raising questions about its role in DNA damage induced by ionizing radiation, in which low-energy electrons are known to play an important part. It was recently suggested that ICD can be triggered efficiently and site-selectively by resonantly core-exciting a target atom, which then transforms through Auger decay into an ionic species with sufficiently high excitation energy to permit ICD to occur. Here we show experimentally that resonant Auger decay can indeed trigger ICD in dimers of both molecular nitrogen and carbon monoxide. By using ion and electron momentum spectroscopy to measure simultaneously the charged species created in the resonant-Auger-driven ICD cascade, we find that ICD occurs in less time than the 20 femtoseconds it would take for individual molecules to undergo dissociation. Our experimental confirmation of this process and its efficiency may trigger renewed efforts to develop resonant X-ray excitation schemes for more localized and targeted cancer radiation therapy.

  1. Neutron scattering in dimers

    DEFF Research Database (Denmark)

    Gudel, H. U.; Furrer, A.; Kjems, Jørgen


    Insulating compounds containing dimers of transition metal and rare earth ions have been studied by inelastic neutron scattering (INS). Energy splittings can be directly determined, and the corresponding parameters are easily extracted from the experimental data. The intensities of dimer excitati......Insulating compounds containing dimers of transition metal and rare earth ions have been studied by inelastic neutron scattering (INS). Energy splittings can be directly determined, and the corresponding parameters are easily extracted from the experimental data. The intensities of dimer...

  2. Coherent Electronic Coupling versus Localization in Individual Molecular Dimers

    NARCIS (Netherlands)

    Lippitz, Markus; Hübner, Christian G.; Christ, Thomas; Eichner, Holger; Bordat, Patrice; Herrmann, Andreas; Müllen, Klaus; Basché, Thomas


    We have investigated electronic excitation transfer in individual molecular dimers by time and spectrally resolved confocal fluorescence microscopy. The single molecule measurements allow for directly probing the distribution of the electronic coupling strengths due to static disorder in the polymer

  3. Thymine Dimerization in DNA is an Ultrafast Photoreaction


    Schreier, Wolfgang J.; Schrader, Tobias E.; Koller, Florian O.; Gilch, Peter; Crespo-Hernández, Carlos E.; Swaminathan, Vijay N.; Carell, Thomas; Zinth, Wolfgang; Kohler, Bern


    Femtosecond time-resolved infrared spectroscopy is used to study the formation of cyclobutane dimers in the all-thymine oligonucleotide (dT)18 by ultraviolet light at 272 nanometers. The appearance of marker bands in time-resolved spectra indicate that dimers are fully formed ∼1 picosecond after ultraviolet excitation. The ultrafast appearance of this mutagenic photolesion points to an approximately barrierless excited-state reaction for bases that are properly oriented at the instant of ligh...

  4. Non-iterative triple excitations in equation-of-motion coupled-cluster theory for electron attachment with applications to bound and temporary anions. (United States)

    Jagau, Thomas-C


    The impact of residual electron correlation beyond the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) approximation on positions and widths of electronic resonances is investigated. To establish a method that accomplishes this task in an economical manner, several approaches proposed for the approximate treatment of triple excitations are reviewed with respect to their performance in the electron attachment (EA) variant of EOM-CC theory. The recently introduced EOM-CCSD(T)(a)* method [D. A. Matthews and J. F. Stanton, J. Chem. Phys. 145, 124102 (2016)], which includes non-iterative corrections to the reference and the target states, reliably reproduces vertical attachment energies from EOM-EA-CC calculations with single, double, and full triple excitations in contrast to schemes in which non-iterative corrections are applied only to the target states. Applications of EOM-EA-CCSD(T)(a)* augmented by a complex absorbing potential (CAP) to several temporary anions illustrate that shape resonances are well described by EOM-EA-CCSD, but that residual electron correlation often makes a non-negligible impact on their positions and widths. The positions of Feshbach resonances, on the other hand, are significantly improved when going from CAP-EOM-EA-CCSD to CAP-EOM-EA-CCSD(T)(a)*, but the correct energetic order of the relevant electronic states is still not achieved.

  5. Dimerization of MT1-MMP during cellular invasion detected by flourescence resonance energy transfer


    Itoh, Yoshifumi; Palmisano, Ralf; Anilkumar, Narayanapanicker; Nagase, Hideaki; Miyawaki, Atsushi; Seiki, Motoharu


    Abstract Homo-dimerization of the membrane-bound collagenase MT1-MMP is crucial for its collagenolytic activity. However, it has not been clear if this dimerization is regulated during cellular invasion into 3D collagen matrices. To address this question, we established a fluorescence resonance energy transfer system to detect MT1-MMP dimerization and analysed the process in cells invading through 3D collagen. Our data indicates that dimerization occurrs dynamically and constantly ...

  6. Liquid crystal dimers

    CERN Document Server

    Kumar Pal, Santanu


    This book covers in-depth discussion of design principles, synthesis and thermal behavior of all types of liquid crystal (LC) dimers. The text presents recent advances in the field of LC dimers consisting of different mesogenic units such as calamitic, discotic and bent-core molecules. It starts with a chapter on the introduction of liquid crystal dimers, including their odd-even behavior, basic classification of dimers and common mesophases in dimers. The text shows how the molecular architectures are being used to develop new materials to study a range of interesting phenomena such as the biaxial nematic phase containing rod-like and disc-like mesogenic units. Finally, the text presents perspectives related to technological relevance of these dimers such as dopants in LC display mixtures exhibiting faster relaxation time, strong flexoelectric coupling and others to effect control over the properties of these materials.

  7. Photoionization of helium dimers; Photoionisation von Heliumdimeren

    Energy Technology Data Exchange (ETDEWEB)

    Havermeier, Tilo


    The helium dimer is one of the most weakly bound systems in the universe. This makes it an interesting quantum mechanical object for investigation. These Van der Waals Clusters can be produced in an expansion of a cryogenic gas jet through a small nozzle into vacuum. In the present experiment we examine the interaction of He dimers with synchrotron radiation at an energy range from 64 to 78 eV. We observed different pathways leading to single ionization of both He atoms of the dimer compound. This two close standing ions begin now to dissociate in cause of their coulomb potential. All charged fragments were detected in coincidence with a COLTRIMS system. Especially Interatomic Coulombic Decay (ICD) and the two step process (TS1) were clearly identified. Furthermore a distribution of the internuclear distance was obtained from the measured Kinetic Energy Release (KER). (orig.)

  8. D-dimer Test (United States)

    ... Acidosis and Alkalosis Adrenal Insufficiency and Addison Disease Alcoholism Allergies Alzheimer Disease Anemia Angina Ankylosing Spondylitis Anthrax ... know? D-dimer concentrations may rise in the elderly, and false positives may be seen with high ...

  9. Thymine dimer photoreversal in purine-containing trinucleotides. (United States)

    Pan, Zhengzheng; Chen, Jinquan; Schreier, Wolfgang J; Kohler, Bern; Lewis, Frederick D


    Cyclobutane-pyrimidine dimer yields in UV-irradiated DNA are controlled by the equilibrium between forward and reverse photoreactions. Past studies have shown that dimer yields are suppressed at sites adjacent to a purine base, but the underlying causes are unclear. In order to investigate whether this suppression is the result of repair by electron transfer from a neighboring nucleobase, the yields and dynamics of the reverse reaction were studied using trinucleotides containing a cis-syn dimer (TT) flanked on the 5' or the 3' side by adenine or guanine. The probability of forming an excited state on TT or on the purine base was varied by tuning the irradiation wavelength between 240 and 280 nm. Cleavage quantum yields decrease by an order of magnitude over this wavelength range and are less than 1% at 280 nm, a wavelength that excites the purine base with more than 95% probability. Conditional quantum yields of cleavage for the trinucleotides given excitation of TT are similar in magnitude to the quantum yield of cleavage of unmodified TT. These results indicate that within experimental uncertainty all photoreversal in these single-stranded substrates is the result of direct electronic excitation of TT. Photolyase-like repair of TT due to electron transfer from an adjacent purine is negligible in these substrates. Instead, the observed variation in photoreversal quantum yields for adenine- versus guanine-flanked cis-syn dimer could be due to uncertainties in absorption cross sections or to a modest quenching effect by the purine on the excited state of TT. Pump-probe measurements reveal that the excited-state lifetimes of A or G in the dimer-containing trinucleotides are unperturbed by the neighboring dimer, indicating that electron transfer from purine base to TT is not competitive with rapid excited-state deactivation. Pump-probe measurements on unmodified TT in aqueous solution indicate that cleavage is most likely complete on a picosecond or subpicosecond

  10. Time-resolved study of thymine dimer formation


    Marguet, Sylvie; Markovitsi, Dimitra


    The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 ± 0.3) × 10-3, and that of the cyclobutane dimers is (2.8 ± 0.2) × 10-2. No triplet absorption is detected, showing that either the i...

  11. Validation of EMP bounds

    Energy Technology Data Exchange (ETDEWEB)

    Warne, L.K.; Merewether, K.O.; Chen, K.C.; Jorgenson, R.E.; Morris, M.E.; Solberg, J.E.; Lewis, J.G. [Sandia National Labs., Albuquerque, NM (United States); Derr, W. [Derr Enterprises, Albuquerque, NM (United States)


    Test data on canonical weapon-like fixtures are used to validate previously developed analytical bounding results. The test fixtures were constructed to simulate (but be slightly worse than) weapon ports of entry but have known geometries (and electrical points of contact). The exterior of the test fixtures exhibited exterior resonant enhancement of the incident fields at the ports of entry with magnitudes equal to those of weapon geometries. The interior consisted of loaded transmission lines adjusted to maximize received energy or voltage but incorporating practical weapon geometrical constraints. New analytical results are also presented for bounding the energies associated with multiple bolt joints and for bounding the exterior resonant enhancement of the exciting fields.

  12. Bounded Rationality

    National Research Council Canada - National Science Library

    Ballester Pla, Coralio; Hernández, Penélope


    The observation of the actual behavior by economic decision makers in the lab and in the field justifies that bounded rationality has been a generally accepted assumption in many socio-economic models...

  13. Bounding the $\

    CERN Document Server

    Gutiérrez-Rodríguez, A


    A bound on the nu /sup tau / magnetic moment is calculated through the reaction e/sup +/e/sup -/ to nu nu gamma at the Z/sub 1/-pole, and in the framework of a left-right symmetric model at LEP energies. We find that the bound is almost independent of the mixing angle phi of the model in the allowed experimental range for this parameter. (31 refs).

  14. Gemini (dimeric) Surfactants

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 3. Gemini (dimeric) Surfactants - The Two-Faced Molecules. B S Sekhon. General Article Volume 9 Issue 3 March 2004 pp 42-49. Fulltext. Click here to view fulltext PDF. Permanent link: ...

  15. Universal dimer–dimer scattering in lattice effective field theory

    Directory of Open Access Journals (Sweden)

    Serdar Elhatisari


    Full Text Available We consider two-component fermions with short-range interactions and large scattering length. This system has universal properties that are realized in several different fields of physics. In the limit of large fermion–fermion scattering length aff and zero-range interaction, all properties of the system scale proportionally with aff. For the case with shallow bound dimers, we calculate the dimer–dimer scattering phase shifts using lattice effective field theory. We extract the universal dimer–dimer scattering length add/aff=0.618(30 and effective range rdd/aff=−0.431(48. This result for the effective range is the first calculation with quantified and controlled systematic errors. We also benchmark our methods by computing the fermion–dimer scattering parameters and testing some predictions of conformal scaling of irrelevant operators near the unitarity limit.

  16. Noncovalent Interactions in the Catechol Dimer

    Directory of Open Access Journals (Sweden)

    Vincenzo Barone


    Full Text Available Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller–Plesset (MP2 calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T/CBS method.

  17. Determination of the Tetramer-Dimer Equilibrium Constant of Rabbit ...

    African Journals Online (AJOL)

    ... derivatives of rabbit hemoglobin. The constant has been found to be the same for all the derivatives of rabbit hemoglobin, implying that the ligand bound on the heme has no significant effect on the tetramer-dimer dissociation of rabbit hemoglobin. African Journal of Educational Studies in Mathematics and Sciences Vol.

  18. Time-resolved study of thymine dimer formation. (United States)

    Marguet, Sylvie; Markovitsi, Dimitra


    The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 +/- 0.3) x 10-3, and that of the cyclobutane dimers is (2.8 +/- 0.2) x 10-2. No triplet absorption is detected, showing that either the intersystem crossing yield decreases by 1 order of magnitude upon oligomerization (dimers.

  19. Asymmetric monometallic nanorod nanoparticle dimer and related compositions and methods

    KAUST Repository

    Han, Yu


    The fabrication of asymmetric monometallic nanocrystals with novel properties for plasmonics, nanophotonics and nanoelectronics. Asymmetric monometallic plasmonic nanocrystals are of both fundamental synthetic challenge and practical significance. In an example, a thiol-ligand mediated growth strategy that enables the synthesis of unprecedented Au Nanorod-Au Nanoparticle (AuNR-AuNP) dimers from pre-synthesized AuNR seeds. Using high-resolution electron microscopy and tomography, crystal structure and three-dimensional morphology of the dimer, as well as the growth pathway of the AuNP on the AuNR seed, was investigated for this example. The dimer exhibits an extraordinary broadband optical extinction spectrum spanning the UV, visible, and near infrared regions (300 - 1300 nm). This unexpected property makes the AuNR-AuNP dimer example useful for many nanophotonic applications. In two experiments, the dimer example was tested as a surface- enhanced Raman scattering (SERS) substrate and a solar light harvester for photothermal conversion, in comparison with the mixture of AuNR and AuNP. In the SERS experiment, the dimer example showed an enhancement factor about 10 times higher than that of the mixture, when the excitation wavelength (660 nm) was off the two surface plasmon resonance (SPR) bands of the mixture. In the photothermal conversion experiment under simulated sunlight illumination, the dimer example exhibited an energy conversion efficiency about 1.4 times as high as that of the mixture.

  20. Hadron-nucleus bound states

    CERN Document Server

    Yamazaki, T


    A new type of nuclear spectroscopy to study hadron-nucleus bound states is described. The first successful experiment was to search for deeply bound pi sup - states in heavy nuclei using the sup 2 sup 0 sup 8 Pb(d, sup 3 He) reaction at GSI, in which a narrow peak arising from the 2p pi sup - orbital coupled with the neutron-hole states was observed at 135 MeV excitation energy. An improved experiment has just been carried out to separately identify the 1s and 2p pi sup - states. These experiments provide important information on the local potential strength, from which the effective mass of pi sup - is deduced to be 20 MeV. This method will be extended to search for eta and omega bound states as well as for K sup - bound states. The advantage of the bound-state spectroscopy versus invariant mass spectroscopy is emphasized.

  1. Competitive Energy and Electron Transfer in β-Functionalized Free-Base Porphyrin-Zinc Porphyrin Dimer Axially Coordinated to C60 : Synthesis, Supramolecular Formation and Excited-State Processes. (United States)

    Hu, Yi; Thomas, Michael B; Jinadasa, R G Waruna; Wang, Hong; D'Souza, Francis


    Simultaneous occurrence of energy and electron transfer events involving different acceptor sites in a newly assembled supramolecular triad comprised of covalently linked free-base porphyrin-zinc porphyrin dyad, H2 P-ZnP axially coordinated to electron acceptor fullerene, has been successfully demonstrated. The dyad was connected through the β-pyrrole positions of the porphyrin macrocycle instead of the traditionally used meso-positions for better electronic communication. Interestingly, the β-pyrrole functionalization modulated the optical properties to such an extent that it was possible to almost exclusively excite the zinc porphyrin entity in the supramolecular triad. The measured binding constant for the complex with 1:1 molecular stoichiometry was in the order of 104  m-1 revealing moderately stable complex formation. An energy level diagram constructed using optical, electrochemical and computational results suggested that both the anticipated energy and electron events are thermodynamically feasible in the triad. Consequently, it was possible to demonstrate occurrence of excited state energy transfer to the covalently linked H2 P, and electron transfer to the coordinated ImC60 from studies involving steady-state and time-resolved emission, and femto- and nanosecond transient absorption studies. The estimated energy transfer was around 67 % in the dyad with a rate constant of 1.1×109  s-1 . In the supramolecular triad, the charge separated state was rather long-lived although it was difficult to arrive the exact lifetime of charge separated state from nanosecond transient spectral studies due to overlap of strong triplet excited signals of porphyrin in the monitoring wavelength window. Nevertheless, simultaneous occurrence of energy and electron transfer in the appropriately positioned energy and electron acceptor entities in a supramolecular triad was possible to demonstrate in the present study, a step forward to unraveling the complex

  2. Dromions bound states

    Energy Technology Data Exchange (ETDEWEB)

    Maccari, Attilio


    The asymptotic perturbation (AP) method is applied to the study of the nonlinear Klein-Gordon equation in 3+1 dimensions with harmonic potential and external periodic excitation supposed to be in primary resonance with the frequency of a generic mode. The AP method uses two different procedures for the solutions: introducing an asymptotic temporal rescaling and balancing of the harmonic terms with a simple iteration. Standard quantum mechanics can be used to derive the lowest order approximate solution and amplitude and phase modulation equations are obtained. External force-response and frequency-response curves are found and the existence of dromions trapped in bound states is demonstrated.

  3. 50 years thymine dimer. (United States)

    Beukers, Rob; Eker, André P M; Lohman, Paul H M


    Fifty years ago thymine dimer was discovered in the Biochemical and Biophysical Laboratory of Delft Technological University, The Netherlands, by one of the authors of this review (Beukers) as the first environmentally induced DNA lesion. It is one of the photoproducts formed between adjacent pyrimidine bases in DNA by UV irradiation, currently known as cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts. Major lesions found in DNA after in vitro or in vivo UV irradiation are the cis-syn cyclobutane thymine dimer and the thymine-cytosine (6-4) photoproduct. Even after 50 years the study of photo-induced DNA lesions is still going on as is illustrated by the hundreds of papers published every year and the millions hits when browsing the internet for dimer-related information. Living organisms possess efficient and different mechanisms to repair detrimental lesions in their DNA. A unique mechanism to repair CPDs is reversion by either direct interaction with light of short wavelength or by enzymatic photoreactivation. Photophysical mechanisms that induce and reverse molecular bonds in biological macromolecules have been a main focus of research of the group in Delft in the middle of the last century. This review describes the break-through results of these studies which were the result of intense interactions between scientists in the fields of physics, organic chemistry and biochemistry. Philosophically, the "view" of the group in Delft was very appealing: since in nature photolesions are induced in DNA by the sun, how is it possible that repair of these lesions could be accomplished by the same energy source. Evolutionary, it is hardly possible to think of a more efficient repair mechanism.

  4. Dimerization of Receptor Protein-Tyrosine Phosphatase alpha in living cells

    Directory of Open Access Journals (Sweden)

    Gadella Theodorus WJ


    Full Text Available Abstract Background Dimerization is an important regulatory mechanism of single membrane-spanning receptors. For instance, activation of receptor protein-tyrosine kinases (RPTKs involves dimerization. Structural, functional and biochemical studies suggested that the enzymatic counterparts of RPTKs, the receptor protein-tyrosine phosphatases (RPTPs, are inhibited by dimerization, but whether RPTPs actually dimerize in living cells remained to be determined. Results In order to assess RPTP dimerization, we have assayed Fluorescence Resonance Energy Transfer (FRET between chimeric proteins of cyan- and yellow-emitting derivatives of green fluorescent protein, fused to RPTPα, using three different techniques: dual wavelength excitation, spectral imaging and fluorescence lifetime imaging. All three techniques suggested that FRET occurred between RPTPα -CFP and -YFP fusion proteins, and thus that RPTPα dimerized in living cells. RPTPα dimerization was constitutive, extensive and specific. RPTPα dimerization was consistent with cross-linking experiments, using a non-cell-permeable chemical cross-linker. Using a panel of deletion mutants, we found that the transmembrane domain was required and sufficient for dimerization. Conclusions We demonstrate here that RPTPα dimerized constitutively in living cells, which may be mediated by the transmembrane domain, providing strong support for the model that dimerization is involved in regulation of RPTPs.

  5. Separation of antibody monomer-dimer mixtures by frontal analysis. (United States)

    Reck, Jason M; Pabst, Timothy M; Hunter, Alan K; Carta, Giorgio


    The removal of aggregates, particularly soluble dimers, from monoclonal antibodies (mAbs) remains a persistent challenge in downstream processing. In this work, we have examined the separation of an antibody monomer from its dimer on the cation exchange resin Nuvia HR-S (Bio-Rad Laboratories) using frontal analysis. In this process, a mixture of monomer and dimer is continuously fed to the column under conditions where the mixture is favorably bound, resulting in two breakthrough fronts whose monomer and dimer compositions are determined by the multi-component equilibrium and kinetics of the system. Experimentally, the selectivity for dimer was found to vary substantially with ionic strength, being lowest when conditions favor the strongest binding, and increasing to a maximum at intermediate ionic strengths where rapid exchange with the bound monomer can occur. A mechanistic model is developed to describe the competitive binding frontal analysis process, assuming pore diffusion and a significant kinetic resistance to binding as a function of ionic strength. The model was solved numerically and was able to describe both the frontal analysis processes and batch adsorption experimental data, accounting for process parameters such as feed composition and salt concentration. The resulting model can be used to optimize column operating conditions for yield and purity. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Thymine dimer splitting in the TT-G trinucleotide model system: a semiclassical dynamics and TD-DFT study. (United States)

    Yuan, Shuai; Shen, Zhi; Zhang, Wenying; Dou, Yusheng; Lo, Glenn V


    The mechanism leading to bond cleavage of a thymine-thymine cyclobutane dimer (TT) in a model system consisting of the dimer flanked by guanine trinucleotide was studied using semiclassical dynamics simulation. Pulsed laser excitation of the guanine molecule is found to cause electron transfer from the guanine molecule to the dimer, which then dissociates via sequential cleavage of the C5C5' and C6C6' bonds. Subsequently, electrons transfer back to the guanine molecule as the dimer splits into two monomers. The splitting of the cyclobutane dimer was found to be in the femtosecond time scale. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Copper dimer interactions on a thermomechanical superfluid (4)He fountain. (United States)

    Popov, Evgeny; Eloranta, Jussi


    Laser induced fluorescence imaging and frequency domain excitation spectroscopy of the copper dimer (B(1)Σg (+) ←X(1)Σu (+)) in thermomechanical helium fountain at 1.7 K are demonstrated. The dimers penetrate into the fountain provided that their average propagation velocity is ca. 15 m/s. This energy threshold is interpreted in terms of an imperfect fountain liquid-gas interface, which acts as a trap for low velocity dimers. Orsay-Trento density functional theory calculations for superfluid (4)He are used to characterize the dynamics of the dimer solvation process into the fountain. The dimers first accelerate towards the fountain surface and once the surface layer is crossed, they penetrate into the liquid and further slow down to Landau critical velocity by creating a vortex ring. Theoretical lineshape calculations support the assignment of the experimentally observed bands to Cu2 solvated in the bulk liquid. The vibronic progressions are decomposed of a zero-phonon line and two types of phonon bands, which correlate with solvent cavity interface compression (t < 200 fs) and expansion (200 < t < 500 fs) driven by the electronic excitation. The presented experimental method allows to perform molecular spectroscopy in bulk superfluid helium where the temperature and pressure can be varied.

  8. Anions of the hydrogen-bonded thymine dimer: ab initio study (United States)

    Jalbout, Abraham F.; Smets, Johan; Adamowicz, Ludwik


    Theoretical calculations have been performed to determine the ability of the hydrogen-bonded thymine dimer to form stable anions. The major conclusions of this work are: (i) three of the hydrogen-bonded conformers of the thymine dimer can form stable dipole-bound anions with excess electrons; (ii) thymine dimer can form a covalent anion that has a structure dissimilar from the structures of the neutral dimer; (iii) in the covalent thymine-dimer anion the excess electron is localized in a π-orbital on one of the thymine molecules and this molecule shows an out-of-plane distortion; (iv) the covalent thymine-dimer anion is stable with respect to an adiabatic electron detachment.

  9. Bound Exciton Complexes (United States)

    Meyer, B. K.

    In the preceding chapter, we concentrated on the properties of free excitons. These free excitons may move through the sample and hit a trap, a nonradiative or a radiative recombination center. At low temperatures, the latter case gives rise to either deep center luminescence, mentioned in Sect. 7.1 and discussed in detail in Chap. 9, or to the luminescence of bound exciton complexes (BE or BEC). The chapter continues with the most prominent of these BECs, namely A-excitons bound to neutral donors. The next aspects are the more weakly BEs at ionized donors. The Sect. 7.4 treats the binding or localization energies of BEC from a theoretical point of view, while Sect. 7.5 is dedicated to excited states of BECs, which contain either holes from deeper valence bands or an envelope function with higher quantum numbers. The last section is devoted to donor-acceptor pair transitions. There is no section devoted specifically to excitons bound to neutral acceptors, because this topic is still partly controversially discussed. Instead, information on these A0X complexes is scattered over the whole chapter, however, with some special emphasis seen in Sects. 7.1, 7.4, and 7.5.

  10. Angle-Resolved Plasmonic Properties of Single Gold Nanorod Dimers

    Institute of Scientific and Technical Information of China (English)

    Jian Wu; Xuxing Lu; Qiannan Zhu; Junwei Zhao; Qishun Shen; Li Zhan; Weihai Ni


    Through wet-chemical assembly methods, gold nanorods were placed close to each other and formed a dimer with a gap distance*1 nm, and hence degenerated plasmonic dipole modes of individual nanorods coupled together to produce hybridized bonding and antibonding resonance modes. Previous studies using a condenser for illumination result in averaged signals over all excitation angles. By exciting an individual dimer obliquely at different angles, we demonstrate that these two new resonance modes are highly tunable and sensitive to the angle between the excitation polarization and the dimer orientation, which follows cos2u dependence. Moreover, for dimer structures with various structure angles, the resonance wavelengths as well as the refractive index sensitivities were found independent of the structure angle. Cal-culated angle-resolved plasmonic properties are in good agreement with the measurements. The assembled nanostructures investigated here are important for fundamental researches as well as potential applications when they are used as building blocks in plasmon-based optical and optoelectronic devices.

  11. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio


    Full Text Available The observation of the actual behavior by economic decision makers in the lab and in the field justifies that bounded rationality has been a generally accepted assumption in many socio-economic models. The goal of this paper is to illustrate the difficulties involved in providing a correct definition of what a rational (or irrational agent is. In this paper we describe two frameworks that employ different approaches for analyzing bounded rationality. The first is a spatial segregation set-up that encompasses two optimization methodologies: backward induction and forward induction. The main result is that, even under the same state of knowledge, rational and non-rational agents may match their actions. The second framework elaborates on the relationship between irrationality and informational restrictions. We use the beauty contest (Nagel, 1995 as a device to explain this relationship.

    La observación del comportamiento de los agentes económicos tanto en el laboratorio como en la vida real justifica que la racionalidad acotada sea un supuesto aceptado en numerosos modelos socio-económicos. El objetivo de este artículo es ilustrar las dificultades que conlleva una correcta definición de qué es un agente racional (irracional. En este artículo se describen dos marcos que emplean diferentes metodologías para analizar la racionalidad acotada. El primero es un modelo de segregación espacial donde se contrastan dos metodologías de optimización: inducción hacia atrás y hacia adelante. El resultado principal es que, incluso con el mismo nivel de conocimiento, tanto agentes racionales como irracionales podrían coincidir en sus acciones. El segundo marco trabaja sobre la relación entre irracionalidad y restricción de información. Se utiliza el juego llamado “beauty contest” (Nagel 1995 como mecanismo para explicar dicha relación.

  12. Sequence-Specific DNA Binding by a Short Peptide Dimer (United States)

    Talanian, Robert V.; McKnight, C. James; Kim, Peter S.


    A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4^circC. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.

  13. Selective amine catalysed steroidal dimerization

    Indian Academy of Sciences (India)

    Synthesis of steroidal dimers: Selective amine catalysed steroidal dimerization. SHAMSUZZAMANa,∗, MOHD GULFAM ALAMa,b and TABASSUM SIDDIQUIa. aDepartment of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh 202 002, India. bSchool of Distance Education (Chemical Science Programme), ...

  14. Discrete Dipole Approximation Simulation of Nearly Touching Plasmonic Au Dimers and Influence of Particle Shape Assembly on Optical Response. (United States)

    Xu, Xi-Bin; Wang, Yu-Ying; Yi, Zao; Li, Xi-Bo; Luo, Jiang-Shan; Luo, Bing-Chi; Yi, You-Gen; Tang, Yong-Jian


    The method Discrete Dipole Approximation (DDA) is used to calculate the extinction spectra and field distribution of three types of dimers. In the paper we provide a systematic analysis of the optical response of different nanoscopic dimer structures with relatively small gap distances. A description is given about how the energy and excitation cross sections of dimer plasmons depend on nanoparticle separation. Resonance peaks of dimers show red-shift compared with single nanoparticle. Dimers formed by different single particle display distinct optical response. Interaction junctions in dimers can serve as hot spots for field enhancement. Field distribution in gaps made of two flat planes is nearly continuous. Changing gaps between two particles in dimers can tune the resonance wavelength effectively as well as different particle ensembles. Existence of sharp corners can attract and change field distribution. It is not effective volume but the effective cross-section that dominates the extinction efficiency.

  15. Radiative and rovibrational collisional relaxation of sodium dimer (United States)

    Bayram, Burcin; Horton, Tim; McFarland, Jacob


    Radiative and rovibrational collisional relaxation of sodium dimer of the A1Σu+ (8,30) state have been measured by direct observation of the decay fluorescence. Sodium molecular vapor is created in a heatpipe oven at 600 K and excited using a 6-ns pulsed dye laser pumped by a Nd:YAG, operating at 532 nm. The preliminary lifetime measurement was done by directly acquiring lifetime data through boxcar averager from the stored oscilloscope trace of the fluorescence. Analysis of the exponential decay of the fluorescence allows us to obtain the radiative lifetime. By introducing the argon buffer gas and varying the pressure of the heatpipe, a collisional cross section between excited sodium dimer and ground state argon atom collision can be extracted using Stern-Volmer relation.

  16. Species A rotavirus NSP3 acquires its translation inhibitory function prior to stable dimer formation.

    Directory of Open Access Journals (Sweden)

    Hugo I Contreras-Treviño

    Full Text Available Species A rotavirus non-structural protein 3 (NSP3 is a translational regulator that inhibits or, under some conditions, enhances host cell translation. NSP3 binds to the translation initiation factor eIF4G1 and evicts poly-(A binding protein (PABP from eIF4G1, thus inhibiting translation of polyadenylated mRNAs, presumably by disrupting the effect of PABP bound to their 3'-ends. NSP3 has a long coiled-coil region involved in dimerization that includes a chaperone Hsp90-binding domain (HS90BD. We aimed to study the role in NSP3 dimerization of a segment of the coiled-coil region adjoining the HS90BD. We used a vaccinia virus system to express NSP3 with point mutations in conserved amino acids in the coiled-coil region and determined the effects of these mutations on translation by metabolic labeling of proteins as well as on accumulation of stable NSP3 dimers by non-dissociating Western blot, a method that separates stable NSP3 dimers from the monomer/dimerization intermediate forms of the protein. Four of five mutations reduced the total yield of NSP3 and the formation of stable dimers (W170A, K171E, R173E and R187E:K191E, whereas one mutation had the opposite effects (Y192A. Treatment with the proteasome inhibitor MG132 revealed that stable NSP3 dimers and monomers/dimerization intermediates are susceptible to proteasome degradation. Surprisingly, mutants severely impaired in the formation of stable dimers were still able to inhibit host cell translation, suggesting that NSP3 dimerization intermediates are functional. Our results demonstrate that rotavirus NSP3 acquires its function prior to stable dimer formation and remain as a proteasome target throughout dimerization.

  17. Relative stabilities and the spectral signatures of stacked and hydrogen-bonded dimers of serotonin (United States)

    Dev, S.; Giri, K.; Majumder, M.; Sathyamurthy, N.


    The O-HṡṡṡN hydrogen-bonded dimer of serotonin is shown to be more stable than the stacked dimer in its ground electronic state, by using the Møller-Plesset second-order perturbation theory (MP2) and the 6-31g** basis set. The vertical excitation energy for the lowest π → π* transition for the monomer as well as the dimer is predicted by time-dependent density functional theory. The experimentally observed red shift of excitation wavelength on oligomerisation is explained in terms of the change in the HOMO-LUMO energy gap due to complex formation. The impact of dimer formation on the proton magnetic resonance spectrum of serotonin monomer is also examined.

  18. Dynamics and mechanism of DNA repair in a biomimetic system: flavin-thymine dimer adduct. (United States)

    Kao, Ya-Ting; Song, Qin-Hua; Saxena, Chaitanya; Wang, Lijuan; Zhong, Dongping


    To mimic photolyase for efficient repair of UV-damaged DNA, numerous biomimetic systems have been synthesized, but all show low repair efficiency. The molecular mechanism of this low-efficiency process is still poorly understood. Here we report our direct mapping of the repair processes of a flavin-thymine dimer adduct with femtosecond resolution. We followed the entire dynamic evolution and observed direct electron transfer (ET) from the excited flavin to the thymine dimer in 79 ps. We further observed two competitive pathways, productive dimer ring splitting within 435 ps and futile back-ET in 95 ps. Our observations reveal that the underlying mechanism for the low repair quantum yield of flavin-thymine dimer adducts is the short-lived excited flavin moiety and the fast dynamics of futile back-ET without repair. © 2012 American Chemical Society

  19. Quasi-bounded sets

    Directory of Open Access Journals (Sweden)

    Jan Kucera


    Full Text Available It is proved in [1] & [2] that a set bounded in an inductive limit E=indlim En of Fréchet spaces is also bounded in some En iff E is fast complete. In the case of arbitrary locally convex spaces En every bounded set in a fast complete indlim En is quasi-bounded in some En, though it may not be bounded or even contained in any En. Every bounded set is quasi-bounded. In a Fréchet space every quasi-bounded set is also bounded.

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

    Momeni, Mohammad R; Brown, Alex


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

  1. Structure of the indole-benzene dimer revisited. (United States)

    Biswal, Himansu S; Gloaguen, Eric; Mons, Michel; Bhattacharyya, Surjendu; Shirhatti, Pranav R; Wategaonkar, Sanjay


    The structure of the indole-benzene dimer has been investigated using experimental techniques, namely, UV spectroscopy and infrared-ultraviolet (IR/UV) double resonance spectroscopy, combined with quantum chemical calculations such as MP2 and dispersion corrected DFT methods. The red shift of the indole N-H stretch frequency in the dimer provides direct evidence that the experimentally observed indole-benzene dimer is an N-H···π bound hydrogen bonded complex. Theoretical investigations suggest that the potential energy surface (PES) of the complex is rather flat along the coordinate describing the tilt angle between the molecular planes of indole and benzene, with several minima of similar energies, namely, parallel displaced (PD), right-angle T-shaped (T), and other intermediate structures which can be categorized as tilted T-shaped (T') and tilted parallel displaced (PD') structures. Three different computational methods, namely, RI-MP2, RI-B97-D, and PBE1-DCP, are used to arrive at a new structural assignment after assessing their performance in predicting the structure of the pyrrole dimer, for which accurate experimental data are available. By comparing the computed IR spectra of PD, T, and T'/PD' structures with the experimental IR spectrum, the tilted T-shaped (T') structure was assigned to the indole-benzene dimer. The empirically dispersion-corrected functionals (RI-B97-D and PBE1-DCP) correctly reproduce the experimental IR spectrum whereas the popular post-Hartree-Fock, MP2 method gives disappointing results. These results are also in agreement with the experimental dissociation energy (D(0)) reported in the literature. The N-H stretch frequency of the indole-benzene dimer has been found to be a more pertinent parameter for the structural assignment than the dissociation energy (D(0)). © 2011 American Chemical Society

  2. A Model for Dimerization of the SOX Group E Transcription Factor Family.

    Directory of Open Access Journals (Sweden)

    Sarah N Ramsook

    Full Text Available Group E members of the SOX transcription factor family include SOX8, SOX9, and SOX10. Preceding the high mobility group (HMG domain in each of these proteins is a thirty-eight amino acid region that supports the formation of dimers on promoters containing tandemly inverted sites. The purpose of this study was to obtain new structural insights into how the dimerization region functions with the HMG domain. From a mutagenic scan of the dimerization region, the most essential amino acids of the dimerization region were clustered on the hydrophobic face of a single, predicted amphipathic helix. Consistent with our hypothesis that the dimerization region directly contacts the HMG domain, a peptide corresponding to the dimerization region bound a preassembled HMG-DNA complex. Sequence conservation among Group E members served as a basis to identify two surface exposed amino acids in the HMG domain of SOX9 that were necessary for dimerization. These data were combined to make a molecular model that places the dimerization region of one SOX9 protein onto the HMG domain of another SOX9 protein situated at the opposing site of a tandem promoter. The model provides a detailed foundation for assessing the impact of mutations on SOX Group E transcription factors.

  3. Electron Capture Dissociation of Weakly Bound Polypeptide Polycationic Complexes

    DEFF Research Database (Denmark)

    Haselmann, Kim F; Jørgensen, Thomas J D; Budnik, Bogdan A


    We have previously reported that, in electron capture dissociation (ECD), rupture of strong intramolecular bonds in weakly bound supramolecular aggregates can proceed without dissociation of weak intermolecular bonds. This is now illustrated on a series of non-specific peptide-peptide dimers...

  4. The Ammonia Dimer Revisited (United States)

    Dawes, Richard; Van Der Avoird, Ad


    The conclusion from microwave spectra by Nelson, Fraser, and Klemperer that the ammonia dimer has a nearly cyclic structure led to much debate about the issue of whether (NH_3)_2 is hydrogen bonded. This structure was surprising because most {ab initio} calculations led to a classical, nearly linear, hydrogen-bonded structure. An obvious explanation of the discrepancy between the outcome of these calculations and the microwave data which led Nelson {et al.} to their ``surprising structure'' might be the effect of vibrational averaging: the electronic structure calculations focus on finding the minimum of the intermolecular potential, the experiment gives a vibrationally averaged structure. Isotope substitution studies seemed to indicate, however, that the complex is nearly rigid. Additional data became available from high-resolution molecular beam far-infrared spectroscopy in the Saykally group. These spectra, displaying large tunneling splittings, indicate that the complex is very floppy. The seemingly contradictory experimental data were explained when it became possible to calculate the vibration-rotation-tunneling (VRT) states of the complex on a six-dimensional intermolecular potential surface. The potential used was a simple model potential, with parameters fitted to the far-infrared data. Now, for the first time, a six-dimensional potential was computed by high level {ab initio} methods and this potential will be used in calculations of the VRT states of (NH_3)_2 and (ND_3)_2. So, we will finally be able to answer the question whether the conclusions from the model calculations are indeed a valid explanation of the experimental data. D. Nelson, G. T. Fraser, and W. Klemperer J. Chem. Phys. 83 6201 (1985) J. G. Loeser, C. A. Schmuttenmaer, R. C. Cohen, M. J. Elrod, D. W. Steyert, R. J. Saykally, R. E. Bumgarner, and G. A. Blake J. Chem. Phys. 97 4727 (1992) E. H. T. Olthof, A. van der Avoird, and P. E. S. Wormer J. Chem. Phys. 101 8430 (1994) E. H. T. Olthof

  5. Excitation Dynamics and Relaxation in a Molecular Heterodimer

    CERN Document Server

    Balevicius, V; Abramavicius, D; Mancal, T; Valkunas, L


    The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the energy gap of the molecular excitation, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

  6. Adventures in Holographic Dimer Models

    Energy Technology Data Exchange (ETDEWEB)

    Kachru, Shamit; /Stanford U., Phys. Dept. /SLAC; Karch, Andreas; /Washington U., Seattle; Yaida, Sho; /Stanford U., Phys. Dept.


    We abstract the essential features of holographic dimer models, and develop several new applications of these models. Firstly, semi-holographically coupling free band fermions to holographic dimers, we uncover novel phase transitions between conventional Fermi liquids and non-Fermi liquids, accompanied by a change in the structure of the Fermi surface. Secondly, we make dimer vibrations propagate through the whole crystal by way of double trace deformations, obtaining nontrivial band structure. In a simple toy model, the topology of the band structure experiences an interesting reorganization as we vary the strength of the double trace deformations. Finally, we develop tools that would allow one to build, in a bottom-up fashion, a holographic avatar of the Hubbard model.

  7. Adventures in holographic dimer models (United States)

    Kachru, Shamit; Karch, Andreas; Yaida, Sho


    We abstract the essential features of holographic dimer models, and develop several new applications of these models. Firstly, semi-holographically coupling free band fermions to holographic dimers, we uncover novel phase transitions between conventional Fermi liquids and non-Fermi liquids, accompanied by a change in the structure of the Fermi surface. Secondly, we make dimer vibrations propagate through the whole crystal by way of double trace deformations, obtaining nontrivial band structure. In a simple toy model, the topology of the band structure experiences an interesting reorganization as we vary the strength of the double trace deformations. Finally, we develop tools that would allow one to build, in a bottom-up fashion, a holographic avatar of the Hubbard model.

  8. Quantum non-demolition detection of polar molecule complexes: dimers, trimers, tetramers (United States)

    Mekhov, Igor B.


    An optical nondestructive method for in situ detection of the bound states of ultracold polar molecules is developed. It promises a minimally destructive measurement scheme up to a physically exciting quantum non-demolition (QND) level. The detection of molecular complexes beyond simple pairs of quantum particles (dimers, known, e.g., from the BEC-BCS theory) is suggested, including three-body (trimer) and four-body (tertramer) complexes trapped by one-dimensional tubes. The intensity of the scattered light is sensitive to the molecule number fluctuations beyond the mean-density approximation. Such fluctuations are very different for different complexes, which leads to radically different light scattering. This type of research extends ‘quantum optics of quantum gases’ to the field of ultracold molecules. Merging the quantum optical and ultracold gas problems will advance experimental efforts towards the study of the light-matter interaction at its ultimate quantum level, where the quantizations of both light and matter are equally important.

  9. Excited states

    CERN Document Server

    Lim, Edward C


    Excited States, Volume I reviews radiationless transitions, phosphorescence microwave double resonance through optical spectra in molecular solids, dipole moments in excited states, luminescence of polar molecules, and the problem of interstate interaction in aromatic carbonyl compounds. The book discusses the molecular electronic radiationless transitions; the double resonance techniques and the relaxation mechanisms involving the lowest triplet state of aromatic compounds; as well as the optical spectra and relaxation in molecular solids. The text also describes dipole moments and polarizab

  10. On the photophysics and photochemistry of the water dimer

    Energy Technology Data Exchange (ETDEWEB)

    Segarra-Marti, Javier; Merchan, Manuela [Instituto de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, 46071 Valencia (Spain); Roca-Sanjuan, Daniel; Lindh, Roland [Department of Chemistry - Angstroem, Theoretical Chemistry Program, Uppsala University, Box 518, 75120 Uppsala (Sweden)


    The photochemistry of the water dimer irradiated by UV light is studied by means of the complete active space perturbation theory//complete active space self-consistent field (CASPT2//CASSCF) method and accurate computational approaches like as minimum energy paths. Both electronic structure computations and ab initio molecular dynamics simulations are carried out. The results obtained show small shifts relative to a single water molecule on the vertical excitation energies of the dimer due to the hydrogen bond placed between the water donor (W{sub D}) and the water acceptor (W{sub A}). A red-shift and a blue-shift are predicted for the W{sub D} and W{sub A}, respectively, supporting previous theoretical and experimental results. The photoinduced chemistry of the water dimer is described as a process occurring between two single water molecules in which the effect of the hydrogen bond plays a minor role. Thus, the photoinduced decay routes correspond to two photodissociation processes, one for each water molecule. The proposed mechanism for the decay channels of the lowest-lying excited states of the system is established as the photochemical production of a hydrogen-bonded H{sub 2}O Horizontal-Ellipsis HO species plus a hydrogen H atom.

  11. Resonant coherent excitation of channeled ions

    Energy Technology Data Exchange (ETDEWEB)

    Datz, S.; Moak, C.D.; Crawford, O.H.; Krause, H.F.; Dittner, P.F.; Gomez del Campo, J.; Biggerstaff, J.A.; Miller, P.D.; Hvelplund, P.; Knudsen, H.


    We have observed resonant excitation of swift channeled hydrogenlike ions (Z = 5 to Z = 9) and heliumlike F/sup 7 +/ which arises from a coherent periodic perturbation by the atoms in the bounding crystal rows. The resonance excitation was seen through the reduction in the transmission of fixed-charge-state ions through channels in thin crystals of Au and Ag.

  12. Van der Waals potential and vibrational energy levels of the ground state radon dimer (United States)

    Sheng, Xiaowei; Qian, Shifeng; Hu, Fengfei


    In the present paper, the ground state van der Waals potential of the Radon dimer is described by the Tang-Toennies potential model, which requires five essential parameters. Among them, the two dispersion coefficients C6 and C8 are estimated from the well determined dispersion coefficients C6 and C8 of Xe2. C10 is estimated by using the approximation equation that C6C10/C82 has an average value of 1.221 for all the rare gas dimers. With these estimated dispersion coefficients and the well determined well depth De and Re the Born-Mayer parameters A and b are derived. Then the vibrational energy levels of the ground state radon dimer are calculated. 40 vibrational energy levels are observed in the ground state of Rn2 dimer. The last vibrational energy level is bound by only 0.0012 cm-1.

  13. Direct Observation of Thymine Dimer Repair in DNA by Photolyase (United States)

    Zhong, Dongping


    Departments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, 191 West Woodruff Avenue, OH 43210. Photolyase uses light energy to split ultraviolet-induced cyclobutane pyrimidine dimers in damaged DNA, but its molecular mechanism has never been directly revealed. We report here the direct mapping of catalytic processes through femtosecond synchronization of the enzymatic dynamics with the repair function. We observed direct electron transfer from the excited flavin cofactor to the dimer in 170 ps and back electron transfer from the repaired thymines in 560 ps. Both reactions are strongly modulated by active-site solvation to achieve maximum repair efficiency. These results show that the photocycle of DNA repair by photolyase is through a radical mechanism and completed on subnanosecond time scale at the dynamic active site with no net electron change in redox states of the flavin cofactor.

  14. Time-resolved study of ICD in Ne dimers using FEL radiation

    Energy Technology Data Exchange (ETDEWEB)

    Schnorr, K., E-mail: [Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany); Senftleben, A. [Universität Kassel, 34132 Kassel (Germany); Schmid, G.; Augustin, S.; Kurka, M. [Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany); Rudenko, A. [J.R. Macdonald Laboratory, Kansas State University, Manhattan, KS 66506 (United States); Foucar, L. [Max-Planck-Institut für medizinische Forschung, 69120 Heidelberg (Germany); Broska, A.; Meyer, K. [Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany); Anielski, D.; Boll, R. [Deutsches Elektronen-Synchrotron, 22607 Hamburg (Germany); Rolles, D. [J.R. Macdonald Laboratory, Kansas State University, Manhattan, KS 66506 (United States); Kübel, M.; Kling, M.F. [Physics Department, Ludwig-Maximilians-Universität München, 85748 Garching (Germany); Jiang, Y.H. [Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210 (China); Mondal, S.; Tachibana, T.; Ueda, K. [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577 (Japan); Marchenko, T.; Simon, M. [Laboratoire de Chimie Physique-Matière et Rayonnement, UPMC and CNRS, 75231 Paris (France); and others


    Interatomic Coulombic Decay (ICD) is a relaxation phenomenon, which takes place in weakly bound atomic and molecular systems, typically within a few to hundreds of femtoseconds depending on the system and the particular decay mechanism. The creation of ICD-active states requires the production of highly excited systems, usually populated by innershell ionization or excitation. To this end, XUV and X-ray radiation from synchrotrons was conventionally applied for the majority of experiments due to the desired state-selective ionization of certain sub-shells. The advent of Free-Electron Lasers (FELs) has enabled an entirely new class of experiments, which finally allow to trace ICD directly in the time domain due to the femtosecond pulse duration. Within this paper, the first time-resolved ICD measurement using an XUV-pump–XUV-probe scheme will be discussed in detail. The experiment was performed on neon dimers and ICD was triggered by removing a 2s electron from one of the neon atoms using a 58 eV pulse from the FEL in Hamburg (FLASH). The onset of ICD was probed with a delayed copy of the trigger pulse that further ionized one of the two Ne{sup +} ions emerging after ICD. Thus, the delay-dependent yield of coincident Ne{sup +} + Ne{sup 2+} ion pairs contains the lifetime of the 2s-innershell vacancy decaying via ICD. The result of 150 fs ± 50 fs is in good agreement with theory but only for those calculations that explicitly take nuclear motion into account.

  15. Braneworld black holes and entropy bounds

    Directory of Open Access Journals (Sweden)

    Y. Heydarzade


    Full Text Available The Bousso's D-bound entropy for the various possible black hole solutions on a 4-dimensional brane is checked. It is found that the D-bound entropy here is apparently different from that of obtained for the 4-dimensional black hole solutions. This difference is interpreted as the extra loss of information, associated to the extra dimension, when an extra-dimensional black hole is moved outward the observer's cosmological horizon. Also, it is discussed that N-bound entropy is hold for the possible solutions here. Finally, by adopting the recent Bohr-like approach to black hole quantum physics for the excited black holes, the obtained results are written also in terms of the black hole excited states.

  16. Braneworld black holes and entropy bounds (United States)

    Heydarzade, Y.; Hadi, H.; Corda, C.; Darabi, F.


    The Bousso's D-bound entropy for the various possible black hole solutions on a 4-dimensional brane is checked. It is found that the D-bound entropy here is apparently different from that of obtained for the 4-dimensional black hole solutions. This difference is interpreted as the extra loss of information, associated to the extra dimension, when an extra-dimensional black hole is moved outward the observer's cosmological horizon. Also, it is discussed that N-bound entropy is hold for the possible solutions here. Finally, by adopting the recent Bohr-like approach to black hole quantum physics for the excited black holes, the obtained results are written also in terms of the black hole excited states.

  17. Topological edge states of bound photon pairs (United States)

    Gorlach, Maxim A.; Poddubny, Alexander N.


    We predict the existence of interaction-driven edge states of bound two-photon quasiparticles in a dimer periodic array of nonlinear optical cavities. The energy spectrum of photon pairs is dramatically richer than in the noninteracting case or in a simple lattice, featuring collapse and revival of multiple edge and bulk modes as well as edge states in continuum. We link the edge-state existence to the two-photon quantum walk graph connectivity. Our results offer a route to control quantum entanglement and provide insights into the physics of many-body topological states.

  18. Dynamics and energetics of Ge(001) dimers

    NARCIS (Netherlands)

    van Houselt, Arie; van Gastel, Raoul; Poelsema, Bene; Zandvliet, Henricus J.W.


    The dynamic behavior of surface dimers on Ge(001) has been studied by positioning the tip of a scanning tunneling microscope over single flip-flopping dimers and measuring the tunneling current as a function of time. We observe that not just symmetric, but also asymmetric appearing dimers exhibit

  19. Bound states and the Bekenstein bound

    Energy Technology Data Exchange (ETDEWEB)

    Bousso, Raphael


    We explore the validity of the generalized Bekenstein bound, S<= pi M a. We define the entropy S as the logarithm of the number of states which have energy eigenvalue below M and are localized to a flat space region of width alpha. If boundary conditions that localize field modes are imposed by fiat, then the bound encounters well-known difficulties with negative Casimir energy and large species number, as well as novel problems arising only in the generalized form. In realistic systems, however, finite-size effects contribute additional energy. We study two different models for estimating such contributions. Our analysis suggests that the bound is both valid and nontrivial if interactions are properly included, so that the entropy S counts the bound states of interacting fields.

  20. Infrared spectra of acetylene dimers and acetylene-nitrogen: (DCCD) 2, H-bonded DCCD-HCCH, and DCCD-NN in the 4.1 μm region (United States)

    Lauzin, Clément; Moazzen-Ahmadi, N.; McKellar, A. R. W.


    Infrared spectra of the weakly-bound T-shaped acetylene dimers DCCD-DCCD and DCCD-HCCH are studied in the region of the DCCD ν3 fundamental (˜2440 cm -1) using a pulsed supersonic slit-jet expansion and a tunable diode laser probe. The K a = 0 ← 1 and 1 ← 0 subbands, corresponding to the vibration of the DCCD monomer at the "top" of the T, are analyzed. Compared to the analogous spectrum of HCCH-HCCH, the present results are much less perturbed. The tunneling splitting for (DCCD) 2 in the excited state is determined to be 141 MHz, a big reduction from the previously determined ground state value of 424 MHz. The dimer A rotational constants show a large apparent increase upon vibrational excitation, and we discuss whether this increase is real. The linear DCCD-NN complex is also observed as an impurity in the spectrum, and it too is found to be unperturbed, in contrast with HCCH-NN.

  1. Parity lifetime of bound states in a proximitized semiconductor nanowire

    DEFF Research Database (Denmark)

    Higginbotham, Andrew Patrick; Albrecht, Sven Marian; Kirsanskas, Gediminas


    superconductor layer, yielding an isolated, proximitized nanowire segment. We identify Andreev-like bound states in the semiconductor via bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound...... state in the semiconductor exceeding 10 ms....

  2. Dimeric guaianolides from Artemisia absinthium. (United States)

    Turak, Ablajan; Shi, She-Po; Jiang, Yong; Tu, Peng-Fei


    Five dimeric guaianolides, absinthins A-E, and seven known dimeric guaianolides were isolated from Artemisia absinthium. Their structures were elucidated based on 1D- and 2D-NMR experiments, including (1)H NMR, (13)C NMR, DEPT, (1)H-(1)H COSY, HSQC, HMBC, and NOESY, and through HRESIMS data analysis. The absolute configuration of the known compound, anabsinthin, was determined by X-ray crystallographic analysis. The isolated compounds were tested to assess their inhibitory activities on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in BV-2 cells; absinthin C and isoanabsinthin exhibited significant inhibitory effects with IC50 values of 1.52 and 1.98μM, respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Antiparallel dimer and actin assembly†


    Grintsevich, Elena E.; Phillips, Martin; Pavlov, Dmitry; Phan, Mai; Reisler, Emil; Muhlrad, Andras


    Antiparallel dimer (APD) is a unique actin species, which can be detected in the early stages of actin polymerization. In this work, we introduce novel tools to examine the effects of the APD on actin polymerization. We document that bifunctional methanothiosulfonate (MTS) reagents are an attractive alternative to the routinely used p-phenylenemaleimide (pPDM) for APD detection, allowing for a fast and efficient cross-linking under conditions of actin polymerization at neutral pH. We report a...

  4. Excited Delirium

    Directory of Open Access Journals (Sweden)

    Takeuchi, Asia


    Full Text Available Excited (or agitated delirium is characterized by agitation, aggression, acute distress and sudden death, often in the pre-hospital care setting. It is typically associated with the use of drugs that alter dopamine processing, hyperthermia, and, most notably, sometimes with death of the affected person in the custody of law enforcement. Subjects typically die from cardiopulmonary arrest, although the cause is debated. Unfortunately an adequate treatment plan has yet to be established, in part due to the fact that most patients die before hospital arrival. While there is still much to be discovered about the pathophysiology and treatment, it is hoped that this extensive review will provide both police and medical personnel with the information necessary to recognize and respond appropriately to excited delirium. [West J Emerg Med. 2011;12(1:77-83.

  5. Physical Uncertainty Bounds (PUB)

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, Diane Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Dean L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)


    This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switching out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.

  6. Structure of a Rabbit Muscle Fructose-1,6-Bisphosphate Aldolase A Dimer Variant

    Energy Technology Data Exchange (ETDEWEB)

    Sherawat,M.; Tolan, D.; Allen, K.


    Fructose-1,6-bisphosphate aldolase (aldolase) is an essential enzyme in glycolysis and gluconeogenesis. In addition to this primary function, aldolase is also known to bind to a variety of other proteins, a property that may allow it to perform 'moonlighting' roles in the cell. Although monomeric and dimeric aldolases possess full catalytic activity, the enzyme occurs as an unusually stable tetramer, suggesting a possible link between the oligomeric state and these noncatalytic cellular roles. Here, the first high-resolution X-ray crystal structure of rabbit muscle D128V aldolase, a dimeric form of aldolase mimicking the clinically important D128G mutation in humans associated with hemolytic anemia, is presented. The structure of the dimer was determined to 1.7 Angstroms resolution with the product DHAP bound in the active site. The turnover of substrate to produce the product ligand demonstrates the retention of catalytic activity by the dimeric aldolase. The D128V mutation causes aldolase to lose intermolecular contacts with the neighboring subunit at one of the two interfaces of the tetramer. The tertiary structure of the dimer does not significantly differ from the structure of half of the tetramer. Analytical ultracentrifugation confirms the occurrence of the enzyme as a dimer in solution. The highly stable structure of aldolase with an independent active site is consistent with a model in which aldolase has evolved as a multimeric scaffold to perform other noncatalytic functions.

  7. Structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant. (United States)

    Sherawat, Manashi; Tolan, Dean R; Allen, Karen N


    Fructose-1,6-bisphosphate aldolase (aldolase) is an essential enzyme in glycolysis and gluconeogenesis. In addition to this primary function, aldolase is also known to bind to a variety of other proteins, a property that may allow it to perform 'moonlighting' roles in the cell. Although monomeric and dimeric aldolases possess full catalytic activity, the enzyme occurs as an unusually stable tetramer, suggesting a possible link between the oligomeric state and these noncatalytic cellular roles. Here, the first high-resolution X-ray crystal structure of rabbit muscle D128V aldolase, a dimeric form of aldolase mimicking the clinically important D128G mutation in humans associated with hemolytic anemia, is presented. The structure of the dimer was determined to 1.7 angstroms resolution with the product DHAP bound in the active site. The turnover of substrate to produce the product ligand demonstrates the retention of catalytic activity by the dimeric aldolase. The D128V mutation causes aldolase to lose intermolecular contacts with the neighboring subunit at one of the two interfaces of the tetramer. The tertiary structure of the dimer does not significantly differ from the structure of half of the tetramer. Analytical ultracentrifugation confirms the occurrence of the enzyme as a dimer in solution. The highly stable structure of aldolase with an independent active site is consistent with a model in which aldolase has evolved as a multimeric scaffold to perform other noncatalytic functions.

  8. The DMM Bound

    DEFF Research Database (Denmark)

    Emiris, Ioannis Z.; Mourrain, Bernard; Tsigaridas, Elias


    In this paper we derive aggregate separation bounds, named after Davenport-Mahler-Mignotte (DMM), on the isolated roots of polynomial systems, specifically on the minimum distance between any two such roots. The bounds exploit the structure of the system and the height of the sparse (or toric) re...... bound on the number of steps that subdivision-based algorithms perform in order to isolate all real roots of a polynomial system. This leads to the first complexity bound of Milne's algorithm [22] in 2D....

  9. Resonant multiphoton fragmentation spectrum of niobium dimer cation. (United States)

    Aydin, M; Lombardi, John R


    Resonant multiphoton fragmentation spectra of niobium dimer cation (Nb2(+)) have been obtained by utilizing laser vaporization of a Nb metal target. Ions are mass-selected with a time-of-flight mass spectrometer followed by a mass gate and then fragmented with a pulsed dye laser, and the resulting fragment ions are detected with a second time-of-flight reflectron mass spectrometer and multichannel plate. Photon resonances are detected by monitoring ion current as a function of fragmentation laser wavelength. A rich but complex spectrum of the cation is obtained. The bands display a characteristic multiplet structure that may be interpreted as due to transitions from the ground state X4Sigma(Omega g)- to several excited states, (B/D)4Pi(Omega u) and 4Sigma(Omega u)-. The ground state X4sigma(+/-1/2g)- is derived from the electron configuration pi(u)4 1sigma(g)2 2sigma(g)1 delta(g)2. The two spin-orbit components are split by 145 cm(-1) due to a strong second-order isoconfigurational spin-orbit interaction with the low-lying 2Sigma(+/-1/2g)+ state. The vibrational frequencies of the ground state and the excited-state of Nb2(+) are identified as well as molecular spin-orbit constants (A(SO)) in the excited state. The electronic structure of niobium dimer cation was investigated using density functional theory. For the electronic ground state, the predicted spectroscopic properties were in good agreement with experiment. Calculations on excited states reveal congested manifolds of quartet and doublet electronic states in the range 0-30,000 cm(-1), reflecting the multitude of possible electronic promotions among the 4d- and 5s-based molecular orbitals. Comparisons are drawn between Nb2(+) and the prevalent isoelectronic molecules V2(+)/NbV(+)/Nb2/V2/NbV2.

  10. Solitary waves in dimer binary collision model (United States)

    Ahsan, Zaid; Jayaprakash, K. R.


    Solitary wave propagation in nonlinear diatomic (dimer) chains is a very interesting topic of research in the study of nonlinear lattices. Such waves were recently found to be supported by the essentially nonlinear granular lattice and Toda lattice. An interesting aspect of this discovery is attributed to the realization of a spectrum of the mass ratio (the only system parameter governing the dynamics) that supports the propagation of such waves corresponding to the considered interaction potential. The objective of this exposition is to explore solitary wave propagation in the dimer binary collision (BC) model. Interestingly, the dimer BC model supports solitary wave propagation at a discrete spectrum of mass ratios similar to those observed in granular and Toda dimers. Further, we report a qualitative and one-to-one correspondence between the spectrum of the mass ratio corresponding to the dimer BC model and those corresponding to granular and Toda dimer chains.

  11. Dimer geometry, amoebae and a vortex dimer model (United States)

    Nash, Charles; O'Connor, Denjoe


    We present a geometrical approach and introduce a connection for dimer problems on bipartite and non-bipartite graphs. In the bipartite case the connection is flat but has non-trivial {Z}2 holonomy round certain curves. This holonomy has the universality property that it does not change as the number of vertices in the fundamental domain of the graph is increased. It is argued that the K-theory of the torus, with or without punctures, is the appropriate underlying invariant. In the non-bipartite case the connection has non-zero curvature as well as non-zero Chern number. The curvature does not require the introduction of a magnetic field. The phase diagram of these models is captured by what is known as an amoeba. We introduce a dimer model with negative edge weights which correspond to vortices. The amoebae for various models are studied with particular emphasis on the case of negative edge weights. Vortices give rise to new kinds of amoebae with certain singular structures which we investigate. On the amoeba of the vortex full hexagonal lattice we find the partition function corresponds to that of a massless Dirac doublet.

  12. Enhanced Chiral Recognition by Cyclodextrin Dimers

    Directory of Open Access Journals (Sweden)

    Bart Jan Ravoo


    Full Text Available In this article we investigate the effect of multivalency in chiral recognition. To this end, we measured the host-guest interaction of a β-cyclodextrin dimer with divalent chiral guests. We report the synthesis of carbohydrate-based water soluble chiral guests functionalized with two borneol, menthol, or isopinocampheol units in either (+ or (– configuration. We determined the interaction of these divalent guests with a β-cyclodextrin dimer using isothermal titration calorimetry. It was found that—in spite of a highly unfavorable conformation—the cyclodextrin dimer binds to guest dimers with an increased enantioselectivity, which clearly reflects the effect of multivalency.

  13. Dimerization of 3He in 3He-4He dilute mixtures filling narrow channels (United States)

    Bashkin, Eugene P.; Wojdylo, John


    We consider dimerization of 3He in a dilute solution of 3He in superfluid 4He filling straight narrow channels that can be found in nanoscale porous media. Dimer formation is facilitated by the restricted geometry and occurs despite the fact that in bulk fluid the interparticle interaction is too weak to lead to a bound state. Dimerization results in the effective ``bosonization'' of the system: a Bose quantum fluid of (3He)2 arises in place of the 3He Fermi component. At high temperatures, when the 3He impurity quasiparticles form a Maxwell-Boltzmann gas, a drastic change in the thermodynamics occurs due to the presence of dimers. The specific heat and magnetic susceptibility of the 3He component, which we calculate at arbitrary degrees of dimerization, show a marked deviation from behavior expected of an undimerized 3He component. We show that the binding energy-which depends on the channel width-is expected to be sufficiently high to make experimental observation feasible. The presence of (3He)2 dimers gives rise to an extra absorption mechanism for first sound propagating through the superfluid 4He, due to resonant absorption and decay of dimers in the acoustic field. We have calculated the absorption coefficient. Several experiments suggest themselves, utilizing, perhaps, K-L zeolites or carbon nanotubes. If the dimers themselves turn out to be attractive, then quadrumers may appear: it may even be the case that a single 3He polymer will form over the entire length of the channel.

  14. Bounded Parikh Automata

    Directory of Open Access Journals (Sweden)

    Michaël Cadilhac


    Full Text Available The Parikh finite word automaton model (PA was introduced and studied by Klaedtke and Ruess in 2003. Here, by means of related models, it is shown that the bounded languages recognized by PA are the same as those recognized by deterministic PA. Moreover, this class of languages is the class of bounded languages whose set of iterations is semilinear.

  15. Bounded Gaussian process regression

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand; Nielsen, Jens Brehm; Larsen, Jan


    We extend the Gaussian process (GP) framework for bounded regression by introducing two bounded likelihood functions that model the noise on the dependent variable explicitly. This is fundamentally different from the implicit noise assumption in the previously suggested warped GP framework. We...

  16. Chirped-Frequency Excitation of Gravitationally Bound Ultracold Neutrons


    Manfredi, Giovanni; Morandi, Omar; Friedland, Lazar; Jenke, Tobias; Abele, Hartmut


    Ultracold neutrons confined in the Earth's gravitational field display quantized energy levels that have been observed for over a decade. In recent resonance spectroscopy experiments [T. Jenke et al., Nature Phys. 7, 468 (2011)], the transition between two such gravitational quantum states was driven by the mechanical oscillation of the plates that confine the neutrons. Here we show that, by applying a sinusoidal modulation with slowly varying frequency (chirp), the neutrons can be brought to...

  17. Model Studies of CBES (Chemically Bound Excited States) Decomposition. (United States)


    the nuclear coordinates. Since photons carry virtually no momentum, radiative decay is strictly forbidden. Molecules, such as FN3, which are...thermometer. Stainless steel cooling coils in the annulus between the reaction kettle and the pot were 7 Y*’ IL He COLD MASS TRAP FLOWMETER VACUUM I UV... SPACER T PYREX HN3 KETTLE ~~~TEFLON .v, COATED0 PADDLE H20 0 0 E FLECTRICALLY NaN 3 AND HEATED POT STEARIC ACID 0 0 0 DRAIN OIL Fig. 3 Detailed view of HN

  18. Bounding Species Distribution Models (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.


    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  19. Intervalence-resonant Raman spectroscopy of strongly coupled mixed-valence cluster dimers of ruthenium. (United States)

    Rocha, Reginaldo C; Brown, Mac G; Londergan, Casey H; Salsman, J Catherine; Kubiak, Clifford P; Shreve, Andrew P


    Resonance Raman spectroelectrochemistry (RR-SEC) at -20 degrees C has been performed on the pyrazine-bridged dimer of mu-oxo-centered trinuclear ruthenium-acetate "clusters"--[(dmap)(CO)(mu-OAc)6(mu3-O)Ru3(mu-L(b))Ru3(mu3-O)(mu-OAc)6(CO)(dmap)]n (where dmap = 4-(dimethylamino)pyridine and L(b) = pyrazine-h4 and pyrazine-d4)-in three oxidation states: n = 0, -1, and -2. In the one-electron reduced, "mixed-valent" state (overall -1 charge and a single odd electron; formal oxidation states [II, II, III]-[III, III, II] on the metal centers), the Raman excitation at 800 nm is resonant with a cluster-to-cluster intervalence charge-transfer (IVCT) band. Under these conditions, scattering enhancement is observed for all four totally symmetric vibrational modes of the bridging pyrazine ligand (nu8a, nu9a, nu1, and nu6a) in the investigated spectral range (100-2000 cm(-1)), and there is no evidence of activity in non-totally symmetric vibrations. Resonantly enhanced Raman peaks related to peripheral pyridyl (dmap) ligand modes and low-frequency features arising from the trigonal Ru3O cluster core and the cluster[Ru]-[N]ligand vibrations were also observed in the spectra of the intermediate-valence (n = -1) cluster dimer. The vibrational assignments and interpretations proposed in this work were reinforced by observation of characteristic isotopic frequency shifts accompanying deuteration of the bridging pyrazine. The results reveal that the fully symmetric (A(g)) vibrational motions of the organic bridge are coupled to the nominally metal cluster-to-metal cluster fast intramolecular electron transfer (ET) and provide validation of the near-delocalized description according to a predicted three-site/three-state (e.g., metal-bridge-metal) vibronic coupling model, in which the important role of the bridging ligand in mediating electronic communication and delocalization between charge centers is explicitly considered. Further compelling evidence supporting an extended five

  20. Excited-State Deactivation of Branched Phthalocyanine Compounds. (United States)

    Zhu, Huaning; Li, Yang; Chen, Jun; Zhou, Meng; Niu, Yingli; Zhang, Xinxing; Guo, Qianjin; Wang, Shuangqing; Yang, Guoqiang; Xia, Andong


    The excited-state relaxation dynamics and chromophore interactions in two phthalocyanine compounds (bis- and trisphthalocyanines) are studied by using steady-state and femtosecond transient absorption spectral measurements, where the excited-state energy-transfer mechanism is explored. By exciting phthalocyanine compounds to their second electronically excited states and probing the subsequent relaxation dynamics, a multitude of deactivation pathways are identified. The transient absorption spectra show the relaxation pathway from the exciton state to excimer state and then back to the ground state in bisphthalocyanine (bis-Pc). In trisphthalocyanine (tris-Pc), the monomeric and dimeric subunits are excited and the excitation energy transfers from the monomeric vibrationally hot S1 state to the exciton state of a pre-associated dimer, with subsequent relaxation to the ground state through the excimer state. The theoretical calculations and steady-state spectra also show a face-to-face conformation in bis-Pc, whereas in tris-Pc, two of the three phthalocyanine branches form a pre-associated face-to-face dimeric conformation with the third one acting as a monomeric unit; this is consistent with the results of the transient absorption experiments from the perspective of molecular structure. The detailed structure-property relationships in phthalocyanine compounds is useful for exploring the function of molecular aggregates in energy migration of natural photosynthesis systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Dimeric (isoquinoline)(N-salicylidene-D,L-glutamato)copper(II) ethanol solvate. (United States)

    Langer, Vratislav; Gyepesová, Dalma; Kohútová, Mária; Valent, Aladár


    The title racemic complex, bis[mu-N-(2-oxidobenzylidene)-D,L-glutamato(2-)]bis[(isoquinoline)copper(II)] ethanol disolvate, [Cu(2)(C(12)H(11)NO(5))(2)(C(9)H(7)N)(2)].2C(2)H(6)O, adopts a square-pyramidal Cu(II) coordination mode with a tridentate N-salicylideneglutamato Schiff base dianion and an isoquinoline ligand bound in the basal plane. The apex of the pyramid is occupied by a phenolic O atom from the adjacent chelate molecule at an apical distance of 2.487 (3) A, building a dimer located on the crystallographic inversion center. The Cu...Cu spacing within the dimers is 3.3264 (12) A. The ethanol solvent molecules are hydrogen bonded to the dimeric complex molecules, forming infinite chains in the a direction. The biological activity of the title complex has been studied.

  2. A dimeric sesquiterpene, gochnatiolide A

    Directory of Open Access Journals (Sweden)

    Hui-Ping Xiong


    Full Text Available The title compound [systematic name: 5′a-hydroxy-1′,3,6,8′-tetrakis(methylene-3a,4,5,5′,5′a,6,6′,6a,7,7′,7′a,8′,9a,9b,10′a,10′b-hexadecahydrospiro[azuleno[4,5-b]furan-9(2H,3′-[3H]benz[1,8]azuleno[4,5-b]furan]-2,2′,8,9′(1′H,3H,4′H-tetrone acetone 0.92-solvate], C30H30O7·0.92C3H6O, is a dimeric sequiterpene formed by a cyclohexane system connecting two monomeric sesquiterpene lactone units of dehydrozaluzanin C. It was isolated from Ainsliaea henryi.

  3. Identification of two quanta simultaneous vibrational transitions in the dimer water trapped in inert matrices

    Energy Technology Data Exchange (ETDEWEB)

    Tremblay, B. [UPMC Universite Pierre et Marie Curie, UMR 7075, Laboratoire de Dynamique, Interactions et Reactivite (LADIR), F-75005 Paris (France); CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Reactivite (LADIR), F-75005 Paris (France); Bouteiller, Y. [Universite Paris-Nord, CNRS, Laboratoire de Physique des lasers, UMR 7538, 93430 Villetaneuse (France); Perchard, J.P., E-mail: [UPMC Universite Pierre et Marie Curie, UMR 7075, Laboratoire de Dynamique, Interactions et Reactivite (LADIR), F-75005 Paris (France); CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Reactivite (LADIR), F-75005 Paris (France)


    Graphical abstract: Simultaneous vibrational transitions of both proton donor and proton acceptor molecules of the water dimer trapped in Ne, Ar and N{sub 2} matrices have been identified. Display Omitted Research highlights: {yields} Observation of simultaneous vibrational transition (ST) within the water dimer. {yields} Proof of resonances involving ST's using {sup 18}O/{sup 16}O isotopic mixtures. {yields} The experimental resonance parameters agree with the predictions of ab initio calculations. - Abstract: Two quanta transitions involving the vibrational excitation of both proton donor (PD) and proton acceptor (PA) molecules of the water dimer trapped in inert matrices, a particular case of similtaneous transitions, have been identified. They are characterized by weaker intensity and smaller anharmonicity than the usual combinations of PD or PA. In some cases their intensity is strongly enhanced by quasi perfect resonances with PD combinations, as proved by decoupling effects in {sup 18}O/{sup 16}O isotopic mixtures.

  4. Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers (United States)

    Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Cho, Kwang-Jin; Dolino, Drew M.; Chen, Wei; Li, Hongyang; Grant, Barry J.; Hancock, John F.; Gorfe, Alemayehu A.


    Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers. For validation we used mutagenesis, electron microscopy and biochemical assays under non-denaturing conditions. We show that partial disruption of a predicted interface through charge reversal mutation of apposed residues reduces oligomerization while introduction of cysteines at these positions enhanced dimerization likely through the formation of an intermolecular disulfide bond. Free energy calculations indicated that K-Ras dimerization involves direct but weak protein-protein interactions in solution, consistent with the notion that dimerization is facilitated by membrane binding. Taken together, our atomically detailed analyses provide unique mechanistic insights into K-Ras dimer formation and membrane organization as well as the conformational fluctuations and equilibrium thermodynamics underlying these processes.

  5. Virial Expansion Bounds (United States)

    Tate, Stephen James


    In the 1960s, the technique of using cluster expansion bounds in order to achieve bounds on the virial expansion was developed by Lebowitz and Penrose (J. Math. Phys. 5:841, 1964) and Ruelle (Statistical Mechanics: Rigorous Results. Benjamin, Elmsford, 1969). This technique is generalised to more recent cluster expansion bounds by Poghosyan and Ueltschi (J. Math. Phys. 50:053509, 2009), which are related to the work of Procacci (J. Stat. Phys. 129:171, 2007) and the tree-graph identity, detailed by Brydges (Phénomènes Critiques, Systèmes Aléatoires, Théories de Jauge. Les Houches 1984, pp. 129-183, 1986). The bounds achieved by Lebowitz and Penrose can also be sharpened by doing the actual optimisation and achieving expressions in terms of the Lambert W-function. The different bound from the cluster expansion shows some improvements for bounds on the convergence of the virial expansion in the case of positive potentials, which are allowed to have a hard core.

  6. Nonequilibrium quantum bounds to Landauer's principle: Tightness and effectiveness (United States)

    Campbell, Steve; Guarnieri, Giacomo; Paternostro, Mauro; Vacchini, Bassano


    We assess two different nonequilibrium quantum Landauer bounds: the traditional approach based on the change in entropy, referred to as the "entropic bound," and one based on the details of the dynamical map, referred to as the "thermodynamic bound." By first restricting to a simple exactly solvable model of a single two-level system coupled to a finite-dimensional thermal environment and by exploiting an excitation-preserving interaction, we establish the dominant role played by the population terms in dictating the tightness of these bounds with respect to the dissipated heat and clearly establish that coherences only affect the entropic bound. Furthermore, we show that sharp boundaries between the relative performance of the two quantities emerge and find that there are clear instances where both approaches return a bound weaker than Clausius' statement of the second law, rendering them ineffective. Finally, we show that our results extend to generic interaction terms.

  7. The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion. (United States)

    Schulte, Kathrin; Pawlowski, Nikolaus; Faelber, Katja; Fröhlich, Chris; Howard, Jonathan; Daumke, Oliver


    The immunity-related GTPases (IRGs) constitute a powerful cell-autonomous resistance system against several intracellular pathogens. Irga6 is a dynamin-like protein that oligomerizes at the parasitophorous vacuolar membrane (PVM) of Toxoplasma gondii leading to its vesiculation. Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization. We determined the crystal structure of an oligomerization-impaired Irga6 mutant bound to a non-hydrolyzable GTP analog. Contrary to the previous model, the structure shows that the GTPase domains dimerize in a parallel fashion. The nucleotides in the center of the interface participate in dimerization by forming symmetric contacts with each other and with the switch I region of the opposing Irga6 molecule. The latter contact appears to activate GTP hydrolysis by stabilizing the position of the catalytic glutamate 106 in switch I close to the active site. Further dimerization contacts involve switch II, the G4 helix and the trans stabilizing loop. The Irga6 structure features a parallel GTPase domain dimer, which appears to be a unifying feature of all dynamin and septin superfamily members. This study contributes important insights into the assembly and catalytic mechanisms of IRG proteins as prerequisite to understand their anti-microbial action.

  8. Structure of a rabbit muscle fructose-1, 6-bisphosphate aldolase A dimer variant

    Energy Technology Data Exchange (ETDEWEB)

    Sherawat, Manashi [Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2394 (United States); Tolan, Dean R., E-mail: [Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215 (United States); Allen, Karen N., E-mail: [Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2394 (United States)


    The X-ray crystallographic structure of a dimer variant of fructose-1, 6-bisphosphate aldolase demonstrates a stable oligomer that mirrors half of the native tetramer. The presence of product demonstrates that this is an active form. Fructose-1, 6-bisphosphate aldolase (aldolase) is an essential enzyme in glycolysis and gluconeogenesis. In addition to this primary function, aldolase is also known to bind to a variety of other proteins, a property that may allow it to perform ‘moonlighting’ roles in the cell. Although monomeric and dimeric aldolases possess full catalytic activity, the enzyme occurs as an unusually stable tetramer, suggesting a possible link between the oligomeric state and these noncatalytic cellular roles. Here, the first high-resolution X-ray crystal structure of rabbit muscle D128V aldolase, a dimeric form of aldolase mimicking the clinically important D128G mutation in humans associated with hemolytic anemia, is presented. The structure of the dimer was determined to 1.7 Å resolution with the product DHAP bound in the active site. The turnover of substrate to produce the product ligand demonstrates the retention of catalytic activity by the dimeric aldolase. The D128V mutation causes aldolase to lose intermolecular contacts with the neighboring subunit at one of the two interfaces of the tetramer. The tertiary structure of the dimer does not significantly differ from the structure of half of the tetramer. Analytical ultracentrifugation confirms the occurrence of the enzyme as a dimer in solution. The highly stable structure of aldolase with an independent active site is consistent with a model in which aldolase has evolved as a multimeric scaffold to perform other noncatalytic functions.

  9. Universal bounds in even-spin CFTs

    Energy Technology Data Exchange (ETDEWEB)

    Qualls, Joshua D. [Department of Physics, National Taiwan University,Taipei, Taiwan (China)


    We prove using invariance under the modular S− and ST−transformations that every unitary two-dimensional conformal field theory (CFT) having only even-spin primary operators (with no extended chiral algebra and with right- and left-central charges c,c̃>1) contains a primary operator with dimension Δ{sub 1} satisfying 0<Δ{sub 1}<((c+c̃)/24)+0.09280…. After deriving both analytical and numerical bounds, we discuss how to extend our methods to bound higher conformal dimensions before deriving lower and upper bounds on the number of primary operators in a given energy range. Using the AdS{sub 3}/CFT{sub 2} dictionary, the bound on Δ{sub 1} proves the lightest massive excitation in appropriate theories of 3D matter and gravity with cosmological constant Λ<0 can be no heavier than 1/8G{sub N}+O(√(−Λ)); the bounds on the number of operators are related via AdS/CFT to the entropy of states in the dual gravitational theory. In the flat-space approximation, the limiting mass is exactly that of the lightest BTZ black hole.

  10. Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences (United States)

    Ai, Yue-Jie; Zhang, Feng; Cui, Gang-Long; Luo, Yi; Fang, Wei-Hai


    2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized π1π∗ excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed.

  11. Single-Molecule Rotational Switch on a Dangling Bond Dimer Bearing. (United States)

    Godlewski, Szymon; Kawai, Hiroyo; Kolmer, Marek; Zuzak, Rafał; Echavarren, Antonio M; Joachim, Christian; Szymonski, Marek; Saeys, Mark


    One of the key challenges in the construction of atomic-scale circuits and molecular machines is to design molecular rotors and switches by controlling the linear or rotational movement of a molecule while preserving its intrinsic electronic properties. Here, we demonstrate both the continuous rotational switching and the controlled step-by-step single switching of a trinaphthylene molecule adsorbed on a dangling bond dimer created on a hydrogen-passivated Ge(001):H surface. The molecular switch is on-surface assembled when the covalent bonds between the molecule and the dangling bond dimer are controllably broken, and the molecule is attached to the dimer by long-range van der Waals interactions. In this configuration, the molecule retains its intrinsic electronic properties, as confirmed by combined scanning tunneling microscopy/spectroscopy (STM/STS) measurements, density functional theory calculations, and advanced STM image calculations. Continuous switching of the molecule is initiated by vibronic excitations when the electrons are tunneling through the lowest unoccupied molecular orbital state of the molecule. The switching path is a combination of a sliding and rotation motion over the dangling bond dimer pivot. By carefully selecting the STM conditions, control over discrete single switching events is also achieved. Combined with the ability to create dangling bond dimers with atomic precision, the controlled rotational molecular switch is expected to be a crucial building block for more complex surface atomic-scale devices.

  12. Sensing Properties of a Fabry-Perot Dielectric Structure and Dimer Nanoparticles

    Directory of Open Access Journals (Sweden)

    A. Polemi


    Full Text Available We investigate the use of a Fabry-Perot dielectric structure combined with differently shaped nanoparticles for Surface Enhanced Raman Scattering. In particular, we show how an ideal two-layer Fabry-Perot configuration enhances the local surface field of silver nanoparticles positioned on the surface of the structure. We develop the concept using disc dimers and then extend the discussion to bowtie nanoparticles. The structure is excited by a single emitter, which couples to the nanoparticles through the dielectric layers, producing a wide aperture field that can be used to excite multiple dimers. We show how an array of nanoparticles can be properly arranged in order to increase the total scattering signal generated from the structure. The layered geometry produces robust field properties in between nanoparticles, making the overall sensing characteristics less sensitive to the interparticle seperation distance and incident polarization.

  13. Switchable directional scattering of electromagnetic radiation with subwavelength asymmetric silicon dimers. (United States)

    Albella, Pablo; Shibanuma, Toshihiko; Maier, Stefan A


    High refractive index dielectric nanoparticles show high promise as a complementary nanophotonics platform due to compared with plasmonic nanostructures low absorption losses and the co-existence of magnetic and electric resonances. Here we explore their use as resonantly enhanced directional scatterers. We theoretically demonstrate that an asymmetric dimer of silicon nanoparticles shows tuneable directional scattering depending on the frequency of excitation. This is due to the interference between electric and magnetic dipoles excited in each nanoparticle, enabling directional control of the scattered light. Interestingly, this control can be achieved regardless of the polarization direction with respect to the dimer axis; however, difference in the polarization can shift the wavelengths at which the directional scattering is achieved. We also explore the application of such an asymmetric nanoantenna as a tuneable routing element in a nanometer scale, suggesting applications in optical nanocircuitry.

  14. Photoinduced dissociation of cyclobutane thymine dimer studied by semiclassical dynamics simulation. (United States)

    Dou, Yusheng; Xiong, Shanshan; Wu, Weifeng; Yuan, Shuai; Tang, Hong


    Photoinduced dissociation of the thymine dimer is studied in a semiclassical dynamics simulation. The simulation follows excitation of an isolated thymine dimer by a 25 fs fwhm laser pulse, and finds that dissociation proceeds via an asynchronously concerted mechanism, in which the C(5)-C(5)' bond breaks soon after application of the laser pulse, followed by cleavage of the C(6)-C(6)' bond. The dissociation results in two thymine monomers, one in an electronically excited state and the other in the ground state. The former decays to the electronic ground state through an avoided crossing induced by deformation of the pyrimidine ring at the C(5)' and C(6)' sites. Copyright 2010 Elsevier B.V. All rights reserved.

  15. Quantum dimer model for the pseudogap metal. (United States)

    Punk, Matthias; Allais, Andrea; Sachdev, Subir


    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S = 1/2, charge +e fermionic dimers. The model realizes a "fractionalized Fermi liquid" with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8 × 8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments.

  16. Photon emission statistics and photon tracking in single-molecule spectroscopy of molecular aggregates : Dimers and trimers

    NARCIS (Netherlands)

    Bloemsma, E. A.; Knoester, J.


    Based on the generating function formalism, we investigate broadband photon statistics of emission for single dimers and trimers driven by a continuous monochromatic laser field. In particular, we study the first and second moments of the emission statistics, which are the fluorescence excitation

  17. Intermolecular Coulombic Decay (ICD) Occuring in Triatomic Molecular Dimer (United States)

    Iskandar, Wael; Gatton, Averell; Gaire, Bishwanath; Champenois, Elio; Larsen, Kirk; Shivaram, Niranjan; Moradmand, Ali; Severt, Travis; Williams, Joshua; Slaughter, Daniel; Weber, Thorsten


    For over two decades, the production of ICD process has been extensively investigated theoretically and experimentally in different systems bounded by a week force (ex. van-der-Waals or Hydrogen force). Furthermore, the ICD process has been demonstrated a strong implication in biological system (DNA damage and DNA repair mechanism) because of the production of genotoxic low energy electrons during the decay cascade. Studying large complex system such as triatomic molecular dimer may be helpful for further exploration of ``Auger electron driven cancer therapy''. The present experiment investigates the dissociation dynamics happened in collision between a photons and CO2 dimer. We will focus more specifically on the CO2++CO2+ fragmentation channel and the detection in coincidence of the two ionic fragments and the two electrons will be done using a COld Target Recoil Ion Momentum Spectroscopy (COLTRIMS). The measurements of the Kinetic Energy Release of the two fragments and the relative angular distribution of the electrons in the molecular frame reveal that the ICD is the only mechanism responsible for the production of this fragmentation channel.

  18. Temperature-sensitive photoreactivation of cyclobutane thymine dimer in soybean. (United States)

    Yamamoto, Ayumi; Tanbir, Najrana; Hirouchi, Tokuhisa; Teranishi, Mika; Hidema, Jun; Morioka, Hiroshi; Yamamoto, Kazuo


    UV radiation induces the formation of two classes of photoproducts in DNA, the cyclobutane pyrimidine dimer (CPD) and the pyrimidine 6-4 pyrimidone photoproduct. CPDs in plants are repaired by class II CPD photolyase via a UV-A/blue light-dependent mechanism. The genes for the class II CPD photolyase have been cloned from higher plants such as Arabidopsis, Cucumis sativus (cucumber), Oryza sativa (rice) and Spinacia oleracea (spinach). Flavin adenine dinucleotide (FAD) has been identified as a cofactor. Here we report the isolation and characterization of the CPD photolyase cDNA from soybean (Glycin max). The sequence of amino acids predicted from the cDNA sequence was highly homologous to sequences of higher plant class II CPD photolyases. When the cDNA was expressed in a photolyase-deficient Escherichia coli, photoreactivation activity was partially restored by illumination with a fluorescent light. The purified enzyme showed CPD binding and light-dependent photoreactivation activities in vitro. When soybean CPD photolyase was heat-treated in vitro from 25 degrees C to 45 degrees C for 3 min, thymine dimer-binding activity and photoreactivation activity were decreased, and FAD was released from the enzyme. On the other hand, when the enzyme-CPD complex was heat-treated, photoreactivation activity was stable. We argue that FAD in the soybean CPD photolyase is labile for temperature, but once the enzyme-CPD complex has formed, FAD becomes tightly bound to the enzyme or complex.

  19. Dynamical properties of photogenerated polarons in one-dimensional dimerized Mott Insulators (United States)

    Moriya, K.; Maeshima, N.; Hino, K. I.


    We study physical properties of photogenerated electron-lattice coupled states, polarons, in one-dimensional (1D) Peierls-Hubbard model with classical lattice distortion by means of the density matrix renormalization group method. The numerical results show novel midgap peaks in optical response spectra of polarons for large on-site Coulomb interaction U. These midgap peaks originate from charge-transfer excitations within the dimer in polarons.

  20. Magnetic excitations of Kitaev-Heisenberg models on honeycomb lattices (United States)

    Yamada, Takuto; Suzuki, Takafumi; Suga, Sei-ichiro


    We investigate ground state energies and low-energy excitations of the S = 1/2 Kitaev-Heisenberg model on honeycomb lattices by using dimer series expansions. We find that dimer series expansions can approach the close vicinity of the Kitaev limit, where the Heisenberg interaction is absent, in the lower order expansion than the Ising series expansion. When the system approaches the Kitaev limit, low-lying modes in the zigzag and Néel phases become flatter except for the Bragg wave numbers.

  1. Bounded Tamper Resilience

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre; Faust, Sebastian; Mukherjee, Pratyay


    a bounded tamper and leakage resilient CCA secure public key cryptosystem based on the DDH assumption. We first define a weaker CPA-like security notion that we can instantiate based on DDH, and then we give a general compiler that yields CCA-security with tamper and leakage resilience. This requires...... a public tamper-proof common reference string. Finally, we explain how to boost bounded tampering and leakage resilience (as in 1. and 2. above) to continuous tampering and leakage resilience, in the so-called floppy model where each user has a personal hardware token (containing leak- and tamper...

  2. Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation

    KAUST Repository

    Kim, Jeong Joo


    Cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) is a key regulator of smooth muscle and vascular tone and represents an important drug target for treating hypertensive diseases and erectile dysfunction. Despite its importance, its activation mechanism is not fully understood. To understand the activation mechanism, we determined a 2.5 Å crystal structure of the PKG I regulatory (R) domain bound with cGMP, which represents the activated state. Although we used a monomeric domain for crystallization, the structure reveals that two R domains form a symmetric dimer where the cGMP bound at high-affinity pockets provide critical dimeric contacts. Small-angle X-ray scattering and mutagenesis support this dimer model, suggesting that the dimer interface modulates kinase activation. Finally, structural comparison with the homologous cyclic AMP-dependent protein kinase reveals that PKG is drastically different from protein kinase A in its active conformation, suggesting a novel activation mechanism for PKG. Kim et al. obtain the first crystal structure of the PKG I R domain bound with cGMP representing its activated state. It reveals a symmetric R dimer where cGMP molecules provide dimeric contacts. This R-R interaction prevents the high-affinity inhibitory interaction between R-C domain and sustains activation. © 2016 Elsevier Ltd.

  3. Synthesis and biological evaluation of 2-benzoylpyridine thiosemicarbazones in a dimeric system: structure-activity relationship studies on their anti-proliferative and iron chelation efficacy. (United States)

    Lukmantara, Adeline Y; Kalinowski, Danuta S; Kumar, Naresh; Richardson, Des R


    Thiosemicarbazone chelators represent an exciting class of biologically active compounds that show great potential as anti-tumor agents. Our previous studies demonstrated the potent anti-tumor activity of the 2'-benzoylpyridine thiosemicarbazone series. While extensive studies have been performed on monomeric thiosemicarbazone compounds, dimeric thiosemicarbazone chelators have received comparatively less attention. Thus, it was of interest to investigate the anti-proliferative activity and iron chelation efficacy of dimeric thiosemicarbazones. Two classes of dimeric thiosemicarbazones were designed and synthesized. The first class consisted of two benzoylpyridine-based thiosemicarbazone units connected via a hexane or dodecane alkyl bridge, while the second class of dimer consisted of two thiosemicarbazones attached to a 2,6-dibenzoylpyridine core. These dimeric ligands demonstrated greater anti-proliferative activity than the clinically used iron chelator, desferrioxamine. This study highlights the importance of optimal lipophilicity as a factor influencing the cytotoxicity and iron chelation efficacy of these chelators. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Synthesis of new dimeric carvacrol compounds

    Directory of Open Access Journals (Sweden)

    Uttam B. More


    Full Text Available The polymer supported carvacrol anion was reacted with 1,2-dibromoethane, 1,4-dibromoethane, oxalyl dichloride, malonyl dichloride, succinyl dichloride, glutaroyl dichloride, and adipoyl dichloride to afford the corresponding dimeric carvacryl ethers or esters

  5. Formation of cystine slipknots in dimeric proteins.

    Directory of Open Access Journals (Sweden)

    Mateusz Sikora

    Full Text Available We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher.

  6. Congruent Docking of Dimeric Kinesin and ncd into Three-dimensional Electron Cryomicroscopy Maps of Microtubule–Motor ADP Complexes (United States)

    Hirose, Keiko; Löwe, Jan; Alonso, Maria; Cross, Robert A.; Amos, Linda A.


    We present a new map showing dimeric kinesin bound to microtubules in the presence of ADP that was obtained by electron cryomicroscopy and image reconstruction. The directly bound monomer (first head) shows a different conformation from one in the more tightly bound empty state. This change in the first head is amplified as a movement of the second (tethered) head, which tilts upward. The atomic coordinates of kinesin·ADP dock into our map so that the tethered head associates with the bound head as in the kinesin dimer structure seen by x-ray crystallography. The new docking orientation avoids problems associated with previous predictions; it puts residues implicated by proteolysis-protection and mutagenesis studies near the microtubule but does not lead to steric interference between the coiled-coil tail and the microtubule surface. The observed conformational changes in the tightly bound states would probably bring some important residues closer to tubulin. As expected from the homology with kinesin, the atomic coordinates of nonclaret disjunctional protein (ncd)·ADP dock in the same orientation into the attached head in a map of microtubules decorated with dimeric ncd·ADP. Our results support the idea that the observed direct interaction between the two heads is important at some stages of the mechanism by which kinesin moves processively along microtubules. PMID:10359615

  7. Bioactive dimeric carbazole alkaloids from Murraya koenigii. (United States)

    Uvarani, Chokkalingam; Sankaran, Mathan; Jaivel, Nanjundan; Chandraprakash, Kumarasamy; Ata, Athar; Mohan, Palathurai S


    Phytochemical studies on the CHCl3 extract of the fruit pulp of Murraya koenigii afforded three new dimeric carbazole alkaloids, bisgerayafolines A-C (1-3). Bisgerayafolines A-C (1-3) are structurally unique dimeric carbazole alkaloids comprising geranyl moieties incorporated in their structures. Compounds 1-3 exhibited various levels of antioxidant, anti-α-glucosidase, DNA binding, and cytotoxic activities and protein interactions.

  8. Prediction of thymine dimer repair by electron transfer from photoexcited 8-aminoguanine or its deprotonated anion. (United States)

    Sieradzan, Iwona; Marchaj, Marzena; Anusiewicz, Iwona; Skurski, Piotr; Simons, Jack


    Electronic structure methods are used to estimate differences in reaction barriers for transfer of an electron from singlet ππ* excited 8-aminoguanine (A) or deprotonated 8-aminoguanine anion (A(-)) to a proximal thymine dimer site compared to barriers when ππ* excited 8-oxoguanine (O) or deprotonated 8-oxoguanine (O(-)) serve as the electron donor. It is predicted that the barrier for photoexcited A should be lower than for photoexcited O, and the barrier for photoexcited A(-) should be lower than for photoexcited O(-). Moreover, A, O(-), and A(-) are predicted to have ππ* excited states at energies near where O does, which allows them to be excited by photons low enough in energy to avoid exciting or ionizing any of DNA's bases. The origin of the differences in barriers is suggested to be the lower ionization potential of A compared to O and the lower electron detachment energy of A(-) compared to O(-). Because O and O(-) have been experimentally shown to produce thymine dimer repair, it is proposed that A and A(-) are promising repair agents deserving experimental study.

  9. Intermolecular potential energy surface for CS2 dimer. (United States)

    Farrokhpour, Hossein; Mombeini, Zainab; Namazian, Mansoor; Coote, Michelle L


    A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface. Copyright © 2010 Wiley Periodicals, Inc.

  10. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José


    This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.

  11. Born Level Bound States (United States)

    Hoyer, Paul


    Bound state poles in the S-matrix of perturbative QED are generated by the divergence of the expansion in α . The perturbative corrections are necessarily singular when expanding around free, {O}( α ^0 ) in and out states that have no overlap with finite-sized atomic wave functions. Nevertheless, measurables such as binding energies do have well-behaved expansions in powers of α (and log α ). It is desirable to formulate the concept of "lowest order" for gauge theory bound states such that higher order corrections vanish in the α → 0 limit. This may allow to determine a lowest order term for QCD hadrons which incorporates essential features such as confinement and chiral symmetry breaking, and thus can serve as the starting point of a useful perturbative expansion. I discuss a "Born" (no loop, lowest order in \\hbar ) approximation. Born level states are bound by gauge fields which satisfy the classical field equations. Gauss' law determines a distinct field A^0({\\varvec{x}}) for each instantaneous position of the charges. A Poincaré covariant boundary condition for the gluon field leads to a confining potential for q\\bar{q} and qqq states. In frames where the bound state is in motion the classical gauge field is obtained by a Lorentz boost of the rest frame field.

  12. Mass spectrum bound state systems with relativistic corrections

    Energy Technology Data Exchange (ETDEWEB)

    Dineykhan, M; Zhaugasheva, S A [Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, Dubna (Russian Federation); Toinbaeva, N Sh; Jakhanshir, A [al-Farabi Kazak National University, 480012 Almaty (Kazakhstan)


    Based on the investigation of the asymptotic behaviour of the polarization loop function for charged n scalar particles in an external gauge field, we determine the interaction Hamiltonian including relativistic corrections. The mass spectrum of the bound state is analytically derived. The mechanism for arising of the constituent mass of the relativistic bound-state forming particles is explained. The mass and the constituent mass of the two-, three- and n-body relativistic bound states are calculated taking into account relativistic corrections. The corrections arising due to the one- and two-loop electron polarization to the energy spectrum of muonic hydrogen with orbital and radial excitations are calculated.

  13. Relation between properties of long-range diatomic bound states

    DEFF Research Database (Denmark)

    Spirko, Vladimir; Sauer, Stephan P. A.; Szalewicz, Krzysztof


    Long-range states of diatomic molecules have average values of internuclear separations at least one order of magnitude larger than the equilibrium value of R. For example, the helium dimer 4He2 has a single bound state with of about 50 Å. We show that the properties of these states, such as ...>, the dissociation energy, or the s-wave scattering length, can be related by simple, yet very accurate formulas if a potential energy curve is known. By examining a range of ab initio and empirical helium dimer potentials, as well as scaling these potentials, we found that the formulas remain accurate even if very...

  14. Role of adenine in thymine-dimer repair by reduced flavin-adenine dinucleotide. (United States)

    Li, Guifeng; Sichula, Vincent; Glusac, Ksenija D


    We present a study of excited-state behavior of reduced flavin cofactors using femtosecond optical transient absorption spectroscopy. The reduced flavin cofactors studied were in two protonation states: flavin-adenine dinucleotide (FADH2 and FADH-) and flavin-mononucleotide (FMNH2 and FMNH-). We find that FMNH- exhibits multiexponential decay dynamics due to the presence of two bent conformers of the isoalloxazine ring. FMNH2 exhibits an additional fast deactivation component that is assigned to an iminol tautomer. Reduced flavin cofactors also exhibit a long-lived component that is attributed to the semiquinone and the hydrated electron that are produced in photoinduced electron transfer to the solvent. The presence of adenine in FADH2 and FADH- further changes the excited-state dynamics due to intramolecular electron transfer from the isoalloxazine to the adenine moiety of cofactors. This electron transfer is more pronounced in FADH2 due to pi-stacking interactions between two moieties. We further studied cyclobutane thymine dimer (TT-dimer) repair via FADH- and FMNH- and found that the repair is much more efficient in the case of FADH-. These results suggest that the adenine moiety plays a significant role in the TT-dimer repair dynamics. Two possible explanations for the adenine mediation are presented: (i) a two-step electron transfer process, with the initial electron transfer occurring from flavin to adenine moiety of FADH-, followed by a second electron transfer from adenine to TT-dimer; (ii) the preconcentration of TT-dimer molecules around the flavin cofactor due to the hydrophobic nature of the adenine moiety.

  15. Imaging study of vibrational predissociation of the HCl-acetylene dimer: pair-correlated distributions. (United States)

    Li, Guosheng; Parr, Jessica; Fedorov, Igor; Reisler, Hanna


    The state-to-state predissociation dynamics of the HCl-acetylene dimer were studied following excitation in the asymmetric C-H (asym-CH) stretch and the HCl stretch. Velocity map imaging (VMI) and resonance enhanced multiphoton ionization (REMPI) were used to determine pair-correlated product energy distributions. Different vibrational predissociation mechanisms were observed for the two excited vibrational levels. Following excitation in the of the asym-CH stretch fundamental, HCl fragments in upsilon = 0 and j = 4-7 were observed and no HCl in upsilon = 1 was detected. The fragments' center-of-mass (c.m.) translational energy distributions were derived from images of HCl (j = 4-7), and were converted to rotational state distributions of the acetylene co-fragment by assuming that acetylene is generated with one quantum of C-C stretch (nu(2)) excitation. The acetylene pair-correlated rotational state distributions agree with the predictions of the statistical phase space theory, restricted to acetylene fragments in 1nu(2). It is concluded that the predissociation mechanism is dominated by the initial coupling of the asym-CH vibration to a combination of C-C stretch and bending modes in the acetylene moiety. Vibrational energy redistribution (IVR) between acetylene bending and the intermolecular dimer modes leads to predissociation that preserves the C-C stretch excitation in the acetylene product while distributing the rest of the available energy statistically. The predissociation mechanism following excitation in the Q band of the dimer's HCl stretch fundamental was quite different. HCl (upsilon = 0) rotational states up to j = 8 were observed. The rovibrational state distributions in the acetylene co-fragment derived from HCl (j = 6-8) images were non-statistical with one or two quanta in acetylene bending vibrational excitation. From the observation that all the HCl(j) translational energy distributions were similar, it is proposed that there exists a

  16. D-dimers (DD) in CVST. (United States)

    Wang, Hui Fang; Pu, Chuan Qiang; Yin, Xi; Tian, Cheng Lin; Chen, Ting; Guo, Jun Hong; Shi, Qiang


    We were interested in further confirming whether D-dimers (DD) are indeed elevated in cerebral venous sinus thrombosis (CVST) as reported in those studies. CVST patients who had a plasma D-dimer test (139 cases) were included and divided into two groups: elevated D-dimer group (EDG) (>0.5 μg/mL; 65 cases) and normal D-dimer group (NDG) (≤0.5 μg/mL; 74 cases). The two groups were compared in terms of demographic data, clinical manifestation, laboratory and imaging data, using inferential statistical methods. The chi-squared and Fisher exact test showed that, compared to the NDG (74 cases), patients with elevated D-dimer levels were more likely to have a shorter symptom duration (SD) (30 ± 83.9 versus 90 ± 58.9 d, p = 0.003), more risk factors (75.4% versus 52.7%, p = 0.006), higher multiple venous sinus involvement (75.4% versus 59.5%, p = 0.037), increased fibrinogen (43.1% versus 18.9%, p = 0.037) and higher levels of blood glucose (18.3% versus 11%, p = 0.037). According to correlation analyses, D-dimer levels were positively correlated with number of venous sinuses involvement (NVS) (r = 0.321, p = 0.009) in the EDG. Multivariate logistic regression analysis showed that SD (OR, 0.025; 95% CI, 1.324-6.043; p = 0.000), NVS (OR, 1.573; 95% CI, 1.15-2.151; p = 0.005) and risk factors (OR, 3.321; 95% CI, 1.451-7.564; p = 0.004) were significantly different between the two groups. D-dimer is elevated in patients with acute/subacute CVST.

  17. Properties of Excitons Bound to Ionized Donors

    DEFF Research Database (Denmark)

    Skettrup, Torben; Suffczynski, M.; Gorzkowski, W.


    Binding energies, interparticle distances, oscillator strengths, and exchange corrections are calculated for the three-particle complex corresponding to an exciton bound to an ionized donor. The results are given as functions of the mass ratio of the electron and hole. Binding of the complex...... is obtained for mass ratios up to 0.426. The interparticle distances are up to 50 times larger than the corresponding exciton radius. The oscillator strengths are about 104 times greater than those of free excitons, while the exchange corrections for the complex are comparable to those of free excitions...

  18. Calix[4]arene supported clusters: a dimer of [Mn(III)Mn(II)] dimers

    DEFF Research Database (Denmark)

    Taylor, Stephanie M; McIntosh, Ruaraidh D; Beavers, Christine M


    Phosphinate ligands allow for the transformation of a calix[4]arene supported [Mn(III)(2)Mn(II)(2)] tetramer cluster motif into an unusual [Mn(III)Mn(II)](2) dimer of dimers; the clusters self-assemble in the crystal to form bi-layer arrays reminiscent of the typical packing of calixarene solvates....

  19. The generalized pseudospectral approach to the bound states of the ...

    Indian Academy of Sciences (India)

    Abstract. The generalized pseudospectral (GPS) method is employed to calculate the bound states of the Hulthén and the Yukawa potentials in quantum mechanics, with special emphasis on higher excited states and stronger couplings. Accurate energy eigenvalues, expectation values and radial probability densities are ...

  20. Dimerization and enzymatic activity of fungal 17β-hydroxysteroid dehydrogenase from the short-chain dehydrogenase/reductase superfamily

    Directory of Open Access Journals (Sweden)

    Kristan Katja


    Full Text Available Abstract Background 17β-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus (17β-HSDcl is a member of the short-chain dehydrogenase/reductase (SDR superfamily. SDR proteins usually function as dimers or tetramers and 17β-HSDcl is also a homodimer under native conditions. Results We have investigated here which secondary structure elements are involved in the dimerization of 17β-HSDcl and examined the importance of dimerization for the enzyme activity. Sequence similarity with trihydroxynaphthalene reductase from Magnaporthe grisea indicated that Arg129 and His111 from the αE-helices interact with the Asp121, Glu117 and Asp187 residues from the αE and αF-helices of the neighbouring subunit. The Arg129Asp and His111Leu mutations both rendered 17β-HSDcl monomeric, while the mutant 17β-HSDcl-His111Ala was dimeric. Circular dichroism spectroscopy analysis confirmed the conservation of the secondary structure in both monomers. The three mutant proteins all bound coenzyme, as shown by fluorescence quenching in the presence of NADP+, but both monomers showed no enzymatic activity. Conclusion We have shown by site-directed mutagenesis and structure/function analysis that 17β-HSDcl dimerization involves the αE and αF helices of both subunits. Neighbouring subunits are connected through hydrophobic interactions, H-bonds and salt bridges involving amino acid residues His111 and Arg129. Since the substitutions of these two amino acid residues lead to inactive monomers with conserved secondary structure, we suggest dimerization is a prerequisite for catalysis. A detailed understanding of this dimerization could lead to the development of compounds that will specifically prevent dimerization, thereby serving as a new type of inhibitor.

  1. PSD-95 uncoupling from NMDA receptors by Tat-N-dimer ameliorates neuronal depolarisation in cortical spreading depression

    DEFF Research Database (Denmark)

    Kucharz, Krzysztof; Søndergaard Rasmussen, Ida; Bach, Anders


    , UCCB01-144 (Tat-N-dimer) ameliorates the persistent effects of cortical spreading depression on cortical function. Using in vivo two-photon microscopy in somatosensory cortex in mice, we show that fluorescently labelled Tat-N-dimer readily crosses blood-brain barrier and accumulates in nerve cells...... depression on cortical blood flow and CMRO2 We suggest that uncoupling of PSD-95 from NMDA receptors reduces overall neuronal excitability and the amplitude of the spreading depolarisation wave. These findings may be of interest for understanding the neuroprotective effects of the nNOS/PSD-95 uncoupling...

  2. Dynamic interplay between adhesive and lateral E-cadherin dimers

    DEFF Research Database (Denmark)

    Klingelhöfer, Jörg; Laur, Oscar Y; Troyanovsky, Regina B


    E-cadherin, an adhesive transmembrane protein of epithelial adherens junctions, forms two types of detergent-resistant dimers: adhesive dimers consisting of cadherin molecules derived from two neighboring cells and lateral dimers incorporating cadherins of the same cell. Both dimers depend...... on the integrity of the same residue, Trp156. While the relative amounts of these complexes are not certain, we show here that in epithelial A-431 cells, adhesive dimers may be a prevalent form. Inactivation of the calcium-binding sites, located between successive cadherin ectodomains, drastically reduced...... the amount of adhesive dimers and concomitantly increased the amount of lateral dimers. A similar interdependence of adhesive and lateral dimers was observed in digitonin-permeabilized cells. In these cells, adhesive dimers immediately disassembled after lowering the Ca2+ concentration below 0.1 m...

  3. Contribution of boundness and motion of nucleons to the EMC effect


    Birbrair, B. L.; Ryskin, M.G; Ryazanov, V. I.


    The kinematical corrections to the structure function of nucleon in nucleus due to the boundness and motion of nucleons arise from the excitation of the doorway states for one-nucleon transfer reactions in the deep inelastic scattering on nuclei.

  4. New Insights into Molecular Organization of Human Neuraminidase-1: Transmembrane Topology and Dimerization Ability (United States)

    Maurice, Pascal; Baud, Stéphanie; Bocharova, Olga V.; Bocharov, Eduard V.; Kuznetsov, Andrey S.; Kawecki, Charlotte; Bocquet, Olivier; Romier, Beatrice; Gorisse, Laetitia; Ghirardi, Maxime; Duca, Laurent; Blaise, Sébastien; Martiny, Laurent; Dauchez, Manuel; Efremov, Roman G.; Debelle, Laurent


    Neuraminidase 1 (NEU1) is a lysosomal sialidase catalyzing the removal of terminal sialic acids from sialyloconjugates. A plasma membrane-bound NEU1 modulating a plethora of receptors by desialylation, has been consistently documented from the last ten years. Despite a growing interest of the scientific community to NEU1, its membrane organization is not understood and current structural and biochemical data cannot account for such membrane localization. By combining molecular biology and biochemical analyses with structural biophysics and computational approaches, we identified here two regions in human NEU1 - segments 139-159 (TM1) and 316-333 (TM2) - as potential transmembrane (TM) domains. In membrane mimicking environments, the corresponding peptides form stable α-helices and TM2 is suited for self-association. This was confirmed with full-size NEU1 by co-immunoprecipitations from membrane preparations and split-ubiquitin yeast two hybrids. The TM2 region was shown to be critical for dimerization since introduction of point mutations within TM2 leads to disruption of NEU1 dimerization and decrease of sialidase activity in membrane. In conclusion, these results bring new insights in the molecular organization of membrane-bound NEU1 and demonstrate, for the first time, the presence of two potential TM domains that may anchor NEU1 in the membrane, control its dimerization and sialidase activity.

  5. Structure of active dimeric human telomerase. (United States)

    Sauerwald, Anselm; Sandin, Sara; Cristofari, Gaël; Scheres, Sjors H W; Lingner, Joachim; Rhodes, Daniela


    Telomerase contains a large RNA subunit, TER, and a protein catalytic subunit, TERT. Whether telomerase functions as a monomer or dimer has been a matter of debate. Here we report biochemical and labeling data that show that in vivo-assembled human telomerase contains two TERT subunits and binds two telomeric DNA substrates. Notably, catalytic activity requires both TERT active sites to be functional, which demonstrates that human telomerase functions as a dimer. We also present the three-dimensional structure of the active full-length human telomerase dimer, determined by single-particle EM in negative stain. Telomerase has a bilobal architecture with the two monomers linked by a flexible interface. The monomer reconstruction at 23-Å resolution and fitting of the atomic structure of the TERT subunit from beetle Tribolium castaneum into the EM density reveals the spatial relationship between RNA and protein subunits, providing insights into telomerase architecture.

  6. Dynamics of UV-excited uracil, thymine, and cytosine (United States)

    Hudock, Hanneli

    The excited state dynamics of nucleic acids has been a subject of much experimental and theoretical interest. Nucleic acid bases readily absorb UV radiation, which can lead to mutagenic dimer formation. The dynamics of UV-excited nucleic acids is an important step in understanding how these dimers form. The pyrimidine bases (uracil, thymine, and cytosine) have been studied with ab initio multiple spawning molecular dynamics and high level electronic structure methods. This work has involved both gas-phase and aqueous dynamics as well as simulation of the time-resolved photoelectron spectrum, transient absorption, fluorescence, and reaction rates. With these findings, complete relaxation mechanisms are proposed for the pyrimidines and comparisons are made directly to experimental results.

  7. End binding proteins are obligatory dimers.

    Directory of Open Access Journals (Sweden)

    Indrani Sen

    Full Text Available End binding (EB proteins are responsible for the recruitment of an array of microtubule plus-end tracking proteins (+TIPs to growing microtubules ends. EBs encompass an N-terminal calponin homology domain that confers microtubule tip tracking activity to the protein. The C-terminal domain of EBs contains a coiled coil that mediates the parallel dimerization of EB monomers. This part of the protein is also responsible for partner binding. While dimerization is not essential for microtubule tip tracking by EBs it is a prerequisite for +TIP partner binding. The concentration of EBs in cells has been estimated to be in the range of hundreds of nanomoles. In contrast, in in vitro single molecule experiments EB concentrations of subnanomoles are employed. From a mechanistic point of view it is important to assess the oligomerization state of EBs at physiologically and experimentally relevant protein concentrations, in particular if the goal of a study is to model the behavior of EB-dependent dynamic +TIP networks. Here we have determined the stability of the EB1 and EB3 dimers using multi-angle light scattering and fluorescence analytical ultracentrifugation. We show that these EBs form stable dimers and do not dissociate even at very low nanomolar concentrations. The dimers remained stable at both room temperature as well as at the physiologically relevant temperature of 37°C. Together, our results reveal that EBs are obligatory dimers, a conclusion that has implications for the mechanistic understanding of these key proteins involved in the orchestration of dynamic protein networks at growing microtubule ends.

  8. Synthesis of Methoxyethyl Nucleoside Dimer Phosphoramidates

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Gi Weon; Kang, Yong Han [Hanyang University, Ansan (Korea, Republic of)


    Four types of methoxyethyl (MOE) nucleoside phosphoramidites, which are categorized as second-generation building blocks of antisense oligonucleotide drugs, were synthesized. Also, three types of MOE nucleoside dimer phosphoramidites were synthesized to increase the efficiency and oligomer purity in solid phase synthesis. The block-like dimer phosphoramidites can prevent or minimize the formation of the (N-1) mer impurity, thereby affording the fabrication of pure oligonucleotides and reducing the synthesis time by performing coupling reactions in the order of 2 + 2 + 2.

  9. A Novel Dimer of α-Tocopherol

    Directory of Open Access Journals (Sweden)

    Anjan Patel


    Full Text Available Decomposition of the complex 4, formed between the α-tocopherol ortho-quinone methide (2 and NMMO, by fast heating from −78∘C to 70∘C in inert solvents produces a novel α-tocopherol dimer with 6H,12H-dibenzo[b,f][1,5]dioxocine structure (5 which—in contrast to the well-known spiro-dimer of α-tocopherol (3—is symmetrical. This is the first example of a direct reaction of the highly transient zwitterionic, aromatic precursor 2a in the formation of the ortho-quinone methide 2.

  10. Gauge Fields as Composite Boundary Excitations

    CERN Document Server

    Ferrara, Sergio; Ferrara, Sergio; Fronsdal, Christian


    We investigate representations of the conformal group that describe "massless" particles in the interior and at the boundary of anti-de Sitter space. It turns out that massless gauge excitations in anti-de Sitter are gauge "current" operators at the boundary. Conversely, massless excitations at the boundary are topological singletons in the interior. These representations lie at the threshold of two "unitary bounds" that apply to any conformally invariant field theory. Gravity and Yang-Mills gauge symmetry in anti-De Sitter is translated to global translational symmetry and continuous R-symmetry of the boundary superconformal field theory.

  11. Chemically induced contraction and stretching of a linear rotaxane dimer. (United States)

    Jimenez-Molero, Maria Consuelo; Dietrich-Buchecker, Christiane; Sauvage, Jean-Pierre


    Copper(I)-induced assembly of two self-complementary identical units, which consist of a ring that incorporates a 1,10-phenanthroline group attached to a small filament containing a second 1,10-phenanthroline (phen) group, leads quantitatively to a doubly threaded complex. Each copper(I) center is four-coordinate and is located inside a ring and bound to a phen from the macrocyle. The two other coordination sites are occupied by a phen from the filament connected to the other ring. An X-ray structure of the dicopper(I) complex unambiguously demonstrates the doubly threaded nature of the system. The molecule has C(2) symmetry in the crystal. This is an extended form with a Cu small middle dot small middle dot small middle dotCu separation of 18.3 A and an overall length close to 40 A. Further synthetic work, which utilizes the two terminal phenolic functions of the previous dicopper(I) complex, gives rise to a more complex system in which both filaments have been prolonged in opposite directions by 2,2':6',2"-terpyridine (terpy) motifs and bulky stoppers. The organic backbone is that of a rotaxane dimer. Although redox cycling of Cu(I) to Cu(II) did not lead to intramolecular rearrangement, simple chemical reactions induced large conformational changes. The rotaxane dimer was set in motion as follows. The dicopper(I) complex, which is in an extended conformation, was demetallated by using KCN. From the free ligand, the dizinc complex was formed quantitatively at room temperature. (1)H NMR data show that a new conformation is obtained: each Zn(II) is five-coordinate (phen + terpy), and the molecule is in a contracted conformation. This process is reminiscent of biological muscles in the sense that the two filaments of this system can be moved along one another in a gliding motion that keeps the whole system together, but which converts a stretched compound (overall length approximately equal to 83 A) into a contracted species (overall length approximately equal to 65

  12. Nuclear-polarization correction to the bound-electron g factor in heavy hydrogenlike ions. (United States)

    Nefiodov, A V; Plunien, G; Soff, G


    The influence of nuclear polarization on the bound-electron g factor in heavy hydrogenlike ions is investigated. Numerical calculations are performed for the K- and L-shell electrons taking into account the dominant virtual nuclear excitations. This determines the ultimate limit for tests of QED utilizing measurements of the bound-electron g factor in highly charged ions.

  13. Nuclear-polarization correction to the bound-electron g factor in heavy hydrogenlike ions


    Nefiodov, A. V.; Plunien, G.; Soff, G.


    The influence of nuclear polarization on the bound-electron $g$ factor in heavy hydrogenlike ions is investigated. Numerical calculations are performed for the K- and L-shell electrons taking into account the dominant virtual nuclear excitations. This determines the ultimate limit for tests of QED utilizing measurements of the bound-electron $g$ factor in highly charged ions.

  14. Tuning near-field enhancements on an off-resonance nanorod dimer via temporally shaped femtosecond laser (United States)

    Du, Guangqing; Yang, Qing; Chen, Feng; Lu, Yu; Wu, Yanmin; Ou, Yan; Hou, Xun


    We theoretically investigated ultrafast thermal dynamics tuning of near-field enhancements on an off-resonance gold nanorod dimer via temporally shaped femtosecond (fs) laser double pulses. The nonequilibrium thermal excitation is self-consistently coupled into a near-field scattering model for exploring the ultrafast near-field enhancement effects. It is revealed that the near electric-field localized within the gold nanorod dimer can be largely promoted via optimizing the temporal separation and the pulse energy ratio of temporally shaped femtosecond laser double pulses. The results are explained as thermal dynamics manipulation of plasmon resonances in the nanorod dimer via tailoring temporally shaped femtosecond laser. This study provides basic understanding for tuning near-field properties on poorly fabricated metallic nano-structures via temporally shaped femtosecond laser, which can find potential applications in the fields such as fs super-resolution near-field imaging, near-field optical tweezers, and fs photothermal therapy.

  15. Excited State Dynamics of DNA and RNA bases (United States)

    Hudock, Hanneli; Levine, Benjamin; Martinez, Todd


    Recent ultrafast spectroscopic experiments have reported excited state lifetimes for DNA and RNA bases and assigned these lifetimes to various electronic states. We have used theoretical and simulation methods to describe the excited state dynamics of these bases in an effort to provide a mechanistic explanation for the observed lifetimes. Our simulations are based on ab initio molecular dynamics, where the electronic and nuclear Schrodinger equations are solved simultaneously. The results are further verified by comparison to high-level ab initio electronic structure methods, including dynamic electron correlation effects through multireference perturbation theory, at important points along the dynamical pathways. Our results provide an explanation of the photochemical mechanism leading to nonradiative decay of the electronic excited states and some suggestions as to the origin of the different lifetimes. Comparisons between pyrimidines illustrate how chemical differences impact excited state dynamics and may play a role in explaining the propensity for dimer formation in thymine.

  16. cGAS dimerization entangles DNA recognition. (United States)

    Kranzusch, Philip J; Vance, Russell E


    Detection of foreign DNA in the cell cytosol triggers potent antiviral responses. In this issue of Immunity, Li et al. (2013) provide new structural and biochemical data indicating that a cytosolic DNA sensor, cyclic GMP-AMP synthase (cGAS), is activated by DNA-induced dimerization. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Ligand regulation of a constitutively dimeric EGF receptor (United States)

    Freed, Daniel M.; Alvarado, Diego; Lemmon, Mark A.


    Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers.

  18. Thymine Dimer Formation probed by Time-Resolved Vibrational Spectroscopy (United States)

    Schreier, Wolfgang J.; Schrader, Tobias E.; Roller, Florian O.; Gilch, Peter; Zinth, Wolfgang; Kohler, Bern

    Cyclobutane pyrimidine dimers are the major photoproducts formed when DNA is exposed to UV light. Femtosecond time-resolved vibrational spectroscopy reveals that thymine dimers are formed in thymidine oligonucleotides in an ultrafast photoreaction.

  19. Efficient photosensitized splitting of the thymine dimer/oxetane unit on its modifying beta-cyclodextrin by a binding electron donor. (United States)

    Tang, Wen-Jian; Song, Qin-Hua; Wang, Hong-Bo; Yu, Jing-Yu; Guo, Qing-Xiang


    Two modified beta-cyclodextrins (beta-CDs) with a thymine dimer and a thymine oxetane adduct respectively, TD-CD and Ox-CD, have been prepared, and utilized to bind an electron-rich chromophore, indole or N,N-dimethylaniline (DMA), to form a supramolecular complex. We have examined the photosensitized splitting of the dimer/oxetane unit in TD-CD/Ox-CD by indole or DMA via an electron-transfer pathway, and observed high splitting efficiencies of the dimer/oxetane unit. On the basis of measurements of fluorescence spectra and splitting quantum yields, it is suggested that the splitting reaction occurs in a supramolecular complex by an inclusion interaction between the modified beta-CDs and DMA or indole. The back electron transfer, which leads low splitting efficiencies for the covalently-linked chromophore-dimer/oxetane compounds, is suppressed in the non-covalently-bound complex, and the mechanism has been discussed.

  20. Photo-induced strengthening of weak bonding in noble gas dimers

    Energy Technology Data Exchange (ETDEWEB)

    Miyamoto, Yoshiyuki; Miyazaki, Takehide [Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Rubio, Angel [Nano-Bio Spectroscopy group and ETSF Scientific Development Centre, Centro de Física de Materiales CSIC-UPV/EHU-MPC and DIPC, Universidad del País Vasco UPV/EHU, Avenida de Tolosa 72, E-20018 San Sebastian (Spain); Zhang, Hong, E-mail: [College of Physical Science and Technology, Sichuan University, Chengdu, Sichuan 610065 (China)


    We demonstrate through extensive first-principles time-dependent density functional calculations that attractive van der Waals interaction between closed-shell atoms can be enhanced by light with constant spatial intensity. We illustrate this general phenomenon for a He dimer as a prototypical case of complex van der Waals interactions and show that when excited by light with a frequency close to the 1s → 2p He-atomic transition, an attractive force larger than 7 pN is produced. This force gain is manifested as a larger acceleration of He-He contraction under an optical field. The concerted dynamical motions of the He atoms together with polarity switching of the charge-induced dipole cause the contraction of the dimer. These findings are relevant for the photo-induced control of weakly bonded molecular species, either in gas phase or in solution.

  1. Phase diagram study of a dimerized spin-S zig-zag ladder. (United States)

    Matera, J M; Lamas, C A


    The phase diagram of a frustrated spin-S zig-zag ladder is studied through different numerical and analytical methods. We show that for arbitrary S, there is a family of Hamiltonians for which a fully-dimerized state is an exact ground state, being the Majumdar-Ghosh point for a particular member of the family. We show that the system presents a transition between a dimerized phase to a Néel-like phase for S = 1/2, and spiral phases can appear for large S. The phase diagram is characterized by means of a generalization of the usual mean field approximation. The novelty in the present implementation is to consider the strongest coupled sites as the unit cell. The gap and the excitation spectrum is analyzed through the random phase approximation. Also, a perturbative treatment to obtain the critical points is discussed. Comparisons of the results with numerical methods like the Density Matrix Renormalization Group are also presented.

  2. Quantum dimer model on the triangular lattice: Semiclassical and variational approaches to vison dispersion and condensation (United States)

    Misguich, Grégoire; Mila, Frédéric


    After reviewing the concept of vison excitations in Z2 dimer liquids, we study the liquid-crystal transition of the quantum dimer model on the triangular lattice by means of a semiclassical spin-wave approximation to the dispersion of visons in the context of a “soft-dimer” version of the model. This approach captures some important qualitative features of the transition: continuous nature of the transition, linear dispersion at the critical point, and 12×12 symmetry-breaking pattern. In a second part, we present a variational calculation of the vison dispersion relation at the Rokhsar-Kivelson (RK) point, which reproduces the qualitative shape of the dispersion relation and the order of magnitude of the gap. This approach provides a simple but reliable approximation of the vison wave functions at the RK point.

  3. Isovector monopole excitation energies

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, J.D.; Lipparini, E.; Stringary, S.


    Using a hydrodynamical model whose parameters have been adjusted to fit the polarizability and excitation energy of the giant dipole nuclear resonance we predict excitation energies of the isovector monopole resonance. The predicted values are in good agreement with experimental data. The mass dependence of the excitation energy is strongly influenced by nuclear geometry.

  4. Refining Multivariate Value Set Bounds (United States)

    Smith, Luke Alexander

    Over finite fields, if the image of a polynomial map is not the entire field, then its cardinality can be bounded above by a significantly smaller value. Earlier results bound the cardinality of the value set using the degree of the polynomial, but more recent results make use of the powers of all monomials. In this paper, we explore the geometric properties of the Newton polytope and show how they allow for tighter upper bounds on the cardinality of the multivariate value set. We then explore a method which allows for even stronger upper bounds, regardless of whether one uses the multivariate degree or the Newton polytope to bound the value set. Effectively, this provides an alternate proof of Kosters' degree bound, an improved Newton polytope-based bound, and an improvement of a degree matrix-based result given by Zan and Cao.

  5. Universal bosonic tetramers of dimer-atom-atom structure


    Deltuva, A.


    Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.

  6. Ultraviolet Spectrum And Chemical Reactivity Of CIO Dimer (United States)

    Demore, William B.; Tschuikow-Roux, E.


    Report describes experimental study of ultraviolet spectrum and chemical reactivity of dimer of chlorine monoxide (CIO). Objectives are to measure absorption cross sections of dimer at near-ultraviolet wavelengths; determine whether asymmetrical isomer (CIOCIO) exists at temperatures relevant to Antarctic stratosphere; and test for certain chemical reactions of dimer. Important in photochemistry of Antarctic stratosphere.

  7. Determination of the Tetramer-Dimer Equilibrium Constant of Rabbit ...

    African Journals Online (AJOL)

    Hemoglobin is a tetrameric protein which is able to dissociate into dimers. The dimers can in turn dissociate into tetramers. It has been found that dimers are more reactive than tetramers. The difference in the reactivity of these two species has been used to determine the tetramerdimer dissociation constant of various ...

  8. 21 CFR 176.120 - Alkyl ketene dimers. (United States)


    ... Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers. Alkyl ketene dimers may... section. (a) The alkyl ketene dimers are manufactured by the dehydrohalogenation of the acyl halides... an adjuvant in the manufacture of paper and paperboard under such conditions that the alkyl ketene...

  9. Measurement of pyrimidine dimers in spheroplasts of Bacillus subtilis

    Energy Technology Data Exchange (ETDEWEB)

    Hadden, C.T.


    A method is described for making spheroplasts of Bacillus subtilis which are permeable to exogenous enzymes. Conditions are described for measuring small numbers of pyrimidine dimers in the DNA of uv-irradiated cells by use of a partially purified Micrococcus luteus extract containing an enzyme specific for pyrimidine dimers. The system will detect as few as 10 to 12 pyrimidine dimers per genome.

  10. Excitation equilibria in plasmas; a classification

    Energy Technology Data Exchange (ETDEWEB)

    Mullen, J.A.M. van der (Eindhoven Univ. of Tech. (Netherlands). Physics Dept.)


    This review gives a classification of the excitation kinetics ruled by electrons in plasmas. It is a study on the atomic state distribution function (ASDF) and its relation with underlying processes, which, for the case of an electron excitation kinetics (EEK) plasma, is merely a competition between free and bound electrons, the same particles in different circumstances. In a quasi steady state the population density of an atomic state results from production-destruction balances in equilibrium. If all balances are proper, i.e., consist of each other's inverse processes, then the ASDF is described by the Boltzmann-Saha relation. In other cases the balance will be denoted as improper, the ASDF will deviate from the equilibrium shape, but reflecting the underlying improper balances, it may give information about the plasma. Four improper balances and their impact on the ASDF are dealt with. An important feature is that improper balances are associated with particle transport. Special attention is paid to the distribution function of the excitation saturation balance in which the overpopulated bound electrons are subjected to frequent interactions with free electrons and the energy distribution of the free electrons is taken over. This distribution, denoted as the bound Maxwell distribution, is experimentally found in several ionizing plasmas. Its recombining counterpart, the deexcitation saturation balance, creates under certain conditions inversion in the ASDF, the basis for the recombination laser. (orig.).

  11. Cryogenic fluorescence and absorption spectroscopy studies on monomeric and dimeric species of 2-butylamino-6-methyl-4-nitropyridine N-oxide (United States)

    de Klerk, Joost S.; Szemik-Hojniak, Anna; Ariese, Freek; Gooijer, Cees


    2-Butylamino-6-methyl-4-nitropyridine- N-oxide (2B6M) belongs to a group of compounds that can undergo not only excited-state intra-, but also intermolecular proton transfer. The latter of course requires the presence of dimeric species. Previously, we have shown that for 2B6M in aprotic non-polar solvents in the liquid state such dimers play no role. Under these conditions, only one single monomeric species exists, exhibiting anomalous fluorescence behavior, i.e. proton transfer not only starting from the lowest excited electronic singlet state, but also from higher excited states. However, we also noted that under frozen, crystalline matrix conditions more species show up in the spectra. In order to study this multi-species system in more detail, we present absorption and fluorescence experiments on 2B6M, recorded in n-octane at various temperatures between 293 and 5 K. High-resolution spectra are included, not only in fluorescence but also in absorption. We demonstrate that under cryogenic conditions three species can be discerned, two of these providing high-resolution spectra with their main 0-0 lines around 452 and 465 nm, respectively. A detailed vibrational analysis of their emission spectra is included. The third species gives broad-banded spectra, in absorption extending to about 520 nm with its long-wavelength maximum around 460 nm, in emission with a maximum around 535 nm. We tentatively assign the three species to a monomer, a H-bonded dimer and a strongly interacting (π-π-stacked) dimer, respectively. We conclude from the excitation spectra that (anomalous) intramolecular proton transfer at higher excited states is still operative under cryogenic conditions. Indications for excited-state intermolecular proton transfer in the stacked dimeric species were not found.

  12. Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

    Energy Technology Data Exchange (ETDEWEB)

    Nath, Seema; Banerjee, Ramanuj; Sen, Udayaditya, E-mail:


    Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.

  13. Quantum marginals from pure doubly excited states (United States)

    Maciążek, Tomasz; Tsanov, Valdemar


    The possible spectra of one-particle reduced density matrices that are compatible with a pure multipartite quantum system of finite dimension form a convex polytope. We introduce a new construction of inner- and outer-bounding polytopes that constrain the polytope for the entire quantum system. The outer bound is sharp. The inner polytope stems only from doubly excited states. We find all quantum systems, where the bounds coincide giving the entire polytope. We show, that those systems are: (i) any system of two particles (ii) L qubits, (iii) three fermions on N≤slant 7 levels, (iv) any number of bosons on any number of levels and (v) fermionic Fock space on N≤slant 5 levels. The methods we use come from symplectic geometry and representation theory of compact Lie groups. In particular, we study the images of proper momentum maps, where our method describes momentum images for all representations that are spherical.

  14. Multi-frequency excitation

    KAUST Repository

    Younis, Mohammad I.


    Embodiments of multi-frequency excitation are described. In various embodiments, a natural frequency of a device may be determined. In turn, a first voltage amplitude and first fixed frequency of a first source of excitation can be selected for the device based on the natural frequency. Additionally, a second voltage amplitude of a second source of excitation can be selected for the device, and the first and second sources of excitation can be applied to the device. After applying the first and second sources of excitation, a frequency of the second source of excitation can be swept. Using the methods of multi- frequency excitation described herein, new operating frequencies, operating frequency ranges, resonance frequencies, resonance frequency ranges, and/or resonance responses can be achieved for devices and systems.

  15. Spectra of van der Waals complexes (dimers) with applications to planetary atmospheres (United States)

    Fox, Kenneth; Kim, Sang J.


    Spectral features observed in the atmosphere of Titan by the Voyager IR experiment have been attributed to weakly bound complexes of N2 and H2, dominant and minor constituents, respectively. The abundance of H2-N2 dimers there was computed. Current calculations include quantitative spectral line positions and intensities for N2-Ar and CO2-CO2 relating to Titan and Earth, and to Mars and Venus, respectively. This work suggests applications to spectra of planetary atmospheres obtained in spacecraft missions.

  16. Unusual chemical bonding in the beryllium dimer and its twelve vibrational levels (United States)

    Mitin, A. V.


    The ab initio calculations have shown that the atoms in the beryllium dimer are covalently bound at the low-lying vibrational energy levels with ν = 0-4, while at the higher levels with ν = 5-11 the atoms are bonded by the van der Waals forces near the right turning points. The developed ab initio modified EMO potential function, in distinction with the original EMO function, which was used for a description of the experimental vibrational levels, not only has the correct dissociation energy, but also describes all twelve vibrational energy levels with a smaller RMS error of less than 0.4 cm-1.

  17. Enhancing the power conversion efficiency of dye-sensitized solar cells via molecular plasmon-like excitations. (United States)

    Li, Jian-Hao; Gryn'ova, Ganna; Prlj, Antonio; Corminboeuf, Clémence


    We introduce a tactic for employing molecular plasmon-like excitations to enhance solar-to-electric power conversion efficiency of dye-sensitized solar cells. We offer general design principles of dimeric dyes, in which a strong plasmonic interaction between two π-conjugated moieties is promoted. The π-stacked conformations of these dimeric dyes result in a desirable broadened absorption and a longer absorption onset wavelength.

  18. Dark excitations in monolayer transition metal dichalcogenides

    DEFF Research Database (Denmark)

    Deilmann, Thorsten; Thygesen, Kristian Sommer


    Monolayers of transition metal dichalcogenides (TMDCs) possess unique optoelectronic properties, including strongly bound excitons and trions. To date, most studies have focused on optically active excitations, but recent experiments have highlighted the existence of dark states, which are equally...... important in many respects. Here, we use ab initio many-body calculations to unravel the nature of the dark excitations in monolayer MoSe2, MoS2, WSe2, andWS(2). Our results show that all these monolayer TMDCs host dark states as their lowest neutral and charged excitations. We further show that dark...... excitons possess larger binding energies than their bright counterparts while the opposite holds for trions....

  19. Plasmonic rod dimers as elementary planar chiral meta-atoms

    CERN Document Server

    Zhukovsky, Sergei V; Chigrin, Dmitry N


    Electromagnetic response of metallic rod dimers is theoretically calculated for arbitrary planar arrangement of rods in the dimer. It is shown that dimers without an in-plane symmetry axis exhibit elliptical dichroism and act as "atoms" in planar chiral metamaterials. Due to a very simple geometry of the rod dimer, such planar metamaterials are much easier in fabrication than conventional split-ring or gammadion-type structures, and lend themselves to a simple analytical treatment based on coupled dipole model. Dependencies of metamaterial's directional asymmetry on the dimer's geometry are established analytically and confirmed in numerical simulations.

  20. Bounding approaches to system identification

    CERN Document Server

    Norton, John; Piet-Lahanier, Hélène; Walter, Éric


    In response to the growing interest in bounding error approaches, the editors of this volume offer the first collection of papers to describe advances in techniques and applications of bounding of the parameters, or state variables, of uncertain dynamical systems. Contributors explore the application of the bounding approach as an alternative to the probabilistic analysis of such systems, relating its importance to robust control-system design.

  1. with Bounded Failure Intensity

    Directory of Open Access Journals (Sweden)

    Preeti Wanti Srivastava


    Full Text Available This paper deals with the Bayes prediction of the future failures of a deteriorating repairable mechanical system subject to minimal repairs and periodic overhauls. To model the effect of overhauls on the reliability of the system a proportional age reduction model is assumed and the 2-parameter Engelhardt-Bain process (2-EBP is used to model the failure process between two successive overhauls. 2-EBP has an advantage over Power Law Process (PLP models. It is found that the failure intensity of deteriorating repairable systems attains a finite bound when repeated minimal repair actions are combined with some overhauls. If such a data is analyzed through models with unbounded increasing failure intensity, such as the PLP, then pessimistic estimates of the system reliability will arise and incorrect preventive maintenance policy may be defined. On the basis of the observed data and of a number of suitable prior densities reflecting varied degrees of belief on the failure/repair process and effectiveness of overhauls, the prediction of the future failure times and the number of failures in a future time interval is found. Finally, a numerical application is used to illustrate the advantages from overhauls and sensitivity analysis of the improvement parameter carried out.

  2. Revisiting the optical $PT$-symmetric dimer

    CERN Document Server

    Morales, J D Huerta; López-Aguayo, S; Rodríguez-Lara, B M


    Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of $\\mathcal{PT}$-symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical $\\mathcal{PT}$-symmetric dimer, a two-waveguide coupler were the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar $N$-waveguide couplers that are the optical realization of Lorentz group in 2+1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of Ehrenfest theorem.

  3. Revisiting the Optical PT-Symmetric Dimer

    Directory of Open Access Journals (Sweden)

    José Delfino Huerta Morales


    Full Text Available Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of PT -symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical PT -symmetric dimer, a two-waveguide coupler where the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry-based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar N-waveguide couplers that are the optical realization of the Lorentz group in 2 + 1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of the Ehrenfest theorem.

  4. Fibrillar dimer formation of islet amyloid polypeptides

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Chi-cheng [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); de Pablo, Juan J. [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)


    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  5. Strongly bound noncovalent (SO3)n:H2CO complexes (n = 1, 2). (United States)

    Azofra, Luis Miguel; Alkorta, Ibon; Scheiner, Steve


    The potential energy surfaces (PES) for the SO3:H2CO and (SO3)2:H2CO complexes were thoroughly examined at the MP2/aug-cc-pVDZ computational level. Heterodimers and trimers are held together primarily by SO chalcogen bonds, supplemented by weaker CHO and/or OC bonds. The nature of the interactions is probed by a variety of means, including electrostatic potentials, AIM, NBO, energy decomposition, and electron density redistribution maps. The most stable dimer is strongly bound, with an interaction energy exceeding 10 kcal mol(-1). Trimers adopt the geometry of the most stable dimer, with an added SO3 molecule situated so as to interact with both of the original molecules. The trimers are strongly bound, with total interaction energies of more than 20 kcal mol(-1). Most such trimers show positive cooperativity, with shorter SO distances, and three-body interaction energies of nearly 3 kcal mol(-1).

  6. Effect of phosphorylation on EGFR dimer stability probed by single-molecule dynamics and FRET/FLIM. (United States)

    Coban, Oana; Zanetti-Dominguez, Laura C; Matthews, Daniel R; Rolfe, Daniel J; Weitsman, Gregory; Barber, Paul R; Barbeau, Jody; Devauges, Viviane; Kampmeier, Florian; Winn, Martyn; Vojnovic, Borivoj; Parker, Peter J; Lidke, Keith A; Lidke, Diane S; Ameer-Beg, Simon M; Martin-Fernandez, Marisa L; Ng, Tony


    Deregulation of epidermal growth factor receptor (EGFR) signaling has been correlated with the development of a variety of human carcinomas. EGF-induced receptor dimerization and consequent trans- auto-phosphorylation are among the earliest events in signal transduction. Binding of EGF is thought to induce a conformational change that consequently unfolds an ectodomain loop required for dimerization indirectly. It may also induce important allosteric changes in the cytoplasmic domain. Despite extensive knowledge on the physiological activation of EGFR, the effect of targeted therapies on receptor conformation is not known and this particular aspect of receptor function, which can potentially be influenced by drug treatment, may in part explain the heterogeneous clinical response among cancer patients. Here, we used Förster resonance energy transfer/fluorescence lifetime imaging microscopy (FRET/FLIM) combined with two-color single-molecule tracking to study the effect of ATP-competitive small molecule tyrosine kinase inhibitors (TKIs) and phosphatase-based manipulation of EGFR phosphorylation on live cells. The distribution of dimer on-times was fitted to a monoexponential to extract dimer off-rates (koff). Our data show that pretreatment with gefitinib (active conformation binder) stabilizes the EGFR ligand-bound homodimer. Overexpression of EGFR-specific DEP-1 phosphatase was also found to have a stabilizing effect on the homodimer. No significant difference in the koff of the dimer could be detected when an anti-EGFR antibody (425 Snap single-chain variable fragment) that allows for dimerization of ligand-bound receptors, but not phosphorylation, was used. These results suggest that both the conformation of the extracellular domain and phosphorylation status of the receptor are involved in modulating the stability of the dimer. The relative fractions of these two EGFR subpopulations (interacting versus free) were obtained by a fractional-intensity analysis of

  7. An interpretation of the absorption and emission spectra of the gold dimer using modern theoretical tools

    DEFF Research Database (Denmark)

    Geethalakshmi, K. R.; Ruiperez, F.; Knecht, S.


    The excited states of the gold dimer have been investigated using modern theoretical tools including the multiconfigurational exact molecular mean-field intermediate Hamiltonian Fock-space Coupled Cluster, X2Cmmf-IHFSCC, and the complete active space self-consistent field followed by second order...... perturbation theory, CASSCF/CASPT2. The computed optically active transitions have been benchmarked against the available experimental data and compared with time-dependent density functional theory, TDDFT, results, both in the two-and four-component schemes. We explored in great detail several spectroscopic...

  8. ExtremeBounds: Extreme Bounds Analysis in R

    Directory of Open Access Journals (Sweden)

    Marek Hlavac


    Full Text Available This article introduces the R package ExtremeBounds to perform extreme bounds analysis (EBA, a sensitivity test that examines how robustly the dependent variable of a regression model is related to a variety of possible determinants. ExtremeBounds supports Leamer's EBA that focuses on the upper and lower extreme bounds of regression coefficients, as well as Sala-i-Martin's EBA which considers their entire distribution. In contrast to existing alternatives, it can estimate models of a variety of user-defined sizes, use regression models other than ordinary least squares, incorporate non-linearities in the model specification, and apply custom weights and standard errors. To alleviate concerns about the multicollinearity and conceptual overlap of examined variables, ExtremeBounds allows users to specify sets of mutually exclusive variables, and can restrict the analysis to coefficients from regression models that yield a variance inflation factor within a prespecified limit.

  9. Palmitoylated APP Forms Dimers, Cleaved by BACE1.

    Directory of Open Access Journals (Sweden)

    Raja Bhattacharyya

    Full Text Available A major rate-limiting step for Aβ generation and deposition in Alzheimer's disease brains is BACE1-mediated cleavage (β-cleavage of the amyloid precursor protein (APP. We previously reported that APP undergoes palmitoylation at two cysteine residues (Cys186 and Cys187 in the E1-ectodomain. 8-10% of total APP is palmitoylated in vitro and in vivo. Palmitoylated APP (palAPP shows greater preference for β-cleavage than total APP in detergent resistant lipid rafts. Protein palmitoylation is known to promote protein dimerization. Since dimerization of APP at its E1-ectodomain results in elevated BACE1-mediated cleavage of APP, we have now investigated whether palmitoylation of APP affects its dimerization and whether this leads to elevated β-cleavage of the protein. Here we report that over 90% of palAPP is dimerized while only ~20% of total APP forms dimers. PalAPP-dimers are predominantly cis-oriented while total APP dimerizes in both cis- and trans-orientation. PalAPP forms dimers 4.5-times more efficiently than total APP. Overexpression of the palmitoylating enzymes DHHC7 and DHHC21 that increase palAPP levels and Aβ release, also increased APP dimerization in cells. Conversely, inhibition of APP palmitoylation by pharmacological inhibitors reduced APP-dimerization in coimmunoprecipitation and FLIM/FRET assays. Finally, in vitro BACE1-activity assays demonstrate that palmitoylation-dependent dimerization of APP promotes β-cleavage of APP in lipid-rich detergent resistant cell membranes (DRMs, when compared to total APP. Most importantly, generation of sAPPβ-sAPPβ dimers is dependent on APP-palmitoylation while total sAPPβ generation is not. Since BACE1 shows preference for palAPP dimers over total APP, palAPP dimers may serve as novel targets for effective β-cleavage inhibitors of APP as opposed to BACE1 inhibitors.

  10. Excited states 2

    CERN Document Server

    Lim, Edward C


    Excited States, Volume 2 is a collection of papers that deals with molecules in the excited states. The book describes the geometries of molecules in the excited electronic states. One paper describes the geometries of a diatomic molecule and of polyatomic molecules; it also discusses the determination of the many excited state geometries of molecules with two, three, or four atoms by techniques similar to diatomic spectroscopy. Another paper introduces an ordered theory related to excitons in pure and mixed molecular crystals. This paper also presents some experimental data such as those invo

  11. Effect of optical excitation energy on the red luminescence of Eu3+ in GaN (United States)

    Peng, H. Y.; Lee, C. W.; Everitt, H. O.; Lee, D. S.; Steckl, A. J.; Zavada, J. M.


    Photoluminescence (PL) excitation spectroscopy mapped the photoexcitation wavelength dependence of the red luminescence (D05→F27) from GaN:Eu. Time-resolved PL measurements revealed that for excitation at the GaN bound exciton energy, the decay transients are almost temperature insensitive between 86 K and 300 K, indicating an efficient energy transfer process. However, for excitation energies above or below the GaN bound exciton energy, the decaying luminescence indicates excitation wavelength- and temperature-dependent energy transfer influenced by intrinsic and Eu3+-related defects.

  12. Roughness effect on the efficiency of dimer antenna based biosensor

    Directory of Open Access Journals (Sweden)

    D. Barchiesi


    Full Text Available The fabrication process of nanodevices is continually improved. However, most of the nanodevices, such as biosensors present rough surfaces with mean roughness of some nanometers even if the deposition rate of material is more controlled. The effect of roughness on performance of biosensors was fully addressed for plane biosensors and gratings, but rarely addressed for biosensors based on Local Plasmon Resonance. The purpose of this paper is to evaluate numerically the influence of nanometric roughness on the efficiency of a dimer nano-biosensor (two levels of roughness are considered. Therefore, we propose a general numerical method, that can be applied to any other nanometric shape, to take into account the roughness in a three dimensional model. The study focuses on both the far-field, which corresponds to the experimental detected data, and the near-field, responsible for exciting and then detecting biological molecules. The results suggest that the biosensor efficiency is highly sensitive to the surface roughness. The roughness can produce important shifts of the extinction efficiency peak and a decrease of its amplitude resulting from changes in the distribution of near-field and absorbed electric field intensities.

  13. Bound state densities and the Helmholtz free energy

    Directory of Open Access Journals (Sweden)

    Souza S.R.


    Full Text Available Bohr's conception of the compound nucleus is based on the idea of ‘longlived’ nuclear states in which all single particles are bound. We briefly discuss the properties of the density of bound states and then use two prescriptions, that of Brack and Quentin and that of Bonche, Levit e Vautherin to calculate the equivalent temperaturedependent quantity – the Helmholtz free energy.We compare the temperature dependence of the latter, as well as that of the excitation energy and entropy, obtained using the two prescriptions in self-consistent calculations within the relativistic Hartree and Skyrme models. We then discuss the extended, temperature-dependent liquid-drop approximation to the excitation and free energies obtained from fits to the self-consistent calculations over a wide range of charge and mass numbers.

  14. Spin relaxation via exchange with donor impurity-bound electrons (United States)

    Appelbaum, Ian

    In the Bir-Aronov-Pikus depolarization process affecting conduction electrons in p-type cubic semiconductors, spin relaxation is driven by exchange with short-lived valence band hole states. We have identified an analogous spin relaxation mechanism in nominally undoped silicon at low temperatures, when many electrons are bound to dilute dopant ion potentials. Inelastic scattering with externally injected conduction electrons accelerated by electric fields can excite transitions into highly spin-orbit-mixed bound excited states, driving strong spin relaxation of the conduction electrons via exchange interaction. We reveal the consequences of this spin depolarization mechanism both below and above the impact ionization threshold, where conventional charge and spin transport are restored. Based upon: Lan Qing, Jing Li, Ian Appelbaum, and Hanan Dery, Phys Rev. B 91, 241405(R) (2015). We acknowledge support from NSF, DTRA, and ONR.

  15. Keto-enol tautomerization and intermolecular proton transfer in photoionized cyclopentanone dimer in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arup K.; Chatterjee, Piyali; Chakraborty, Tapas, E-mail: [Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A Raja S. C. Mullick Road, Jadavpur, Kolkata 700032 (India)


    Time-of-flight mass spectra of cyclopentanone and its clusters cooled in a supersonic jet expansion have been measured following 4-, 3-, and 2-photon ionizations by the 2nd, 3rd, and 4th harmonic wavelengths, respectively, of a Q-switched Nd:YAG laser. The mass spectra reveal signatures of energetically favored keto to enol tautomerization of the molecular ion leading to intermolecular proton transfer, and this observation is found sharply dependent on the ionization wavelengths used. Electronic structure calculation predicts that in spite of the energetic preference, keto-enol conversion barrier of isolated molecular ion is high. However, the barrier is significantly reduced in a CH⋯O hydrogen-bonded dimer of the molecule. The transition states associated with tautomeric conversion of both cyclopentanone monomer and dimer cations have been identified by means of intrinsic reaction co-ordinate calculation. In a supersonic jet expansion, although a weakly bound dimer is readily generated, the corresponding cation and also the protonated counterpart are observed only for ionization by 532 nm. For other two ionization wavelengths, these species do not register in the mass spectra, where the competing reaction channels via α-cleavage of the ring become dominant. In contrast to the report of a recent study, we notice that the intact molecular ion largely survives fragmentations when ionized from the 2-photon resonant 3p Rydberg state as intermediate using nanosecond laser pulses, and the corresponding resonant 3-photon ionization spectrum has been recorded probing the intact molecular ion.

  16. IR/UV and UV/UV double-resonance study of guaiacol and eugenol dimers (United States)

    Longarte, Asier; Redondo, Carolina; Fernández, José A.; Castaño, Fernando


    Guaiacol (2-methoxyphenol) and eugenol (4-allyl-2-methoxyphenol) molecules are biologically active phenol derivatives with an intramolecular -OH⋯OCH3 hydrogen bond (H bond). Pulsed supersonic expansions of mixtures of either of the two molecules with He yield weakly bound homodimers as well as other higher-order complexes. A number of complementary and powerful laser spectroscopic techniques, including UV-UV and IR-UV double resonances, have been employed to interrogate the species formed in the expansion in order to get information on their structures and spectroscopic properties. The interpretation of the spectra of eugenol dimer is complex and required a previous investigation on a similar but simpler molecule both to gain insight into the possible structures and support the conclusions. Guaiacol (2-methoxyphenol) has been used for that purpose. The combination of the broad laser study combined with ab initio calculations at the Becke 3 Lee-Yang-Parr/6-31+G(d) level has provided the isomer structures, the potential-energy wells, and shed light on the inter- and intramolecular interactions involved. Guaiacol homodimer has been shown to have a single isomer whereas eugenol dimer has at least two. The comparison between the computed geometries of the dimers, their respective energies, and the vibrational normal modes permits the identification of the spectra.

  17. Bounds for Asian basket options (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle


    In this paper we propose pricing bounds for European-style discrete arithmetic Asian basket options in a Black and Scholes framework. We start from methods used for basket options and Asian options. First, we use the general approach for deriving upper and lower bounds for stop-loss premia of sums of non-independent random variables as in Kaas et al. [Upper and lower bounds for sums of random variables, Insurance Math. Econom. 27 (2000) 151-168] or Dhaene et al. [The concept of comonotonicity in actuarial science and finance: theory, Insurance Math. Econom. 31(1) (2002) 3-33]. We generalize the methods in Deelstra et al. [Pricing of arithmetic basket options by conditioning, Insurance Math. Econom. 34 (2004) 55-57] and Vanmaele et al. [Bounds for the price of discrete sampled arithmetic Asian options, J. Comput. Appl. Math. 185(1) (2006) 51-90]. Afterwards we show how to derive an analytical closed-form expression for a lower bound in the non-comonotonic case. Finally, we derive upper bounds for Asian basket options by applying techniques as in Thompson [Fast narrow bounds on the value of Asian options, Working Paper, University of Cambridge, 1999] and Lord [Partially exact and bounded approximations for arithmetic Asian options, J. Comput. Finance 10 (2) (2006) 1-52]. Numerical results are included and on the basis of our numerical tests, we explain which method we recommend depending on moneyness and time-to-maturity.

  18. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and long...

  19. Market access through bound tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal


    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and longterm...

  20. Explicit correlation treatment of the potential energy surface of CO{sub 2} dimer

    Energy Technology Data Exchange (ETDEWEB)

    Kalugina, Yulia N., E-mail: [Tomsk State University, 36 Lenin Ave., Tomsk 634050 (Russian Federation); Buryak, Ilya A. [Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Moscow (Russian Federation); Chemistry Department, Lomonosov Moscow State University, Moscow (Russian Federation); Ajili, Yosra [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Bd Descartes, 77454 Marne-La-Vallée (France); Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA Université de Tunis El Manar (Tunisia); Vigasin, Andrei A. [Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Moscow (Russian Federation); Jaidane, Nejm Eddine [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications - LSAMA Université de Tunis El Manar (Tunisia); Hochlaf, Majdi [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Bd Descartes, 77454 Marne-La-Vallée (France)


    We present an extensive study of the four-dimensional potential energy surface (4D-PES) of the carbon dioxide dimer, (CO{sub 2}){sub 2}. This PES is developed over the set of intermolecular coordinates. The electronic computations are carried out at the explicitly correlated coupled cluster method with single, double, and perturbative triple excitations [CCSD(T)-F12] level of theory in connection with the augmented correlation-consistent aug-cc-pVTZ basis set. An analytic representation of the 4D-PES is derived. Our extensive calculations confirm that “Slipped Parallel” is the most stable form and that the T-shaped structure corresponds to a transition state. Later on, this PES is employed for the calculations of the vibrational energy levels of the dimer. Moreover, the temperature dependence of the dimer second virial coefficient and of the first spectral moment of rototranslational collision-induced absorption spectrum is derived. For both quantities, a good agreement is found between our values and the experimental data for a wide range of temperatures. This attests to the high quality of our PES. Generally, our PES and results can be used for modeling CO{sub 2} supercritical fluidity and examination of its role in planetary atmospheres. It can be also incorporated into dynamical computations of CO{sub 2} capture and sequestration. This allows deep understanding, at the microscopic level, of these processes.

  1. A peroxide-bridged imidazole dimer formed from a photochromic naphthalene-bridged imidazole dimer. (United States)

    Hatano, Sayaka; Abe, Jiro


    2,4,5-Triphenylimidazole (lophine) is known as the first chemiluminescence substrate, and its oxidized derivative, the 2,4,5-triphenylimidazolyl radical, corresponds to the coloured species in the photochromic reaction of hexaarylbiimidazole (HABI). We report the first direct observation of the O(2) adduct of the imidazolyl radical that forms the end-on peroxide-bridged imidazole dimer. The ring-opening reaction of the peroxide-bridged imidazole dimer leading to the formation of an N-benzoylbenzamidine derivative supports the presence of the 4,5-epidioxide of lophine as a reaction intermediate of its chemiluminescence. This journal is © the Owner Societies 2012

  2. Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage (United States)

    Knips, Alexander; Zacharias, Martin


    The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA.

  3. γ-Irradiation of Thymine Dimers in Aqueous Solution (United States)

    Deering, R. A.; Snipes, Wallace


    Thymine dimers were irradiated in aqueous solution with 60Co γ-rays in N2 or O2. Thymine and unidentified non-UV-absorbing products appeared. The thymine was identified by spectrophotometry, chromatography, and ability to support the growth of Escherichia coli 15 T-. Residual dimer was determined by a UV-reversibility assay. The G-values for dimer breakage were approximately equal in N2 and O2. At low γ-doses, about two thymines were produced per dimer broken in N2, whereas only about one thymine appeared per dimer broken in O2. For dimer irradiated in frozen solution, the yield of thymine was at least 100 times less than in liquid. PMID:4934290

  4. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze


    Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.

  5. On intense energy exchange and localization in periodic FPU dimer chains (United States)

    Starosvetsky, Y.; Manevitch, L. I.


    Dynamics of periodically heterogeneous, nonlinear lattices is a subject of intense research in great variety of aspects of theoretical and applied physics. In fact almost all the studies pursued to date in the field of lattice dynamics have been mostly concerned with the analysis of stationary and near stationary regimes. However, not much has been done with respect to highly non-stationary processes existing in periodically heterogeneous nonlinear lattices such as FPU dimers etc. The system under consideration in the present paper is the FPU dimer chain given to periodic boundary conditions and composed of two identical cells of particles. Each cell of the chain comprises exactly one heavy particle succeeded by a group of N light particles of identical masses (i.e. 1:N dimer chain). In the current work we present an extensive analytical study of the mechanism of the formation of highly non-stationary regimes excited in FPU dimer chains subject to periodic boundary conditions. In particular we show that the initial excitation provided to a single group of light particles (belonging to a single cell), may lead to the two opposing regimes, namely energy localization on the same (initially excited) group of light particles as well as the recurrent (near complete) energy exchanges between the two groups of light particles of both cells. It is important to emphasize that for both the regimes heavy particles remain near completely stationary. An analytical study of the dynamics of the system under consideration reveals the threshold value of the parameter of nonlinearity (stiffness nonlinearity) above which the initial energy supplied to a specific group of light particles of the chain gets permanently localized on it. The developed analytical procedure correctly predicts the threshold value for the transition from the regime of strong energy exchange between the two groups of light particles to the permanent energy localization on a single group. It should be emphasized

  6. Dimeric assembly of enterocyte brush border enzymes

    DEFF Research Database (Denmark)

    Danielsen, E M


    The noncovalent, dimeric assembly of small intestinal brush border enzymes was studied by sedimentation analysis in density gradients of extracts of pulse-labeled pig jejunal mucosal explants. Like aminopeptidase N (EC, sucrase-isomaltase (EC, aminopeptidase A (EC 3...... appearance of the liposome-reconstituted enzyme [Norén et al. (1986) J. Biol. Chem. 261, 12306-12309], showing only the inner, membrane-anchored domains of the monomers to be in close contact with one another while the outer domains are far apart. In contrast to the other brush border enzymes studied...

  7. Fano Transparency in Rounded Nanocube Dimers Induced by Gap Plasmon Coupling. (United States)

    Pellarin, Michel; Ramade, Julien; Rye, Jan Michael; Bonnet, Christophe; Broyer, Michel; Lebeault, Marie-Ange; Lermé, Jean; Marguet, Sylvie; Navarro, Julien R G; Cottancin, Emmanuel


    Homodimers of noble metal nanocubes form model plasmonic systems where the localized plasmon resonances sustained by each particle not only hybridize but also coexist with excitations of a different nature: surface plasmon polaritons confined within the Fabry-Perot cavity delimited by facing cube surfaces (i.e., gap plasmons). Destructive interference in the strong coupling between one of these highly localized modes and the highly radiating longitudinal dipolar plasmon of the dimer is responsible for the formation of a Fano resonance profile and the opening of a spectral window of anomalous transparency for the exciting light. We report on the clear experimental evidence of this effect in the case of 50 nm silver and 160 nm gold nanocube dimers studied by spatial modulation spectroscopy at the single particle level. A numerical study based on a plasmon mode analysis leads us to unambiguously identify the main cavity mode involved in this process and especially the major role played by its symmetry. The Fano depletion dip is red-shifted when the gap size is decreasing. It is also blue-shifted and all the more pronounced that the cube edge rounding is large. Combining nanopatch antenna and plasmon hybridization descriptions, we quantify the key role of the face-to-face distance and the cube edge morphology on the spectral profile of the transparency dip.

  8. Quantum Transfer Energy and Nonlocal Correlation in a Dimer with Time-Dependent Coupling Effect (United States)

    El-Shishtawy, Reda M.; Berrada, K.; C. Haddon, Robert; Al-Hadeethi, Yas F.; H. Al-Heniti, Saleh.; Raffah, Bahaaudin M.


    The presence of coherence phenomenon due to the interference of probability amplitude terms, is one of the most important features of quantum mechanics theory. Recent experiments show the presence of quantum processes whose coherence provided over suddenly large interval-time. In particular, photosynthetic mechanisms in light-harvesting complexes provide oscillatory behaviors in quantum mechanics due to quantum coherence. In this work, we investigate the coherent quantum transfer energy for a single-excitation and nonlocal correlation in a dimer system modelled by a two-level atom system with and without time-dependent coupling effect. We analyze and explore the required conditions that are feasible with real experimental realization for optimal transfer of quantum energy and generation of nonlocal quantum correlation. We show that the enhancement of the probability for a single-excitation transfer energy is greatly benefits from the combination of the energy detuning and time-dependent coupling effect. We investigate the presence of quantum correlations in the dimer using the entanglement of formation. We also find that the entanglement between the donor and acceptor is very sensitive to the physical parameters and it can be generated during the coherent energy transfer. On the other hand, we study the dynamical behavior of the quantum variance when performing a measurement on an observable of the density matrix operator. Finally, an interesting relationship between the transfer probability, entanglement and quantum variance is explored during the time evolution in terms of the physical parameters.

  9. Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization

    DEFF Research Database (Denmark)

    Vinther, Tine N.; Norrman, Mathias; Strauss, Holger M.


    in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic ß-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization...

  10. Synthesis of dimeric lactose and dimeric (sialyl) Lewis(X) glycolipids. (United States)

    Gege, Christian; Schmidt, Richard R


    To investigate structural requirements for the homophilic interaction between carbohydrates on planar model membranes, divalent derivatives with enforced proximity between the two carbohydrate epitopes (lactose, Lewis(X), and sialyl Lewis(X)) were synthesized by use of a dimeric membrane anchor as scaffold.

  11. Cytotoxic sesquiterpene lactone dimers isolated from Inula japonica. (United States)

    Xu, Xing-Yu; Sun, Peng; Guo, De-An; Liu, Xuan; Liu, Jun-Hua; Hu, Li-Hong


    Two new sesquiterpene lactone dimers, neojaponicone B (1) and inulanolide E (2) along with five known sesquiterpene lactone dimers (3-7, resp.) were isolated from the aerial parts of Inula japonica Thunb. The chemical structures of 1 and 2 were elucidated by detailed spectroscopic analysis. The relative configuration of 2 was confirmed by biomimetic transformation from the known sesquiterpene lactone dimer inulanolide A (3). The cytotoxicities of the isolated sesquiterpene lactone dimers were evaluated against 6T-CEM and Jurkat cell lines. All compounds showed potent cytotoxicities with IC50 value of 2.2-5.9μm. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Computational Lower Bounds Using Diagonalization

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 7. Computational Lower Bounds Using Diagonalization - Languages, Turing Machines and Complexity Classes. M V Panduranga Rao. General Article Volume 14 Issue 7 July 2009 pp 682-690 ...

  13. DFT calculations for the high-temperature structure of (EDO-TTF)2PF6: Identification of an electronic molecular dimer (United States)

    Iwano, Kaoru; Shimoi, Yukihiro


    Density-functional theory (DFT) calculations are performed based on the high-temperature structure of (EDO-TTF)2PF6, a quasi-one-dimensional molecular compound that shows both thermal and photoinduced phase transitions. In this structure, the EDO-TTF molecules are one-dimensionally aligned, accompanied with weak dimerization. Contrary to a common sense, our DFT calculations reveal that the pair having a shorter mutual distance has a weaker intermolecular coupling than the pair with a longer one; the latter is appropriate to be called an electronic dimer. We also estimate the corresponding transfer energies and discuss their relevance to spin correlations and optical excitations.

  14. Conical intersections S0/S1 of thymine mediating the non-radiative photodestruction of cyclobutane dimers: a CASSCF level study (United States)

    Kancheva, P. B.; Delchev, V. B.


    Three new conical intersections S0/S1 (cis-anti, trans-syn and trans-anti) were fond which mediate the processes of photo-induced formation of cyclobutane thymine dimers. Their structures were optimized at the CASSCF(2,2) (Complete Active Space Self Consistent Field method) level of theory with the minimal bases set STO-3G*. The geometries were explored with respect to their structural and electron features. The found conical intersections S0/S1 give a clear indication that they could be included in the internal conversions of the 1ππ* excited states of the stacked dimers to cyclobutane photodimers and vice versa.

  15. Excited states 4

    CERN Document Server

    Lim, Edward C


    Excited States, Volume 4 is a collection of papers that deals with the excited states of molecular activity. One paper investigates the resonance Raman spectroscopy as the key to vibrational-electronic coupling. This paper reviews the basic theory of Raman scattering; it also explains the derivation of the Raman spectra, excitation profiles, and depolarization ratios for simple resonance systems. Another paper reviews the magnetic properties of triplet states, including the zero-field resonance techniques, the high-field experiments, and the spin Hamiltonian. This paper focuses on the magnetic

  16. Nuclear expansion with excitation

    Energy Technology Data Exchange (ETDEWEB)

    De, J.N. [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India); Departament d' Estructura i Constituents de la Materia, Facultat de Fisica, Universitat de Barcelona, Diagonal 647, 08028 Barcelona (Spain); Samaddar, S.K. [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India); Vinas, X. [Departament d' Estructura i Constituents de la Materia, Facultat de Fisica, Universitat de Barcelona, Diagonal 647, 08028 Barcelona (Spain); Centelles, M. [Departament d' Estructura i Constituents de la Materia, Facultat de Fisica, Universitat de Barcelona, Diagonal 647, 08028 Barcelona (Spain)]. E-mail:


    The expansion of an isolated hot spherical nucleus with excitation energy and its caloric curve are studied in a thermodynamic model with the SkM{sup *} force as the nuclear effective two-body interaction. The calted results are shown to compare well with the recent experimental data from energetic nuclear collisions. The fluctuations in temperature and density are also studied. They are seen to build up very rapidly beyond an excitation energy of {approx}9 MeV/u. Volume-conserving quadrupole deformation in addition to expansion indicates, however, nuclear disassembly above an excitation energy of {approx}4 MeV/u.

  17. Bound-state energy of the three-dimensional Ising model in the broken-symmetry phase: suppressed finite-size corrections. (United States)

    Nishiyama, Yoshihiro


    The low-lying spectrum of the three-dimensional Ising model is investigated numerically; we made use of an equivalence between the excitation gap and the reciprocal correlation length. In the broken-symmetry phase, the magnetic excitations are attractive, forming a bound state with an excitation gap m_{2} (mass-gap ratio as m_{2}/m_{1}=1.84(3) .

  18. Bounded Rationality in Transposition Processes

    DEFF Research Database (Denmark)

    Vollaard, Hans; Martinsen, Dorte Sindbjerg


    perspective may affect the commonly employed explanatory factors of administrative capacities, misfit and the heterogeneity of preferences among veto players. To prevent retrospective rationalisation of the transposition process, this paper traces this process as it unfolded in Denmark and the Netherlands....... As bounded rationality is apparent in the transposition processes in these relatively well-organised countries, future transposition studies should devote greater consideration to the bounded rationality perspective....

  19. Experimental and DFT dimer modeling studies of the H-bond induced-vibration modes of l-β-Homoserine. (United States)

    Yalagi, Shashikala; Tonannavar, J; Yenagi, Jayashree


    The vibrational spectra for l-β-Homoserine have been measured (IR absorption: 4000-400cm(-1)/Raman spectra: 4000-200cm(-1)). Characteristic vibrational modes of ammonium (-NH3(+)), carboxylate (-CO2(-)) and hydroxyl (-OH) groups across the 3700-1400cm(-1) are all identified to have originated in inter-molecular hydrogen bonding involving these functional groups. DFT calculations at B3LYP/6-311++G(d, p) level have yielded a single neutral monomer in the gas phase. Since as a member of the amino acids which are known to possess zwitterionic structure in condensed phase, the neutral monomer of l-β-Homoserine is optimized to a zwitterionic structure in a water medium. Consideration of two dimer structures, one dimer with -NH‧‧‧O bond and another -OH‧‧‧O bond, has given rise to vibrational modes that satisfactorily fit to all the observed absorption and Raman bands. It is found that the dimer with -OH‧‧‧O bond (binding energy, 8.896kcal/mol) is more tightly bound than the dimer with -NH‧‧‧O bond (8.363kcal/mol). Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Structural Insights into a Unique Dimeric DEAD-Box Helicase CshA that Promotes RNA Decay. (United States)

    Huen, Jennifer; Lin, Chia-Liang; Golzarroshan, Bagher; Yi, Wan-Li; Yang, Wei-Zen; Yuan, Hanna S


    CshA is a dimeric DEAD-box helicase that cooperates with ribonucleases for mRNA turnover. The molecular mechanism for how a dimeric DEAD-box helicase aids in RNA decay remains unknown. Here, we report the crystal structure and small-angle X-ray scattering solution structure of the CshA from Geobacillus stearothermophilus. In contrast to typical monomeric DEAD-box helicases, CshA is exclusively a dimeric protein with the RecA-like domains of each protomer forming a V-shaped structure. We show that the C-terminal domains protruding outward from the tip of the V-shaped structure is critical for mediating strong RNA binding and is crucial for efficient RNA-dependent ATP hydrolysis. We also show that RNA remains bound with CshA during ATP hydrolysis cycles and thus bulk RNAs could be unwound and degraded in a processive manner through cooperation between exoribonucleases and CshA. A dimeric helicase is hence preserved in RNA-degrading machinery for efficient RNA turnover in prokaryotes and eukaryotes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. The role of dimerization in prion replication. (United States)

    Tompa, Peter; Tusnády, Gábor E; Friedrich, Peter; Simon, István


    The central theme in prion diseases is the conformational transition of a cellular protein from a physiologic to a pathologic (so-called scrapie) state. Currently, two alternative models exist for the mechanism of this autocatalytic process; in the template assistance model the prion is assumed to be a monomer of the scrapie conformer, whereas in the nucleated polymerization model it is thought to be an amyloid rod. A recent variation on the latter assumes disulfide reshuffling as the mechanism of polymerization. The existence of stable dimers, let alone their mechanistic role, is not taken into account in either of these models. In this paper we review evidence supporting that the dimerization of either the normal or the scrapie state, or both, has a decisive role in prion replication. The contribution of redox changes, i.e., the temporary opening and possible rearrangement of the intramolecular disulfide bridge is also considered. We present a model including these features largely ignored so far and show that it adheres satisfactorily to the observed phenomenology of prion replication.

  2. Modelling study of dimerization in mammalian defensins

    Directory of Open Access Journals (Sweden)

    Verma Chandra


    Full Text Available Abstract Background Defensins are antimicrobial peptides of innate immunity functioning by non-specific binding to anionic phospholipids in bacterial membranes. Their cationicity, amphipathicity and ability to oligomerize are considered key factors for their action. Based on structural information on human β-defensin 2, we examine homologous defensins from various mammalian species for conserved functional physico-chemical characteristics. Results Based on homology greater than 40%, structural models of 8 homologs of HBD-2 were constructed. A conserved pattern of electrostatics and dynamics was observed across 6 of the examined defensins; models backed by energetics suggest that the defensins in these 6 organisms are characterized by dimerization-linked enhanced functional potentials. In contrast, dimerization is not energetically favoured in the sheep, goat and mouse defensins, suggesting that they function efficiently as monomers. Conclusion β-defensin 2 from some mammals may work as monomers while those in others, including humans, work as oligomers. This could potentially be used to design human defensins that may be effective at lower concentrations and hence have therapeutic benefits.

  3. A retrospective evaluation of the age-adjusted D-dimer versus the conventional D-dimer for pulmonary embolism. (United States)

    Sheele, Johnathan M; Tang, Annie; Farhan, Obada; Morris, Nathan


    : The conventional D-dimer cut-off value of at least 500 μg FEU/l has good sensitivity but poor specificity for identifying pulmonary embolism. An elevated age-adjusted D-dimer value (age in years × 10 μg FEU/l) for patients at least 50 years old has been recommended as a better cut-off with adequate sensitivity and improved specificity for identifying pulmonary embolism compared with the conventional value. We retrospectively reviewed 3117 patient encounters in which a D-dimer was ordered. The D-dimer value, age of the patient, and the computed tomography radiology report was evaluated. The sensitivity and specificity of the age-adjusted D-dimer was calculated using bootstrapping. With an assumed 99% sensitivity for the conventional D-dimer cut-off the specificity was 39.2% [95% confidence interval (CI): 37.5-41.0%]. The sensitivity of the age-adjusted D-dimer was 91.8% (95% CI: 83.8-97.2%) with a specificity of 51.0% (95% CI: 49.1-53.1%). The sensitivity of the age-adjusted D-dimer was unacceptably low compared with the conventional D-dimer cut-off.

  4. Interaction between thymine dimer and flavin-adenine dinucleotide: a DFT and direct ab initio molecular dynamics study. (United States)

    Tachikawa, Hiroto; Kawabata, Hiroshi


    The interaction between the fully reduced flavin-adenine dinucleotide (FADH (-)) and thymine dimer (T) 2 has been investigated by means of density functional theory (DFT) calculations. The charges of FADH (-) and (T) 2 were calculated to be -0.9 and -0.1, respectively, at the ground state. By photoirradiation, an electron transfer occurred from FADH (-) to (T) 2 at the first excited state. Next, the reaction dynamics of electron capture of (T) 2 have been investigated by means of the direct ab initio molecular dynamics (MD) method (HF/3-21G(d) and B3LYP/6-31G(d) levels) in order to elucidate the mechanism of the repair process of thymine dimer caused by the photoenzyme. The thymine dimer has two C-C single bonds between thymine rings (C 5-C 5' and C 6-C 6' bonds) at the neutral state, which is expressed by (T) 2. After the electron capture of (T) 2, the C 5-C 5' bond was gradually elongated and then it was preferentially broken. The time scale of the C-C bond breaking and formation of the intermediate with a single bond (T) 2 (-) was estimated to be 100-150 fs. The present calculations confirmed that the repair reaction of thymine dimer takes place efficiently via an electron-transfer process from the FADH (-) enzyme.

  5. Excited states of {sup 4}He droplets

    Energy Technology Data Exchange (ETDEWEB)

    Guardiola, R.; Navarro, J.; Portesi, M.


    We study low-lying excited states of {sup 4}He clusters up to a cluster size of 40 atoms in a variational framework. The ansatz wave function combines two- and three-body correlations, coming from a translationally invariant configuration interaction description, and Jastrow-type short-range correlation. We have previously used this scheme to determine the ground-state energies of {sup 4}He and {sup 3}He clusters. Here we present an extension of this ansatz wave function having a good quantum angular momentum L. The variational procedure is applied independently to the cases with L=0,2,4, and upper bounds for the corresponding energies are thus obtained. Moreover, centroid energies for L excitations are calculated through the use of sum rules. A comparison with previous calculations is also made.

  6. Search for excited states in 25O (United States)

    Jones, M. D.; Fossez, K.; Baumann, T.; DeYoung, P. A.; Finck, J. E.; Frank, N.; Kuchera, A. N.; Michel, N.; Nazarewicz, W.; Rotureau, J.; Smith, J. K.; Stephenson, S. L.; Stiefel, K.; Thoennessen, M.; Zegers, R. G. T.


    Background: Theoretical calculations suggest the presence of low-lying excited states in 25O. Previous experimental searches by means of proton knockout on 26F produced no evidence for such excitations. Purpose: We search for excited states in 25O using the 24O(d ,p ) 25O reaction. The theoretical analysis of excited states in unbound O,2725 is based on the configuration interaction approach that accounts for couplings to the scattering continuum. Method: We use invariant-mass spectroscopy to measure neutron-unbound states in 25O. For the theoretical approach, we use the complex-energy Gamow Shell Model and Density Matrix Renormalization Group method with a finite-range two-body interaction optimized to the bound states and resonances of O-2623, assuming a core of 22O. We predict energies, decay widths, and asymptotic normalization coefficients. Results: Our calculations in a large s p d f space predict several low-lying excited states in 25O of positive and negative parity, and we obtain an experimental limit on the relative cross section of a possible Jπ=1/2 + state with respect to the ground state of 25O at σ1 /2 +/σg .s .=0 .25-0.25+1.0 . We also discuss how the observation of negative parity states in 25O could guide the search for the low-lying negative parity states in 27O. Conclusion: Previous experiments based on the proton knockout of 26F suffered from the low cross sections for the population of excited states in 25O because of low spectroscopic factors. In this respect, neutron transfer reactions carry more promise.

  7. Disrupting Dimerization Translocates Soluble Epoxide Hydrolase to Peroxisomes.

    Directory of Open Access Journals (Sweden)

    Jonathan W Nelson

    Full Text Available The epoxyeicosatrienoic acid (EET neutralizing enzyme soluble epoxide hydrolase (sEH is a neuronal enzyme, which has been localized in both the cytosol and peroxisomes. The molecular basis for its dual localization remains unclear as sEH contains a functional peroxisomal targeting sequence (PTS. Recently, a missense polymorphism was identified in human sEH (R287Q that enhances its peroxisomal localization. This same polymorphism has also been shown to generate weaker sEH homo-dimers. Taken together, these observations suggest that dimerization may mask the sEH PTS and prevent peroxisome translocation. In the current study, we test the hypothesis that dimerization is a key regulator of sEH subcellular localization. Specifically, we altered the dimerization state of sEH by introducing substitutions in amino acids responsible for the dimer-stabilizing salt-bridge. Green Fluorescent Protein (GFP fusions of each of mutants were co-transfected into mouse primary cultured cortical neurons together with a PTS-linked red fluorescent protein to constitutively label peroxisomes. Labeled neurons were analyzed using confocal microscopy and co-localization of sEH with peroxisomes was quantified using Pearson's correlation coefficient. We find that dimer-competent sEH constructs preferentially localize to the cytosol, whereas constructs with weakened or disrupted dimerization were preferentially targeted to peroxisomes. We conclude that the sEH dimerization status is a key regulator of its peroxisomal localization.

  8. Disrupting Dimerization Translocates Soluble Epoxide Hydrolase to Peroxisomes. (United States)

    Nelson, Jonathan W; Das, Anjali J; Barnes, Anthony P; Alkayed, Nabil J


    The epoxyeicosatrienoic acid (EET) neutralizing enzyme soluble epoxide hydrolase (sEH) is a neuronal enzyme, which has been localized in both the cytosol and peroxisomes. The molecular basis for its dual localization remains unclear as sEH contains a functional peroxisomal targeting sequence (PTS). Recently, a missense polymorphism was identified in human sEH (R287Q) that enhances its peroxisomal localization. This same polymorphism has also been shown to generate weaker sEH homo-dimers. Taken together, these observations suggest that dimerization may mask the sEH PTS and prevent peroxisome translocation. In the current study, we test the hypothesis that dimerization is a key regulator of sEH subcellular localization. Specifically, we altered the dimerization state of sEH by introducing substitutions in amino acids responsible for the dimer-stabilizing salt-bridge. Green Fluorescent Protein (GFP) fusions of each of mutants were co-transfected into mouse primary cultured cortical neurons together with a PTS-linked red fluorescent protein to constitutively label peroxisomes. Labeled neurons were analyzed using confocal microscopy and co-localization of sEH with peroxisomes was quantified using Pearson's correlation coefficient. We find that dimer-competent sEH constructs preferentially localize to the cytosol, whereas constructs with weakened or disrupted dimerization were preferentially targeted to peroxisomes. We conclude that the sEH dimerization status is a key regulator of its peroxisomal localization.

  9. Exact Solution of a Generalized Nonlinear Schrodinger Equation Dimer

    DEFF Research Database (Denmark)

    Christiansen, Peter Leth; Maniadis, P.; Tsironis, G.P.


    We present exact solutions for a nonlinear dimer system defined throught a discrete nonlinear Schrodinger equation that contains also an integrable Ablowitz-Ladik term. The solutions are obtained throught a transformation that maps the dimer into a double Sine-Gordon like ordinary nonlinear...

  10. Stochastic optimization-based study of dimerization kinetics

    Indian Academy of Sciences (India)

    We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end, we study dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and combine it with three different optimization ...

  11. D-Dimer and thrombus burden in acute pulmonary embolism. (United States)

    Keller, Karsten; Beule, Johannes; Balzer, Jörn Oliver; Dippold, Wolfgang


    Thrombus burden in pulmonary embolism (PE) is associated with higher D-Dimer-levels and poorer prognosis. We aimed to investigate i) the influence of right ventricular dysfunction (RVD), deep venous thrombosis (DVT), and high-risk PE-status on D-Dimer-levels and ii) effectiveness of D-Dimer to predict RVD in normotensive PE patients. Overall, 161 PE patients were analyzed retrospectively, classified in 5 subgroups of thrombus burden according to clinical indications and compared regarding D-Dimer-levels. Linear regression models were computed to investigate the association between D-Dimer and the groups. In hemodynamically stable PE patients, a ROC curve was calculated to assess the effectiveness of D-Dimer for predicting RVD. Overall, 161 patients (60.9% females, 54.0% aged >70 years) were included in this analysis. The D-Dimer-level was associated with group-category in a univariate linear regression model (β 0.050 (95%CI 0.002-0.099), P = .043). After adjustment for age, sex, cancer, and pneumonia in a multivariate model we observed an association between D-Dimer and group-category with borderline significance (β 0.047 (95%CI 0.002-0.096), P = .058). The Kruskal-Wallis test demonstrated that D-Dimer increased significantly with higher group-category. In 129 normotensive patients, patients with RVD had significantly higher D-Dimer values compared to those without (1.73 (1.11/3.48) vs 1.17 (0.65/2.90) mg/l, P = .049). A ROC curve showed an AUC of 0.61, gender non-specific, with calculated optimal cut-off of 1.18 mg/l. Multi-variate logistic regression model confirmed an association between D-Dimer >1.18 mg/l and RVD (OR2.721 (95%CI 1.196-6.190), P = .017). Thrombus burden in PE is related to elevated D-Dimer levels, and D-Dimer values >1.18 mg/l were predictive for RVD in normotensive patients. D-Dimer levels were influenced by DVT, but not by cancer, pneumonia, age, or renal impairment. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. Large D-Dimer Fluctuation in Normal Pregnancy

    DEFF Research Database (Denmark)

    Hedengran, Katrine K; Andersen, Malene R; Stender, Steen


    pregnancies were recruited. D-dimer was repeatedly measured during pregnancy, at active labor, and on the first and second postpartum days. Percentiles for each gestational week were calculated. Each individual D-dimer was normalized by transformation into percentiles for the relevant gestational age...... or delivery group. The range in percentage points during the pregnancy and the delivery was calculated, and reference intervals were calculated for each pregnancy trimester, during vaginal delivery and scheduled and emergency cesarean section, and for the first and second day postpartum. Results. D......-dimer increased during pregnancy; the maximal fluctuation was approximately 20 percentile points in approximately half of the women. In one out of ten women, the D-dimer values fluctuated by more than 50 percentile points. Conclusions. Due to the biological variation in D-dimer within each individual woman during...

  13. Antiparallel coiled-coil–mediated dimerization of myosin X (United States)

    Lu, Qing; Ye, Fei; Wei, Zhiyi; Wen, Zilong; Zhang, Mingjie


    Processive movements of unconventional myosins on actin filaments generally require motor dimerization. A commonly accepted myosin dimerization mechanism is via formation of a parallel coiled-coil dimer by a stretch of amino acid residues immediately carboxyl-terminal to the motor’s lever-arm domain. Here, we discover that the predicted coiled-coil region of myosin X forms a highly stable, antiparallel coiled-coil dimer (anti-CC). Disruption of the anti-CC either by single-point mutations or by replacement of the anti-CC with a parallel coiled coil with a similar length compromised the filopodial induction activity of myosin X. We further show that the anti-CC and the single α-helical domain of myosin X are connected by a semirigid helical linker. The anti-CC–mediated dimerization may enable myosin X to walk on both single and bundled actin filaments. PMID:23012428

  14. Space-bounded communication complexity

    DEFF Research Database (Denmark)

    Brody, Joshua Eric; Chen, Shiteng; Papakonstantinou, Periklis A.


    -obliviousness shows up. For this model we also introduce new techniques through which certain limitations of space-bounded computation are revealed. One of the main motivations of this work is in understanding the difference in the use of space when computing the following functions: Equality (EQ), Inner Product (IP......In the past thirty years, Communication Complexity has emerged as a foundational tool to proving lower bounds in many areas of computer science. Its power comes from its generality, but this generality comes at a price---no superlinear communication lower bound is possible, since a player may...... communicate his entire input. However, what if the players are limited in their ability to recall parts of their interaction? We introduce memory models for 2-party communication complexity. Our general model is as follows: two computationally unrestricted players, Alice and Bob, each have s(n) bits of memory...

  15. Real-space investigation of energy transfer in heterogeneous molecular dimers (United States)

    Imada, Hiroshi; Miwa, Kuniyuki; Imai-Imada, Miyabi; Kawahara, Shota; Kimura, Kensuke; Kim, Yousoo


    Given its central role in photosynthesis and artificial energy-harvesting devices, energy transfer has been widely studied using optical spectroscopy to monitor excitation dynamics and probe the molecular-level control of energy transfer between coupled molecules. However, the spatial resolution of conventional optical spectroscopy is limited to a few hundred nanometres and thus cannot reveal the nanoscale spatial features associated with such processes. In contrast, scanning tunnelling luminescence spectroscopy has revealed the energy dynamics associated with phenomena ranging from single-molecule electroluminescence, absorption of localized plasmons and quantum interference effects to energy delocalization and intervalley electron scattering with submolecular spatial resolution in real space. Here we apply this technique to individual molecular dimers that comprise a magnesium phthalocyanine and a free-base phthalocyanine (MgPc and H2Pc) and find that locally exciting MgPc with the tunnelling current of the scanning tunnelling microscope generates a luminescence signal from a nearby H2Pc molecule as a result of resonance energy transfer from the former to the latter. A reciprocating resonance energy transfer is observed when exciting the second singlet state (S2) of H2Pc, which results in energy transfer to the first singlet state (S1) of MgPc and final funnelling to the S1 state of H2Pc. We also show that tautomerization of H2Pc changes the energy transfer characteristics within the dimer system, which essentially makes H2Pc a single-molecule energy transfer valve device that manifests itself by blinking resonance energy transfer behaviour.

  16. α-Synuclein Dimers Impair Vesicle Fission during Clathrin-Mediated Synaptic Vesicle Recycling

    Directory of Open Access Journals (Sweden)

    Audrey T. Medeiros


    Full Text Available α-Synuclein is a presynaptic protein that regulates synaptic vesicle (SV trafficking. In Parkinson’s disease (PD and several other neurodegenerative disorders, aberrant oligomerization and aggregation of α-synuclein lead to synaptic dysfunction and neurotoxicity. Despite evidence that α-synuclein oligomers are generated within neurons under physiological conditions, and that altering the balance of monomers and oligomers contributes to disease pathogenesis, how each molecular species of α-synuclein impacts SV trafficking is currently unknown. To address this, we have taken advantage of lamprey giant reticulospinal (RS synapses, which are accessible to acute perturbations via axonal microinjection of recombinant proteins. We previously reported that acute introduction of monomeric α-synuclein inhibited SV recycling, including effects on the clathrin pathway. Here, we report the effects of α-synuclein dimers at synapses. Similar to monomeric α-synuclein, both recombinant α-synuclein dimers that were evaluated bound to small liposomes containing anionic lipids in vitro, but with reduced efficacy. When introduced to synapses, the α-synuclein dimers also induced SV recycling defects, which included a build up of clathrin-coated pits (CCPs with constricted necks that were still attached to the plasma membrane, a phenotype indicative of a vesicle fission defect. Interestingly, both α-synuclein dimers induced longer necks on CCPs as well as complex, branching membrane tubules, which were distinct from the CCPs induced by a dynamin inhibitor, Dynasore. In contrast, monomeric α-synuclein induced a buildup of free clathrin-coated vesicles (CCVs, indicating an inhibition of clathrin-mediated endocytosis at a later stage during the clathrin uncoating process. Taken together, these data further support the conclusion that excess α-synuclein impairs SV recycling. The data additionally reveal that monomeric and dimeric α-synuclein produce

  17. Graphene plasmonics: multiple sharp Fano resonances in silver split concentric nanoring/disk resonator dimers on a metasurface (United States)

    Ahmadivand, Arash; Sinha, Raju; Pala, Nezih


    We introduce a platform based on plasmonic metamaterials to design various optical devices. A simple structure brokenring with a nanodisk at the center is utilized to excite and hybridize the plasmon resonant modes. We show that the proposed nanoantenna is able to support strong sub- and superradiant plasmon resonances because of its unique geometrical features. Using the concentric ring/disk in a dimer orientation as a nanoantenna on a multilayer metasurface consisting of graphene monolayer, we induced double sharp plasmonic Fano resonant modes in the transmission window across the visible to the near-infrared region. Considering the strong polarization-dependency of the broken-ring/disk dimer antenna, it is shown that the proposed plasmonic metamaterial can be tailored as an optical router device for fast switching applications. This understanding opens new paths to employ plasmonic metamaterials with simple geometrical nanoscale blocks for sensing and switching applications.

  18. Pi-dimer of an aniline dimer: an ESR-UV-vis spectroelectrochemical study. (United States)

    Petr, Andreas; Wei, Di; Kvarnström, Carita; Ivaska, Ari; Dunsch, Lothar


    It is shown for the first time that the most important intermediate formed during aniline polymerization, the p-aminodiphenylamine, forms a pi-dimer under oxidation at room temperature in acidified organic solvents that are used in electropolymerization. N-Phenylquinonediimine, which is generally assumed to be formed under oxidation, is only formed in basic solutions and in ionic liquids. Most of the mechanistic studies reported so far take the formation of N-phenylquinonediimine under consideration, although it is not consistent with the UV-vis spectra measured during oxidation of p-aminodiphenylamine. The formation of a pi-dimer is very well consistent with the electronic spectra of the oxidation product. In this way the pi-dimer is very important for the interpretation of the UV-vis spectra of higher oligomers and polyaniline as well. Furthermore, it offers a new interpretation of the redox behavior of p-aminodiphenylamine as found by cyclic voltammetry and has to be considered in the mechanism of the electrochemical polyaniline formation.

  19. Excitations in organic solids

    CERN Document Server

    Agranovich, Vladimir M


    During the last decade our expertise in nanotechnology has advanced considerably. The possibility of incorporating in the same nanostructure different organic and inorganic materials has opened up a promising field of research, and has greatly increased the interest in the study of properties of excitations in organic materials. In this book not only the fundamentals of Frenkel exciton and polariton theory are described, but also the electronic excitations and electronic energytransfers in quantum wells, quantum wires and quantum dots, at surfaces, at interfaces, in thin films, in multilayers,

  20. Excitation Methods for Bridge Structures

    Energy Technology Data Exchange (ETDEWEB)

    Farrar, C.R.; Duffy, T.A.; Cornwell, P.J.; Doebling, S.W.


    This paper summarizes the various methods that have been used to excited bridge structures during dynamic testing. The excitation methods fall into the general categories of ambient excitation methods and measured-input excitation methods. During ambient excitation the input to the bridge is not directly measured. In contrast, as the category label implies, measured-input excitations are usually applied at a single location where the force input to the structure can be monitored. Issues associated with using these various types of measurements are discussed along with a general description of the various excitation methods.

  1. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.


    This paper describes how one can compute interval-valued statistical measures given limited information about the underlying distribution. The particular focus is on a bounded derivative of a probability density function and its combination with other available statistical evidence for computing ...

  2. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

    nuclear physics changed drastically as the new generation of accelerators started providing more and more rare isotopes, which are away from the line of stability. These weakly bound nuclei are found to exhibit new forms of nuclear matter and unprecedented exotic behaviour. The low breakup thresholds of these rare ...

  3. Distance bounds on quantum dynamics (United States)

    Lidar, Daniel A.; Zanardi, Paolo; Khodjasteh, Kaveh


    We derive rigorous upper bounds on the distance between quantum states in an open-system setting in terms of the operator norm between Hamiltonians describing their evolution. We illustrate our results with an example taken from protection against decoherence using dynamical decoupling.

  4. Moderate deviations for bounded subsequences

    Directory of Open Access Journals (Sweden)

    George Stoica


    Full Text Available We study Davis' series of moderate deviations probabilities for Lp-bounded sequences of random variables (p>2. A certain subseries therein is convergent for the same range of parameters as in the case of martingale difference or i.i.d. sequences.

  5. Excited states using semistochastic heat-bath configuration interaction (United States)

    Holmes, Adam A.; Umrigar, C. J.; Sharma, Sandeep


    We extend our recently developed heat-bath configuration interaction (HCI) algorithm, and our semistochastic algorithm for performing multireference perturbation theory, to calculate excited-state wavefunctions and energies. We employ time-reversal symmetry, which reduces the memory requirements by more than a factor of two. An extrapolation technique is introduced to reliably extrapolate HCI energies to the full CI limit. The resulting algorithm is used to compute fourteen low-lying potential energy surfaces of the carbon dimer using the cc-pV5Z basis set, with an estimated error in energy of 30-50 μHa compared to full CI. The excitation energies obtained using our algorithm have a mean absolute deviation of 0.02 eV compared to experimental values.

  6. Paclitaxel dimers assembling nanomedicines for treatment of cervix carcinoma. (United States)

    Pei, Qing; Hu, Xiuli; Liu, Shi; Li, Yang; Xie, Zhigang; Jing, Xiabin


    Poor water solubility and adverse side effects pose a challenge for clinical application of paclitaxel (PTX). In this work, a series of PTX dimers are synthesized by coupling two PTX molecules with dicarboxylic acids. As-synthesized PTX dimers form stable nanoparticles in aqueous solution without using any surfactants or adjuvants, and the solubility of PTX in water increases by 2500-fold compared to that of free PTX. These nanoparticles with high content of PTX are internalized by cancer cells and exhibit comparable cytotoxicity with Taxol. Furthermore, when the PTX dimers are incorporated into methoxypoly(ethylene glycol)2K-block-poly(d, l-lactide)2K (PEG-PDLLA) micelles, the loading content of PTX dimers is as high as 85wt%. The formed nanoparticles possess the high stability in biological conditions. Both in vitro and in vivo experiments show that these (PTX dimer)/PEG-PDLLA formulations possess effective cellular uptake and potent cytotoxicity, and exhibit reduced systemic toxicity and enhanced antitumor efficacy towards human cervical tumor. We believe these PTX dimers-based nanoparticles would be an alternative formulation for PTX, and such drug dimer assembling behaviors could be extended to other therapeutic agents. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Advances in Chemistry and Pharmacology of Triterpenoid Synthetic Dimers. (United States)

    Bednarczyk-Cwynar, Barbara; Günther, Andrzej


    This review focuses on advances in chemistry and pharmacology of synthetic triterpenoid dimers, obtained from natural compounds. Synthetic triterpenoid dimers are divided into specific subgroups based on the structure of main triterpenoid monomeric skeleton. Synthetic triterpenoid derivatives of dimeric structure can be obtained through the covalent linkage of the C-3 hydroxyl or another group, via the C-2 atom or the C-17 carboxyl group (mainly anhydrides, amides or esters). Some triterpenes can undergo chemical transformations leading to the formation of cyclic dimers or other types of dimers. Most of the obtained triterpenoid dimers have been subjected to pharmacological tests evaluating their biological activity, mainly antiviral (HIV-1 RT, HCVpp, VSVpp, HIV-RT-C8166-CCR5), cytotoxic (against e.g. 388, MCF-7, SF-268, NCIH460, KM20L2, DU-145, Hep-G2, A549, BGC-823, PC-3), anti-inflammatory (iNOS, RAW 264.7) and antidiabetic (RMGPa inhibition). The authors also reported the ability of some of the obtained cyclic triterpenoid dimers to recognize anions and to form self-assembled structures. Copyright© Bentham Science Publishers; For any queries, please email at

  8. The PH Domain of PDK1 Exhibits a Novel, Phospho-Regulated Monomer-Dimer Equilibrium With Important Implications for Kinase Domain Activation: Single Molecule and Ensemble Studies† (United States)

    Ziemba, Brian P.; Pilling, Carissa; Calleja, Véronique; Larijani, Banafshé; Falke, Joseph J.


    Phosphoinositide-Dependent Kinase-1 (PDK1) is an essential master kinase recruited to the plasma membrane by the binding of its C-terminal PH domain to the signaling lipid phosphatidylinositol-3,4-5-trisphosphate (PIP3). Membrane binding leads to PDK1 phospho-activation, but despite the central role of PDK1 in signaling and cancer biology this activation mechanism remains poorly understood. PDK1 has been shown to exist as a dimer in cells, and one crystal structure of its isolated PH domain exhibits a putative dimer interface. It has been proposed that phosphorylation of PH domain residue T513 (or the phospho-mimetic T513E mutation) may regulate a novel PH domain dimer-monomer equilibrium, thereby converting an inactive PDK1 dimer to an active monomer. However, the oligomeric state(s) of the PH domain on the membrane have not yet been determined, nor whether a negative charge at position 513 is sufficient to regulate its oligomeric state. The present study investigates the binding of purified WT and T513E PDK1 PH domains to lipid bilayers containing the PIP3 target lipid, using both single molecule and ensemble measurements. Single molecule analysis of the brightness of fluorescent PH domain shows that the PIP3-bound WT PH domain on membranes is predominantly dimeric, while the PIP3-bound T513E PH domain is monomeric, demonstrating that negative charge at the T513 position is sufficient to dissociate the PH domain dimer and is thus likely to play a central role in PDK1 monomerization and activation. Single molecule analysis of 2-D diffusion of PH domain-PIP3 complexes reveals that the dimeric WT PH domain diffuses at the same rate a single lipid molecule, indicating that only one of its two PIP3 binding sites is occupied and there is little protein penetration into the bilayer as observed for other PH domains. The 2-D diffusion of T513E PH domain is slower, suggesting the negative charge disrupts local structure in a way that enables greater protein insertion into

  9. Multipair excitations in the two-dimensional electron gas (United States)

    Pederiva, F.; Emperador, A.; Lipparini, E.


    We present a sum-rule study of spin multipair excitations in the two-dimensional electron gas. The cubic-energy-weighted sum rule m3=∫S(q,ω)ω3dω is microscopically calculated taking into account the effect of dynamical correlations. The comparison among exact sum rules and the ones derived within Landau theory allows us to give a proper estimate of the average spin multipair excitation energy and a rigorous lower bound for the multipair contribution to the static form factor in the low-q limit. The relative importance of spin multipair excitations in two- and three-dimensional electron gases is discussed. Finally, numerical results of the contribution of multipair excitations to the m3 sum rule in the density channel are given.

  10. Coupling of electrons to intermolecular phonons in molecular charge transfer dimers: A resonance Raman study (United States)

    Pedron, D.; Speghini, A.; Mulloni, V.; Bozio, R.


    We report resonance Raman scattering (RRS) spectra and Raman excitation profiles (REP) of a system containing π dimers of identical molecular radical ions measured with laser excitation in resonance with the charge transfer (CT) transition. A Peierls-Hubbard (PH) Hamiltonian has been used to model the investigated system and to calculate its optical and RRS properties. Results are reported for two polyoxometallate salts of tetrathiafulvalene (TTF), namely (TTF)2(W6O19) and (TTF)2(Mo6O19) whose structures contain almost isolated (TTF+)2 dimers. The RRS spectra of (TTF)2(W6O19), measured in resonance with the CT absorption band centered at 832 nm, show three phonon modes located at 55, 90, and 116 cm-1 which are strongly resonance enhanced. These modes have been associated to the out-of-phase combinations of the translational motions of the two molecules composing the dimer. Such modes are effective in modulating the intradimer transfer integral, thus providing an efficient mechanism for coupling with the electronic system and for enhancement of the scattering intensity at resonance with the CT transition. The REP for the three strongly coupled modes of (TTF)2(W6O19) have been measured with laser excitation wavelengths ranging from 740 to 930 nm. Quantitative analysis of the REP data has been performed based on a perturbative solution of the PH model to second order in the electron-molecular-vibration (EMV) and electron-intermolecular-phonon (EIP) interactions. The CT absorption profile and the REP's have been calculated using a time correlator technique and the model parameters have been optimized in order to fit the experimental REP data. Infrared vibronic absorptions of (TTF)2(W6O19), originated by the EMV coupling, have been measured and independent information on the electronic parameters of the PH model have been derived. This has made the choice of the fitting parameters used for the REP calculations rather unambiguous and has allowed us to obtain, for the

  11. Positron excitation of neon (United States)

    Parcell, L. A.; Mceachran, R. P.; Stauffer, A. D.


    The differential and total cross section for the excitation of the 3s1P10 and 3p1P1 states of neon by positron impact were calculated using a distorted-wave approximation. The results agree well with experimental conclusions.

  12. Hardness and excitation energy

    Indian Academy of Sciences (India)

    It is shown that the first excitation energy can be given by the Kohn-Sham hardness (i.e. the energy difference of the ground-state lowest unoccupied and highest occupied levels) plus an extra term coming from the partial derivative of the ensemble exchange-correlation energy with respect to the weighting factor in the ...

  13. Excitation of Stellar Pulsations

    DEFF Research Database (Denmark)

    Houdek, G.


    In this review I present an overview of our current understanding of the physical mechanisms that are responsible for the excitation of pulsations in stars with surface convection zones. These are typically cooler stars such as the δ Scuti stars, and stars supporting solar-like oscillations....

  14. Human white blood cells contain cyclobutyl pyrimidine dimer photolyase

    Energy Technology Data Exchange (ETDEWEB)

    Sutherland, B.M.; Bennett, P.V. [Brookhaven National Lab., Upton, NY (United States)


    Although enzymatic photoreactivation of cyclobutyl pyrimidine dimers in DNA is present in almost all organisms, its presence in placental mammals is controversial. We tested human white blood cells for photolyase by using three defined DNAs (suprecoiled pET-2, nonsupercoiled bacteriphage {lambda}, and a defined-sequence 287-bp oligonucleotide), two dimer-specific endonucleases (T4 endonuclease V and UV endonuclease from Micrococcus luteus), and three assay methods. We show that human white blood cells contain photolyase that can photorepair pyrimidine dimers in defined supercoiled and linear DNAs and in a 287-bp oligonucleotide and that human photolyase is active on genomic DNA in intact human cells. 44 refs., 3 figs.

  15. Subsurface dimerization in III-V semiconductor (001) surfaces

    DEFF Research Database (Denmark)

    Kumpf, C.; Marks, L.D.; Ellis, D.


    We present the atomic structure of the c(8 X 2) reconstructions of InSb-, InAs-, and GaAs-(001) surfaces as determined by surface x-ray diffraction using direct methods. Contrary to common belief, group III dimers are not prominent on the surface, instead subsurface dimerization of group m atoms ...... takes place in the second bilayer, accompanied by a major rearrangement of the surface atoms above the dimers to form linear arrays. By varying the occupancies of four surface sites the (001)-c(8 X 2) reconstructions of III-V semiconductors can be described in a unified model....

  16. Dimeric Surfactants: Promising Ingredients of Cosmetics and Toiletries

    Directory of Open Access Journals (Sweden)

    Naveen Kumar


    Full Text Available Surfactants are an essential ingredient for cosmetic, toiletries and personal care products for enhancing their performance. Dimeric surfactants demonstrate superiority compared to conventional surfactants in all areas of application. Dimeric surfactants are extremely promising for utilization in various cosmetic formulations viz. shampoo, lotions, creams, conditioners etc. These surfactants possess extremely unique surface properties viz. lower surface tension, unique micellization, low critical micelle concentration (CMC and antimicrobial activity, higher solubilization etc. Dimerics enhance the performances of cosmetics in an extraordinary manner and provide eco-friendly preparations for human epidermis.

  17. Evidence of anti-parallel dimer formation of 4-cyano-4'-alkyl biphenyls in isotropic cyclohexane solution. (United States)

    Takabatake, Shunzo; Shikata, Toshiyuki


    The formation of anti-parallel dimers of two liquid crystal forming 4-cyano-4'-alkyl biphenyls (nCB, n = 5 (pentyl) and n = 8 (octyl)) was confirmed in an isotropic cyclohexane solution (nCB-cH). In addition to high frequency dielectric relaxation (DR) measurements up to 50 GHz, fluorescence emission (FE) experiments in the wavelength range from 280 to 500 nm were carried out to investigate the molecular dynamics of the nCB molecules. The DR spectra of solutions at intermediate to high concentrations were comprised of two dynamic modes. A fast mode with a relaxation time of ca. 90 ps was assigned to the free rotations of monomeric nCB molecules. The slow mode with a relaxation time of ca. 400 ps was attributed to the dissociation process of the anti-parallel dimers ((nCB)2). The Kirkwood factor (g(K)), a measure of the orientational correlation between the dipole moments of the cyano groups, was markedly less than unity for the slow mode, which demonstrated the formation of anti-parallel dimers, (nCB)2. The equilibrium constant for anti-parallel dimer formation in an isotropic solution, i.e., for the reaction, 2nCB ↔ (nCB)2, which was determined via the DR data increased with an increase in the concentration of nCB. Under extremely dilute conditions, a sharp fluorescence emission signal attributed to the nCB monomer was observed at 325 nm in FE spectrum measurements. However, at the moderate to high concentrations used in the DR measurements where the slow mode was clearly observed, a broad FE signal at 390 nm was observed, which was assigned to excimer emission (including emission from the excited ground state dimers). The relative intensity of the excimer emission to the monomer emission significantly increased with an increase in the concentration. Moreover, the equilibrium constant for the excimer formation reasonably agreed with that for the anti-parallel dimer formation evaluated by the DR data. Consequently, the results of the FE measurements evidently

  18. Five intermolecular vibrations of the CO2 dimer observed via infrared combination bands (United States)

    Norooz Oliaee, J.; Dehghany, M.; Rezaei, Mojtaba; McKellar, A. R. W.; Moazzen-Ahmadi, N.


    The weakly bound van der Waals dimer (CO2)2 has long been of considerable theoretical and experimental interest. Here, we study its low frequency intermolecular vibrations by means of combination bands in the region of the CO2 monomer ν3 fundamental (≈2350 cm-1), which are observed using a tunable infrared laser to probe a pulsed supersonic slit jet expansion. With the help of a recent high level ab initio calculation by Wang, Carrington, and Dawes, four intermolecular frequencies are assigned: the in-plane disrotatory bend (22.26 cm-1); the out-of-plane torsion (23.24 cm-1); twice the disrotatory bend (31.51 cm-1); and the in-plane conrotatory bend (92.25 cm-1). The disrotatory bend and torsion, separated by only 0.98 cm-1, are strongly mixed by Coriolis interactions. The disrotatory bend overtone is well behaved, but the conrotatory bend is highly perturbed and could not be well fitted. The latter perturbations could be due to tunneling effects, which have not previously been observed experimentally for CO2 dimer. A fifth combination band, located 1.3 cm-1 below the conrotatory bend, remains unassigned.

  19. Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. (United States)

    Tamulaitiene, Giedre; Jovaisaite, Virginija; Tamulaitis, Gintautas; Songailiene, Inga; Manakova, Elena; Zaremba, Mindaugas; Grazulis, Saulius; Xu, Shuang-Yong; Siksnys, Virginijus


    Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within or close to their DNA target sites, they form different oligomeric assemblies ranging from monomers, dimers, tetramers to higher order oligomers to generate a double strand break in DNA. Type IIP restriction endonuclease AgeI recognizes a palindromic sequence 5΄-A/CCGGT-3΄ and cuts it ('/' denotes the cleavage site) producing staggered DNA ends. Here, we present crystal structures of AgeI in apo and DNA-bound forms. The structure of AgeI is similar to the restriction enzymes that share in their target sites a conserved CCGG tetranucleotide and a cleavage pattern. Structure analysis and biochemical data indicate, that AgeI is a monomer in the apo-form both in the crystal and in solution, however, it binds and cleaves the palindromic target site as a dimer. DNA cleavage mechanism of AgeI is novel among Type IIP restriction endonucleases. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Water dimers in the atmosphere III: equilibrium constant from a flexible potential. (United States)

    Scribano, Yohann; Goldman, Nir; Saykally, R J; Leforestier, Claude


    We present new results for the water dimer equilibrium constant K(p)(T) in the range 190-390 K, using a flexible potential energy surface fitted to spectroscopical data. The increased numerical complexity due to explicit consideration of the monomer vibrations is handled via an adiabatic (6 + 6)d decoupling between intra- and intermolecular modes. The convergence of the canonical partition function of the dimer is ensured by computing all energy levels up to dissociation for total angular momentum values J = 0-5 and using an extrapolation scheme to higher values. The newly calculated values for K(p)(T) are in very good agreement with available experimental data at room temperature. At higher temperatures, an analysis of the convergence of the partition function reveals that quasi-bound states are likely to contribute to the equilibrium constant. Additional thermodynamical quantities (deltaG, deltaH, deltaS, and C(p)) have also been determined and fit to quadratic expressions a + bT + cT2.

  1. A Dimeric Bis(melamine)-Substituted Bispidine for Efficient Transmembrane H+/Cl-Cotransport. (United States)

    Shinde, Sopan Valiba; Talukdar, Pinaki


    A 3,7-diazabicyclo[3.3.1]nonane linking to two melamines is a unique transmembrane H + /Cl - carrier. In the solid state, the V-shaped compound forms a HCl-bound zig-zag network through cooperative protonation and hydrogen bond interactions. In the lipid membrane, the receptor forms a dimeric self-assembly involving multiple H + and Cl - leading to the efficient transport of the acid. The pH-dependent Cl - efflux observed for the compound was rationalized based on a gradual protonation model that confers an active transmembrane carrier at physiological pH. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Solvation of Mg in Helium-4: Are there Meta-stable Mg Dimers ?

    CERN Document Server

    Krotscheck, Eckhard


    Experiments on the formation of magnesium complexes in $^4$He nanodroplets were interpreted as the observation of the formation of weakly bound magnesium complexes. We present results for single Mg and Mg dimer solvation using the hypernetted chain / Euler-Lagrange method as well as path integral Monte Carlo simulations. We find that the phonon-mediated, indirect Mg-Mg interaction adds an oscillatory component to the direct Mg-Mg interaction. We undertake a step-by-step examination of the ingredients of the calculation of the phonon-induced interaction, comparing the results of semi-analytic HNC-EL calculations for bulk and single impurity results with experiments as well as Monte Carlo data. We do not find evidence for a sufficiently strong secondary minimum in the effective Mg-Mg interaction to support a metastable state.

  3. Using Protein Dimers to Maximize the Protein Hybridization Efficiency with Multisite DNA Origami Scaffolds.

    Directory of Open Access Journals (Sweden)

    Vikash Verma

    Full Text Available DNA origami provides a versatile platform for conducting 'architecture-function' analysis to determine how the nanoscale organization of multiple copies of a protein component within a multi-protein machine affects its overall function. Such analysis requires that the copy number of protein molecules bound to the origami scaffold exactly matches the desired number, and that it is uniform over an entire scaffold population. This requirement is challenging to satisfy for origami scaffolds with many protein hybridization sites, because it requires the successful completion of multiple, independent hybridization reactions. Here, we show that a cleavable dimerization domain on the hybridizing protein can be used to multiplex hybridization reactions on an origami scaffold. This strategy yields nearly 100% hybridization efficiency on a 6-site scaffold even when using low protein concentration and short incubation time. It can also be developed further to enable reliable patterning of a large number of molecules on DNA origami for architecture-function analysis.

  4. Competing Deactivation Channels for Excited π-Stacked Cytosines

    Directory of Open Access Journals (Sweden)

    Shuai Yuan


    Full Text Available The deactivation of π-stacked cytosine molecules following excitation by ultrashort laser pulses was studied using semiclassical dynamics simulations. Another deactivation channel was found to compete with a previously reported path that led to dimerization. For both pathways, the initial excited state was found to form a charge-separated neutral exciton state, which forms an excimer state by charge transfer. When the interbase distance becomes less than 3 Å, charge recombination occurs due to strong intermolecular interaction, ultimately leading to an avoided crossing. Results indicate that the C2–N1–C6–C5 and C2′–N1′–C6′–C5′ dihedral angles play a significant role in the vibronic coupling between the highest occupied molecular orbital (HOMO and the lowest unoccupied molecular orbital (LUMO. Vibrational energy distribution determines the fate of the excimer at the avoided crossing. Higher-amplitude vibration of C5 or C6 atoms leads to a nonadiabatic transition to the electronic ground state (a photophysical pathway; otherwise, a chemical reaction leading to the formation of cyclobutane type dimer occurs as found in earlier studies. The S1 and S0 potential energy surfaces calculated at TD-DFT level and the simulated trajectories were found to be consistent with CASPT2 results.

  5. Imaging the state-specific vibrational predissociation of the C2H2-NH3 hydrogen-bonded dimer. (United States)

    Parr, Jessica A; Li, Guosheng; Fedorov, Igor; McCaffery, Anthony J; Reisler, Hanna


    The state-to-state vibrational predissociation (VP) dynamics of the hydrogen-bonded ammonia-acetylene dimer were studied following excitation in the asymmetric CH stretch. Velocity map imaging (VMI) and resonance-enhanced multiphoton ionization (REMPI) were used to determine pair-correlated product energy distributions. Following vibrational excitation of the asymmetric CH stretch fundamental, ammonia fragments were detected by 2 + 1 REMPI via the B1E'' acetylene co-fragment. The latter is always generated with one or two quanta of bending excitation. All the distributions could be fit well when using a dimer dissociation energy of D0 = 900 +/- 10 cm(-1). Only channels with maximum translational energy acetylene co-fragment pair-correlated with specific rovibrational states of ammonia appear statistical as well. The vibrational-state distributions, however, show distinct state specificity among channels with low translational energy release. The predominant channel is NH3(1nu2) + C2H2(2nu4 or 1nu4 + 1nu5), where nu4 and nu5 are the trans- and cis-bend vibrations of acetylene, respectively. A second observed channel, with much lower population, is NH3(2nu2) + C2H2(1nu4). No products are generated in which the ammonia is in the vibrational ground state or the asymmetric bend (1nu4) state, nor is acetylene ever generated in the ground vibrational state or with CC stretch excitation. The angular momentum (AM) model of McCaffery and Marsh is used to estimate impact parameters in the internal collisions that give rise to the observed rotational distributions. These calculations show that dissociation takes place from bent geometries, which can also explain the propensity to excite fragment bending levels. The low recoil velocities associated with the observed channels facilitate energy exchange in the exit channel, which results in statistical-like fragment rotational distributions.

  6. Resonantly Trapped Bound State in the Continuum Laser

    CERN Document Server

    Lepetit, Thomas; Kodigala, Ashok; Bahari, Babak; Fainman, Yeshaiahu; Kanté, Boubacar


    Cavities play a fundamental role in wave phenomena from quantum mechanics to electromagnetism and dictate the spatiotemporal physics of lasers. In general, they are constructed by closing all "doors" through which waves can escape. We report, at room temperature, a bound state in the continuum laser that harnesses optical modes residing in the radiation continuum but nonetheless may possess arbitrarily high quality factors. These counterintuitive cavities are based on resonantly trapped symmetry-compatible modes that destructively interfere. Our experimental demonstration opens exciting avenues towards coherent sources with intriguing topological properties for optical trapping, biological imaging, and quantum communication.

  7. Nanomechanical properties of vimentin intermediate filament dimers

    Energy Technology Data Exchange (ETDEWEB)

    Qin Zhao; Buehler, Markus J [Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-235A and B, Cambridge, MA 02139 (United States); Kreplak, Laurent, E-mail: mbuehler@MIT.ED [Department of Physics and Atmospheric Science, Dalhousie University, Halifax, NS, B3H 3J5 (Canada)


    The cell's cytoskeleton, providing the cell with structure and shape, consists of a complex array of structural proteins, including microtubules, microfilaments and intermediate filaments. Intermediate filaments play a crucial role in mechanotransduction and in providing mechanical stability to cells, in particular under large deformation. By utilizing molecular simulation, here we report a nanomechanical analysis of vimentin intermediate filament dimers, the basic building blocks of intermediate filaments. We describe a detailed analysis of the mechanical properties and associated deformation mechanisms, and find that mechanical stretch induces a transition from alpha-helices to beta-sheets, a phenomenon known as alpha-beta transition. A comparison of the Young's modulus predicted from simulation with experimental measurements is provided, and good agreement is found. We present an analysis of structural changes during deformation, domain unfolding patterns, rate dependence of the rupture force and associated changes in the energy landscape, and conclude with a discussion of potential implications for mechanobiology and the development of de novo protein materials.

  8. Tuneable, non-degenerated, nonlinear, parametrically-excited amplifier (United States)

    Dolev, Amit; Bucher, Izhak


    The proposed parametric amplifier scheme can be tuned to amplify a wide range of input frequencies by altering the parametric excitation with no need to physically modify the oscillator. Parametric amplifiers had been studied extensively, although most of the work focused on amplifiers that are parametrically excited at a frequency twice the amplifier's natural frequency. These amplifiers are confined to amplifying predetermined frequencies. The proposed parametric amplifier's bandwidth is indeed tuneable to nearly any input frequency, not bound to be an integer multiple of a natural frequency. In order to tune the stiffness and induce a variable frequency parametric excitation, a digitally controlled electromechanical element must be incorporated in the realization. We introduce a novel parametric amplifier with nonlinearity, Duffing type hardening, that bounds the otherwise unlimited amplitude. Moreover, we present a multi degree of freedom system in which a utilization of the proposed method enables the projection of low frequency vector forces on any eigenvector and corresponding natural frequency of the system, and thus to transform external excitations to a frequency band where signal levels are considerably higher. Using the method of multiple scales, analytical expressions for the responses have been retrieved and verified numerically. Parametric studies of the amplifiers' gain, sensitivities and spatial projection of the excitation on the system eigenvectors were carried out analytically. The results demonstrate the advantage of the proposed approach over existing schemes. Practical applications envisaged for the proposed method will be outlined.

  9. UV-light exposure of insulin: pharmaceutical implications upon covalent insulin dityrosine dimerization and disulphide bond photolysis.

    Directory of Open Access Journals (Sweden)

    Manuel Correia

    Full Text Available In this work we report the effects of continuous UV-light (276 nm, ~2.20 W.m(-2 excitation of human insulin on its absorption and fluorescence properties, structure and functionality. Continuous UV-excitation of the peptide hormone in solution leads to the progressive formation of tyrosine photo-product dityrosine, formed upon tyrosine radical cross-linkage. Absorbance, fluorescence emission and excitation data confirm dityrosine formation, leading to covalent insulin dimerization. Furthermore, UV-excitation of insulin induces disulphide bridge breakage. Near- and far-UV-CD spectroscopy shows that UV-excitation of insulin induces secondary and tertiary structure losses. In native insulin, the A and B chains are held together by two disulphide bridges. Disruption of either of these bonds is likely to affect insulin's structure. The UV-light induced structural changes impair its antibody binding capability and in vitro hormonal function. After 1.5 and 3.5 h of 276 nm excitation there is a 33.7% and 62.1% decrease in concentration of insulin recognized by guinea pig anti-insulin antibodies, respectively. Glucose uptake by human skeletal muscle cells decreases 61.7% when the cells are incubated with pre UV-illuminated insulin during 1.5 h. The observations presented in this work highlight the importance of protecting insulin and other drugs from UV-light exposure, which is of outmost relevance to the pharmaceutical industry. Several drug formulations containing insulin in hexameric, dimeric and monomeric forms can be exposed to natural and artificial UV-light during their production, packaging, storage or administration phases. We can estimate that direct long-term exposure of insulin to sunlight and common light sources for indoors lighting and UV-sterilization in industries can be sufficient to induce irreversible changes to human insulin structure. Routine fluorescence and absorption measurements in laboratory experiments may also induce changes

  10. Very narrow excited Ωc baryons (United States)

    Karliner, Marek; Rosner, Jonathan L.


    Recently, LHCb reported the discovery of five extremely narrow excited Ωc baryons decaying into Ξc+K-. We interpret these baryons as bound states of a c quark and a P -wave s s diquark. For such a system, there are exactly five possible combinations of spin and orbital angular momentum. The narrowness of the states could be a signal that it is hard to pull apart the two s quarks in a diquark. We predict two of spin 1 /2 , two of spin 3 /2 , and one of spin 5 /2 , all with negative parity. Of the five states, two can decay in S -wave, and three can decay in D -wave. Some of the D -wave states might be narrower than the S -wave states. We discuss the relations among the five masses expected in the quark model and the likely spin assignments, and we compare them with the data. A similar pattern is expected for negative-parity excited Ωb states. An alternative interpretation is noted in which the heaviest two states are 2 S excitations with JP=1 /2+ and 3 /2+, while the lightest three are those with JP=3 /2- , 3 /2- , 5 /2- , expected to decay via D -waves. In this case, we expect JP=1 /2- Ωc states around 2904 and 2978 MeV.

  11. Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains: Implications for Actin Filament Nucleation

    Energy Technology Data Exchange (ETDEWEB)

    Rebowski, Grzegorz; Namgoong, Suk; Boczkowska, Malgorzata; Leavis, Paul C.; Navaza, Jorge; Dominguez, Roberto (IBS); (BBRI); (UPENN-MED)


    Actin filament nucleators initiate polymerization in cells in a regulated manner. A common architecture among these molecules consists of tandem WASP homology 2 domains (W domains) that recruit three to four actin subunits to form a polymerization nucleus. We describe a low-resolution crystal structure of an actin dimer assembled by tandem W domains, where the first W domain is cross-linked to Cys374 of the actin subunit bound to it, whereas the last W domain is followed by the C-terminal pointed end-capping helix of thymosin {beta}4. While the arrangement of actin subunits in the dimer resembles that of a long-pitch helix of the actin filament, important differences are observed. These differences result from steric hindrance of the W domain with intersubunit contacts in the actin filament. We also determined the structure of the first W domain of Vibrio parahaemolyticus VopL cross-linked to actin Cys374 and show it to be nearly identical with non-cross-linked W-Actin structures. This result validates the use of cross-linking as a tool for the study of actin nucleation complexes, whose natural tendency to polymerize interferes with most structural methods. Combined with a biochemical analysis of nucleation, the structures may explain why nucleators based on tandem W domains with short inter-W linkers have relatively weak activity, cannot stay bound to filaments after nucleation, and are unlikely to influence filament elongation. The findings may also explain why nucleation-promoting factors of the Arp2/3 complex, which are related to tandem-W-domain nucleators, are ejected from branch junctions after nucleation. We finally show that the simple addition of the C-terminal pointed end-capping helix of thymosin {beta}4 to tandem W domains can change their activity from actin filament nucleation to monomer sequestration.

  12. Lower bounds in differential privacy


    De, Anindya


    This is a paper about private data analysis, in which a trusted curator holding a confidential database responds to real vector-valued queries. A common approach to ensuring privacy for the database elements is to add appropriately generated random noise to the answers, releasing only these {\\em noisy} responses. In this paper, we investigate various lower bounds on the noise required to maintain different kind of privacy guarantees.

  13. Geometry of Homogeneous Bounded Domains

    CERN Document Server

    Vesentini, E


    This title includes: S.G. Gindikin, I.I. Pjateckii-Sapiro, E.B. Vinberg: Homogeneous Kahler manifolds; S.G. Greenfield: Extendibility properties of real submanifolds of Cn; W. Kaup: Holomorphische Abbildungen in Hyperbolische Raume; A. Koranyi: Holomorphic and harmonic functions on bounded symmetric domains; J.L. Koszul: Formes harmoniques vectorielles sur les espaces localement symetriques; S. Murakami: Plongements holomorphes de domaines symetriques; and E.M. Stein: The analogues of Fatous' theorem and estimates for maximal functions.

  14. Wronskian method for bound states

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, Francisco M, E-mail: [INIFTA (UNLP, CONICET), Division Quimica Teorica, Boulevard 113 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)


    We propose a simple and straightforward method based on Wronskians for the calculation of bound-state energies and wavefunctions of one-dimensional quantum-mechanical problems. We explicitly discuss the asymptotic behaviour of the wavefunction and show that the allowed energies make the divergent part vanish. As illustrative examples we consider an exactly solvable model, the Gaussian potential well, and a two-well potential proposed earlier for the interpretation of the infrared spectrum of ammonia.

  15. Crystal electric field and dimer splitting in Cs{sub 3}Er{sub 2}X{sub 9} (X=Cl, Br)

    Energy Technology Data Exchange (ETDEWEB)

    Allenspach, P.; Furrer, A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Guedel, H.U.; Furer, N. [Bern Univ. (Switzerland); Buettner, H. [Institut Max von Laue - Paul Langevin, 75 - Paris (France)


    Inelastic neutron scattering technique was used to measure the crystal electric field (CEF) splitting of Cs{sub 3}Er{sub 2}Cl{sub 9}. Besides a low lying magnetic excitation at around 2 meV all the other transitions are in agreement with CEF transitions found in optical measurements. Similar additional low-lying magnetic transitions were found in Cs{sub 3}Er{sub 2}Br{sub 9}. While excitations of the rare-earth dimers most likely play a role, the size of the splitting and its absence in optical spectra still remain a mystery. (author) 2 figs., 5 refs.

  16. Cyclotron transitions of bound ions (United States)

    Bezchastnov, Victor G.; Pavlov, George G.


    A charged particle in a magnetic field possesses discrete energy levels associated with particle rotation around the field lines. The radiative transitions between these levels are the well-known cyclotron transitions. We show that a bound complex of particles with a nonzero net charge displays analogous transitions between the states of confined motion of the entire complex in the field. The latter bound-ion cyclotron transitions are affected by a coupling between the collective and internal motions of the complex and, as a result, differ from the transitions of a "reference" bare ion with the same mass and charge. We analyze the cyclotron transitions for complex ions by including the coupling within a rigorous quantum approach. Particular attention is paid to comparison of the transition energies and oscillator strengths to those of the bare ion. Selection rules based on integrals of collective motion are derived for the bound-ion cyclotron transitions analytically, and the perturbation and coupled-channel approaches are developed to study the transitions quantitatively. Representative examples are considered and discussed for positive and negative atomic and cluster ions.

  17. Antiplasmodial dimeric chalcone derivatives from the roots of Uvaria siamensis. (United States)

    Salae, Abdul-Wahab; Chairerk, Orapan; Sukkoet, Piyanut; Chairat, Therdsak; Prawat, Uma; Tuntiwachwuttikul, Pittaya; Chalermglin, Piya; Ruchirawat, Somsak


    Four dimeric chalcone derivatives, 8″,9″-dihydrowelwitschin H, uvarins A-C, a naphthalene derivative, 2-hydroxy-3-methoxy-6-(4'- hydroxyphenyl)naphthalene, and the known dimeric chalcones, dependensin and welwitschin E, flavonoids, a cyclohexane oxide derivative, an aromatic aldehyde were isolated from the roots of Uvaria siamensis (Annonaceae). The structures of the compounds were elucidated by spectroscopic analysis, as well as by comparison with literature data. The isolated compounds with a sufficient amount for biological assays were evaluated for their antimalarial, antimycobacterial, and cytotoxic activities. The dimeric chalcones 8″,9″-dihydrowelwitschin H, uvarins B and C, dependensin and welwitschin E showed strong antiplasmodial activity with IC50 values of 3.10, 3.02, 3.09, 4.21 and 3.99 μg/mL, respectively. A possible biosynthesis pathway of the dimeric chalcones is discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Predicting thymine dimerization yields from molecular dynamics simulations. (United States)

    Law, Yu Kay; Azadi, Javad; Crespo-Hernández, Carlos E; Olmon, Eric; Kohler, Bern


    It was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)(18) are fully formed in dimers in DNA. Conformations obtained from simulations of thymidylyl-(3'-5')-thymidine in various cosolvents were classified as dimerizable or nondimerizable depending on the distance between the C5-C6 double bonds of the adjacent thymine bases and the torsion angle between them. The quantum yield of cyclobutane pyrimidine dimer formation was calculated as the number of dimerizable conformations divided by the total number of conformations. The experimental quantum yields measured in the different solvents were satisfactorily reproduced using physically reasonable values for the two parameters. The mean dimerizable structure computed by averaging all of the dimerizable cis-syn conformations is structurally similar to the actual cis-syn dimer. Compared to the canonical B-form TT step, the most important structural property of a dimerizable conformation is its reduced helical twist angle of 22 degrees.

  19. Relativistic effects in the study of weakly bound F and Be nuclei

    Indian Academy of Sciences (India)



    Jan 3, 2018 ... Abstract. Relativistic effects are employed to describe the weakly bound nuclei of 17F and 11Be. In order to calculate the energy levels of the ground state and the excited states of these nuclei, we solved the Dirac equation with pseudospin symmetry in the shell model by using the basic concept of ...

  20. Relativistic effects in the study of weakly bound 17 F and 11 Be nuclei

    Indian Academy of Sciences (India)

    Relativistic effects are employed to describe the weakly bound nuclei of 17 F and 11 B e . In order to calculate the energy levels of the ground state and the excited states of these nuclei, we solved the Dirac equation with pseudospin symmetry in the shell model by using the basic concept of supersymmetric shape ...

  1. The effect of impurity on transition frequency of bound polaron in ...

    Indian Academy of Sciences (India)

    and the excitation energy as functions of the Coulomb-bound potential, the electron– phonon coupling strength, the transverse effective confinement length and the ellipsoid aspect ratio. 2. Theory model. As shown in figure 1, the electron under consideration is moving in a polar crystal QR with three-dimensional anisotropic ...

  2. Stability of bound species during alkene reactions on solid acids (United States)

    Sarazen, Michele L.; Iglesia, Enrique


    This study reports the thermodynamics of bound species derived from ethene, propene, n-butene, and isobutene on solid acids with diverse strength and confining voids. Density functional theory (DFT) and kinetic data indicate that covalently bound alkoxides form C-C bonds in the kinetically relevant step for dimerization turnovers on protons within TON (0.57 nm) and MOR (0.67 nm) zeolitic channels and on stronger acids HPW (polyoxometalate clusters on silica). Turnover rates for mixed alkenes give relative alkoxide stabilities; the respective adsorption constants are obtained from in situ infrared spectra. Tertiary alkoxides (from isobutene) within larger voids (MOR, HPW) are more stable than less substituted isomers but are destabilized within smaller concave environments (TON) because framework distortions are required to avoid steric repulsion. Adsorption constants are similar on MOR and HPW for each alkoxide, indicating that binding is insensitive to acid strength for covalently bound species. DFT-derived formation free energies for alkoxides with different framework attachments and backbone length/structure agree with measurements when dispersion forces, which mediate stabilization by confinement in host-guest systems, are considered. Theory reveals previously unrecognized framework distortions that balance the C-O bond lengths required for covalency with host-guest distances that maximize van der Waals contacts. These distortions, reported here as changes in O-atom locations and dihedral angles, become stronger for larger, more substituted alkoxides. The thermodynamic properties reported here for alkoxides and acid hosts differing in size and conjugate-anion stability are benchmarked against DFT-derived free energies; their details are essential to design host-guest pairs that direct alkoxide species toward specific products.

  3. Frenkel and Charge-Transfer Excitations in Donor-acceptor Complexes from Many-Body Green's Functions Theory. (United States)

    Baumeier, Björn; Andrienko, Denis; Rohlfing, Michael


    Excited states of donor-acceptor dimers are studied using many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation. For a series of prototypical small-molecule based pairs, this method predicts energies of local Frenkel and intermolecular charge-transfer excitations with the accuracy of tens of meV. Application to larger systems is possible and allowed us to analyze energy levels and binding energies of excitons in representative dimers of dicyanovinyl-substituted quarterthiophene and fullerene, a donor-acceptor pair used in state of the art organic solar cells. In these dimers, the transition from Frenkel to charge transfer excitons is endothermic and the binding energy of charge transfer excitons is still of the order of 1.5-2 eV. Hence, even such an accurate dimer-based description does not yield internal energetics favorable for the generation of free charges either by thermal energy or an external electric field. These results confirm that, for qualitative predictions of solar cell functionality, accounting for the explicit molecular environment is as important as the accurate knowledge of internal dimer energies.

  4. Exotic nuclear excitations

    CERN Document Server

    Pancholi, S C


    By providing the reader with a foundational background in high spin nuclear structure physics and exploring exciting current discoveries in the field, this book presents new phenomena in a clear and compelling way. The quest for achieving the highest spin states has resulted in some remarkable successes which this monograph will address in comprehensive detail. The text covers an array of pertinent subject matter, including the rotational alignment and bandcrossings, magnetic rotation, triaxial strong deformation and wobbling motion and chirality in nuclei. Dr. Pancholi offers his readers a clearly-written and up-to-date treatment of the topics covered. The prerequisites for a proper appreciation are courses in nuclear physics and nuclear models and measurement techniques of observables like gamma-ray energies, intensities, multi-fold coincidences, angular correlations or distributions, linear polarization, internal conversion coefficients, short lifetime (pico-second range) of excited states etc. and instrum...

  5. Coexistence of Scattering Enhancement and Suppression by Plasmonic Cavity Modes in Loaded Dimer Gap-Antennas

    CERN Document Server

    Zhang, Qiang; Li, Meili; Han, Dezhuan; Gao, Lei


    Plasmonic nanoantenna is of promising applications in optical sensing, single-molecular detection, and enhancement of optical nonlinear effect, surface optical spectroscopy, photochemistry, photoemission, photovoltaics, etc. Here we show that in a carefully-designed dimer gap-antenna made by two metallic nanorods, the longitudinal plasmon antenna mode (AM) of bonding dipoles can compete with the transverse plasmonic cavity modes (CMs), yielding dramatically enhanced or suppressed scattering efficiency, depending on the CMs symmetry characteristics (e.g., the radial order n and the azimuthal quantum number m ). More specifically, it is demonstrated that an appropriately loaded gap layer enables substantial excitation of toroidal moment and its strong interaction with the AM dipole moment, resulting in Fano- or electromagnetically induced transparency (EIT)-like profile in the scattering spectrum. However, for CMs with nonzero azimuthal number, the spectrum features a cumulative signature of the respective AM a...

  6. Excitable scale free networks (United States)

    Copelli, M.; Campos, P. R. A.


    When a simple excitable system is continuously stimulated by a Poissonian external source, the response function (mean activity versus stimulus rate) generally shows a linear saturating shape. This is experimentally verified in some classes of sensory neurons, which accordingly present a small dynamic range (defined as the interval of stimulus intensity which can be appropriately coded by the mean activity of the excitable element), usually about one or two decades only. The brain, on the other hand, can handle a significantly broader range of stimulus intensity, and a collective phenomenon involving the interaction among excitable neurons has been suggested to account for the enhancement of the dynamic range. Since the role of the pattern of such interactions is still unclear, here we investigate the performance of a scale-free (SF) network topology in this dynamic range problem. Specifically, we study the transfer function of disordered SF networks of excitable Greenberg-Hastings cellular automata. We observe that the dynamic range is maximum when the coupling among the elements is critical, corroborating a general reasoning recently proposed. Although the maximum dynamic range yielded by general SF networks is slightly worse than that of random networks, for special SF networks which lack loops the enhancement of the dynamic range can be dramatic, reaching nearly five decades. In order to understand the role of loops on the transfer function we propose a simple model in which the density of loops in the network can be gradually increased, and show that this is accompanied by a gradual decrease of dynamic range.

  7. Dimer representations of the Temperley–Lieb algebra

    Energy Technology Data Exchange (ETDEWEB)

    Morin-Duchesne, Alexi, E-mail: [Institut de Recherche en Mathématique et Physique, Université Catholique de Louvain, Louvain-la-Neuve, B-1348 (Belgium); Rasmussen, Jørgen, E-mail: [School of Mathematics and Physics, University of Queensland St Lucia, Brisbane, Queensland 4072 (Australia); Ruelle, Philippe, E-mail: [Institut de Recherche en Mathématique et Physique, Université Catholique de Louvain, Louvain-la-Neuve, B-1348 (Belgium)


    A new spin-chain representation of the Temperley–Lieb algebra TL{sub n}(β=0) is introduced and related to the dimer model. Unlike the usual XXZ spin-chain representations of dimension 2{sup n}, this dimer representation is of dimension 2{sup n−1}. A detailed analysis of its structure is presented and found to yield indecomposable zigzag modules.

  8. Dimeric analogs of immunosuppressive decapeptide fragment of ubiquitin. (United States)

    Kluczyk, Alicja; Cydzik, Marzena; Biernat, Monika; Bąchor, Remigiusz; Pasikowski, Paweł; Stefanowicz, Piotr; Artym, Jolanta; Zimecki, Michał; Szewczuk, Zbigniew


    Our previous studies revealed that ubiquitin and its decapeptide fragment with the LEDGRTLSDY sequence, located on the exposed molecule loop, strongly suppressed the immune response. This suggested that the loop may serve as a functional epitope of ubiquitin molecule and that a possible mechanism of biological action of the synthesized peptides is associated with interfering in interactions of ubiquitin with other molecules. Ubiquitin is known to exist in oligomeric forms, which can interact with various oligomeric receptors. We designed and synthesized new dimeric analogs of the ubiquitin fragment, to probe whether dimeric peptides may have higher affinity towards the ubiquitin receptors responsible for immunosuppression, which are believed to form oligomeric structures. Three dimerization strategies, N-terminus to N-terminus, C-terminus to C-terminus, and N-terminus to C-terminus (head-to-tail) via PEG derivatives were used to synthesize the dimeric peptides on solid support. In the course of our research, we developed a new and straightforward procedure of dimerization where α-amino groups of the C-terminal lysine residues of two peptide fragments were linked by PEG spacer directly on solid support. The effect of dimeric analogs on the immunological response was tested in the AFC in vitro experiment. The immunological tests showed that the head-to-tail dimerization caused a more profound increase in the biological activity than other tested dimerization methods. Our results suggest that such orientation of peptide components may correspond to orientation of the hypothetic ubiquitin receptors responsible for the immunomodulatory activity. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.

  9. Dimers on Surface Graphs and Spin Structures. I

    DEFF Research Database (Denmark)

    Cimasoni, David; Reshetikhin, Nicolai


    Partition functions for dimers on closed oriented surfaces are known to be alternating sums of Pfaffians of Kasteleyn matrices. In this paper, we obtain the formula for the coefficients in terms of discrete spin structures.......Partition functions for dimers on closed oriented surfaces are known to be alternating sums of Pfaffians of Kasteleyn matrices. In this paper, we obtain the formula for the coefficients in terms of discrete spin structures....

  10. The influence of strain on the diffusion of Si dimers on Si(001)

    NARCIS (Netherlands)

    Zoethout, E.; Zoethout, E.; Gurlu, O.; Gürlü, O.; Zandvliet, Henricus J.W.; Poelsema, Bene


    The influence of lattice mismatch-induced tensile strain on the diffusion of Si dimers on Si(001) has been studied. The rate of surface diffusion of a Si dimer along the substrate dimer rows is relatively insensitive to tensile strain, whereas the rate of diffusion for a Si dimer across the

  11. Tubulin dimers oligomerize before their incorporation into microtubules.

    Directory of Open Access Journals (Sweden)

    Julien Mozziconacci

    Full Text Available In the presence of GTP, purified dimers of alpha- and beta-tubulin will interact longitudinally and laterally to self-assemble into microtubules (MTs. This property provides a powerful in vitro experimental system to describe MT dynamic behavior at the micrometer scale and to study effects and functioning of a large variety of microtubule associated proteins (MAPs. Despite the plethora of such data produced, the molecular mechanisms of MT assembly remain disputed. Electron microscopy (EM studies suggested that tubulin dimers interact longitudinally to form short oligomers which form a tube by lateral interaction and which contribute to MT elongation. This idea is however challenged: Based on estimated association constants it was proposed that single dimers represent the major fraction of free tubulin. This view was recently supported by measurements suggesting that MTs elongate by addition of single tubulin dimers. To solve this discrepancy, we performed a direct measurement of the longitudinal interaction energy for tubulin dimers. We quantified the size distribution of tubulin oligomers using EM and fluorescence correlation spectroscopy (FCS. From the distribution we derived the longitudinal interaction energy in the presence of GDP and the non-hydrolysable GTP analog GMPCPP. Our data suggest that MT elongation and nucleation involves interactions of short tubulin oligomers rather than dimers. Our approach provides a solid experimental framework to better understand the role of MAPs in MT nucleation and growth.

  12. Ring opening of a resin-bound chiral aziridine with phenol nucleophiles

    DEFF Research Database (Denmark)

    Ottesen, Lars Korsgaard; Jaroszewski, Jerzy W; Franzyk, Henrik


    An efficient and versatile solid-phase route for the preparation of aryl-alkyl ethers is described. Regioselective ring opening of a resin-bound chiral aziridine with phenolic nucleophiles constitutes the key feature of the present protocol that allows incorporation of fluorescent moieties...... and subsequent on-resin protecting group interconversion. Initial experiments demonstrated that a competing oligomerization may occur by concomitant attacks of transient nosylamide anions on neighboring aziridines, resulting in formation of dimeric and trimeric byproduct. Expectedly, the significance...... of this alternative reaction pathway was strongly dependent on resin loading, and a low loading (protected coumaryl amino acid building blocks, which were...

  13. Participation of the extracellular domain in (pro)renin receptor dimerization

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki-Nakagawa, Chiharu [The United Graduate School of Agricultural Sciences, Gifu University, Gifu (Japan); Nishimura, Misa; Tsukamoto, Tomoko; Aoyama, Sho [Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu (Japan); Ebihara, Akio; Suzuki, Fumiaki [The United Graduate School of Agricultural Sciences, Gifu University, Gifu (Japan); Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu (Japan); Nakagawa, Tsutomu, E-mail: [The United Graduate School of Agricultural Sciences, Gifu University, Gifu (Japan); Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu (Japan)


    Highlights: • The (pro)renin receptor [(P)RR] is a regulator of the renin–angiotensin system. • The region responsible for (P)RR dimerization was investigated. • (P)RR extracellular domain constructs were retained intracellularly. • The extracellular domain of (P)RR is responsible for its dimerization. • Novel insight into the regulatory mechanism of soluble (P)RR secretion is provided. - Abstract: The (pro)renin receptor [(P)RR] induces the catalytic activation of prorenin, as well as the activation of the mitogen-activated protein kinase (MAPK) signaling pathway; as such, it plays an important regulatory role in the renin–angiotensin system. (P)RR is known to form a homodimer, but the region participating in its dimerization is unknown. Using glutathione S-transferase (GST) as a carrier protein and a GST pull-down assay, we investigated the interaction of several (P)RR constructs with full-length (FL) (P)RR in mammalian cells. GST fusion proteins with FL (P)RR (GST-FL), the C-terminal M8-9 fragment (GST-M8-9), the extracellular domain (ECD) of (P)RR (GST-ECD), and the (P)RR ECD with a deletion of 32 amino acids encoded by exon 4 (GST-ECDd4) were retained intracellularly, whereas GST alone was efficiently secreted into the culture medium when transiently expressed in COS-7 cells. Immunofluorescence microscopy showed prominent localization of GST-ECD to the endoplasmic reticulum. The GST pull-down analysis revealed that GST-FL, GST-ECD, and GST-ECDd4 bound FLAG-tagged FL (P)RR, whereas GST-M8-9 showed little or no binding when transiently co-expressed in HEK293T cells. Furthermore, pull-down analysis using His-tag affinity resin showed co-precipitation of soluble (P)RR with FL (P)RR from a stable CHO cell line expressing FL h(P)RR with a C-terminal decahistidine tag. These results indicate that the (P)RR ECD participates in dimerization.

  14. Assessment of quantum chemical methods and basis sets for excitation energy transfer

    Energy Technology Data Exchange (ETDEWEB)

    Fink, Reinhold F. [Institute of Physical Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg (Germany); Pfister, Johannes; Zhao Hongmei [Institute of Organic Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg (Germany); Engels, Bernd [Institute of Organic Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg (Germany)], E-mail:


    The validity of several standard quantum chemical approaches and other models for the prediction of exciton energy transfer is investigated using the HOMO-LUMO excited states of benzene dimer as an example. The configuration interaction singles (CIS), time-dependent Hartree-Fock (TD-HF), time dependent density functional theroy (TD-DFT), and complete-active-space self-consistent-field (CASSCF) methods are applied with a supermolecule approach and compared to the previously established monomer transition density method and the ideal dipole approximation. Strong and physically incorrect admixture of charge-transfer states makes TD-DFT inappropriate for investigations of potential energy surfaces in such dimer systems. CIS, TD-HF and CASSCF perform qualitatively correct. TD-HF seems to be a particularly appropriate method due to its general applicability and overall good performance for the excited state and for transition properties. Double-zeta basis sets with polarisation functions are found to be sufficient to predict transfer rates of dipole allowed excitations. Efficient excitation energy transfer is predicted between degenerate excited states while avoided curve crossings of nearly spaced {pi}-aggregates are identified as a possible trapping mechanism.

  15. Rovibrational Quantum Dynamics of the Methane-Water Dimer (United States)

    Sarka, János; Császár, Attila; Mátyus, Edit


    The challenging quantum dynamical description of the CH_4.H_2O complex has been solved variationally to provide theoretical explanation and assignment to the high-resolution spectroscopic measurements of the methane-water dimer carried out some twenty years ago. The computational results are in excellent agreement with the reported experimental transitions and the experimentally observed reversed rovibrational sequences, i.e., formally negative rotational excitation energies, are also obtained in the computations. In order to better understand the origin of these peculiar features in the energy-level spectrum, we studied all four possible combinations of the light and heavy isotopologues of methane and water and analyzed their rovibrational states using two limiting model systems: the rigidly rotating (RR) molecule and the coupled rotor (CR) system corresponding to the coupling of the two rotating monomers. All rovibrational quantum dynamical computations^{a,c} were carried out with rigid monomers and J = 0,1,2 total angular momentum quantum numbers using the fourth-age quantum chemical code GENIUSH and two different methane-water potential energy surfaces (PES). The numerical and formal analysis of the wave functions give insight into a fascinating complex world worth for further theoretical and experimental inquiries. J. Sarka, A. G. Császár, S. C. Althorpe, D. J. Wales and E. Mátyus, Phys. Chem. Chem. Phys. 18, 22816 (2016). L. Dore, R. C. Cohen, C. A. Schmuttenmaer, K. L. Busarow, M. J. Elrod, J. G. Loeser and R. J. Saykally, J. Chem. Phys. 100, 863 (1994). J. Sarka, A. G. Császár and E. Mátyus, Phys. Chem. Chem. Phys. accepted for publication (2017).} E. Mátyus, G. Czakó and A. G. Császár, J. Chem. Phys. 130, 134112 (2009). C. Fábri, E. Mátyus and A. G. Császár, J. Chem. Phys. 134, 074105 (2011). O. Akin-Ojo and K. Szalewicz, J. Chem. Phys. 123, 134311 (2005). C. Qu, R. Conte, P. L. Houston and J. M. Bowman, Phys. Chem. Chem. Phys. 17, 8172 (2015).

  16. Lower bounds for randomized Exclusive Write PRAMs

    Energy Technology Data Exchange (ETDEWEB)

    MacKenzie, P.D.


    In this paper we study the question: How useful is randomization in speeding up Exclusive Write PRAM computations? Our results give further evidence that randomization is of limited use in these types of computations. First we examine a compaction problem on both the CREW and EREW PRAM models, and we present randomized lower bounds which match the best deterministic lower bounds known. (For the CREW PRAM model, the lower bound is asymptotically optimal.) These are the first non-trivial randomized lower bounds known for the compaction problem on these models. We show that our lower bounds also apply to the problem of approximate compaction. Next we examine the problem of computing boolean functions on the CREW PRAM model, and we present a randomized lower bound, which improves on the previous best randomized lower bound for many boolean functions, including the OR function. (The previous lower bounds for these functions were asymptotically optimal, but we improve the constant multiplicative factor.) We also give an alternate proof for the randomized lower bound on PARITY, which was already optimal to within a constant additive factor. Lastly, we give a randomized lower bound for integer merging on an EREW PRAM which matches the best deterministic lower bound known. In all our proofs, we use the Random Adversary method, which has previously only been used for proving lower bounds on models with Concurrent Write capabilities. Thus this paper also serves to illustrate the power and generality of this method for proving parallel randomized lower bounds.

  17. Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles.

    Directory of Open Access Journals (Sweden)

    Benjamin A Hall

    Full Text Available Bacterial chemoreceptors provide an important model for understanding signalling processes. In the serine receptor Tsr from E. coli, a binding event in the periplasmic domain of the receptor dimer causes a shift in a single transmembrane helix of roughly 0.15 nm towards the cytoplasm. This small change is propagated through the ≈ 22 nm length of the receptor, causing downstream inhibition of the kinase CheA. This requires interactions within a trimer of receptor dimers. Additionally, the signal is amplified across a 53,000 nm(2 array of chemoreceptor proteins, including ≈ 5,200 receptor trimers-of-dimers, at the cell pole. Despite a wealth of experimental data on the system, including high resolution structures of individual domains and extensive mutagenesis data, it remains uncertain how information is communicated across the receptor from the binding event to the downstream effectors. We present a molecular model of the entire Tsr dimer, and examine its behaviour using coarse-grained molecular dynamics and elastic network modelling. We observe a large bending in dimer models between the linker domain HAMP and coiled-coil domains, which is supported by experimental data. Models of the trimer of dimers, built from the dimer models, are more constrained and likely represent the signalling state. Simulations of the models in a 70 nm diameter vesicle with a biologically realistic lipid mixture reveal specific lipid interactions and oligomerisation of the trimer of dimers. The results indicate a mechanism whereby small motions of a single helix can be amplified through HAMP domain packing, to initiate large changes in the whole receptor structure.

  18. Dimer-atom-atom recombination in the universal four-boson system


    Deltuva, A.


    The dimer-atom-atom recombination process in the system of four identical bosons with resonant interactions is studied. The description uses the exact Alt, Grassberger and Sandhas equations for the four-particle transition operators that are solved in the momentum-space framework. The dimer-dimer and atom-trimer channel contributions to the ultracold dimer-atom-atom recombination rate are calculated. The dimer-atom-atom recombination rate greatly exceeds the three-atom recombination rate.

  19. Polaronic exciton in self-organized assemblies of protonated meso-tetraphenylporphine dimers and water at room temperature (United States)

    Udal'tsov, Alexander V.


    Assemblies consisting of protonated meso-tetraphenylporphine (TPP) dimers and water have been investigated by UV-vis and infrared (IR) spectroscopy and by atomic force microscopy (AFM) in thin layers. Features of electronic absorption spectra of the assemblies are interpreted in terms of hole polaron combined with exciton theory using quantum well with parameters obtained from the dimer structure. It appears to be hole polaron moving defines kinetic energy of polaronic exciton confined in a quantum well when the electron absorbs photon. Hole polaron characteristics such as polaron self-energy, energy of Frank-Condon transitions, and radius of hole polaron moving through water are found to be 1.38 eV, 0.2445 eV, and 0.246 Å, respectively. A doublet at 1944, 1960 cm-1 (0.2412, 0.2432 eV) observed in IR spectra matches the energy of Frank-Condon transitions. Excitation energies estimated using molecular parameters for polaronic excitons in pure water and in the TPP dimers are found in a good agreement with the experimental data.

  20. Can $\\beta$-decay probe excited state halos?

    CERN Multimedia


    In the first experiment at the newly constructed ISOLDE Facility the first-forbidden $\\beta$-decay of $^{17}$Ne into the first excited state of $^{17}$F has been measured. It is a factor two faster than the corresponding mirror decay and thus gives one of the largest recorded asymmetries for $\\beta$-decays feeding bound final states. Shell-model calculations can only reproduce the asymmetry if the halo structure of the $^{17}$F state is taken into account.

  1. Para-quinodimethane-bridged perylene dimers and pericondensed quaterrylenes: The effect of the fusion mode on the ground states and physical properties

    KAUST Repository

    Das, Soumyajit


    Polycyclic hydrocarbon compounds with a singlet biradical ground state show unique physical properties and promising material applications; therefore, it is important to understand the fundamental structure/biradical character/physical properties relationships. In this study, para-quinodimethane (p-QDM)-bridged quinoidal perylene dimers 4 and 5 with different fusion modes and their corresponding aromatic counterparts, the pericondensed quaterrylenes 6 and 7, were synthesized. Their ground-state electronic structures and physical properties were studied by using various experiments assisted with DFT calculations. The proaromatic p-QDM-bridged perylene monoimide dimer 4 has a singlet biradical ground state with a small singlet/triplet energy gap (-2.97 kcalmol-1), whereas the antiaromatic s-indacene-bridged N-annulated perylene dimer 5 exists as a closed-shell quinoid with an obvious intramolecular charge-transfer character. Both of these dimers showed shorter singlet excited-state lifetimes, larger two-photon-absorption cross sections, and smaller energy gaps than the corresponding aromatic quaterrylene derivatives 6 and 7, respectively. Our studies revealed how the fusion mode and aromaticity affect the ground state and, consequently, the photophysical properties and electronic properties of a series of extended polycyclic hydrocarbon compounds. A matter of fusion mode! Fusion of a para-quinodimethane (p-QDM) subunit at the peri and β positions of perylene dimers leads to systems with different ground states, that is, open and closed shell (see picture). These systems showed large two-photon absorption cross sections and ultrafast excited-state dynamics relative to their corresponding pericondensed aromatic quaterrylene counterparts. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Towards Automatic Resource Bound Analysis for OCaml


    Hoffmann, Jan; Das, Ankush; Weng, Shu-Chun


    This article presents a resource analysis system for OCaml programs. This system automatically derives worst-case resource bounds for higher-order polymorphic programs with user-defined inductive types. The technique is parametric in the resource and can derive bounds for time, memory allocations and energy usage. The derived bounds are multivariate resource polynomials which are functions of different size parameters that depend on the standard OCaml types. Bound inference is fully automatic...

  3. Distance hijacking attacks on distance bounding protocols


    Cremers, Cas; Rasmussen, Kasper Bonne; Čapkun, Srdjan


    Distance bounding protocols are typically analyzed with respect to three types of attacks: Distance Fraud, Mafia Fraud, and Terrorist Fraud. We define and analyze a fourth main type of attack on distance bounding protocols, called Distance Hijacking. We show that many proposed distance bounding protocols are vulnerable to this type of attack, and we propose solutions to make these protocols resilient to Distance Hijacking. We further show that verifying distance bounding protocols using exist...

  4. Purity- and Gaussianity-bounded uncertainty relations (United States)

    Mandilara, A.; Karpov, E.; Cerf, N. J.


    Bounded uncertainty relations provide the minimum value of the uncertainty assuming some additional information on the state. We derive analytically an uncertainty relation bounded by a pair of constraints, those of purity and Gaussianity. In a limiting case this uncertainty relation reproduces the purity-bounded derived by Man’ko and Dodonov and the Gaussianity-bounded one (Mandilara and Cerf 2012 Phys. Rev. A 86 030102R).

  5. Detection of rhodopsin dimerization in situ by PIE-FCCS, a time-resolved fluorescence spectroscopy. (United States)

    Smith, Adam W


    Rhodopsin self-associates in the plasma membrane. At low concentrations, the interactions are consistent with a monomer-dimer equilibrium (Comar et al., J Am Chem Soc 136(23):8342-8349, 2014). At high concentrations in native tissue, higher-order clusters have been observed (Fotiadis et al., Nature 421:127-128, 2003). The physiological role of rhodopsin dimerization is still being investigated, but it is clear that a quantitative assessment is essential to determining the function of rhodopsin clusters in vision. To quantify rhodopsin interactions, I will outline the theory and methodology of a specialized time-resolved fluorescence spectroscopy for measuring membrane protein-protein interactions called pulsed-interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS). The strength of this technique is its ability to quantify rhodopsin interactions in situ (i.e., a live cell plasma membrane). There are two reasons for restricting the scope to live cell membranes. First, the compositional heterogeneity of the plasma membrane creates a complex milieu with thousands of lipid, protein, and carbohydrate species. This makes it difficult to infer quaternary interactions from detergent solubilized samples or construct a model phospholipid bilayer that recapitulates all of the interactions present in native membranes. Second, organizational structure and dynamics is a key feature of the plasma membrane, and fixation techniques like formaldehyde cross-linking and vitrification will modulate the interactions. PIE-FCCS is based on two-color fluorescence imaging with time-correlated single-photon counting (TCSPC) (Becker et al., Rev Sci Instrum 70:1835-1841, 1999). By time-tagging every detected photon, the data can be analyzed as a fluorescence intensity distribution, fluorescence lifetime histogram, or fluorescence (cross-)correlation spectra (FCS/FCCS) (Becker, Advanced time-correlated single-photon counting techniques, Springer, Berlin, 2005). These

  6. Near-threshold vibrational excitation of acetylene by positron impact (United States)

    de Oliveira, Eliane M.; Lima, Marco A. P.; Sanchez, Sergio D.'A.; Varella, Márcio T. Do N.


    We report vibrational excitation cross sections for C-C and C-H symmetric stretch modes of acetylene by positron impact. The contribution of these infrared inactive modes to the annihilation parameter is also addressed. The Feshbach projection operator approach was employed to vibrationally resolve e+-acetylene scattering phase shifts obtained with the Schwinger multichannel method. The present results point out a virtual state pole at the equilibrium geometry of acetylene that becomes a bound state as either bond is stretched, in qualitative agreement with previous calculations for small hydrocarbons. The vibrational couplings are stronger for the C-C mode, giving rise to a bound state pole within the Franck-Condon region of the vibrational ground state. These bound and virtual states give rise to sharp threshold structures (vibrational resonances) in both the vibrational excitation cross sections and the annihilation parameter (Zeff). We found fair agreement between the present calculations and previously reported e+-acetylene vibrational excitation cross sections.

  7. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    Massaro, D.


    This thesis studies the effect of individual bounded rationality on aggregate macroeconomic dynamics. Boundedly rational agents are specified as using simple heuristics in their decision making. An important aspect of the type of bounded rationality described in this thesis is that the population of

  8. Labeling schemes for bounded degree graphs

    DEFF Research Database (Denmark)

    Adjiashvili, David; Rotbart, Noy Galil


    graphs. Our results complement a similar bound recently obtained for bounded depth trees [Fraigniaud and Korman, SODA 2010], and may provide new insights for closing the long standing gap for adjacency in trees [Alstrup and Rauhe, FOCS 2002]. We also provide improved labeling schemes for bounded degree...

  9. Upper bound on quantum stabilizer codes (United States)

    Li, Zhuo; Xing, Li-Juan


    By studying sets of operators having constant weight, we present an analytical upper bound on the pure quantum stabilizer codes whose underlying quantum system can be of arbitrary dimension, which outperforms the well-known quantum Hamming bound, the optimal analytical upper bound so far for small code length.

  10. Photosensitized splitting of thymine dimer or oxetane unit by a covalently N-linked carbazole via electron transfer in different marcus regions. (United States)

    Wu, Qing-Qing; Song, Qin-Hua


    Although many similarities exist between the two classes of enzymes, cyclobutane photolyases and (6-4) photolyases have certain important differences. The most significant difference is in their repair quantum yields, cyclobutane photolyases with a uniformly high efficiency (0.7-0.98) and very low repair efficiency for (6-4) photolyases (0.05-0.1). To understand the significant difference, we prepared two classes of model compounds, covalently N-linked dimer- (1) or oxetane-carbazole (2) compounds with a dimethylene or trimethylene group as a linker. Under light irradiation, the dimer or oxetane unit of model compounds can be sensitized to split by the excited carbazole via an intramolecular electron transfer. The splitting reaction of dimer or oxetane unit in model compounds is strongly solvent dependent. In nonpolar solvents, such as cyclohexane or THF, no fluorescence quenching of the carbazole moiety of model compounds relative to a free carbazole, N-methylcarbazole, was observed and thus no splitting occurred. In polar solvents, two classes of model compounds reveal two reverse solvent effects on the splitting quantum yield. One is an inverse relation between the quantum yield and the polarity of the solvent for dimer-model systems, and another is a normal relation for oxetane-model systems. This phenomenon was also observed with another two classes of model compounds, covalently linked dimer- or oxetane-indole. Based on Marcus theory and thermodynamic data, it has been rationalized that the two reverse solvent effects derive from back electron transfer in the splitting process lying in the different Marcus regions. Back electron transfer lies in the Marcus inverted region for dimer-model systems and the normal region for oxetane-model systems. From repair solvent behavior of the two classes of model compounds, we gained some insights into the major difference in the repair efficiency for the two classes of photolyases.

  11. Efficient numerical technique for calculating the properties of interacting dimers in the Peierls-Hubbard model (United States)

    Sous, John; Chakraborty, Monodeep; Krems, Roman; Berciu, Mona


    We develop a method to compute the Green's function for two particles in an infinite chain and coupled to phonons by interactions that modulate their hopping as described by the Peierls/Su-Schrieffer-Heeger (SSH) model. The method is based on a variational approximation to the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy and is shown to agree with exact digaonalization calculations. We show that the properties of bipolarons arising in such models is qualitatively different from those of the well-studied Holstein bipolarons. In particular, we show that depending on the particle statistics, strongly bound bipolarons may or may not form. In the case of hard-core bosons, we demonstrate novel effects for dimers such as sharp transitions and self-trapping. In the case of soft-core particles/ spinfull fermions, we show that the mediated interactions lead to overscreeing of the bare Hubbard U repulsion resulting in the formation of strongly bound bipolarons. This work was supported by NSERC of Canada and the Stewart Blusson Quantum Matter Institute.

  12. Effects of crossed states on photoluminescence excitation spectroscopy of InAs quantum dots

    Directory of Open Access Journals (Sweden)

    Lin Chien-Hung


    Full Text Available Abstract In this report, the influence of the intrinsic transitions between bound-to-delocalized states (crossed states or quasicontinuous density of electron-hole states on photoluminescence excitation (PLE spectra of InAs quantum dots (QDs was investigated. The InAs QDs were different in size, shape, and number of bound states. Results from the PLE spectroscopy at low temperature and under a high magnetic field (up to 14 T were compared. Our findings show that the profile of the PLE resonances associated with the bound transitions disintegrated and broadened. This was attributed to the coupling of the localized QD excited states to the crossed states and scattering of longitudinal acoustical (LA phonons. The degree of spectral linewidth broadening was larger for the excited state in smaller QDs because of the higher crossed joint density of states and scattering rate.

  13. Fluorescence images of DNA-bound YOYO between coupled silver particles. (United States)

    Zhang, Jian; Fu, Yi; Lakowicz, Joseph R


    Oligonucleotide-bound silver particles were coupled through hybridization with target complementary oligonucleotides. YOYO molecules were intercalated into DNA duplexes bound between the coupled metal particles. Fluorescence images of YOYO molecules were monitored by scanning confocal microscopy. Relative to the free single YOYO, the emission brightness of the image was enhanced 80-fold after intercalating the fluorophores into the DNA duplexes between the coupled silver particles. Some images of the labeled metal particle dimers were observed to be dumbbell-shaped, suggesting that the stretching of intercalated YOYO molecules was restricted because of the orientation effect of fluorophores. The shortened lifetime of YOYO molecules between the coupled metal particles indicated that the fluorescence was enhanced via a near-field interaction mechanism between the fluorophore and the metal nanoparticle.

  14. Crystal Structure of NFAT Bound to the HIV-1 LTR Tandem κB Enhancer Element

    Energy Technology Data Exchange (ETDEWEB)

    Bates, Darren L.; Barthel, Kristen K.B.; Wu, Yongqing; Kalhor, Reza; Stroud, James C.; Giffin, Michael J.; Chen, Lin (UCLA); (Colorado)


    Here, we have determined the crystal structure of the DNA binding domain of NFAT bound to the HIV-1 long terminal repeat (LTR) tandem {kappa}B enhancer element of 3.05 {angstrom} resolution. NFAT binds as a dimer to the upstream {kappa}B site (Core II), but as a monomer to the 3' end of the downstream {kappa}B site (Core I). The DNA shows a significant bend near the 5' end of Core I, where a lysine residue from NFAT bound to the 3' end of Core II inserts into the minor groove and seems to cause DNA bases to flip out. Consistent with this structural feature, the 5' end of Core I become hypersensitive to dimethylsulfate in the in vivo footprinting upon transcriptional activation of the HIV-1 LTR. Our studies provide a basis for futher investigating the functional mechanism of NFAT in HIV-1 transcription and replication.

  15. Two-body bound and edge states in the extended SSH Bose-Hubbard model (United States)

    Di Liberto, M.; Recati, A.; Carusotto, I.; Menotti, C.


    We study the bosonic two-body problem in a Su-Schrieffer-Heeger dimerized chain with on-site and nearest-neighbor interactions. We find two classes of bound states. The first, similar to the one induced by on-site interactions, has its center of mass on the strong link, whereas the second, existing only thanks to nearest-neighbor interactions, is centered on the weak link. We identify energy crossings between these states and analyse them using exact diagonalization and perturbation theory. In the presence of open boundary conditions, novel strongly-localized edge-bound states appear in the spectrum as a consequence of the interplay between lattice geometry, on-site and nearest-neighbor interactions. Contrary to the case of purely on-site interactions, such EBS persist even in the strongly interacting regime.

  16. Preference for bridging versus terminal ligands in magnesium dimers. (United States)

    Lioe, Hadi; White, Jonathan M; O'Hair, Richard A J


    Magnesium dimers play important roles in inorganic and organometallic chemistry. This study evaluates the inherent bridging ability of a range of different ligands in magnesium dimers. In the first part, the Cambridge Structural Database is interrogated to establish the frequency of different types of ligands found in bridging versus terminal positions in two key structural motifs: one in which there are two bridging ligands (the D(2h) "Mg(2)(μ-X(2))" structure); the other in which there are three bridging ligands (the C(3v) "Mg(2)(μ-X(3))" structure). The most striking finding from the database search is the overwhelming preference for magnesium dimers possessing two bridging ligands. The most common bridging ligands are C-, N-, and O-based. In the second part, DFT calculations (at the B3LYP/6-311+G(d) level of theory) are carried out to examine a wider range of structural types for dimers consisting of the stoichiometries Mg(2)Cl(3)R and Mg(2)Cl(2)R(2), where R = CH(3), SiH(3), NH(2), PH(2), OH, SH, CH(2)CH(3), CH=CH(2), C≡CH, Ph, OAc, F and Br. Consistent with the database search, the most stable magnesium dimers are those that contain two bridging ligands. Furthermore, it was demonstrated that the electronic effect of the bridging ligands is important in influencing the stability of the magnesium dimers. The preference for a bridging ligand, which reflects its ability to stabilize a magnesium dimer, follows the order: OH > NH(2) > C≡CH > SH > Ph > Br > PH(2) = CH=CH(2) > CH(2)CH(3) > CH(3) > SiH(3). Finally, the role that the ether solvent Me(2)O has on the stability of isomeric Mg(2)Cl(2)Me(2) dimers was studied. It was found that the first solvent molecule stabilizes the dimers, while the second solvent molecule can either have a stabilizing or destabilizing effect, depending on the isomer structure.

  17. D-dimer and BNP levels in acute aortic dissection. (United States)

    Sbarouni, Eftihia; Georgiadou, Panagiota; Marathias, Aikaterini; Geroulanos, Stefanos; Kremastinos, Dimitrios Th


    Early diagnosis and treatment are pivotal for patients with acute aortic dissection (AAD). D-dimer is a rule-out diagnostic test for pulmonary embolism but there is evidence that it may also be applicable to AAD. We evaluated plasma D-dimer, white cell blood count (WBC), C-reactive protein (CRP) and N-terminal pro-B-type natriuretic peptide (BNP) in 18 consecutive patients with established AAD, 21 consecutive patients with dilated ascending aortas scheduled for elective surgery and 8 normal subjects. Patients with AAD had significantly higher elevated D-dimer, compared to chronic aneurysms and normal controls (pD-dimer level higher than 700 ng/ml had a sensitivity of 94% and specificity of 59% for diagnosis of AAD. The WBC count was also significantly increased compared to the other groups (pD-dimer can be used as a 'rule-out' test in patients with suspected AAD and seems useful in the discrimination between AAD and chronic uncomplicated aneurysms, unlike CRP and BNP plasma levels.

  18. Cytotoxicity of bovine seminal ribonuclease: monomer versus dimer. (United States)

    Lee, J Eugene; Raines, Ronald T


    Bovine seminal ribonuclease (BS-RNase) is a homologue of bovine pancreatic ribonuclease (RNase A). Unlike RNase A, BS-RNase has notable toxicity for human tumor cells. Wild-type BS-RNase is a homodimer linked by two intermolecular disulfide bonds. This quaternary structure endows BS-RNase with resistance to inhibition by the cytosolic ribonuclease inhibitor protein (RI), which binds tightly to RNase A and monomeric BS-RNase. Here, we report on the creation and analysis of monomeric variants of BS-RNase that evade RI but retain full enzymatic activity. The cytotoxic activity of these monomeric variants exceeds that of the wild-type dimer by up to 30-fold, indicating that the dimeric structure of BS-RNase is not required for cytotoxicity. Dimers of these monomeric variants are more cytotoxic than wild-type BS-RNase, suggesting that the cytotoxicity of the wild-type enzyme is limited by RI inhibition following dissociation of the dimer in the reducing environment of the cytosol. Finally, the cytotoxic activity of these dimers is less than that of the constituent monomers, indicating that their quaternary structure is a liability. These data provide new insight into structure-function relationships of BS-RNase. Moreover, BS-RNase monomers described herein are more toxic to human tumor cells than is any known variant or homologue of RNase A including Onconase, an amphibian homologue in phase III clinical trials for the treatment of unresectable malignant mesothelioma.

  19. Synthesis of a distinct water dimer inside fullerene C70 (United States)

    Zhang, Rui; Murata, Michihisa; Aharen, Tomoko; Wakamiya, Atsushi; Shimoaka, Takafumi; Hasegawa, Takeshi; Murata, Yasujiro


    The water dimer is an ideal chemical species with which to study hydrogen bonds. Owing to the equilibrium between the monomer and oligomer structure, however, selective generation and separation of a genuine water dimer has not yet been achieved. Here, we report a synthetic strategy that leads to the successful encapsulation of one or two water molecules inside fullerene C70. These endohedral C70 compounds offer the opportunity to study the intrinsic properties of a single water molecule without any hydrogen bonding, as well as an isolated water dimer with a single hydrogen bond between the two molecules. The unambiguously determined off-centre position of water in (H2O)2@C70 by X-ray diffraction provides insights into the formation of (H2O)2@C70. Subsequently, the 1H NMR spectroscopic measurements for (H2O)2@C70 confirmed the formation of a single hydrogen bond rapidly interchanging between the encapsulated water dimer. Our theoretical calculations revealed a peculiar cis-linear conformation of the dimer resulting from confinement effects inside C70.

  20. Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein from Helicobacter pylori: Role of Multiple Metal Binding Sites

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Rong; Munger, Christine; Asinas, Abdalin; Benoit, Stephane L.; Miller, Erica; Matte, Allan; Maier, Robert J.; Cygler, Miroslaw (McGill); (Georgia); (Biotech Res.)


    The crystal structure of the urease maturation protein UreE from Helicobacter pylori has been determined in its apo form at 2.1 {angstrom} resolution, bound to Cu{sup 2+} at 2.7 {angstrom} resolution, and bound to Ni{sup 2+} at 3.1 {angstrom} resolution. Apo UreE forms dimers, while the metal-bound enzymes are arranged as tetramers that consist of a dimer of dimers associated around the metal ion through coordination by His102 residues from each subunit of the tetramer. Comparison of independent subunits from different crystal forms indicates changes in the relative arrangement of the N- and C-terminal domains in response to metal binding. The improved ability of engineered versions of UreE containing hexahistidine sequences at either the N-terminal or C-terminal end to provide Ni{sup 2+} for the final metal sink (urease) is eliminated in the H102A version. Therefore, the ability of the improved Ni{sup 2+}-binding versions to deliver more nickel is likely an effect of an increased local concentration of metal ions that can rapidly replenish transferred ions bound to His102.

  1. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas


    A system consisting of parallel optical wireless channels with a total average intensity constraint is studied. Capacity upper and lower bounds for this system are derived. Under perfect channel-state information at the transmitter (CSIT), the bounds have to be optimized with respect to the power allocation over the parallel channels. The optimization of the lower bound is non-convex, however, the KKT conditions can be used to find a list of possible solutions one of which is optimal. The optimal solution can then be found by an exhaustive search algorithm, which is computationally expensive. To overcome this, we propose low-complexity power allocation algorithms which are nearly optimal. The optimized capacity lower bound nearly coincides with the capacity at high SNR. Without CSIT, our capacity bounds lead to upper and lower bounds on the outage probability. The outage probability bounds meet at high SNR. The system with average and peak intensity constraints is also discussed.

  2. Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. (United States)

    Walsh, M A; Otwinowski, Z; Perrakis, A; Anderson, P M; Joachimiak, A


    Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.

  3. The Cramer-Rao Bound and DMT Signal Optimisation for the Identification of a Wiener-Type Model

    Directory of Open Access Journals (Sweden)

    H. Koeppl


    Full Text Available In linear system identification, optimal excitation signals can be determined using the Cramer-Rao bound. This problem has not been thoroughly studied for the nonlinear case. In this work, the Cramer-Rao bound for a factorisable Volterra model is derived. The analytical result is supported with simulation examples. The bound is then used to find the optimal excitation signal out of the class of discrete multitone signals. As the model is nonlinear in the parameters, the bound depends on the model parameters themselves. On this basis, a three-step identification procedure is proposed. To illustrate the procedure, signal optimisation is explicitly performed for a third-order nonlinear model. Methods of nonlinear optimisation are applied for the parameter estimation of the model. As a baseline, the problem of optimal discrete multitone signals for linear FIR filter estimation is reviewed.

  4. Performance Bounds of Quaternion Estimators. (United States)

    Xia, Yili; Jahanchahi, Cyrus; Nitta, Tohru; Mandic, Danilo P


    The quaternion widely linear (WL) estimator has been recently introduced for optimal second-order modeling of the generality of quaternion data, both second-order circular (proper) and second-order noncircular (improper). Experimental evidence exists of its performance advantage over the conventional strictly linear (SL) as well as the semi-WL (SWL) estimators for improper data. However, rigorous theoretical and practical performance bounds are still missing in the literature, yet this is crucial for the development of quaternion valued learning systems for 3-D and 4-D data. To this end, based on the orthogonality principle, we introduce a rigorous closed-form solution to quantify the degree of performance benefits, in terms of the mean square error, obtained when using the WL models. The cases when the optimal WL estimation can simplify into the SWL or the SL estimation are also discussed.

  5. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan


    Exact eigenvalues, eigenvectors, and principal vectors of operators with infinite dimensional ranges can rarely be found. Therefore, one must approximate such operators by finite rank operators, then solve the original eigenvalue problem approximately. Serving as both an outstanding text for graduate students and as a source of current results for research scientists, Spectral Computations for Bounded Operators addresses the issue of solving eigenvalue problems for operators on infinite dimensional spaces. From a review of classical spectral theory through concrete approximation techniques to finite dimensional situations that can be implemented on a computer, this volume illustrates the marriage of pure and applied mathematics. It contains a variety of recent developments, including a new type of approximation that encompasses a variety of approximation methods but is simple to verify in practice. It also suggests a new stopping criterion for the QR Method and outlines advances in both the iterative refineme...

  6. On order bounded subsets of locally solid Riesz spaces | Hong ...

    African Journals Online (AJOL)

    In a topological Riesz space there are two types of bounded subsets: order bounded subsets and topologically bounded subsets. It is natural to ask (1) whether an order bounded subset is topologically bounded and (2) whether a topologically bounded subset is order bounded. A classical result gives a partial answer to (1) ...

  7. Composition dependence of magneto-optical response in Ag/Co dimer nanodot arrays

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Yaning; Deng, Chenhua; Yan, Lijuan [School of Chemistry and Materials Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004 (China); Tang, Zhixiong; Tang, Shaolong [Nanjing National Laboratory of Microstructures, Jiangsu Provincial Laboratory for Nanotechnology and Department of Physics, Nanjing University, Nanjing 210093 (China); Xu, Xiaohong, E-mail: [School of Chemistry and Materials Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004 (China)


    In this work, we fabricated ordered Ag/Co dimer nanodot arrays by using anodic aluminum oxide (AAO) templates combined with magnetron sputtering. First of all, we studied the optical properties of the nanodot arrays with different Ag/Co ratios while keeping the total thickness constant. The sharp absorption peaks were found in visible spectral range due to the excitation of localized surface plasmon resonances (LSPR) of Ag/Co nanodot arrays, and the absorption peak decreases and slightly blue shifts with the decreasing of Ag ratio. Further, we explored the magneto-optical (MO) properties of nanodot arrays, and found that the excitation of LSPR induces electromagnetic (EM) enhancement near the surface of the Co, which exhibits a sizable MO activity. - Highlights: • An enhanced MO activity is obtained by designing Ag/Co composite nano- structure. • AAO template is a feasible method to get the uniformly distributed nanoparticles. • Few people studied the MO activity of a long-range highly ordered nanodot arrays.

  8. Spectroscopic signatures of proton transfer dynamics in the water dimer cation

    Energy Technology Data Exchange (ETDEWEB)

    Kamarchik, Eugene; Kostko, Oleg; Bowman, Joel M.; Ahmed, Musahid; Krylov, Anna I.


    Using full dimensional EOM-IP-CCSD/aug-cc-pVTZ potential energy surfaces, the photoelectron spectrum, vibrational structure, and ionization dynamics of the water dimer radical cation, (H2O)+2, were computed. We also report an experimental photoelectron spectrum which is derived from photoionization efficiency measurements and compares favorably with the theoretical spectrum. The vibrational structure is also compared with the recent experimental work of Gardenier et al. [J. Phys. Chem. A 113, 4772 (2009)] and the recent theoretical calculations by Cheng et al. [J. Phys. Chem. A 113 13779 (2009)]. A reduced dimensionality nuclear Hamiltonian was used to compute the ionization dynamics for both the ground state and first excited state of the cation. The dynamics show markedly different behavior and spectroscopic signatures depending on which state of the cation is accessed by the ionization. Ionization to the ground-state cation surface induces a hydrogen transfer which is complete within 50 femtoseconds, whereas ionization to the first excited state results in a much slower process.

  9. CINE: Comet INfrared Excitation (United States)

    de Val-Borro, Miguel; Cordiner, Martin A.; Milam, Stefanie N.; Charnley, Steven B.


    CINE calculates infrared pumping efficiencies that can be applied to the most common molecules found in cometary comae such as water, hydrogen cyanide or methanol. One of the main mechanisms for molecular excitation in comets is the fluorescence by the solar radiation followed by radiative decay to the ground vibrational state. This command-line tool calculates the effective pumping rates for rotational levels in the ground vibrational state scaled by the heliocentric distance of the comet. Fluorescence coefficients are useful for modeling rotational emission lines observed in cometary spectra at sub-millimeter wavelengths. Combined with computational methods to solve the radiative transfer equations based, e.g., on the Monte Carlo algorithm, this model can retrieve production rates and rotational temperatures from the observed emission spectrum.

  10. Characterization of oxygen dimer-enriched silicon detectors

    CERN Document Server

    Boisvert, V; Moll, M; Murin, L I; Pintilie, I


    Various types of silicon material and silicon p+n diodes have been treated to increase the concentration of the oxygen dimer (O2i) defect. This was done by exposing the bulk material and the diodes to 6 MeV electrons at a temperature of about 350 °C. FTIR spectroscopy has been performed on the processed material confirming the formation of oxygen dimer defects in Czochralski silicon pieces. We also show results from TSC characterization on processed diodes. Finally, we investigated the influence of the dimer enrichment process on the depletion voltage of silicon diodes and performed 24 GeV/c proton irradiations to study the evolution of the macroscopic diode characteristics as a function of fluence.

  11. Optofluidic taming of a colloidal dimer with a silicon nanocavity

    Energy Technology Data Exchange (ETDEWEB)

    Pin, C.; Renaut, C. [Groupe d' Optique de Champ Proche - LRC CEA n°DSM-08-36, Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS n°6303- Université de Bourgogne, Dijon (France); University Grenoble Alpes, INAC-SP2M-SINAPS, F-38000 Grenoble, France and CEA, INAC-SP2M-SINAPS, F-38000 Grenoble (France); University Grenoble Alpes, CNRS, CEA-Leti Minatec, LTM, F-38054 Grenoble Cedex (France); Cluzel, B., E-mail:; Fornel, F. de [Groupe d' Optique de Champ Proche - LRC CEA n°DSM-08-36, Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS n°6303- Université de Bourgogne, Dijon (France); Peyrade, D. [University Grenoble Alpes, CNRS, CEA-Leti Minatec, LTM, F-38054 Grenoble Cedex (France); Picard, E.; Hadji, E. [University Grenoble Alpes, INAC-SP2M-SINAPS, F-38000 Grenoble, France and CEA, INAC-SP2M-SINAPS, F-38000 Grenoble (France)


    We report here the optical trapping of a heterogeneous colloidal dimer above a photonic crystal nanocavity used as an on-chip optical tweezer. The trapped dimer consists of a cluster of two dielectric microbeads of different sizes linked by van der Waals forces. The smallest bead, 1 μm in diameter, is observed to be preferentially trapped by the nanotweezer, leaving the second bead untrapped. The rotational nature of the trapped dimer Brownian motion is first evidenced. Then, in the presence of a fluid flow, control of its orientation and rotation is achieved. The whole system is found to show high rotational degrees of freedom, thereby acting as an effective flow-sensitive microscopic optical ball joint.

  12. Metal membrane with dimer slots as a universal polarizer

    DEFF Research Database (Denmark)

    Zhukovsky, Sergei; Zalkovskij, Maksim; Malureanu, Radu


    In this work, we show theoretically and confirm experimentally that thin metal membranes patterned with an array of slot dimers (or their Babinet analogue with metal rods) can function as a versatile spectral and polarization filter. We present a detailed covariant multipole theory for the electr......In this work, we show theoretically and confirm experimentally that thin metal membranes patterned with an array of slot dimers (or their Babinet analogue with metal rods) can function as a versatile spectral and polarization filter. We present a detailed covariant multipole theory......-shaped, and T-shaped. These particular shapes of dimers are found to be sensitive to variations of the slots lengths and orientation of elements. Theoretical results are well supported by full-wave three-dimensional simulations. Our findings were verified experimentally on the metal membranes fabricated using...

  13. Role of Solvent, pH, and Molecular Size in Excited-State Deactivation of Key Eumelanin Building Blocks: Implications for Melanin Pigment Photostability

    DEFF Research Database (Denmark)

    Gauden, M.; Pezzella, A.; Panzella, L.


      Ultrafast time-resolved fluorescence spectroscopy has been used to investigate the excited state dynamics of the basic eumelanin building block 5,6-dihydroxyindole-2-carboxylic acid  (DHICA) its acetylated, methylated and carboxylic ester derivatives as well as two oligomers, a dimer and a trim...

  14. N-Annulated perylene-substituted and fused porphyrin dimers with intense near-infrared one-photon and two-photon absorption

    KAUST Repository

    Luo, Jie


    Fusion of two N-annulated perylene (NP) units with a fused porphyrin dimer along the S0-S1 electronic transition moment axis has resulted in new near-infrared (NIR) dyes 1a/1b with very intense absorption (ε>1.3×105M-1cm-1) beyond 1250nm. Both compounds displayed moderate NIR fluorescence with fluorescence quantum yields of 4.4×10-6 and 6.0×10-6 for 1a and 1b, respectively. The NP-substituted porphyrin dimers 2a/2b have also been obtained by controlled oxidative coupling and cyclodehydrogenation, and they showed superimposed absorptions of the fused porphyrin dimer and the NP chromophore. The excited-state dynamics of all of these compounds have been studied by femtosecond transient absorption measurements, which revealed porphyrin dimer-like behaviour. These new chromophores also exhibited good nonlinear optical susceptibility with large two-photon absorption cross-sections in the NIR region due to extended π-conjugation. Time-dependent density functional theory calculations have been performed to aid our understanding of their electronic structures and absorption spectra.

  15. The majority of lipoprotein lipase in plasma is bound to remnant lipoproteins: A new definition of remnant lipoproteins. (United States)

    Sato, Koichi; Okajima, Fumikazu; Miyashita, Kazuya; Imamura, Shigeyuki; Kobayashi, Junji; Stanhope, Kimber L; Havel, Peter J; Machida, Tetsuo; Sumino, Hiroyuki; Murakami, Masami; Schaefer, Ernst; Nakajima, Katsuyuki


    Lipoprotein lipase (LPL) is a multifunctional protein and a key enzyme involved in the regulation of lipoprotein metabolism. We determined the lipoproteins to which LPL is bound in the pre-heparin and post-heparin plasma. Tetrahydrolipstatin (THL), a potent inhibitor of serine lipases, was used to block the lipolytic activity of LPL, thereby preventing changes in the plasma lipoproteins due to ex vivo lipolysis. Gel filtration was performed to obtain the LPL elution profiles in plasma and the isolated remnant lipoproteins (RLP). When ex vivo lipolytic activity was inhibited by THL in the post-heparin plasma, majority of the LPL was found in the VLDL elution range, specifically in the RLP as inactive dimers. However, in the absence of THL, most of the LPL was found in the HDL elution range as active dimers. Furthermore, majority of the LPL in the pre-heparin plasma was found in the RLP as inactive form, with broadly diffused lipoprotein profiles in the presence and absence of THL. It is suggested that during lipolysis in vivo, the endothelial bound LPL dimers generates RLP, forming circulating RLP-LPL complexes in an inactive form that subsequently binds and initiates receptor-mediated catabolism. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Using tolerance bounds in scientific investigations

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, J.R.


    Assessment of the variability in population values plays an important role in the analysis of scientific data. Analysis of scientific data often involves developing a bound on a proportion of a population. Sometimes simple probability bounds are obtained using formulas involving known mean and variance parameters and replacing the parameters by sample estimates. The resulting bounds are only approximate and fail to account for the variability in the estimated parameters. Tolerance bounds provide bounds on population proportions which account for the variation resulting from the estimated mean and variance parameters. A beta content, gamma confidence tolerance interval is constructed so that a proportion beta of the population lies within the region bounded by the interval with confidence gamma. An application involving corrosion measurements is used to illustrate the use of tolerance bounds for different situations. Extensions of standard tolerance intervals are applied to generate regression tolerance bounds, tolerance bounds for more general models of measurements collected over time, and tolerance intervals for varying precision data. Tolerance bounds also provide useful information for designing the collection of future data.

  17. Solution structure of the dimeric cytoplasmic domain of syndecan-4

    DEFF Research Database (Denmark)

    Shin, J; Lee, W; Lee, D


    between peptides at physiological pH. Commensurately, the NMR structures demonstrate that syndecan-4L is a compact intertwined dimer with a symmetric clamp shape in the central variable V region with a root-mean-square deviation between backbone atom coordinates of 0.95 A for residues Leu(186)-Ala(195...... in the center of the dimeric twist similar to our previously reported 4V structure. The overall topology of the central variable region within the 4L structure is very similar to that of 4V complexed with the phosphatidylinositol 4,5-bisphosphate; however, the intersubunit interaction mode is affected...

  18. Lipopeptides as dimerization inhibitors of HIV-1 protease


    Schramm, H. J.; de Rosny, E.; Reboud-Ravaux, M.; Büttner, J.; Dick, A.; Schramm, W.


    In AIDS therapy, attempts have been made to inhibit the virus-encoded enzymes, e.g, HIV-1 protease, using active site-directed inhibitors. This approach is questionable, however, due to virus mutations and the high toxicity of the drugs, An alternative method to inhibit the dimeric HIV protease is the targeting of the interface region of the protease subunits in order to prevent subunit dimerization and enzyme activity, This approach should be less prone to inactivation by mutation, A list of...

  19. Molecular cloning, characterisation and ligand-bound structure of an azoreductase from Pseudomonas aeruginosa. (United States)

    Wang, Chan-Ju; Hagemeier, Christoph; Rahman, Nawreen; Lowe, Edward; Noble, Martin; Coughtrie, Michael; Sim, Edith; Westwood, Isaac


    The gene PA0785 from Pseudomonas aeruginosa strain PAO1, which is annotated as a probable acyl carrier protein phosphodiesterase (acpD), has been cloned and heterologously overexpressed in Escherichia coli. The purified recombinant enzyme exhibits activity corresponding to that of azoreductase but not acpD. Each recombinant protein molecule has an estimated molecular mass of 23,050 Da and one non-covalently bound FMN as co-factor. This enzyme, now identified as azoreductase 1 from Pseudomonas aeruginosa (paAzoR1), is a flavodoxin-like protein with an apparent molecular mass of 110 kDa as determined by gel-filtration chromatography, indicating that the protein is likely to be tetrameric in solution. The three-dimensional structure of paAzoR1, in complex with the substrate methyl red, was solved at a resolution of 2.18 A by X-ray crystallography. The protein exists as a dimer of dimers in the crystal lattice, with two spatially separated active sites per dimer, and the active site of paAzoR1 was shown to be a well-conserved hydrophobic pocket formed between two monomers. The paAzoR1 enzyme is able to reduce different classes of azo dyes and activate several azo pro-drugs used in the treatment of inflammatory bowel disease (IBD). During azo reduction, FMN serves as a redox centre in the electron-transferring system by mediating the electron transfer from NAD(P)H to the azo substrate. The spectral properties of paAzoR1 demonstrate the hydrophobic interaction between FMN and the active site in the protein. The structure of the ligand-bound protein also highlights the pi-stacking interactions between FMN and the azo substrate.

  20. Calculations on the electronic excited states of ureas and oligoureas. (United States)

    Oakley, Mark T; Guichard, Gilles; Hirst, Jonathan D


    We report CASPT2 calculations on the electronic excited states of several ureas. For monoureas, we find an electric dipole forbidden n --> pi* transition between 180 and 210 nm, dependent on the geometry and substituents of the urea. We find two intense pinb --> pi* transitions between 150 and 210 nm, which account for the absorptions seen in the experimental spectra. The n' --> pi* and pib --> pi* transitions are at wavelengths below 125 nm, which is below the lower limit of the experimental spectra. Parameter sets modeling the charge densities of the electronic transitions have been derived and permit calculations on larger oligoureas, using the exciton matrix method. For glycouril, a urea dimer, both the CASPT2 method and the matrix method yield similar results. Calculations of the electronic circular dichroism spectrum of an oligourea containing eight urea groups indicate that the experimental spectrum cannot be reproduced without the inclusion of electronic excitations involving the side chains. These calculations are one of the first attempts to understand the relationship between the structure and excited states of this class of macromolecule.

  1. Subsurface excitations in a metal

    DEFF Research Database (Denmark)

    Ray, M. P.; Lake, R. E.; Sosolik, C. E.


    We investigate internal hot carrier excitations in a Au thin film bombarded by hyperthermal and low energy alkali and noble gas ions. Excitations within the thin film of a metal-oxide-semiconductor device are measured revealing that ions whose velocities fall below the classical threshold given...... by the free-electron model of a metal still excite hot carriers. Excellent agreement between these results and a nonadiabatic model that accounts for the time-varying ion-surface interaction indicates that the measured excitations are due to semilocalized electrons near the metal surface....

  2. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

    Haranczyk, Maciej; Gutowski, Maciej S; Li, Xiang; Bowen, Kit H


    Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases, are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the new-found anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The discovery of these valence anionic states of adenine was facilitated by the development of: (i) a new experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a new combinatorial/ quantum chemical approach for identification of the most stable tautomers of organic molecules. The computational portion of this work was supported by the: (i) Polish State Committee for Scientific Research (KBN) Grants: DS/8000-4-0140-7 (M.G.) and N204 127 31/2963 (M.H.), (ii) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.), and (iii) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic

  3. From soil to structure, a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. (United States)

    McAndrew, Ryan P; Park, Joshua I; Heins, Richard A; Reindl, Wolfgang; Friedland, Gregory D; D'haeseleer, Patrik; Northen, Trent; Sale, Kenneth L; Simmons, Blake A; Adams, Paul D


    A recent metagenomic analysis sequenced a switchgrass-adapted compost community to identify enzymes from microorganisms that were specifically adapted to switchgrass under thermophilic conditions. These enzymes are being examined as part of the pretreatment process for the production of "second-generation" biofuels. Among the enzymes discovered was JMB19063, a novel three-domain β-glucosidase that belongs to the GH3 (glycoside hydrolase 3) family. Here, we report the structure of JMB19063 in complex with glucose and the catalytic variant D261N crystallized in the presence of cellopentaose. JMB19063 is first structure of a dimeric member of the GH3 family, and we demonstrate that dimerization is required for catalytic activity. Arg-587 and Phe-598 from the C-terminal domain of the opposing monomer are shown to interact with bound ligands in the D261N structure. Enzyme assays confirmed that these residues are absolutely essential for full catalytic activity.

  4. Effects of fluorine substitution on the edge-to-face interaction of the benzene dimer. (United States)

    Riley, Kevin E; Merz, Kenneth M


    To gain some insight into the effects of fluorination on the aromatic-aromatic interactions found in protein-ligand complexes, like those observed in the set of N-(4-sulfamylbenzoyl)benzylamine (SBB) inhibitors bound to Human Carbonic Anhydrase II (HCAII), we have produced potential energy curves for the edge-to-face interactions of a set of fluorinated benzene dimer compounds. All calculations were carried out at the MP2/aug-cc-pVDZ level of theory using the counterpoise method of Boys and Bernardi (Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 553) to account for the basis set superposition error. Fluorine substitutions are made onto the face molecule of the edge-to-face benzene dimer. As one might expect, the substitution of additional fluorines into this system generally resulted in a decrease of the binding energy. It was also found that the positioning of the fluorine substituents on isosubstituted compounds has a large effect on the total binding energy of these types of systems. More specifically, complexes with fluorines that are substituted closer to the hydrogen atoms of the edge benzene will tend to be stabilized by an electrostatic interaction between the partially negative fluorine atoms and the partially positive hydrogen atoms. However, our findings do not explain the recent crystallographic findings for the SBB-HCAII protein-ligand complex, where increased fluorination resulted in closer edge-to-face contacts, which suggests that there are factors, other than edge-to-face aromatic interactions, influencing this system's behavior.

  5. Instanton bound states in ABJM theory

    Energy Technology Data Exchange (ETDEWEB)

    Hatsuda, Yasuyuki [DESY Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics


    The partition function of the ABJM theory receives non-perturbative corrections due to instanton effects. We study these non-perturbative corrections, including bound states of worldsheet instantons and membrane instantons, in the Fermi-gas approach. We require that the total non-perturbative correction should be always finite for arbitrary Chern-Simons level. This finiteness is realized quite non-trivially because each bound state contribution naively diverges at some levels. The poles of each contribution should be canceled out in total. We use this pole cancellation mechanism to find unknown bound state corrections from known ones. We conjecture a general expression of the bound state contribution. Summing up all the bound state contributions, we find that the effect of bound states is simply incorporated into the worldsheet instanton correction by a redefinition of the chemical potential in the Fermi-gas system. Analytic expressions of the 3- and 4-membrane instanton corrections are also proposed.

  6. Axonal Excitability in Amyotrophic Lateral Sclerosis : Axonal Excitability in ALS. (United States)

    Park, Susanna B; Kiernan, Matthew C; Vucic, Steve


    Axonal excitability testing provides in vivo assessment of axonal ion channel function and membrane potential. Excitability techniques have provided insights into the pathophysiological mechanisms underlying the development of neurodegeneration and clinical features of amyotrophic lateral sclerosis (ALS) and related neuromuscular disorders. Specifically, abnormalities of Na+ and K+ conductances contribute to development of membrane hyperexcitability in ALS, thereby leading to symptom generation of muscle cramps and fasciculations, in addition to promoting a neurodegenerative cascade via Ca2+-mediated processes. Modulation of axonal ion channel function in ALS has resulted in significant symptomatic improvement that has been accompanied by stabilization of axonal excitability parameters. Separately, axonal ion channel dysfunction evolves with disease progression and correlates with survival, thereby serving as a potential therapeutic biomarker in ALS. The present review provides an overview of axonal excitability techniques and the physiological mechanisms underlying membrane excitability, with a focus on the role of axonal ion channel dysfunction in motor neuron disease and related neuromuscular diseases.

  7. Suppression of the weakly-bound excited Υ states in HI collisions

    CERN Multimedia


      CMS was able to observe for the first time this phenomenon by comparing last year’s HI collisions at 2.76 TeV/nucleon with the pp collisions that took place at the same energy earlier this year. For more, visit:  

  8. Bounds on CFTs with W3 algebras and AdS3 higher spin theories (United States)

    Apolo, Luis


    The scaling dimension of the first excited state in two-dimensional conformal field theories (CFTs) satisfies a universal upper bound. Using the modular bootstrap, we extend this result to CFTs with W3 algebras which are generically dual to higher spin theories in AdS3 . Assuming unitarity and modular invariance, we show that the conformal weights h , h ¯ of the lightest charged state satisfy h 4 |h -c /24 |/√{10 π c }+O (1 ) . We discuss hints on the existence of stronger bounds and comment on the interpretation of our results in the dual higher spin theory.

  9. Distance hijacking attacks on distance bounding protocols


    Cremers, Cas; Rasmussen, Kasper Bonne; Čapkun, Srdjan


    Distance bounding protocols are typically analyzed with respect to three types of attacks: Distance Fraud, Mafia Fraud, and Terrorist Fraud. We define a fourth main type of attacks on distance bounding protocols, called Distance Hijacking attacks. We show that many proposed distance bounding protocols are vulnerable to these attacks, and we propose solutions to make these protocols resilient to Distance Hijacking. Additionally, we generalize Distance Hijacking to Location Hijacking, to which ...

  10. Boundedly UC spaces: characterisations and preservation | Jain ...

    African Journals Online (AJOL)

    A metric space (X, d) is called a boundedly UC space if every closed and bounded subset of X is a UC space. A metric space (X, d) is called a UC space if each real-valued continuous function on (X, d) is uniformly continuous. In this paper, we study twenty-two equivalent conditions for a metric space to be a boundedly UC ...

  11. Quick and simple estimation of bacteria using a fluorescent paracetamol dimer-Au nanoparticle composite (United States)

    Sahoo, Amaresh Kumar; Sharma, Shilpa; Chattopadhyay, Arun; Ghosh, Siddhartha Sankar


    Rapid, simple and sensitive detection of bacterial contamination is critical for safeguarding public health and the environment. Herein, we report an easy method of detection as well as enumeration of the bacterial cell number on the basis of fluorescence quenching of a non-antibacterial fluorescent nanocomposite, consisting of paracetamol dimer (PD) and Au nanoparticles (NPs), in the presence of bacteria. The composite was synthesized by reaction of paracetamol (p-hydroxyacetanilide) with HAuCl4. The Au NPs of the composite were characterized using UV-Vis spectroscopy, transmission electron microscopy (TEM), X-ray diffraction and selected area electron diffraction analysis. The paracetamol dimer in the composite showed emission peak at 435 nm when excited at 320 nm. The method successfully detected six bacterial strains with a sensitivity of 100 CFU mL-1. The Gram-positive and Gram-negative bacteria quenched the fluorescence of the composite differently, making it possible to distinguish between the two. The TEM analysis showed interaction of the composite with bacteria without any apparent damage to the bacteria. The chi-square test established the accuracy of the method. Quick, non-specific and highly sensitive detection of bacteria over a broad range of logarithmic dilutions within a short span of time demonstrates the potential of this method as an alternative to conventional methods.Rapid, simple and sensitive detection of bacterial contamination is critical for safeguarding public health and the environment. Herein, we report an easy method of detection as well as enumeration of the bacterial cell number on the basis of fluorescence quenching of a non-antibacterial fluorescent nanocomposite, consisting of paracetamol dimer (PD) and Au nanoparticles (NPs), in the presence of bacteria. The composite was synthesized by reaction of paracetamol (p-hydroxyacetanilide) with HAuCl4. The Au NPs of the composite were characterized using UV-Vis spectroscopy

  12. Bounded cohomology of discrete groups

    CERN Document Server

    Frigerio, Roberto


    The author manages a near perfect equilibrium between necessary technicalities (always well motivated) and geometric intuition, leading the readers from the first simple definition to the most striking applications of the theory in 13 very pleasant chapters. This book can serve as an ideal textbook for a graduate topics course on the subject and become the much-needed standard reference on Gromov's beautiful theory. -Michelle Bucher The theory of bounded cohomology, introduced by Gromov in the late 1980s, has had powerful applications in geometric group theory and the geometry and topology of manifolds, and has been the topic of active research continuing to this day. This monograph provides a unified, self-contained introduction to the theory and its applications, making it accessible to a student who has completed a first course in algebraic topology and manifold theory. The book can be used as a source for research projects for master's students, as a thorough introduction to the field for graduate student...

  13. Iminodiacetic acid as bifunctional linker for dimerization of cyclic RGD peptides. (United States)

    Xu, Dong; Zhao, Zuo-Quan; Chen, Shu-Ting; Yang, Yong; Fang, Wei; Liu, Shuang


    In this study, I2P-RGD2 was used as the example to illustrate a novel approach for dimerization of cyclic RGD peptides. The main objective of this study was to explore the impact of bifunctional linkers (glutamic acid vs. iminodiacetic acid) on tumor-targeting capability and excretion kinetics of the 99mTc-labeled dimeric cyclic RGD peptides. HYNIC-I2P-RGD2 was prepared by reacting I2P-RGD2 with HYNIC-OSu in the presence of diisopropylethylamine, and was evaluated for its αvβ3 binding affinity against 125I-echistatin bound to U87MG glioma cells. 99mTc-I2P-RGD2 was prepared with high specific activity (~185GBq/μmol). The athymic nude mice bearing U87MG glioma xenografts were used to evaluate its biodistribution properties and image quality in comparison with those of 99mTc-3P-RGD2. The IC50 value for HYNIC-I2P-RGD2 was determined to be 39±6nM, which was very close to that (IC50=33±5nM) of HYNIC-3P-RGD2. Replacing glutamic acid with iminodiacetic acid had little impact on αvβ3 binding affinity of cyclic RGD peptides. 99mTc-I2P-RGD2 and 99mTc-3P-RGD2 shared similar tumor uptake values over the 2h period, and its αvβ3-specificity was demonstrated by a blocking experiment. The uptake of 99mTc-I2P-RGD2 was significantly lower than 99mTc-3P-RGD2 in the liver and kidneys. The U87MG glioma tumors were visualized by SPECT with excellent contrast using both 99mTc-I2P-RGD2 and 99mTc-3P-RGD2. Iminodiacetic acid is an excellent bifunctional linker for dimerization of cyclic RGD peptides. Bifunctional linkers have significant impact on the excretion kinetics of 99mTc radiotracers. Because of its lower liver uptake and better tumor/liver ratios, 99mTc-I2P-RGD2 may have advantages over 99mTc-3P-RGD2 for diagnosis of tumors in chest region. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Bounded sets in fast complete inductive limits

    Directory of Open Access Journals (Sweden)

    Jan Kucera


    Full Text Available Let E1⊂E2⊂… be a sequence of locally convex spaces with all identity maps: En→En+1 continuous and E=indlim En fast complete. Then each set bounded in E is also bounded in some En iff for any Banach disk B bounded in E and n∈N, the closure of B⋂En in B is bounded in some Em. This holds, in particular, if all spaces En are webbed.

  15. Valuation models and Simon's bounded rationality

    National Research Council Canada - National Science Library

    Alexandra Strommer de Farias Godoi


    This paper aims at reconciling the evidence that sophisticated valuation models are increasingly used by companies in their investment appraisal with the literature of bounded rationality, according...

  16. Some Improved Nonperturbative Bounds for Fermionic Expansions

    Energy Technology Data Exchange (ETDEWEB)

    Lohmann, Martin, E-mail: [Universita di Roma Tre, Dipartimento di Matematica (Italy)


    We reconsider the Gram-Hadamard bound as it is used in constructive quantum field theory and many body physics to prove convergence of Fermionic perturbative expansions. Our approach uses a recursion for the amplitudes of the expansion, discovered in a model problem by Djokic (2013). It explains the standard way to bound the expansion from a new point of view, and for some of the amplitudes provides new bounds, which avoid the use of Fourier transform, and are therefore superior to the standard bounds for models like the cold interacting Fermi gas.

  17. A strongly quasiconvex PAC-Bayesian bound

    DEFF Research Database (Denmark)

    Thiemann, Niklas; Igel, Christian; Wintenberger, Olivier

    We propose a new PAC-Bayesian bound and a way of constructing a hypothesis space, so that the bound is convex in the posterior distribution and also convex in a trade-off parameter between empirical performance of the posterior distribution and its complexity. The complexity is measured by the Ku......We propose a new PAC-Bayesian bound and a way of constructing a hypothesis space, so that the bound is convex in the posterior distribution and also convex in a trade-off parameter between empirical performance of the posterior distribution and its complexity. The complexity is measured...

  18. Structural analysis of the essential resuscitation promoting factor YeaZ suggests a mechanism of nucleotide regulation through dimer reorganization.

    Directory of Open Access Journals (Sweden)

    Inci Aydin

    Full Text Available BACKGROUND: The yeaZ gene product forms part of the conserved network YjeE/YeaZ/YgjD essential for the survival of many gram-negative eubacteria. Among other as yet unidentified roles, YeaZ functions as a resuscitation promoting factor required for survival and resuscitation of cells in a viable but non-culturable (VBNC state. METHODOLOGY/PRINCIPAL FINDINGS: In order to investigate in detail the structure/function relationship of this family of proteins we have performed X-ray crystallographic studies of Vibrio parahaemolyticus YeaZ. The YeaZ structure showed that it has a classic actin-like nucleotide-binding fold. Comparisons of this crystal structure to that of available homologues from E. coli, T. maritima and S. typhimurium revealed two distinctly different modes of dimer formation. In one form, prevalent in the absence of nucleotide, the putative nucleotide-binding site is incomplete, lacking a binding pocket for a nucleotide base. In the second form, residues from the second subunit complete the nucleotide-binding site. This suggests that the two dimer architectures observed in the crystal structures correspond to a free and a nucleotide-bound form of YeaZ. A multiple sequence alignment of YeaZ proteins from different bacteria allowed us to identify a large conserved hydrophobic patch on the protein surface that becomes exposed upon nucleotide-driven dimer re-arrangement. We hypothesize that the transition between two dimer architectures represents the transition between the 'on' and 'off' states of YeaZ. The effect of this transition is to alternately expose and bury a docking site for the partner protein YgjD. CONCLUSIONS/SIGNIFICANCE: This paper provides the first structural insight into the putative mechanism of nucleotide regulation of YeaZ through dimer reorganization. Our analysis suggests that nucleotide binding to YeaZ may act as a regulator or switch that changes YeaZ shape, allowing it to switch partners between YjeE and YgjD.

  19. Manipulation of Squeezed Two-Phonon Bound States using Femtosecond Laser Pulses

    Directory of Open Access Journals (Sweden)

    Nakamura Kazutaka G.


    Full Text Available Two-phonon bound states have been excited exclusively in ZnTe(110 via impulsive stimulated second-order Raman scattering, essentially being squeezed states due to phase coherent excitation of two identical components anticorrelated in the wave vector. By using coherent control technique with a pair of femtosecond laser pulses, the manipulation of squeezed states has been demonstrated in which both the amplitude and lifetime of coherent oscillations of squeezed states are modulated, indicating the feasibility to control the quantum noise and the quantum nature of phonon squeezed states, respectively.

  20. Interatomic Coulombic decay cascades in multiply excited neon clusters (United States)

    Nagaya, K.; Iablonskyi, D.; Golubev, N. V.; Matsunami, K.; Fukuzawa, H.; Motomura, K.; Nishiyama, T.; Sakai, T.; Tachibana, T.; Mondal, S.; Wada, S.; Prince, K. C.; Callegari, C.; Miron, C.; Saito, N.; Yabashi, M.; Demekhin, Ph. V.; Cederbaum, L. S.; Kuleff, A. I.; Yao, M.; Ueda, K.


    In high-intensity laser light, matter can be ionized by direct multiphoton absorption even at photon energies below the ionization threshold. However on tuning the laser to the lowest resonant transition, the system becomes multiply excited, and more efficient, indirect ionization pathways become operative. These mechanisms are known as interatomic Coulombic decay (ICD), where one of the species de-excites to its ground state, transferring its energy to ionize another excited species. Here we show that on tuning to a higher resonant transition, a previously unknown type of interatomic Coulombic decay, intra-Rydberg ICD occurs. In it, de-excitation of an atom to a close-lying Rydberg state leads to electron emission from another neighbouring Rydberg atom. Moreover, systems multiply excited to higher Rydberg states will decay by a cascade of such processes, producing even more ions. The intra-Rydberg ICD and cascades are expected to be ubiquitous in weakly-bound systems exposed to high-intensity resonant radiation. PMID:27917867

  1. Identification of Trimer and Dimer of 4-hydroxy-3-methoxy ...

    African Journals Online (AJOL)

    The effect of intermolecular hydrogen bonding on the molecular structure of vanillin has been studied using negative ion chemical ionization (NICl) mass spectrometry methods. The [Trimer-H2O] and [Dimer-H2O] were observed at m/z 438 and 286 respectively in NICl (CH4) mass spectrum of vanillin. The NICl (Cl) mass ...

  2. Cationic zinc (II) dimers and one dimensional coordination polymer ...

    Indian Academy of Sciences (India)

    A zinc coordination polymer was synthesised by treating in situ generation of 2 in the presence of 4,4′-bipyridine. These new molecules, dimers and polymer, were characterized by FT-IR, NMR, UV-vis, fluorescent and single crystal X-ray diffraction techniques. Zinc polymer is the first example of 1D coordination polymer ...

  3. Dimerization effect of sucrose octasulfate on rat FGF1

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Artur


    signalling pathways. The structure of rat FGF1 crystallized in the presence of SOS has been determined at 2.2 A resolution. SOS-mediated dimerization of FGF1 was observed, which was further supported by gel-filtration experiments. The major contributors to the sulfate-binding sites in rat FGF1 are Lys113...

  4. Photodissociation pathways and lifetimes of protonated peptides and their dimers

    DEFF Research Database (Denmark)

    Gopalan, Aravind; Klærke, Benedikte; Rajput, Jyoti


    rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis...

  5. Peroxynitrous Acid Dimer: Ab Initio Density Functional Study (United States)

    Pathak, Rajeev


    Peroxynitrous acid (PNA) HOONO, isomeric to nitric acid, is a very strong oxidant. A novel dimeric hydrogen-bonded cluster of peroxynitrous acid (PNA-D) is proposed herein; ab inito quantum chemical investigations performed whereupon lead to several stable structures that have a direct bearing on the reactivity of the participating monomers, quantified in terms of the molecular electrostatic potential. The electron-correlation lending stability to PNA and its dimers is gauged through several density functionals namely B3LYP, B3PW91, M06-2X, M06-L, and φ-B97X, etc.; as well as from popular wave-function based second order Møller-Plesset (MP2) perturbation theory, using the basis sets 6-311++G(d,p) and 6-311++G(2d,2p). The infra-red vibrational spectra reveal spectral shifts and intensity redistribution after dimerization. While the lowest energy PNA-D has a perfect inversion symmetry; the other stable dimers emerge as combinations of monomers in different orientation.

  6. Synthesis and biological evaluation of gramicidin S dimers

    NARCIS (Netherlands)

    Grotenbreg, Gijsbert M.; Witte, Martin D.; Hooft, Peter A.V. van; Spalburg, Emile; Reiß, Philipp; Noort, Daan; Neeling, Albert J. de; Koert, Ulrich; Marel, Gijsbert A. van der; Overkleeft, Herman S.; Overhand, Mark


    The design and synthesis of analogues of the cyclic β-sheet peptide gramicidin S (GS), having additional functionalities in their turn regions, is reported. The monomeric GS analogues were transformed into dimers and their activities towards biological membranes, through antimicriobial and hemolytic

  7. Synthesis and Dimerization Behavior of Five Metallophthalocyanines in Different Solvents

    Directory of Open Access Journals (Sweden)

    Zhenhua Cheng


    Full Text Available Metallophthalocyanine (MPc has become one of the metal organic compounds with the largest production and the most widely application, because of its excellent performance in catalytic oxidation. However, aggregation of the MPc in solution, resulting in decreased solubility, greatly limits the performance of application. Studying the behavior of dimerization of MPcs can provide a theoretical basis for solving the problem of the low solubility. So five metallophthalocyanines (FePc, CoPc, NiPc, CuPc, and ZnPc were prepared with improved method and characterized. Dimerization of the five MPcs was measured by UV-Vis spectroscopy separately in N,N-dimethyl formamide (DMF and dimethylsulfoxide (DMSO. The red-shift of maximum absorption wavelength and deviations from Lambert-Beer law with increasing the concentration were observed for all the five MPcs. The dimerization equilibrium constants (K of the five MPcs in DMF were arranged in order of CoPc > ZnPc > CuPc > FePc > NiPc, while in DMSO they were arranged in order of ZnPc > CoPc > FePc > CuPc > NiPc. The type of the central metal and nature of the solvent affect the dimerization of the MPcs.

  8. Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

    Directory of Open Access Journals (Sweden)

    Lukas P. Feilen


    Full Text Available Physiological function and pathology of the Alzheimer’s disease causing amyloid precursor protein (APP are correlated with its cytosolic adaptor Fe65 encompassing a WW and two phosphotyrosine-binding domains (PTBs. The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD including the GYENPTY internalization sequence fingerprint. AICD binding to Fe65-PTB2 opens an intra-molecular interaction causing a structural change and altering Fe65 activity. Here we show that in the absence of the AICD, Fe65-PTB2 forms a homodimer in solution and determine its crystal structure at 2.6 Å resolution. Dimerization involves the unwinding of a C-terminal α-helix that mimics binding of the AICD internalization sequence, thus shielding the hydrophobic binding pocket. Specific dimer formation is validated by nuclear magnetic resonance (NMR techniques and cell-based analyses reveal that Fe65-PTB2 together with the WW domain are necessary and sufficient for dimerization. Together, our data demonstrate that Fe65 dimerizes via its APP interaction site, suggesting that besides intra- also intermolecular interactions between Fe65 molecules contribute to homeostatic regulation of APP mediated signaling.

  9. Family C 7TM receptor dimerization and activation

    DEFF Research Database (Denmark)

    Bonde, Marie Mi; Sheikh, Søren P; Hansen, Jakob Lerche


    to be fully defined. This review presents the biochemical support for family C 7TM receptor dimerization and discusses its importance for receptor biosynthesis, surface expression, ligand binding and activation, since lessons learnt here may well be applicable to the whole superfamily of 7TM receptors....

  10. Asymmetric electron capture in HCI collisions with rare gas dimers (United States)

    Matsumoto, J.; Leredde, A.; Fléchard, X.; Shiromaru, H.; Rangama, J.; Zhou, C. L.; Iskandar, W.; Guillous, S.; Hennecart, D.; Mery, A.; Gervais, B.; Cassimi, A.


    Low-energy collisions between different rare gas dimers (Ar2, Ne2) and different projectiles (O3+, Ar9+, Xe20+) show that the weight of the different fragmentation processes, Coulomb explosion and Radiative Charge Transfer, strongly depends on the projectile charge state. This result is understood in term of impact parameter from which the electrons are captured on the projectile.

  11. TRF2 recruits ORC through TRFH domain dimerization. (United States)

    Higa, Mitsunori; Kushiyama, Tatsunori; Kurashige, Seiichiro; Kohmon, Daisuke; Enokitani, Kouki; Iwahori, Satoko; Sugimoto, Nozomi; Yoshida, Kazumasa; Fujita, Masatoshi


    Telomeres are specialized chromatin structures that prevent the degradation and instability of the ends of linear chromosomes. While telomerase maintains long stretches of the telomeric repeat, the majority of telomeric DNA is duplicated by conventional DNA replication. A fundamental step in eukaryotic DNA replication involves chromatin binding of the origin recognition complex (ORC). In human cells, telomeric repeat binding factor 2 (TRF2) is thought to play a role in the recruitment of ORC onto telomeres. To better understand the mechanism of TRF2-mediated ORC recruitment, we utilized a lacO-LacI protein tethering system in U2OS cells and found that ectopically targeted TRF2, but not TRF1, can recruit ORC onto the lacO array. We further found that the TRF homology (TRFH) dimerization domain of TRF2, but not its mutant defective in dimerization, is sufficient for ORC and minichromosome maintenance (MCM) recruitment. Mutations impairing the dimerization also compromised ORC recruitment by full-length TRF2. Similar results were obtained using immunoprecipitation and GST pull-down assays. Together, these results suggest that dimerized TRF2 recruits ORC and stimulates pre-replication complex (pre-RC) formation at telomeres through the TRFH domain. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations

    NARCIS (Netherlands)

    De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut


    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices

  13. Scyphiphin D, a new iridoid glucoside dimer from Scyphiphora hydrophyllacea. (United States)

    Zeng, Yan-Bo; Mei, Wen-Li; Wang, Hui; Li, Xiao-Na; Dai, Hao-Fu


    From the aerial parts of Scyphiphora hydrophyllacea Gaertn. F., a new iridoid glucoside dimer scyphiphin D (1) and a known iridoid glucoside geniposidic acid (2) were isolated. The structure of this new compound was determined on the basis of HR-FAB-MS, IR, (1)H and (13)C NMR (DEPT), and 2D NMR (HMQC, HMBC, COSY, ROESY) spectral data.

  14. (--AMPELOPSIN A : A DIMER RESVERATROL FROM Dryobalanops oblongifolia (dipterocarpaceae

    Directory of Open Access Journals (Sweden)

    Nanik Siti Aminah


    Full Text Available A dimer resveratrol compound named (--ampelopsin A was isolated from acetone extract of the stem bark of  Dryobalanops oblongifolia (Dipterocarpaceae. The structure of this compound was determined on the basis of NMR spectroscopic data.   Keywords: (--ampelopsin A, Dryobalanops oblongifolia, Dipterocarpaceae

  15. Construction of covalently coupled, concatameric dimers of 7TM receptors

    DEFF Research Database (Denmark)

    Terpager, Marie; Scholl, D Jason; Kubale, Valentina


    7TM receptors are easily fused to proteins such as G proteins and arrestin but because of the fact that their terminals are found on each side of the membrane they cannot be joined directly in covalent dimers. Here, we use an artificial connector comprising a transmembrane helix composed of Leu...

  16. Chemically distinct coupled Cu (II) dimers: Structure and ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 112; Issue 3. Chemically distinct coupled Cu(II) dimers: Structure and physicochemical properties. R Srinivasan R Venkatesan T M Rajendiran P Sambasiva Rao. Volume 112 Issue 3 June 2000 pp 359-359 ...

  17. Facile synthesis of dimer phase of coronene and its optical properties

    Energy Technology Data Exchange (ETDEWEB)

    Hayakawa, T.; Song, H.; Ishii, Y.; Kawasaki, S., E-mail: [Nagoya Institute of Technology, Gokiso, Showa, Nagoya, Aichi (Japan)


    We synthesized very pure dimer phase of coronene by simple heat-treatment and subsequent sublimation purification. It was found that the dimer phase emits very bright red light under the irradiation of low energy ultra-violet light.

  18. Photocrosslinking of human telomeric G-quadruplex loops by anti cyclobutane thymine dimer formation

    National Research Council Canada - National Science Library

    Dian G. T. Su; Huafeng Fang; Michael L. Gross; John-Stephen A. Taylor


    .... UVB irradiation of d[AGGG(TTAGGG) 3 ] in the presence of Na + results in a cis,syn thymine dimer between two adjacent Ts in a TTA loop and a mixture of nonadjacent anti thymine dimers between various loops...

  19. Excited electronic states from a variational approach based on symmetry-projected Hartree--Fock configurations

    CERN Document Server

    Jiménez-Hoyos, Carlos A; Scuseria, Gustavo E


    Recent work from our research group has demonstrated that symmetry-projected Hartree--Fock (HF) methods provide a compact representation of molecular ground state wavefunctions based on a superposition of non-orthogonal Slater determinants. The symmetry-projected ansatz can account for static correlations in a computationally efficient way. Here we present a variational extension of this methodology applicable to excited states of the same symmetry as the ground state. Benchmark calculations on the C$_2$ dimer with a modest basis set, which allows comparison with full configuration interaction results, indicate that this extension provides a high quality description of the low-lying spectrum for the entire dissociation profile. We apply the same methodology to obtain the full low-lying vertical excitation spectrum of formaldehyde, in good agreement with available theoretical and experimental data, as well as to a challenging model $C_{2v}$ insertion pathway for BeH$_2$. The variational excited state methodolo...

  20. Description of ground and excited electronic states by ensemble density functional method with extended active space (United States)

    Filatov, Michael; Martínez, Todd J.; Kim, Kwang S.


    An extended variant of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, the REKS(4,4) method, designed to describe the ground electronic states of strongly multireference systems is modified to enable calculation of excited states within the time-independent variational formalism. The new method, the state-interaction state-averaged REKS(4,4), i.e., SI-SA-REKS(4,4), is capable of describing several excited states of a molecule involving double bond cleavage, polyradical character, or multiple chromophoric units. We demonstrate that the new method correctly describes the ground and the lowest singlet excited states of a molecule (ethylene) undergoing double bond cleavage. The applicability of the new method for excitonic states is illustrated with π stacked ethylene and tetracene dimers. We conclude that the new method can describe a wide range of multireference phenomena.

  1. Topological excitations in magnetic materials

    Energy Technology Data Exchange (ETDEWEB)

    Bazeia, D., E-mail: [Departamento de Física, Universidade Federal da Paraíba, 58051-970 João Pessoa, PB (Brazil); Doria, M.M. [Instituto de Física, Universidade Federal do Rio de Janeiro, Rio de Janeiro (Brazil); Dipartimento di Fisica, Università di Camerino, I-62032 Camerino (Italy); Rodrigues, E.I.B. [Departamento de Física, Universidade Federal da Paraíba, 58051-970 João Pessoa, PB (Brazil)


    In this work we propose a new route to describe topological excitations in magnetic systems through a single real scalar field. We show here that spherically symmetric structures in two spatial dimensions, which map helical excitations in magnetic materials, admit this formulation and can be used to model skyrmion-like structures in magnetic materials.

  2. Plasmid DNA linearization in the antibacterial action of a new fluorescent Ag nanoparticle-paracetamol dimer composite (United States)

    Sahoo, Amaresh Kumar; Sk, Md Palashuddin; Ghosh, Siddhartha Sankar; Chattopadhyay, Arun


    Herein, we report the generation of a composite comprised of p-hydroxyacetanilide dimer and Ag nanoparticles (NPs) by reaction of AgNO3 and p-hydroxyacetanilide. The formation of the composite was established by UV-vis, FTIR and NMR spectroscopy, transmission electron microscopy and X-ray diffraction along with substantiation by mass spectrometry. Interestingly, the composite exhibited an emission spectrum with a peak at 435 nm when excited by light of wavelength 320 nm. The composite showed superior antimicrobial activity with respect to its individual components against a wide range of Gram positive and Gram negative bacteria at relatively low concentrations of Ag NPs and at which there was no apparent cytotoxicity against mammalian cells. Our results suggest that the composite strongly interacted with the bacterial cell walls leading to cell bursting. Interestingly, enhancement in the reactive oxygen species (ROS) generation in bacteria was observed in the presence of the composite. It is proposed that the ROS generation led to oxidation of the dimer to N-acetyl-p-benzoquinone imine (NAPQI). The generated NAPQI acted as a DNA gyrase inhibitor causing cell death following linearization of DNA.Herein, we report the generation of a composite comprised of p-hydroxyacetanilide dimer and Ag nanoparticles (NPs) by reaction of AgNO3 and p-hydroxyacetanilide. The formation of the composite was established by UV-vis, FTIR and NMR spectroscopy, transmission electron microscopy and X-ray diffraction along with substantiation by mass spectrometry. Interestingly, the composite exhibited an emission spectrum with a peak at 435 nm when excited by light of wavelength 320 nm. The composite showed superior antimicrobial activity with respect to its individual components against a wide range of Gram positive and Gram negative bacteria at relatively low concentrations of Ag NPs and at which there was no apparent cytotoxicity against mammalian cells. Our results suggest that the

  3. Tricriticality for dimeric Coulomb molecular crystals in ground state (United States)

    Travěnec, Igor; Šamaj, Ladislav


    We study the ground-state properties of a system of dimers. Each dimer consists in a pair of equivalent charges at a fixed distance, immersed in a neutralizing homogeneous background. All charges interact pairwisely by Coulomb potential. The dimer centers form a two-dimensional rectangular lattice with the aspect ratio α\\in [0, 1] and each dimer is allowed to rotate around its center. The previous numerical simulations, made for the more general Yukawa interaction, indicate that only two basic dimer configurations can appear: either all dimers are parallel or they have two different angle orientations within alternating (checkerboard) sublattices. As the dimer size increases, two second-order phase transitions, related to two kinds of the symmetry breaking in dimer’s orientations, were reported. In this paper, we use a recent analytic method based on an expansion of the interaction energy in Misra functions which converges quickly and provides an analytic derivation of the critical behaviour. Our main result is that there exists a specific aspect ratio of the rectangular lattice α^*=0.714 106 840 000 71\\ldots which divides the space of model’s phases onto two distinct regions. If the lattice aspect ratio α>α* , we recover both types of the second-order phase transitions and find that they are of mean-field type with the critical exponent β = 1/2 . If 0.711 535≤slantα<α* , the phase transition associated with the discontinuity of dimer’s angles on alternating sublattices becomes of first order. For α=α* , the first- and second-order phase transitions meet at the tricritical point, characterized by the different critical index β = 1/4 . Such phenomenon is known from literature about the Landau theory of one-component fields, but in our two-component version the scenario is more complicated: the component which is already in the symmetry-broken state at the tricritical point also interferes and exhibits unexpectedly the mean-field singular

  4. Designer interface peptide grafts target estrogen receptor alpha dimerization

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, S. [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Asare, B.K. [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States); Biswas, P.K., E-mail: [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Rajnarayanan, R.V., E-mail: [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States)


    The nuclear transcription factor estrogen receptor alpha (ERα), triggered by its cognate ligand estrogen, regulates a variety of cellular signaling events. ERα is expressed in 70% of breast cancers and is a widely validated target for anti-breast cancer drug discovery. Administration of anti-estrogen to block estrogen receptor activation is still a viable anti-breast cancer treatment option but anti-estrogen resistance has been a significant bottle-neck. Dimerization of estrogen receptor is required for ER activation. Blocking ERα dimerization is therefore a complementary and alternative strategy to combat anti-estrogen resistance. Dimer interface peptide “I-box” derived from ER residues 503–518 specifically blocks ER dimerization. Recently using a comprehensive molecular simulation we studied the interaction dynamics of ERα LBDs in a homo-dimer. Based on this study, we identified three interface recognition peptide motifs LDKITDT (ERα residues 479–485), LQQQHQRLAQ (residues 497–506), and LSHIRHMSNK (residues 511–520) and reported the suitability of using LQQQHQRLAQ (ER 497–506) as a template to design inhibitors of ERα dimerization. Stability and self-aggregation of peptide based therapeutics poses a significant bottle-neck to proceed further. In this study utilizing peptide grafted to preserve their pharmacophoric recognition motif and assessed their stability and potential to block ERα mediated activity in silico and in vitro. The Grafted peptides blocked ERα mediated cell proliferation and viability of breast cancer cells but did not alter their apoptotic fate. We believe the structural clues identified in this study can be used to identify novel peptidometics and small molecules that specifically target ER dimer interface generating a new breed of anti-cancer agents. - Highlights: • Designer peptide grafts retain core molecular recognition motif during MD simulations. • Designer peptide grafts with Poly-ALA helix form stable

  5. New lower bound for the Capacitated Arc Routing Problem

    DEFF Research Database (Denmark)

    Wøhlk, Sanne


    We present a new lower bound, the Multiple Cuts Node Duplication Lower Bound, for the undirected Capacitated Arc Routing Problem.We prove that this new bound dominates the existing bounds for the problem. Computational results are also provided.......We present a new lower bound, the Multiple Cuts Node Duplication Lower Bound, for the undirected Capacitated Arc Routing Problem.We prove that this new bound dominates the existing bounds for the problem. Computational results are also provided....

  6. The Fc segment of IgE influences the kinetics of dissociation of a symmetrical bivalent ligand from cyclic dimeric complexes. (United States)

    Subramanian, K; Holowka, D; Baird, B; Goldstein, B


    As part of a systematic effort to determine the features of immunoglobulin E-receptor (IgE-Fc epsilon RI) aggregation that are critical for cellular activation, we used fluorescence to examine the dissociation of a soluble bivalent ligand, N, N'-bis[[epsilon-[(2,4-dinitrophenyl)amino]caproyl]-L-tyrosyl]-L-cystine ((DCT)2-cys), from soluble bivalent IgE and its bivalent F(ab')2 and monovalent Fab' fragments. Cross-linking of Fab' fragments by (DCT)2-cys is limited to linear dimers, and we find that (DCT)2-cys dissociation from Fab' occurs with a single kinetic coefficient [(4.2 +/- 0.6) x 10-3 s-1] that corresponds to the lower of the two kinetic coefficients observed with the bivalent IgE [(4.7 +/- 0.7) x 10-2 s-1 and (4.4 +/- 0.3) x 10-3 s-1]. Similarly, the lower value is obtained for dissociation of (DCT)2-cys that is monovalently bound to IgE after incubation with a large excess of the ligand. (DCT)2-cys can bind to bivalent F(ab')2 fragments and form a variety of linear and cyclic aggregates, similarly to IgE, but, unlike IgE, we find that dissociation occurs with a single kinetic coefficient similar to that observed for Fab'. We find that IgE and its (Fab')2 fragments form highly stable cyclic dimer rings with two (DCT)2-cys. We demonstrate that the kinetic coefficients are independent of enhanced fluorescence quenching observed for bound sites in cyclic dimers. Together, the results show that the rate constant for breaking a linear cross-link formed by (DCT)2-cys is the same as that for dissociation of the monovalently bound (DCT)2-cys. Further, they show that opening of a bond in a dimer ring for the F(ab')2 fragment occurs with approximately the same dissociation rate constant as opening a bond in a linear cross-link. This rate constant is about three times smaller than that observed with IgE, suggesting that steric strain is caused by apposed Fc segments in cyclic IgE dimers. Such structural interference may affect the functional consequences of Ig

  7. Photosensitized Cleavage of the Thymine Dimer in DNA via Carbazole Nucleoside


    Yoshimura, Yoshinaga; Taya, Yuta; Matsumura, Hiroshi; Fujimoto, Kenzo


    We report the catalytic repair of a thymine dimer incorporated in a DNA duplex via oligodeoxynucleotide (ODN) containing carbazole nucleoside. The occurrence of an electron transfer between carbazole nucleoside and thymine dimer is evidenced by fluorescence quenching measurements. Carbazole nucleoside acts as a good electron donor for the catalytic repair of a thymine dimer.

  8. Photoinduced repair of a thymine dimer in DNA via carbazole nucleoside. (United States)

    Yoshimura, Yoshinaga; Fujimoto, Kenzo


    We report the photoinduced repair of a thymine dimer incorporated in a DNA duplex via oligodeoxynucleotide (ODN) containing carbazole nucleoside (K). The occurrence of an electron transfer between K and thymine dimer is evidenced by fluorescence quenching measurements. K acts as a good electron donor for the photoinduced repair of a thymine dimer.

  9. A first principles study of fluorescence quenching in rhodamine B dimers : how can quenching occur in dimeric species?

    NARCIS (Netherlands)

    Setiawan, Dani; Kazaryan, Andranik; Martoprawiro, Muhamad Abdulkadir; Filatov, Michael


    Rhodamine B (RhB) is widely used in chemistry and biology due to its high fluorescence quantum yield. In high concentrations, the quantum yield of fluorescence decreases considerably which is attributed to the formation of RhB dimers. In the present work, a possible mechanism of fluorescence

  10. Higher order expansions for the entropy of a dimer or a monomer-dimer system on d-dimensional lattices

    CERN Document Server

    Butera, Paolo; Pernici, Mario


    Recently an expansion as a power series in 1/d has been presented for the specific entropy of a complete dimer covering of a d-dimensional hypercubic lattice. This paper extends from 3 to 10 the number of terms known in the series. Likewise an expansion for the entropy, dependent on the dimer-density p, of a monomer-dimer system, involving a sum sum_k a_k(d) p^k, has been recently offered. We herein extend the number of the known expansion coefficients from 6 to 20 for the hyper-cubic lattices of general dimension d and from 6 to 24 for the hyper-cubic lattices of dimensions d 2. The computations of this paper have led us to make the following marvelous conjecture: "In the case of the hyper-cubic lattices, all the expansion coefficients, a_k(d), are positive"! This paper results from a simple melding of two disparate research programs: one computing to high orders the Mayer series coefficients of a dimer gas, the other studying the development of entropy from these coefficients. An effort is made to make thi...

  11. Entanglement asymmetry for boosted black branes and the bound (United States)

    Mishra, Rohit; Singh, Harvendra


    We study the effects of asymmetry in the entanglement thermodynamics of CFT subsystems. It is found that “boosted” Dp-brane backgrounds give rise to the first law of the entanglement thermodynamics where the CFT pressure asymmetry plays a decisive role in the entanglement. Two different strip like subsystems, one parallel to the boost and the other perpendicular, are studied in the perturbative regime Tthermal ≪ TE. We mainly seek to quantify this entanglement asymmetry as a ratio of the first-order entanglement entropies of the excitations. We discuss the AdS-wave backgrounds at zero temperature having maximum asymmetry from where a bound on entanglement asymmetry is obtained. The entanglement asymmetry reduces as we switch on finite temperature in the CFT while it is maximum at zero temperature.

  12. Excitability constraints on voltage-gated sodium channels.

    Directory of Open Access Journals (Sweden)

    Elaine Angelino


    Full Text Available We study how functional constraints bound and shape evolution through an analysis of mammalian voltage-gated sodium channels. The primary function of sodium channels is to allow the propagation of action potentials. Since Hodgkin and Huxley, mathematical models have suggested that sodium channel properties need to be tightly constrained for an action potential to propagate. There are nine mammalian genes encoding voltage-gated sodium channels, many of which are more than approximately 90% identical by sequence. This sequence similarity presumably corresponds to similarity of function, consistent with the idea that these properties must be tightly constrained. However, the multiplicity of genes encoding sodium channels raises the question: why are there so many? We demonstrate that the simplest theoretical constraints bounding sodium channel diversity--the requirements of membrane excitability and the uniqueness of the resting potential--act directly on constraining sodium channel properties. We compare the predicted constraints with functional data on mammalian sodium channel properties collected from the literature, including 172 different sets of measurements from 40 publications, wild-type and mutant, under a variety of conditions. The data from all channel types, including mutants, obeys the excitability constraint; on the other hand, channels expressed in muscle tend to obey the constraint of a unique resting potential, while channels expressed in neuronal tissue do not. The excitability properties alone distinguish the nine sodium channels into four different groups that are consistent with phylogenetic analysis. Our calculations suggest interpretations for the functional differences between these groups.

  13. Co-Binding of Pharmaceutical Compounds at Mineral Surfaces: Molecular Investigations of Dimer Formation at Goethite/Water Interfaces. (United States)

    Xu, Jing; Marsac, Rémi; Costa, Dominique; Cheng, Wei; Wu, Feng; Boily, Jean-François; Hanna, Khalil


    The emergence of antibiotic and anti-inflammatory agents in aquatic and terrestrial systems is becoming a serious threat to human and animal health worldwide. Because pharmaceutical compounds rarely exist individually in nature, interactions between various compounds can have unforeseen effects on their binding to mineral surfaces. This work demonstrates this important possibility for the case of two typical antibiotic and anti-inflammatory agents (nalidixic acid (NA) and niflumic acid (NFA)) bound at goethite (α-FeOOH) used as a model mineral surface. Our multidisciplinary study, which makes use of batch sorption experiments, vibration spectroscopy and periodic density functional theory calculations, reveals enhanced binding of the otherwise weakly bound NFA caused by unforeseen intermolecular interactions with mineral-bound NA. This enhancement is ascribed to the formation of a NFA-NA dimer whose energetically favored formation (-0.5 eV compared to free molecules) is predominantly driven by van der Waals interactions. A parallel set of efforts also showed that no cobinding occurred with sulfamethoxazole (SMX) because of the lack of molecular interactions with coexisting contaminants. As such, this article raises the importance of recognizing drug cobinding, and lack of cobinding, for predicting and developing policies on the fate of complex mixtures of antibiotics and anti-inflammatory agents in nature.

  14. Bounded rationality and learning in complex markets

    NARCIS (Netherlands)

    Hommes, C.H.; Barkely Rosser Jr, J.


    This chapter reviews some work on bounded rationality, expectation formation and learning in complex markets, using the familiar demand-supply cobweb model. We emphasize two stories of bounded rationality, one story of adaptive learning and another story of evolutionary selection. According to the

  15. Bounded rationality and learning in complex markets

    NARCIS (Netherlands)

    Hommes, C.H.


    This chapter reviews some work on bounded rationality, expectation formation and learning in complex markets, using the familiar demand-supply cobweb model. We emphasize two stories of bounded rationality, one story of adaptive learning and another story of evolutionary selection. According to the

  16. Spatial coagulation with bounded coagulation rate


    Bailleul, Ismael


    We prove that the spatial coagulation equation with bounded coagulation rate is well-posed for all times in a given class of kernels if the convection term of the underlying particle dynamics has divergence bounded below by a positive constant. Multiple coagulations, fragmentation and scattering are also considered.

  17. Schroedinger upper bounds to semirelativistic eigenvalues

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Richard L [Department of Mathematics and Statistics, Concordia University, 1455 de Maisonneuve Boulevard West, Montreal, Quebec, H3G 1M8 (Canada); Lucha, Wolfgang [Institut fuer Hochenergiephysik, Oesterreichische Akademie der Wissenschaften, Nikolsdorfergasse 18, A-1050 Vienna (Austria)


    Problems posed by semirelativistic Hamiltonians of the form H = {radical}(m{sup 2} + p{sup 2}) + V(r) are studied. It is shown that energy upper bounds can be constructed in terms of certain related Schroedinger operators; these bounds include free parameters which can be chosen optimally.

  18. No-arbitrage bounds for financial scenarios

    DEFF Research Database (Denmark)

    Geyer, Alois; Hanke, Michael; Weissensteiner, Alex


    We derive no-arbitrage bounds for expected excess returns to generate scenarios used in financial applications. The bounds allow to distinguish three regions: one where arbitrage opportunities will never exist, a second where arbitrage may be present, and a third, where arbitrage opportunities...

  19. Nonatomic dual bakery algorithm with bounded tokens

    NARCIS (Netherlands)

    Aravind, Alex A.; Hesselink, Wim H.

    A simple mutual exclusion algorithm is presented that only uses nonatomic shared variables of bounded size, and that satisfies bounded overtaking. When the shared variables behave atomically, it has the first-come-first-served property (FCFS). Nonatomic access makes information vulnerable. The

  20. Polynomially Bounded Sequences and Polynomial Sequences

    Directory of Open Access Journals (Sweden)

    Okazaki Hiroyuki


    Full Text Available In this article, we formalize polynomially bounded sequences that plays an important role in computational complexity theory. Class P is a fundamental computational complexity class that contains all polynomial-time decision problems [11], [12]. It takes polynomially bounded amount of computation time to solve polynomial-time decision problems by the deterministic Turing machine. Moreover we formalize polynomial sequences [5].

  1. Upper Bounds on Numerical Approximation Errors

    DEFF Research Database (Denmark)

    Raahauge, Peter


    This paper suggests a method for determining rigorous upper bounds on approximationerrors of numerical solutions to infinite horizon dynamic programming models.Bounds are provided for approximations of the value function and the policyfunction as well as the derivatives of the value function...

  2. On the range of completely bounded maps

    Directory of Open Access Journals (Sweden)

    Richard I. Loebl


    Full Text Available It is shown that if every bounded linear map from a C*-algebra α to a von Neumann algebra β is completely bounded, then either α is finite-dimensional or β⫅⊗Mn, where is a commutative von Neumann algebra and Mn is the algebra of n×n complex matrices.

  3. A polynomial lower bound for testing monotonicity

    NARCIS (Netherlands)

    A. Belovs (Aleksandr); Blais, E. (Eric)


    textabstractWe show that every algorithm for testing n-variate Boolean functions for monotonicity has query complexity Ω(n1/4). All previous lower bounds for this problem were designed for nonadaptive algorithms and, as a result, the best previous lower bound for general (possibly adaptive)

  4. Solvent-Controlled Branching of Localized versus Delocalized Singlet Exciton States and Equilibration with Charge Transfer in a Structurally Well-Defined Tetracene Dimer

    Energy Technology Data Exchange (ETDEWEB)

    Cook, Jasper D. [Department; Carey, Thomas J. [Department; Arias, Dylan H. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Johnson, Justin C. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Damrauer, Niels H. [Department


    A detailed photophysical picture is elaborated for a structurally well-defined and symmetrical bis-tetracene dimer in solution. The molecule was designed for interrogation of the initial photophysical steps (S1 - 1TT) in intramolecular singlet fission (SF). (Triisopropylsilyl)acetylene substituents on the dimer TIPS-BT1 as well as a monomer model TIPS-Tc enable a comparison of photophysical properties, including transient absorption dynamics, as solvent polarity is varied. In nonpolar toluene solutions, TIPS-BT1 decays via radiative and nonradiative pathways to the ground state with no evidence for dynamics related to the initial stages of SF. This contrasts with the behavior of the previously reported unsubstituted dimer BT1 and is likely a consequence of energetic perturbations to the singlet excited-state manifold of TIPS-BT1 by the (trialkylsilyl)acetylene substituents. In polar benzonitrile, two key findings emerge. First, photoexcited TIPS-BT1 shows a bifurcation into both arm-localized (S1-loc) and dimer-delocalized (S1-dim) singlet exciton states. The S1-loc decays to the ground state, and weak temperature dependence of its emissive signatures suggests that once it is formed, it is isolated from S1-dim. Emissive signatures of the S1-dim state, on the other hand, are strongly temperature-dependent, and transient absorption dynamics show that S1-dim equilibrates with an intramolecular charge-transfer state in 50 ps at room temperature. This equilibrium decays to the ground state with little evidence for formation of long-lived triplets nor 1TT. These detailed studies spectrally characterize many of the key states in intramolecular SF in this class of dimers but highlight the need to tune electronic coupling and energetics for the S1 - 1TT photoreaction.

  5. Evaluation of stability difference between asymmetric homochiral dimer in (S)-thalidomide crystal and symmetric heterochiral dimer in (RS)-thalidomide crystal (United States)

    Suzuki, Toshiya; Tanaka, Masahito; Shiro, Motoo; Shibata, Norio; Osaka, Tetsuya; Asahi, Toru


    This article discusses differences in physicochemical properties such as solubility and melting point between (S)-thalidomide and (RS)-thalidomide based on crystal structures determined by X-ray diffraction experiments. Investigation of such differences is of great importance because thalidomide has attracted considerable attention again due to its wide-range bioactivity for intractable diseases. In this article, structures of hydrogen-bonded rings were compared between asymmetric homochiral dimers in (S)-thalidomide crystal and symmetric heterochiral dimers in (RS)-thalidomide crystal. The heterochiral dimer was evaluated to be more stable than the homochiral dimer by the energy calculations for hydrogen-bonded rings in those dimers. These results indicate that differences in physicochemical properties between enantiomeric and racemic thalidomides originate from the difference of structural stability between homochiral and heterochiral dimers.

  6. The PH domain of phosphoinositide-dependent kinase-1 exhibits a novel, phospho-regulated monomer-dimer equilibrium with important implications for kinase domain activation: single-molecule and ensemble studies. (United States)

    Ziemba, Brian P; Pilling, Carissa; Calleja, Véronique; Larijani, Banafshé; Falke, Joseph J


    Phosphoinositide-dependent kinase-1 (PDK1) is an essential master kinase recruited to the plasma membrane by the binding of its C-terminal PH domain to the signaling lipid phosphatidylinositol-3,4,5-trisphosphate (PIP3). Membrane binding leads to PDK1 phospho-activation, but despite the central role of PDK1 in signaling and cancer biology, this activation mechanism remains poorly understood. PDK1 has been shown to exist as a dimer in cells, and one crystal structure of its isolated PH domain exhibits a putative dimer interface. It has been proposed that phosphorylation of PH domain residue T513 (or the phospho-mimetic T513E mutation) may regulate a novel PH domain dimer-monomer equilibrium, thereby converting an inactive PDK1 dimer to an active monomer. However, the oligomeric states of the PH domain on the membrane have not yet been determined, nor whether a negative charge at position 513 is sufficient to regulate its oligomeric state. This study investigates the binding of purified wild-type (WT) and T513E PDK1 PH domains to lipid bilayers containing the PIP3 target lipid, using both single-molecule and ensemble measurements. Single-molecule analysis of the brightness of the fluorescent PH domain shows that the PIP3-bound WT PH domain on membranes is predominantly dimeric while the PIP3-bound T513E PH domain is monomeric, demonstrating that negative charge at the T513 position is sufficient to dissociate the PH domain dimer and is thus likely to play a central role in PDK1 monomerization and activation. Single-molecule analysis of two-dimensional (2D) diffusion of PH domain-PIP3 complexes reveals that the dimeric WT PH domain diffuses at the same rate as a single lipid molecule, indicating that only one of its two PIP3 binding sites is occupied and there is little penetration of the protein into the bilayer as observed for other PH domains. The 2D diffusion of T513E PH domain is slower, suggesting the negative charge disrupts local structure in a way that allows

  7. Bound-states of D-branes in L-R asymmetric superstring vacua

    CERN Document Server

    Bianchi, Massimo


    We discuss bound-states of D-branes in truly L-R asymmetric and thus non-geometric Type II vacuum configurations with extended supersymmetry. We argue for their stability as a result of residual supersymmetry and coupling to R-R potentials surviving in the massless spectrum. We then identify the open string excitations of these L-R asymmetric BPS D-branes. Finally, we briefly comment on possible applications and extensions.

  8. Excited cooper pairs

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Arrietea, M. G.; Solis, M. A.; De Llano, M. [Universidad Nacional Autonoma de Mexico, Mexico, D.F (Mexico)


    Excited cooper pairs formed in a many-fermion system are those with nonzero total center-of mass momentum (CMM). They are normally neglected in the standard Bardeen-Cooper-Schrieffer (BCS) theory of superconductivity for being too few compared with zero CMM pairs. However, a Bose-Einstein condensation picture requires both zero and nonzero CMM pairs. Assuming a BCS model interaction between fermions we determine the populations for all CMM values of Cooper pairs by actually calculating the number of nonzero-CMM pairs relative to that of zero-CMM ones in both 2D and 3D. Although this ratio decreases rapidly with CMM, the number of Cooper pairs for any specific CMM less than the maximum (or breakup of the pair) momentum turns out to be typically larger than about 95% of those with zero-CMM at zero temperature T. Even at T {approx}100 K this fraction en 2D is still as large as about 70% for typical quasi-2D cuprate superconductor parameters. [Spanish] Los pares de cooper excitados formados en un sistema de muchos electrones, son aquellos con momentos de centro de masa (CMM) diferente de cero. Normalmente estos no son tomados en cuenta en la teoria estandar de la superconductividad de Bardeen-Cooper-Schrieffer (BCS) al suponer que su numero es muy pequeno comparados con los pares de centro de masa igual a cero. Sin embargo, un esquema de condensacion Bose-Einstein requiere de ambos pares, con CMM cero y diferente de cero. Asumiendo una interaccion modelo BCS entre los fermiones, determinamos la poblacion de pares cooper con cada uno de todos los posibles valores del CMM calculando el numero de pares con momentos de centro de masa diferente de cero relativo a los pares de CMM igual a cero, en 2D y 3D. Aunque esta razon decrece rapidamente con el CMM, el numero de pares de cooper para cualquier CMM especifico menor que el momento maximo (o rompimiento de par) es tipicamente mas grande que el 95% de aquellos con CMM cero. Aun a T {approx}100 K esta fraccion en 2D es

  9. Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog. (United States)

    Jian, Yajun; Maximowitsch, Egle; Liu, Degang; Adhikari, Surya; Li, Lei; Domratcheva, Tatiana


    Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Contactless friction and the {sup 3}He-{sup 4}He dimer. Studies with the atomic-beam spin-echo spectrometer; Kontaktlose Reibung und das {sup 3}He-{sup 4}He-Dimer. Untersuchungen mit dem Atomstrahlspinechospektrometer

    Energy Technology Data Exchange (ETDEWEB)

    Janke, Matthias


    In this thesis the time of flight resolved atomic beam spin echo method (SEToF) is applied to a {sup 3}He-beam for the first time and studied systematically. This method is shown to be superior to the usual atomic beam spin echo technique. With SEToF it is possible to almost completely remove unpolarized background and to reach a beam polarisation close to 100%. The SEToF technique is shown to be crucial for the first experimental proof of the existence of the {sup 3}He-{sup 4}He dimer. This dimer is the weakest bound van-der-Waals-molecule known to date. Furthermore, a drag force between an atom and a dielectric surface is detected originating from the fluctuating dipole moment of the atom. Not only the measured friction coefficients match their theoretical predictions perfectly, but our data also shows the correct temperature dependence. A great many technological renewals and improvements were installed in the apparatus during this thesis work. They have become necessary or sensible due to the relocation of the physics institute. A few of them are documented and motivated in this thesis.

  11. A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima.

    Directory of Open Access Journals (Sweden)

    Alessia Ruggiero

    Full Text Available The arginine binding protein from Thermatoga maritima (TmArgBP, a substrate binding protein (SBP involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate the atomic level structural properties of this intriguing protein, we determined the crystallographic structures of the apo and the arginine-bound forms of TmArgBP using MAD and SAD methods, respectively. The comparison of the liganded and unliganded models demonstrates that TmArgBP tertiary structure undergoes a very large structural re-organization upon arginine binding. This transition follows the Venus Fly-trap mechanism, although the entity of the re-organization observed in TmArgBP is larger than that observed in homologous proteins. Intriguingly, TmArgBP dimerizes through the swapping of the C-terminal helix. This dimer is stabilized exclusively by the interactions established by the swapping helix. Therefore, the TmArgBP dimer combines a high level of stability and conformational freedom. The structure of the TmArgBP dimer represents an uncommon example of large tertiary structure variations amplified at quaternary structure level by domain swapping. Although the biological relevance of the dimer needs further assessments, molecular modelling suggests that the two TmArgBP subunits may simultaneously interact with two distinct ABC transporters. Moreover, the present protein structures provide some clues about the determinants of the extraordinary stability of the biomolecule

  12. Uniform excitations in magnetic nanoparticles

    Directory of Open Access Journals (Sweden)

    Steen Mørup


    Full Text Available We present a short review of the magnetic excitations in nanoparticles below the superparamagnetic blocking temperature. In this temperature regime, the magnetic dynamics in nanoparticles is dominated by uniform excitations, and this leads to a linear temperature dependence of the magnetization and the magnetic hyperfine field, in contrast to the Bloch T3/2 law in bulk materials. The temperature dependence of the average magnetization is conveniently studied by Mössbauer spectroscopy. The energy of the uniform excitations of magnetic nanoparticles can be studied by inelastic neutron scattering.

  13. Uniform excitations in magnetic nanoparticles

    DEFF Research Database (Denmark)

    Mørup, Steen; Frandsen, Cathrine; Hansen, Mikkel Fougt


    We present a short review of the magnetic excitations in nanoparticles below the superparamagnetic blocking temperature. In this temperature regime, the magnetic dynamics in nanoparticles is dominated by uniform excitations, and this leads to a linear temperature dependence of the magnetization...... and the magnetic hyperfine field, in contrast to the Bloch T3/2 law in bulk materials. The temperature dependence of the average magnetization is conveniently studied by Mössbauer spectroscopy. The energy of the uniform excitations of magnetic nanoparticles can be studied by inelastic neutron scattering....

  14. Thermochemistry of HO2 + HO2 → H2O4: Does HO2 Dimerization Affect Laboratory Studies? (United States)

    Sprague, Matthew K; Irikura, Karl K


    Self-reaction is an important sink for the hydroperoxy radical (HO2) in the atmosphere. It has been suggested (Denis, P. A.; Ornellas, F. R. J. Phys. Chem. A, 2009, 113 (2), 499-506) that the minor product hydrogen tetroxide (HO4H) may act as a reservoir of HO2. Here, we compute the thermochemistry of HO2 self-reactions to determine if either HO4H or the cyclic hydrogen-bound dimer (HO2)2 can act as reservoirs. We computed electronic energies using coupled-cluster calculations in the complete basis set limit, CCSD(T)/CBS[45]//CCSD(T)/cc-pVTZ. Our model chemistry includes corrections for vibrational anharmonicity in the zero-point energy and vibrational partition functions, core-valence correlation, scalar relativistic effects, diagonal Born-Oppenheimer, spin-orbit splitting, and higher-order corrections. We compute the Gibbs energy of dimerization to be (-20.1 ± 1.6) kJ/mol at 298.15 K (2σ uncertainty), and (-32.3 ± 1.5) kJ/mol at 220 K. For atmospherically relevant [HO2] = 10(8) molecules per cm(3), our thermochemistry indicates that dimerization will be negligible, and thus H2O4 species are atmospherically unimportant. Under conditions used in laboratory experiments ([HO2] > 10(12) molecules per cm(3), 220 K), H2O4 formation may be significant. We compute two absorption spectra that could be used for laboratory detection of HO4H: the OH stretch overtone (near-IR) and electronic (UV) spectra.

  15. Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA. (United States)

    Masson, Fanny; Laino, Teodoro; Tavernelli, Ivano; Rothlisberger, Ursula; Hutter, Jürg


    Formation of the thymine dimer is one of the most important types of photochemical damage in DNA, responsible for several biological pathologies. Though specifically designed proteins (photolyases) can efficiently repair this type of damage in living cells, an autocatalytic activity of the DNA itself was recently discovered, allowing for a self-repair mechanism. In this paper, we provide the first molecular dynamics study of the splitting of thymine dimer radical anions, using a quantum mechanical/molecular mechanics (QM/MM) approach based on density functional theory (DFT) to describe the quantum region. A set of seven statistically representative molecular dynamics trajectories is analyzed. Our calculations predict an asynchronously concerted process in which C5-C5' bond breaking is barrierless while C6-C6' bond breaking is characterized by a small free energy barrier. An upper bound of 2.5 kcal/mol for this barrier is estimated. Moreover, the molecular dynamics study and the low free energy barrier involved in C6-C6' bond breaking characterize the full process as being an ultrafast reaction.

  16. Structure of the weakly bound triatomic He2Li and He2Na molecules (United States)

    Suno, Hiroya


    We study the structure of triatomic molecules containing two helium atoms and one alkali-metal atom X (X = Li, Na). The three-body Schrödinger equation is solved in hyperspherical coordinates using the He-He and He-X pair van der Waals potentials available in the literature. We calculate the structural properties of the He2Li and He2Na bound states, and analyze one-dimensional pair and angle distribution functions as well as two-dimensional pair-pair and angle-angle distribution functions. These bound states are characterized by so peculiar weakly bound structures that classifying them into particular sizes and geometrical shapes appears to be elusive. Particularly, the JΠ=0+ excited states of He426Li and He427Li are found to constitute giant triatomic molecules with their size amounting to several hundred bohrs.

  17. From the tunneling dimer to the onset of microsolvation: Infrared spectroscopy of allyl radical water aggregates in helium nanodroplets (United States)

    Leicht, Daniel; Kaufmann, Matin; Pal, Nitish; Schwaab, Gerhard; Havenith, Martina


    The infrared spectrum of allyl:water clusters embedded in helium nanodroplets was recorded. Allyl radicals were produced by flash vacuum pyrolysis and trapped in helium droplets. Deuterated water was added to the doped droplets, and the infrared spectrum of the radical water aggregates was recorded in the frequency range 2570-2820 cm-1. Several absorption bands are observed and assigned to 1:1 and 1:2 allyl:D2O clusters, based on pressure dependent measurements and accompanying quantum chemical calculations. The analysis of the 1:1 cluster spectrum revealed a tunneling splitting as well as a combination band. For the 1:2 cluster, we observe a water dimer-like motif that is bound by one π-hydrogen bond to the allyl radical.

  18. Indirect excitation of ultrafast demagnetization

    National Research Council Canada - National Science Library

    Vodungbo, B; Tudu, B; Perron, J; Delaunay, R; Müller, L; Berntsen, M.H; Grübel, G; Malinowski, G; Weier, C; Gautier, J; Lambert, G; Zeitoun, P; Gutt, C; Jal, E; Reid, A.H; Granitzka, P.W; Jaouen, N; Dakovski, G.L; Moeller, S; Minitti, M.P; Mitra, A; Carron, S; Pfau, B; von Korff Schmising, C; Schneider, M; Eisebitt, S; Lüning, J


    .... Upon excitation with an intense femtosecond-short IR laser pulse, the film exhibits the classical ultrafast demagnetization phenomenon although only a negligible number of IR photons penetrate the aluminum layer...

  19. Transport waves as crystal excitations (United States)

    Cepellotti, Andrea; Marzari, Nicola


    We introduce the concept of transport waves by showing that the linearized Boltzmann transport equation admits excitations in the form of waves that have well-defined dispersion relations and decay times. Crucially, these waves do not represent single-particle excitations, but are collective excitations of the equilibrium distribution functions. We study in detail the case of thermal transport, where relaxons are found in the long-wavelength limit, and second sound is reinterpreted as the excitation of one or several temperature waves at finite frequencies. Graphene is studied numerically, finding decay times of the order of microseconds. The derivation, obtained by a spectral representation of the Boltzmann equation, holds in principle for any crystal or semiclassical transport theory and is particularly relevant when transport takes place in the hydrodynamic regime.

  20. Match-bounded String Rewriting Systems (United States)

    Geser, Alfons; Hofbauer, Dieter; Waldmann, Johannes


    We introduce a new class of automated proof methods for the termination of rewriting systems on strings. The basis of all these methods is to show that rewriting preserves regular languages. To this end, letters are annotated with natural numbers, called match heights. If the minimal height of all positions in a redex is h+1 then every position in the reduct will get height h+1. In a match-bounded system, match heights are globally bounded. Using recent results on deleting systems, we prove that rewriting by a match-bounded system preserves regular languages. Hence it is decidable whether a given rewriting system has a given match bound. We also provide a sufficient criterion for the abence of a match-bound. The problem of existence of a match-bound is still open. Match-boundedness for all strings can be used as an automated criterion for termination, for match-bounded systems are terminating. This criterion can be strengthened by requiring match-boundedness only for a restricted set of strings, for instance the set of right hand sides of forward closures.

  1. Photophysical characterization and time-resolved spectroscopy of a anthradithiophene dimer: exploring the role of conformation in singlet fission

    KAUST Repository

    Dean, Jacob C.


    Quantitative singlet fission has been observed for a variety of acene derivatives such as tetracene and pentacene, and efforts to extend the library of singlet fission compounds is of current interest. Preliminary calculations suggest anthradithiophenes exhibit significant exothermicity between the first optically-allowed singlet state, S1, and 2 × T1 with an energy difference of >5000 cm−1. Given the fulfillment of this ingredient for singlet fission, here we investigate the singlet fission capability of a difluorinated anthradithiophene dimer (2ADT) covalently linked by a (dimethylsilyl)ethane bridge and derivatized by triisobutylsilylethynyl (TIBS) groups. Photophysical characterization of 2ADT and the single functionalized ADT monomer were carried out in toluene and acetone solution via absorption and fluorescence spectroscopy, and their photo-initiated dynamics were investigated with time-resolved fluorescence (TRF) and transient absorption (TA) spectroscopy. In accordance with computational predictions, two conformers of 2ADT were observed via fluorescence spectroscopy and were assigned to structures with the ADT cores trans or cis to one another about the covalent bridge. The two conformers exhibited markedly different excited state deactivation mechanisms, with the minor trans population being representative of the ADT monomer showing primarily radiative decay, while the dominant cis population underwent relaxation into an excimer geometry before internally converting to the ground state. The excimer formation kinetics were found to be solvent dependent, yielding time constants of ∼1.75 ns in toluene, and ∼600 ps in acetone. While the difference in rates elicits a role for the solvent in stabilizing the excimer structure, the rate is still decidedly long compared to most singlet fission rates of analogous dimers, suggesting that the excimer is neither a kinetic nor a thermodynamic trap, yet singlet fission was still not observed. The result

  2. Excited State Properties of Hybrid Perovskites. (United States)

    Saba, Michele; Quochi, Francesco; Mura, Andrea; Bongiovanni, Giovanni


    Metal halide perovskites have come to the attention of the scientific community for the progress achieved in solar light conversion. Energy sustainability is one of the priorities of our society, and materials advancements resulting in low-cost but efficient solar cells and large-area lighting devices represent a major goal for applied research. From a basic point of view, perovskites are an exotic class of hybrid materials combining some merits of organic and inorganic semiconductors: large optical absorption, large mobilities, and tunable band gap together with the possibility to be processed in solution. When a novel class of promising semiconductors comes into the limelight, lively discussions ensue on the photophysics of band-edge excitations, because just the states close to the band edge are entailed in energy/charge transport and light emission. This was the case several decades ago for III-V semiconductors, it has been up to 10 years ago for organics, and it is currently the case for perovskites. Our aim in this Account is to rationalize the body of experimental evidence on perovskite photophysics in a coherent theoretical framework, borrowing from the knowledge acquired over the years in materials optoelectronics. A crucial question is whether photon absorption leads to a population of unbound, conductive free charges or instead excitons, neutral and insulating bound states created by Coulomb interaction just below the energy of the band gap. We first focus on the experimental estimates of the exciton binding energy (Eb): at room temperature, Eb is comparable to the thermal energy kBT in MAPbI3 and increases up to values 2-3kBT in wide band gap MAPbBr3 and MAPbCl3. Statistical considerations predict that these values, even though comparable to or larger than thermal energy, let free carriers prevail over bound excitons for all levels of excitation densities relevant for devices. The analysis of photophysics evidence confirms that all hybrid halide

  3. Indirect excitation of ultrafast demagnetization


    Boris Vodungbo; Bahrati Tudu; Jonathan Perron; Renaud Delaunay; Leonard Müller; Berntsen, Magnus H.; Gerhard Grübel; Grégory Malinowski; Christian Weier; Julien Gautier; Guillaume Lambert; Philippe Zeitoun; Christian Gutt; Emmanuelle Jal; Reid, Alexander H.


    Does the excitation of ultrafast magnetization require direct interaction between the photons of the optical pump pulse and the magnetic layer? Here, we demonstrate unambiguously that this is not the case. For this we have studied the magnetization dynamics of a ferromagnetic cobalt/palladium multilayer capped by an IR-opaque aluminum layer. Upon excitation with an intense femtosecond-short IR laser pulse, the film exhibits the classical ultrafast demagnetization phenomenon although only a ne...

  4. Stochastic Hierarchical Systems: Excitable Dynamics


    Leonhardt, Helmar; Zaks, Michael A.; Falcke, Martin; Schimansky-Geier, Lutz


    We present a discrete model of stochastic excitability by a low-dimensional set of delayed integral equations governing the probability in the rest state, the excited state, and the refractory state. The process is a random walk with discrete states and nonexponential waiting time distributions, which lead to the incorporation of memory kernels in the integral equations. We extend the equations of a single unit to the system of equations for an ensemble of globally coupled oscillators, derive...

  5. Autowaves in moving excitable media

    Directory of Open Access Journals (Sweden)



    Full Text Available Within the framework of kinematic theory of autowaves we suggest a method for analytic description of stationary autowave structures appearing at the boundary between the moving and fixed excitable media. The front breakdown phenomenon is predicted for such structures. Autowave refraction and, particulary, one-side "total reflection" at the boundary is considered. The obtained analytical results are confirmed by computer simulations. Prospects of the proposed method for further studies of autowave dynamics in the moving excitable media are discussed.

  6. Have Gluonic Excitations Been Found?


    Page, Philip R.


    New experimental information on the non-exotic J^PC = 0^-+ isovector seen at 1.8 GeV by VES yields convincing evidence of its excited gluonic (hybrid) nature when a critical study of alternative quarkonium assignments is made in the context of ^3 P_0 decay by flux-tube breaking. Production of this gluonic excitation via meson exchange is promising, although its two photon production vanishes.

  7. D-dimer: An Overview of Hemostasis and Fibrinolysis, Assays, and Clinical Applications. (United States)

    Olson, John D


    D-dimer is the smallest fibrinolysis-specific degradation product found in the circulation. The origins, assays, and clinical use of D-dimer will be addressed. Hemostasis (platelet and vascular function, coagulation, fibrinolysis, hemostasis) is briefly reviewed. D-dimer assays are reviewed. The D-dimer is very sensitive to intravascular thrombus and may be markedly elevated in disseminated intravascular coagulation, acute aortic dissection, and pulmonary embolus. Because of its exquisite sensitivity, negative tests are useful in the exclusion venous thromboembolism. Elevations occur in normal pregnancy, rising two- to fourfold by delivery. D-dimer also rises with age, limiting its use in those >80 years old. There is a variable rise in D-dimer in active malignancy and indicates increased thrombosis risk in active disease. Elevated D-dimer following anticoagulation for a thrombotic event indicates increased risk of recurrent thrombosis. These and other issues are addressed. © 2015 Elsevier Inc. All rights reserved.

  8. Association of atoms into universal dimers using an oscillating magnetic field. (United States)

    Langmack, Christian; Smith, D Hudson; Braaten, Eric


    In a system of ultracold atoms near a Feshbach resonance, pairs of atoms can be associated into universal dimers by an oscillating magnetic field with a frequency near that determined by the dimer binding energy. We present a simple expression for the transition rate that takes into account many-body effects through a transition matrix element of the contact. In a thermal gas, the width of the peak in the transition rate as a function of the frequency is determined by the temperature. In a dilute Bose-Einstein condensate of atoms, the width is determined by the inelastic scattering rates of a dimer with zero-energy atoms. Near an atom-dimer resonance, there is a dramatic increase in the width from inelastic atom-dimer scattering and from atom-atom-dimer recombination. The recombination contribution provides a signature for universal tetramers that are Efimov states consisting of two atoms and a dimer.

  9. Glycine transporter dimers: evidence for occurrence in the plasma membrane

    DEFF Research Database (Denmark)

    Bartholomäus, Ingo; Milan-Lobo, Laura; Nicke, Annette


    membrane based on hydrodynamic and native gel electrophoretic studies. Here, we used cysteine substitution and oxidative cross-linking to show that of GlyT1 and GlyT2 also form dimeric complexes within the plasma membrane. GlyT oligomerization at the cell surface was confirmed for both GlyT1 and GlyT2......Different Na(+)/Cl(-)-dependent neurotransmitter transporters of the SLC6a family have been shown to form dimers or oligomers in both intracellular compartments and at the cell surface. In contrast, the glycine transporters (GlyTs) GlyT1 and -2 have been reported to exist as monomers in the plasma...

  10. d -wave superconductivity in boson+fermion dimer models (United States)

    Goldstein, Garry; Chamon, Claudio; Castelnovo, Claudio


    We present a slave-particle mean-field study of the mixed boson+fermion quantum dimer model introduced by Punk et al. [Proc. Natl. Acad. Sci. USA 112, 9552 (2015), 10.1073/pnas.1512206112] to describe the physics of the pseudogap phase in cuprate superconductors. Our analysis naturally leads to four charge e fermion pockets whose total area is equal to the hole doping p for a range of parameters consistent with the t -J model for high-temperature superconductivity. Here we find that the dimers are unstable to d -wave superconductivity at low temperatures. The region of the phase diagram with d -wave rather than s -wave superconductivity matches well with the appearance of the four fermion pockets. In the superconducting regime, the dispersion contains eight Dirac cones along the diagonals of the Brillouin zone.

  11. Cytotoxic bibenzyl dimers from the stems of Dendrobium fimbriatum Hook. (United States)

    Xu, Feng-Qing; Xu, Fang-Cheng; Hou, Bo; Fan, Wei-Wei; Zi, Cheng-Ting; Li, Yan; Dong, Fa-Wu; Liu, Yu-Qing; Sheng, Jun; Zuo, Zhi-Li; Hu, Jiang-Miao


    The bioassay-guided chemical investigation of the stems of Dendrobium fimbriatum Hook led to the isolation of seven first reported bibenzyl dimers with a linkage of a methylene moiety, fimbriadimerbibenzyls A-G (1-7), together with a new dihydrophenanthrene derivative (S)-2,4,5,9-tetrahydroxy-9,10-dihydrophenanthrene (8) and thirteen known compounds (9-21). The structure of the new compound was established by spectroscopic analysis. Biological evaluation of bibenzyl derivatives against five human cell lines indicated that seven of those compounds exhibited broad-spectrum and cytotoxic activities with IC50 values ranging from 2.2 to 21.2 μM. Those rare bibenzyl dimers exhibited cytotoxic activities in vitro and the cytotoxicity decreased as the number of oxygen-containing groups in the structure decreases. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Mechanically controlled quantum interference in individual π-stacked dimers. (United States)

    Frisenda, Riccardo; Janssen, Vera A E C; Grozema, Ferdinand C; van der Zant, Herre S J; Renaud, Nicolas


    Recent observations of destructive quantum interference in single-molecule junctions confirm the role of quantum effects in the electronic conductance properties of molecular systems. These effects are central to a broad range of chemical and biological processes and may be beneficial for the design of single-molecule electronic components to exploit the intrinsic quantum effects that occur at the molecular scale. Here we show that destructive interference can be turned on or off within the same molecular system by mechanically controlling its conformation. Using a combination of ab initio calculations and single-molecule conductance measurements, we demonstrate the existence of a quasiperiodic destructive quantum-interference pattern along the breaking traces of π-stacked molecular dimers. The results demonstrate that it is possible to control the molecular conductance over more than one order of magnitude and with a sub-ångström resolution by exploiting the subtle structure-property relationship of π-stacked dimers.

  13. D-dimer measurements in acute aortic dissection

    Directory of Open Access Journals (Sweden)

    Vladyslava Bazylevska


    Full Text Available Acute aortic dissection (AAD is a medical emergency with significant morbidity and mortality. The diagnosis can be challenging due to the wide array of presenting symptoms and a broad differential diagnosis. Computed tomographic angiography is currently the gold standard for diagnosis of AAD. However, it carries the risk of contrast and radiation exposure and has a financial burden for patients. Multiple biomarkers have been evaluated as a screening tool for AAD. D-dimer has previously been suggested as a sole rule-out test for AAD. It is rapid and inexpensive, is widely available in the emergency rooms, and is highly sensitive for any thrombotic event. This review article evaluates the evidence for the use of D-dimer assays in the diagnosis of AAD, in differentiation of AAD from acute coronary syndromes, and in risk stratification of AAD patients.

  14. Data on dimer formation between importin α subtypes

    Directory of Open Access Journals (Sweden)

    Yoichi Miyamoto


    Full Text Available This article describes data related to the research article titled “Functional characterization of importin α8 as a classical nuclear localization signal receptor” [1]. A GST pull-down assay showed that both importin α1 and α8, which are classical nuclear localization signal (cNLS receptors, can form a dimer with importin α6, α7, or α8. Importin α8 has higher dimer-forming ability than importin α1. In addition, our data show that either importin α1 or importin α8 can form a heterodimer with importin α3, which exists in a preformed complex with cNLS substrates such as the conventional SV40TNLS or the p53 protein, resulting in the release of the cNLS substrates from importin α3.

  15. Emergence of a Dimer-Dimer Interaction in the Low-Energy Effective Quantum-Dimer Model of a Diamond-Like-Decorated Square-Lattice Heisenberg Antiferromagnets with Further Neighbor Couplings (United States)

    Hirose, Yuhei; Oguchi, Akihide; Fukumoto, Yoshiyuki


    We study spin-1/2 Heisenberg antiferromagnets on a diamond-like-decorated square lattice perturbed by two kinds of further neighbor couplings. In our previous study [" xlink:type="simple">J. Phys. Soc. Jpn. 85, 094002 (2016)], the second-order effective Hamiltonian for the Heisenberg model perturbed by a further neighbor coupling was found to be a square-lattice quantum-dimer model with a finite hopping amplitude, t > 0, and no dimer-dimer interaction, v = 0. In this study, we introduce another kind of further neighbor coupling and show that it leads to an attractive interaction between dimers, which suggests the stabilization of the columnar phase of the square-lattice quantum-dimer model. The calculated v/t is presented as a function of the ratio of the two exchange parameters in the Heisenberg model.

  16. Electron-excited molecule interactions

    Energy Technology Data Exchange (ETDEWEB)

    Christophorou, L.G. (Oak Ridge National Lab., TN (USA) Tennessee Univ., Knoxville, TN (USA). Dept. of Physics)


    In this paper the limited but significant knowledge to date on electron scattering from vibrationally/rotationally excited molecules and electron scattering from and electron impact ionization of electronically excited molecules is briefly summarized and discussed. The profound effects of the internal energy content of a molecule on its electron attachment properties are highlighted focusing in particular on electron attachment to vibrationally/rotationally and to electronically excited molecules. The limited knowledge to date on electron-excited molecule interactions clearly shows that the cross sections for certain electron-molecule collision processes can be very different from those involving ground state molecules. For example, optically enhanced electron attachment studies have shown that electron attachment to electronically excited molecules can occur with cross sections 10{sup 6} to 10{sup 7} times larger compared to ground state molecules. The study of electron-excited molecule interactions offers many experimental and theoretical challenges and opportunities and is both of fundamental and technological significance. 54 refs., 15 figs.

  17. Sound velocity bound and neutron stars. (United States)

    Bedaque, Paulo; Steiner, Andrew W


    It has been conjectured that the velocity of sound in any medium is smaller than the velocity of light in vacuum divided by sqrt[3]. Simple arguments support this bound in nonrelativistic and/or weakly coupled theories. The bound has been demonstrated in several classes of strongly coupled theories with gravity duals and is saturated only in conformal theories. We point out that the existence of neutron stars with masses around two solar masses combined with the knowledge of the equation of state of hadronic matter at "low" densities is in strong tension with this bound.

  18. Lability of copper bound to humic acid


    Mao, Lingchen; Young, Scott D.; Bailey, Liz


    Geochemical speciation models generally include the assumption that all metal bound to humic acid and fulvic acid (HA, FA) is labile. However, in the current study, we determined the presence of a soluble ‘non-labile’ Cu fraction bound to HA extracted from grassland and peat soils. This was quantified by determining isotopically-exchangeable Cu (E-value) and EDTA-extraction of HA-bound Cu, separated by size-exclusion chromatography (SEC) and assayed by coupled ICP-MS. Evidence of time-depend...

  19. Positivity bounds on double parton distributions

    Energy Technology Data Exchange (ETDEWEB)

    Diehl, Markus; Kasemets, Tomas


    Double hard scattering in proton-proton collisions is described in terms of double parton distributions. We derive bounds on these distributions that follow from their interpretation as probability densities, taking into account all possible spin correlations between two partons in an unpolarized proton. These bounds constrain the size of the polarized distributions and can for instance be used to set upper limits on the effects of spin correlations in double hard scattering. We show that the bounds are stable under leading-order DGLAP evolution to higher scales.

  20. Lower bound for the nuclear kinetic energy

    Energy Technology Data Exchange (ETDEWEB)

    Dehesa, J.S. (Granada Univ. (Spain). Dept. de Fisica Nuclear); Galvez, F.J. (Granada Univ. (Spain). Dept. de Fisica Teorica)


    We argue that the kinetic energy of a many-fermion system is bounded from below by Kqsup(-2/3)A sup(5/3) / , with K = 0.565 where q is the number of spin states available to each particle and sup(1/2) is the root mean square radius of the single-particle density. A simple lower bound for the nuclear kinetic energy is found. Numerical values of the bound for several nuclei are shown, and a comparison with some self-consistent calculations and some pseudo-empirical values is made.

  1. Continuous bounded cohomology of locally compact groups

    CERN Document Server


    Recent research has repeatedly led to connections between important rigidity questions and bounded cohomology. However, the latter has remained by and large intractable. This monograph introduces the functorial study of the continuous bounded cohomology for topological groups, with coefficients in Banach modules. The powerful techniques of this more general theory have successfully solved a number of the original problems in bounded cohomology. As applications, one obtains, in particular, rigidity results for actions on the circle, for representations on complex hyperbolic spaces and on Teichmüller spaces. A special effort has been made to provide detailed proofs or references in quite some generality.

  2. R-matrix study of electron impact excitation and dissociation of CH+ ions (United States)

    Chakrabarti, K.; Dora, A.; Ghosh, R.; Choudhury, B. S.; Tennyson, Jonathan


    Electron impact excitation and electron impact dissociation of CH+ ions are studied in the framework of the R-matrix method using the diatomic version of the UK molecular R-matrix codes. A configuration interaction calculation is first performed to yield the potential energy curves of the lowest eight singlet and triplet states of CH+. Scattering calculations are then performed to yield vibrationally-resolved electronic excitations to the lowest three bound states, namely the a {}3{{\\Pi }}, A {}1{{\\Pi }} and the b {}3{{{Σ }}}-. Electron impact dissociation cross sections are obtained from the assumption that all electronic excitations above the dissociation threshold result in dissociation. Bound states of CH and resonance positions and widths of Feshbach resonances in the e-CH+ system are also calculated at the CH+ equilibrium bond length 2.137 a0.

  3. Adaptive Dynamic Surface Control for Generator Excitation Control System

    Directory of Open Access Journals (Sweden)

    Zhang Xiu-yu


    Full Text Available For the generator excitation control system which is equipped with static var compensator (SVC and unknown parameters, a novel adaptive dynamic surface control scheme is proposed based on neural network and tracking error transformed function with the following features: (1 the transformation of the excitation generator model to the linear systems is omitted; (2 the prespecified performance of the tracking error can be guaranteed by combining with the tracking error transformed function; (3 the computational burden is greatly reduced by estimating the norm of the weighted vector of neural network instead of the weighted vector itself; therefore, it is more suitable for the real time control; and (4 the explosion of complicity problem inherent in the backstepping control can be eliminated. It is proved that the new scheme can make the system semiglobally uniformly ultimately bounded. Simulation results show the effectiveness of this control scheme.

  4. Half-Collision Studies of Excited Metal Atom - Molecule Interactions (United States)

    Kleiber, P. D.; Chen, J.; Wong, T. H.


    We report on state-resolved studies of excited state molecular dynamics, including both reactive and nonreactive (energy transfer) processes using half-collision techniques. Scattering state spectroscopy is used to investigate electronic orbital alignment effects on the reactive quenching of excited p-state alkali and alkaline earth metal atoms in collisions with hydrogen and methane. These experiments give information about the shape of the Born-Oppenheimer potential energy surfaces for the collision complex, and about the nonadiabatic interactions that couple the surfaces. Experimental results indicate two distinct reaction mechanisms are operative in the alkali metal-hydrogen quenching system. In complementary experiments, the spectroscopy and dissociation dynamics of weakly bound metal ion-hydrocarbon bimolecular complexes are studied using photofragmentation spectroscopic techniques in a tandem time-of- flight mass spectrometer. Results suggest that the quenching mechanism involves metal ion activation of the hydrocarbon bonds througha bond- stretch insertion process.

  5. Mass spectrum and decay constants of radially excited vector mesons (United States)

    Mojica, Fredy F.; Vera, Carlos E.; Rojas, Eduardo; El-Bennich, Bruno


    We calculate the masses and weak decay constants of flavorless and flavored ground and radially excited JP=1- mesons within a Poincaré covariant continuum framework based on the Bethe-Salpeter equation. We use in both the quark's gap equation and the meson bound-state equation an infrared massive and finite interaction in the leading symmetry-preserving truncation. While our numerical results are in rather good agreement with experimental values where they are available, no single parametrization of the QCD inspired interaction reproduces simultaneously the ground and excited mass spectrum, which confirms earlier work on pseudoscalar mesons. This feature being a consequence of the lowest truncation, we pin down the range and strength of the interaction in both cases to identify common qualitative features that may help to tune future interaction models beyond the rainbow-ladder approximation.

  6. A New Hydroxychavicol Dimer from the Roots of Piper betle

    Directory of Open Access Journals (Sweden)

    Huei-Yu Tu


    Full Text Available A new hydroxychavicol dimer, 2-(g'-hydroxychavicol-hydroxychavicol (1, was isolated from the roots of Piper betle Linn. along with five known compounds, hydroxychavicol (2, aristololactam A II (3, aristololactam B II (4, piperolactam A (5 and cepharadione A (6. The structures of these isolated compounds were elucidated by spectroscopic methods. Compounds 1 and 2 exhibited inhibitory effects on the generation of superoxide anion and the release of elastase by human neutrophils.

  7. Dimerization and DNA recognition rules of mithramycin and its analogues


    Weidenbach, Stevi; Hou, Caixia; Chen, Jhong-Min; Tsodikov, Oleg V.; Rohr, J?rgen


    The antineoplastic and antibiotic natural product mithramycin (MTM) is used against cancer-related hypercalcemia and, experimentally, against Ewing sarcoma and lung cancers. MTM exerts its cytotoxic effect by binding DNA as a divalent metal ion (Me2+)-coordinated dimer and disrupting the function of transcription factors. A precise molecular mechanism of action of MTM, needed to develop MTM analogues selective against desired transcription factors, is lacking. Although it is known that MTM bi...

  8. A new phenylspirodrimane dimer from the fungus Stachybotrys chartarum. (United States)

    Ding, Zhang-Gui; Ding, Jian-Hai; Zhao, Jiang-Yuan; Chunyu, Wei-Xun; Li, Ming-Gang; Gu, Shao-Jie; Wang, Fei; Wen, Meng-Liang


    A new phenylspirodrimane dimer, named stachartarin A (1), was isolated from cultures of the tin mine tailings-associated fungus Stachybotrys chartarum. Its structures were elucidated by means of spectroscopic methods. At the same time, the compound was tested for its cytotoxicity against HL-60, SMMC-7721, A-549, MCF-7, and SW480 cells. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Synthesis and anti-inflammatory activity of phenylbutenoid dimer analogs

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung Soo; Fang, Yuan Ying; Park, Hae Eil [Kangwon National University, Chuncheon (Korea, Republic of)


    Several phenylbutenoid dimer (PBD) analogs were synthesized and evaluated for their inhibitory activities against nitric oxide (NO) production and TNF-α release. The PBD analogs were synthesized via Diels–Alder and subsequent Schlosser reactions as key steps. Among the tested compounds, two analogs (8c, 8f) exhibited much stronger inhibitory activity against LPS-stimulated NO production and TNF-α release in RAW 264.7 cells than that of wogonin.

  10. Multiple-charge transfer and trapping in DNA dimers (United States)

    Tornow, Sabine; Bulla, Ralf; Anders, Frithjof B.; Zwicknagl, Gertrud


    We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated hopping and the bond-bond interaction, which were recently calculated by Starikov [E. B. Starikov, Philos. Mag. Lett. 83, 699 (2003)10.1080/0950083031000151374] for different DNA dimers. The electronic degrees of freedom are coupled to an ohmic or a superohmic bath serving as dissipative environment. We employ the numerical renormalization group method in the nuclear tunneling regime and compare the results to Marcus theory for the thermal activation regime. For realistic parameters, the rate that at least one charge is transferred from the donor to the acceptor in the subspace of two excess electrons significantly exceeds the rate in the single charge sector. Moreover, the dynamics is strongly influenced by the Coulomb matrix elements. We find sequential and pair transfer as well as a regime where both charges remain self-trapped. The transfer rate reaches its maximum when the difference of the on-site and intersite Coulomb matrix element is equal to the reorganization energy which is the case in a guanine/cytosine (GC)-dimer. Charge transfer is completely suppressed for two excess electrons in adenine/thymine (AT)-dimer in an ohmic bath and replaced by damped coherent electron-pair oscillations in a superohmic bath. A finite bond-bond interaction W alters the transfer rate: it increases as function of W when the effective Coulomb repulsion exceeds the reorganization energy (inverted regime) and decreases for smaller Coulomb repulsion.

  11. Protocadherin cis-dimer architecture and recognition unit diversity. (United States)

    Goodman, Kerry M; Rubinstein, Rotem; Dan, Hanbin; Bahna, Fabiana; Mannepalli, Seetha; Ahlsén, Göran; Aye Thu, Chan; Sampogna, Rosemary V; Maniatis, Tom; Honig, Barry; Shapiro, Lawrence


    Clustered protocadherins (Pcdhs) mediate numerous neural patterning functions, including neuronal self-recognition and non-self-discrimination to direct self-avoidance among vertebrate neurons. Individual neurons stochastically express a subset of Pcdh isoforms, which assemble to form a stochastic repertoire of cis-dimers. We describe the structure of a PcdhγB7 cis-homodimer, which includes the membrane-proximal extracellular cadherin domains EC5 and EC6. The structure is asymmetric with one molecule contributing interface surface from both EC5 and EC6, and the other only from EC6. Structural and sequence analyses suggest that all Pcdh isoforms will dimerize through this interface. Site-directed mutants at this interface interfere with both Pcdh cis-dimerization and cell surface transport. The structure explains the known restrictions of cis-interactions of some Pcdh isoforms, including α-Pcdhs, which cannot form homodimers. The asymmetry of the interface approximately doubles the size of the recognition repertoire, and restrictions on cis-interactions among Pcdh isoforms define the limits of the Pcdh recognition unit repertoire.

  12. Self-discrimination of enantiomers in hydrogen-bonded dimers. (United States)

    Alkorta, Ibon; Elguero, Jose


    The homochiral and heterochiral hydrogen-bonded (HB) dimers of a set of small model molecules (alpha-amino alcohols) have been studied by means of ab initio methods. The gas-phase calculations have been carried out with the hybrid HF/DFT B3LYP method and the 6-311++G** basis set. The electron density of the complexes has been analyzed using the atoms in molecules (AIM) methodology, which allows characterization of the HB interactions and additional intermolecular contacts. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the Delta G(solv). The gas-phase results show that the heterochiral dimers are the most stable ones for each case studied, while in solution for several cases, the relative stability is reversed and the homochiral dimers become more stable. The AIM analysis shows the typical bond critical points characteristic of the HB and additional bond critical points denoting, in this case, destabilization of intermolecular interaction as CF(3)...F(3)C and CH(3)...H(3)C contacts.

  13. Photo association in metastable helium in the vicinity of the Bose-Einstein condensation and production of giant dimers; Photo-association de l'helium metastable au voisinage de la condensation de Bose-Einstein et formation de dimeres geants

    Energy Technology Data Exchange (ETDEWEB)

    Leonard, J


    In the vicinity of Bose-Einstein condensation, the collisional properties of a dilute gas of metastable helium (He{sub 2}{sup 3}S) are governed by the rate of ionizing Penning collisions and the s-wave scattering length. In order to investigate these properties, we have carried out new photo-association experiments in which a pair of free atoms absorbs a photon to produce a molecule in an excited electronic state. In particular, we have observed 'giant dimers' for which the autoionizing process is inhibited. Accurate spectra have been acquired by the use of an original 'calorimetric' detection scheme. In addition, we have calculated long-range electronic potentials for the 2{sup 3} S + 2{sup 3} P system. Our asymptotic approach is described in detail, which reproduces the measured binding energies of the giant dimers with very good accuracy. (author)

  14. Phase diagram of the hexagonal lattice quantum dimer model: Order parameters, ground-state energy, and gaps (United States)

    Schlittler, Thiago M.; Mosseri, Rémy; Barthel, Thomas


    The phase diagram of the quantum dimer model on the hexagonal (honeycomb) lattice is computed numerically, extending on earlier work by Moessner, Sondhi, and Chandra. The different ground state phases are studied in detail using several local and global observables. In addition, we analyze imaginary-time correlation functions to determine ground state energies as well as gaps to the first excited states. This leads in particular to a confirmation that the intermediary so-called plaquette phase is gapped. On the technical side, we describe an efficient world-line quantum Monte Carlo algorithm with improved cluster updates that increase acceptance probabilities by taking account of potential terms of the Hamiltonian during the cluster construction. The Monte Carlo simulations are supplemented with variational computations.

  15. Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer. (United States)

    Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José


    The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

  16. Effect of loss on the topological features of dimer chains described by the extended Aubry-André-Harper model (United States)

    Zhao, X. L.; Shi, Z. C.; Yu, C. S.; Yi, X. X.


    By introducing loss to one sublattice of dimer chains described by the extended Aubry-André or Harper (AAH) model, we study the topological features including the winding number, the edge states, Chern number, and spectrum of the chain. We find that the parameter region for the system to have real band-gap closing is increased due to the loss, and the average displacement of the single excitation can indicate the topological features of the chain in the presence of loss on one sublattice. The robustness of the zero energy eigenstate against four kinds of disorders are examined. A feasible experimental apparatus based on coupled waveguides to observe the predictions of this work is proposed.

  17. Excitation energy flow in chlorosome antennas of green photosynthetic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Mimuro, Mamoru (National Institute for Basic Biology, Aichi (Japan)); Nozawa, Tsunenori (Tohoku Univ., Miyagi (Japan)); Tamai, Naoto; Yamazaki, Iwao (Institute for Molecular Science, Aichi (Japan)); Shimada, Keizou (Tokyo Metropolitan Univ. (Japan)); Lin, Su; Knox, R.S. (Univ. of Rochester, NY (USA)); Wittmershaus, B.P.; Brune, D.C.; Blankenship, R.E. (Arizona State Univ., Tempe (USA))


    Energy flow in whole cells of the thermophilic green photosynthetic bacterium Chloroflexus aurantiacus was studied by measurements of time-resolved fluorescence spectra in the picosecond time range, detected by both streak camera and single-photon counting methods. These data characterize the energy-transfer sequence from bacteriochlorophyll c (BChl c), found in membrane-associated antenna structures called chlorosomes, to BChl a in the chlorosome baseplate, then to a BChl a antenna complex in the cytoplasmic membrane, and finally to the photochemical reaction center. Upon selective excitation of BChl c in chlorosomes, the decay time of the emission arising from BChl c was 16 ps. The apparent rise time of the emission from the baseplate pigment was < 3 ps. The time course of the transfer from the baseplate BChl a to the membrane-bound BChl a complex was clearly detected. A major 41-ps decay component of the baseplate BChl a emission corresponded to the rise term found for the membrane-bound BChl a emission. With a kinetic analysis, a model is proposed for the structure and function of the chlorosome antenna system in Chloroflexus aurantiacus. The data suggest that the excitation-transfer process may utilize a novel mechanism that takes advantage of the photophysical properties of aggregated pigments. BChl c molecules form naturally occurring aggregates with oligomeric structures similar to J aggregates, but very different from the organization of antenna pigment-proteins from other photosynthetic organisms. These oligomers absorb light and transfer excitations to a small amount of BChl a antenna proteins in the baseplate. The baseplate acts as an energy-transfer interface between the chlorosome and the antenna protein complexes located within the membrane. The integral membrane antenna complexes in turn deliver the excitations to the reaction center where photosynthesis is initiated by electron-transfer reactions.

  18. Redshift-space limits of bound structures

    NARCIS (Netherlands)

    Duenner, Rolando; Reisenegger, Andreas; Meza, Andres; Araya, Pablo A.; Quintana, Hernan


    An exponentially expanding Universe, possibly governed by a cosmological constant, forces gravitationally bound structures to become more and more isolated, eventually becoming causally disconnected from each other and forming so-called 'island universes'. This new scenario reformulates the question

  19. Quantized breather excitations of Fermi-Pasta-Ulam lattices. (United States)

    Riseborough, Peter S


    We have calculated the lowest energy quantized breather excitations of both the β and the α Fermi-Pasta-Ulam monoatomic lattices and the diatomic β lattice within the ladder approximation. While the classical breather excitations form continua, the quantized breather excitations form a discrete hierarchy labeled by a quantum number n. Although the number of phonons is not conserved, the breather excitations correspond to multiple bound states of phonons. The n=2 breather spectra are composed of resonances in the two-phonon continuum and of discrete branches of infinitely long-lived excitations. The nonlinear attributes of these excitations become more pronounced at elevated temperatures. The calculated n=2 breather and the resonance of the monoatomic β lattice hybridize and exchange identity at the zone boundary and are in reasonable agreement with the results of previous calculations using the number-conserving approximation. However, by contrast, the breather spectrum of the α monoatomic lattice couples resonantly with the single-phonon spectrum and cannot be calculated within a number-conserving approximation. Furthermore, we show that for sufficiently strong nonlinearity, the α lattice breathers can be observed directly through the single-phonon inelastic neutron-scattering spectrum. As the temperature is increased, the single-phonon dispersion relation for the α lattice becomes progressively softer as the lattice instability is approached. For the diatomic β lattice, it is found that there are three distinct branches of n=2 breather dispersion relations, which are associated with three distinct two-phonon continua. The two-phonon excitations form three distinct continua: One continuum corresponds to the motion of two independent acoustic phonons, another to the motion of two independent optic phonons, and the last continuum is formed by propagation of two phonons that are one of each character. Each breather dispersion relation is split off the top

  20. New Spectral Features from Bound Dark Matter

    DEFF Research Database (Denmark)

    Catena, Riccardo; Kouvaris, Chris


    We demonstrate that dark matter particles gravitationally bound to the Earth can induce a characteristic nuclear recoil signal at low energies in direct detection experiments. The new spectral feature we predict can provide the ultimate smoking gun for dark matter discovery for experiments...... with positive signal but unclear background. The new feature is universal, in that the ratio of bound over halo dark matter event rates at detectors is independent of the dark matter-nucleon cross section....

  1. On bounds for symmetric divergence measures (United States)

    Furuichi, S.; Yanagi, K.; Kuriyama, K.


    In the paper [1], tight bounds for symmetric divergence measures applying the results established by G.L.Gilardoni. In this article, we report on two kinds of extensions for the Sason's results, namely a classical q-extension and a non-commutative(quantum) extension. Especially, we improve Sason's bound of the summation of the absolute value for the difference between two probability distributions, applying the parameter q of Tsallis entropy, under a certain assumption.

  2. Stable Bound States of Asymmetric Dark Matter


    Wise, Mark B.; Zhang, Yue


    The simplest renormalizable effective field theories with asymmetric dark matter bound states contain two additional gauge singlet fields one being the dark matter and the other a mediator particle that the dark matter annihilates into. We examine the physics of one such model with a Dirac fermion as the dark matter and a real scalar mediator. For a range of parameters the Yukawa coupling of the dark matter to the mediator gives rise to stable asymmetric dark matter bound states. We derive pr...

  3. Malabsorption of protein bound vitamin B12.


    Dawson, D W; Sawers, A H; Sharma, R K


    Patients with subnormal serum vitamin B12 concentrations were tested for absorption of protein bound vitamin B12 and compared with controls. Absorption of the protein bound vitamin appeared to decrease with increasing age in healthy subjects. Differences between the result of this test and the result of the Schilling test in patients who had undergone gastric surgery were confirmed; such differences were also seen in some patients who had iron deficiency anaemia, an excessive alcohol intake, ...

  4. Dynamic optimization problems with bounded terminal conditions (United States)

    Lee, A. Y.


    Bounded terminal conditions of nonlinear optimization problems are converted to equality terminal conditions via Valentine's device. In so doing, additional unknown parameters are introduced into the problem. The transformed problems can still be easily solved using the sequential gradient-restoration algorithm (SGRA) via a simple augmentation of the unknown parameter vector pi. Three example problems with bounded terminal conditions are solved to verify this technique.

  5. Ultralong range ICD in the He dimer, resonant Auger - ICD cascade processes

    Energy Technology Data Exchange (ETDEWEB)

    Jahnke, Till [IKF, Goethe Universitaet, Max-von-Laue-Str.1, 60438 Frankfurt am Main (Germany)


    Interatomic (or intermolecular) Coulombic Decay (ICD) has become an extensively studied atomic decay process during the last 10 years. The talk shows examples of different systems in which ICD has been examined. In particular helium molecules (so called helium dimers) are presented in which ICD occurs over longest internuclear distances. In ICD electrons of low energy are created as a typical decay product. Such electrons are known to effectively cause DNA double strand breakups suggesting ICD as a possible origin for radiation damage of living tissue. The group of L. Cederbaum recently suggested that ICD can be triggered efficiently and site-selectively by resonant excitation of molecules. They realized that this provides a unique tool to create low energy electrons at a specific site inside a biological system for example in order to damage malignant cells that are tagged using specific marker molecules. Here we show experimentally that resonant Auger induced ICD can indeed be observed in model systems of small nitrogen and carbon monoxide clusters and - as expected - produces low energy electrons. Furthermore our simple model systems are able to prove the efficiency of ICD: it occurs before the individual molecule is able to undergo dissociation, i.e on a timescale <10 fs. Our findings therefore strongly support the idea of resonant Auger-ICD being a promising process to induce radiation damage at a specific site inside a high-Z-tagged cell.

  6. High resolution overtone spectroscopy of the acetylene van der Waals dimer, ((12)C2H2)2. (United States)

    Didriche, K; Lauzin, C; Földes, T; Golebiowski, D; Herman, M; Leforestier, C


    CW-cavity ring down spectroscopy was used to record in a free jet expansion the spectrum of the absorption band in ((12)C(2)H(2))(2) with origin at 6547.6 cm(-1). It is a perpendicular band and corresponds to 2CH excitation in the hat unit of the T-shaped dimer. Calibration (better than ±1 × 10(-3) cm(-1) accuracy) and ring-down time (130 μs) were improved compared to a previous contribution (Didriche et al. Mol. Phys., 2010, 108, 2158-2164). A line-by-line analysis was achieved. Three series of lines were identified involving levels with A(1)(+), E(+) and B(1)(+) ground state tunneling symmetries, confirming the spectral and symmetry analyses reported in the literature for the 1CH excitation band (Fraser et al. J. Chem. Phys., 1988, 89, 6028-6045). 164 vibration-rotation-tunneling lines were assigned in the K(a)' - K(a)'' = 2 - 3, 0 - 1, 2 - 1 and 4 - 3 sub-bands and effective rigid rotor vibration-rotation constants were obtained by simultaneously fitting 1CH and 2CH lines with the same symmetry series. Perturbations affecting the K(a) stacks, in particular, are reported. The tunneling frequency in 2CH is estimated to be ν(tunn)(2CH) = 270 MHz for the K(a) = 0 stack. The rotational temperature is determined to be 23 K from relative line intensities and the lifetime of the dimer in the 2CH hat state is estimated to be 1 ns from individual line widths.

  7. Intermolecular potential functions from spectroscopic properties of weakly bound complexes

    Energy Technology Data Exchange (ETDEWEB)

    Muenter, J.S.


    Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)

  8. The Development and Study of Surface Bound Ruthenium Organometallic Complexes (United States)

    Abbott, Geoffrey Reuben

    The focus of this project has been on the use of mono-diimine ruthenium organometallic complexes, of the general structure [H(Ru)(CO)(L)2(L') 2][PF6] (L=PPh3, DPPENE and L'=Bpy, DcBpy, MBpyC, Phen, AminoPhen) bound to surfaces as luminescent probes. Both biological and inorganic/organic hybrid surfaces have been studied. The complexes were characterized both bound and unbound using standard analytical techniques such as NMR, IR and X-ray crystallography, as well as through several photophysical methods as well. Initially the study focused on how the photophyscial properties of the complexes were affected by incorporation into biological membranes. It was found that by conjugating the probes to a more rigid cholesterol moiety that luminescence was conserved, compared to conjugation with a far more flexible lipid moiety, where luminescence was either lost or reduced. Both the cholesterol and lipid conjugates were able to insert into a lipid membrane, and in the more rigid environment some of the lipid conjugates regained some of their luminescence, but often blue shifted and reduced, depending on the conjugation site. Silica Polyamine Composites (SPCs) were a hybrid material developed in the Rosenberg Lab as useful metal separation materials, that could be easily modified, and had several benefits over current commercially available polymers, or inorganic materials. These SPCs also provided an opportunity for the development of a heterogeneous platform for luminescent complexes as either catalysts or sensors. Upon binding of the luminescent Ru complexes to the surface no loss, or major change in luminescence was seen, however, when bound to the rigid surface a significant increase in excited state lifetime was measured. It is likely that through binding and interacting with the surface that the complexes lost non-radiative decay pathways, resulting in the increase in lifetime, however, these interactions do not seem to affect the energy level of the MLCT band in a

  9. Qualitative point-of-care D-dimer testing compared with quantitative D-dimer testing in excluding pulmonary embolism in primary care

    NARCIS (Netherlands)

    Lucassen, W. A M; Erkens, P. M G; Geersing, G. J.; Büller, H. R.; Moons, K. G M; Stoffers, H. E J H; van Weert, H. C P M


    Background: General practitioners can safely exclude pulmonary embolism (PE) by using the Wells PE rule combined with D-dimer testing. Objective: To compare the accuracy of a strategy using the Wells rule combined with either a qualitative point-of-care (POC) D-dimer test performed in primary care

  10. [The binuclear iron site of the membrane-bound methane hydroxylase from Methylococcus capsulatus (strain M)]. (United States)

    Tumanova, L V; Tukhvatullin, I A; Burbaev, T Sh; Gvozdev, R I; Andersson, K K


    The particulate membrane-bound methane hydroxylase (pMMOH) was isolated from methane-oxidizing cells of Methylococcus capsulatus (strain M). At SDS PAGE, pMMOH displays three bands: 47 (alpha), 27 (beta), and 25 kDa (gamma). The ESR spectrum of pMMOH incubated with hydrogen peroxide (final concentration 20 mM) at 4 degrees C exhibited, along with the copper signal of type I with g = 2.05, signals of cytochrome with g = 3.0 and of high-spin ferriheme with g = 6.00. After incubation at -30 degrees C, additional signals with g 8.5 and 13.5 were observed. These signals, which have not been recorded previously in pMMOH preparations, are due to an intermediate of the pMMOH active site, which arises in the reaction of hydrogen peroxide with pMMOH at -30 degrees C. It was established that this intermediate is a high-spin dimer [Fe(IlI)-Fe(IV)] with S = 9/2 and different degree of rhombic distortion of structure (it is responsible for both signals). Presumably, the signal with g = 8.5 also arises from the same dimer [Fe(III)-Fe(IV)], but with S = 7/2. The presence of the intermediate [Fe(lII)-Fe(IV)] in pMMOH preparations suggests that the original state of the pMMOH active site is the dimer [Fe(III)-Fe(III)] which is located in the beta-subunit and cannot be detected by ESR. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http://

  11. Neutral dipole-dipole dimers: A new field in science (United States)

    Kosower, Edward M.; Borz, Galina


    Dimer formation with dipole neutralization produces species such as low polarity water (LPW) compatible with hydrophobic surfaces (Phys. Chem. Chem. Phys. 2015, 17, 24895-24900) Dimerization and dipole neutralization occurs for N-methylacetamide on polyethylene, a behavior drastically different from its contortions in acetonitrile on AgBr:AgCl planar crystals (AgX) (ChemPhysChem 2014, 15, 3598-3607). The weak infrared absorption of the amide dimer on polyethylene is shown experimentally. Dimerization of palmitic acid is shown along with some of the many ramifications for intracellular systems. Polyoligomers of water are present on polyethylene surfaces. Some high resolution spectra of three of the polyoligomers of water are shown along with a mechanistic scheme for polyoligomer formation and dissolution. The structures of some of the oligomers are known from spectroscopic studies of water on AgX. The scope of the article begins with PE, generally accepted as hydrophobic. The IR of PE revealed not only that water was present but that it appeared in two forms, oligomers (O) and polyoligomers (PO). How did we recognize what they were? These species had been observed as especially strong "marker" peaks in the spectra1 of water placed on planar AgX, a platform developed by Katzir and his coworkers [6]. But there was a problem: the proximity to PE of oligomers with substantial (calculated) dipole moments and thus polarity, including cyclic hexamers of water (chair and boat forms), the cyclic pentamer, the books I and II, and the cyclic trimer [7a]. Another link was needed, a role perfectly fit by the already cited low polarity water (LPW). The choice was experimentally supported by the detection of low intensity absorption in the bending region.Some important generalities flow from these results. What other dimers might be present in the biological or chemical world? Palmitic acid dimer (PAD) would be a candidate for decreasing the polarity of the acid (PA). Another

  12. Sadomasochism, sexual excitement, and perversion. (United States)

    Kernberg, O F


    Sadomasochism, an ingredient of infantile sexuality, is an essential part of normal sexual functioning and love relations, and of the very nature of sexual excitement. Sadomasochistic elements are also present in all sexual perversions. Sadomasochism starts out as the potential for erotic masochism in both sexes, and represents a very early capacity to link aggression with the libidinal elements of sexual excitement. Sexual excitement may be considered a basic affect that overcomes primitive splitting of love and hatred. Erotic desire is a more mature form of sexual excitement. Psychoanalytic exploration makes it possible to uncover the unconscious components of sexual excitement: wishes for symbiotic fusion and for aggressive penetration and intermingling; bisexual identifications; the desire to transgress oedipal prohibitions and the secretiveness of the primal scene, and to violate the boundaries of a teasing and withholding object. The relation between these wishes and the development of erotic idealization processes in both sexes is explored in the context of a critical review of the pertinent psychoanalytic literature.

  13. Coulomb excitation of (31)Mg

    CERN Document Server

    Seidlitz, M; Reiter, P; Bildstein, V; Blazhev, A; Bree, N; Bruyneel, B; Cederkall, J; Clement, E; Davinson, T; van Duppen, P; Ekstrom, A; Finke, F; Fraile, L M; Geibel, K; Gernhauser, R; Hess, H; Holler, A; Huyse, M; Ivanov, O; Jolie, J; Kalkuhler, M; Kotthaus, T; Krucken, R; Lutter, R; Piselli, E; Scheit, H; Stefanescu, I; van de Walle, J; Voulot, D; Warr, N; Wenander, F; Wiens, A


    The ground state properties of ^3^1Mg indicate a change of nuclear shape at N=19 with a deformed J^@p=1/2^+ intruder state as a ground state, implying that ^3^1Mg is part of the ''island of inversion''. The collective properties of excited states were the subject of a Coulomb excitation experiment at REX-ISOLDE, CERN, employing a radioactive ^3^1Mg beam. De-excitation @c-rays were detected by the MINIBALL @c-spectrometer in coincidence with scattered particles in a segmented Si-detector. The level scheme of ^3^1Mg was extended. Spin and parity assignment of the 945 keV state yielded 5/2^+ and its de-excitation is dominated by a strong collective M1 transition. Comparison of the transition probabilities of ^3^0^,^3^1^,^3^2Mg establishes that for th e N=19 magnesium isotope not only the ground state but also excited states are largely dominated by a deformed pf intruder configuration.

  14. A potential new, stable state of the E-cadherin strand-swapped dimer in solution. (United States)

    Schumann-Gillett, Alexandra; Mark, Alan E; Deplazes, Evelyne; O'Mara, Megan L


    E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution.

  15. Tight bounds on computing error-correcting codes by bounded-depth circuits with arbitrary gates

    DEFF Research Database (Denmark)

    Gal, A.; Hansen, Kristoffer Arnsfelt; Koucky, Michal


    We bound the minimum number w of wires needed to compute any (asymptotically good) error-correcting code C:{0,1}Ω(n)→{0,1}n with minimum distance Ω(n), using unbounded fan-in circuits of depth d with arbitrary gates. Our main results are: 1) if d=2, then w=Θ(n (lgn/lglgn)2); 2) if d=3, then w...... bound gives the largest known lower bound for computing any linear map. The upper bounds imply that a (necessarily dense) generator matrix for our code can be written as the product of two sparse matrices. Using known techniques, we also obtain similar (but not tight) bounds for computing pairwise......-independent hash functions. Our lower bounds are based on a superconcentrator-like condition that the graphs of circuits computing good codes must satisfy. This condition is provably intermediate between superconcentrators and their weakenings considered before...

  16. Toward the Application of Three-Dimensional Approach to Few-body Atomic Bound States

    Directory of Open Access Journals (Sweden)

    Hadizadeh M.R.


    Full Text Available The first step toward the application of an effective non partial wave (PW numerical approach to few-body atomic bound states has been taken. The two-body transition amplitude which appears in the kernel of three-dimensional Faddeev-Yakubovsky integral equations is calculated as function of two-body Jacobi momentum vectors, i.e. as a function of the magnitude of initial and final momentum vectors and the angle between them. For numerical calculation the realistic interatomic interactions HFDHE2, HFD-B, LM2M2 and TTY are used. The angular and momentum dependence of the fully off-shell transition amplitude is studied at negative energies. It has been numerically shown that, similar to the nuclear case, the transition amplitude exhibits a characteristic angular behavior in the vicinity of 4He dimer pole.

  17. Tetraquark bound states and resonances in a unitary microscopic quark model: A case study of bound states of two light quarks and two heavy antiquarks (United States)

    Bicudo, P.; Cardoso, M.


    We address q q Q ¯Q ¯ exotic tetraquark bound states and resonances with a fully unitarized and microscopic quark model. We propose a triple string flip-flop potential, inspired by lattice QCD tetraquark static potentials and flux tubes, combining meson-meson and double Y potentials. Our model includes the color excited potential, but neglects the spin-tensor potentials, as well as all the other relativistic effects. To search for bound states and resonances, we first solve the two-body mesonic problem. Then we develop fully unitary techniques to address the four-body tetraquark problem. We fold the four-body Schrödinger equation with the mesonic wave functions, transforming it into a two-body meson-meson problem with nonlocal potentials. We find bound states for some quark masses, including the one reported in lattice QCD. Moreover, we also find resonances and calculate their masses and widths, by computing the T matrix and finding its pole positions in the complex energy plane, for some quantum numbers. However, a detailed analysis of the quantum numbers where binding exists shows a discrepancy with recent lattice QCD results for the l l b ¯ b ¯ tetraquark bound states. We conclude that the string flip-flop models need further improvement.

  18. Indirect excitation of ultrafast demagnetization (United States)

    Vodungbo, Boris; Tudu, Bahrati; Perron, Jonathan; Delaunay, Renaud; Müller, Leonard; Berntsen, Magnus H.; Grübel, Gerhard; Malinowski, Grégory; Weier, Christian; Gautier, Julien; Lambert, Guillaume; Zeitoun, Philippe; Gutt, Christian; Jal, Emmanuelle; Reid, Alexander H.; Granitzka, Patrick W.; Jaouen, Nicolas; Dakovski, Georgi L.; Moeller, Stefan; Minitti, Michael P.; Mitra, Ankush; Carron, Sebastian; Pfau, Bastian; von Korff Schmising, Clemens; Schneider, Michael; Eisebitt, Stefan; Lüning, Jan


    Does the excitation of ultrafast magnetization require direct interaction between the photons of the optical pump pulse and the magnetic layer? Here, we demonstrate unambiguously that this is not the case. For this we have studied the magnetization dynamics of a ferromagnetic cobalt/palladium multilayer capped by an IR-opaque aluminum layer. Upon excitation with an intense femtosecond-short IR laser pulse, the film exhibits the classical ultrafast demagnetization phenomenon although only a negligible number of IR photons penetrate the aluminum layer. In comparison with an uncapped cobalt/palladium reference film, the initial demagnetization of the capped film occurs with a delayed onset and at a slower rate. Both observations are qualitatively in line with energy transport from the aluminum layer into the underlying magnetic film by the excited, hot electrons of the aluminum film. Our data thus confirm recent theoretical predictions.

  19. Magnetic excitations in deformed nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Nojarov, R. [Tuebingen Univ. (Germany). Inst. fuer Theoretische Physik


    Cross sections for inelastic electron scattering and energy distributions of M1 and E2 strengths of K{sup {pi}} - 1{sup +} excitations in titanium, rare-earth, and actinide nuclei are studied microscopically within QRPA. The spin M1 strength has two peaks, isoscalar and isovector, residing between the low-and high-energy orbital M1 strength. The latter is strongly fragmented and lies in the region of the IVGQR, where the (e,e`) cross sections are almost one order of magnitude larger for E2 than for M1 excitations. Comparison with the quantized isovector rotor allows the interpretation of all the orbital M1 excitations at both low and high energies as manifestation of the collective scissors mode. (author).

  20. Excitation optimization for damage detection

    Energy Technology Data Exchange (ETDEWEB)

    Bement, Matthew T [Los Alamos National Laboratory; Bewley, Thomas R [UCSD


    A technique is developed to answer the important question: 'Given limited system response measurements and ever-present physical limits on the level of excitation, what excitation should be provided to a system to make damage most detectable?' Specifically, a method is presented for optimizing excitations that maximize the sensitivity of output measurements to perturbations in damage-related parameters estimated with an extended Kalman filter. This optimization is carried out in a computationally efficient manner using adjoint-based optimization and causes the innovations term in the extended Kalman filter to be larger in the presence of estimation errors, which leads to a better estimate of the damage-related parameters in question. The technique is demonstrated numerically on a nonlinear 2 DOF system, where a significant improvement in the damage-related parameter estimation is observed.