Theoretical investigation of potential energy surface and bound states for the van der Waals complex Ar–BrCl dimer

Energy Technology Data Exchange (ETDEWEB)

Zheng, Rui [School of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou (China); Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan (China); Li, Song, E-mail: lsong@yangtzeu.edu.cn [School of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou (China); Chen, Shan-Jun; Chen, Yan [School of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou (China); Zheng, Li-Min [Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan (China)

2015-09-08

Highlights: • A two-dimensional potential for Ar–BrCl is constructed at the CCSD(T) level. • The PES is characterized by three minima and two saddle points between them. • Bound state calculations were carried out for the complex. - Abstract: The intermolecular potential energy surface (PES) of the ground electronic state for the Ar–BrCl dimer is constructed at the CCSD(T) level with the aug-cc-pVQZ basis set and mid-bond functions. The PES is characterized by three minima and two saddle points. The global minimum corresponding to a collinear Ar–BrCl configuration, which has been observed experimentally, is located at R = 4.10 Å and θ = 2.5° with a well depth of −285.207 cm{sup −1}. A nearly T-shaped structure and an anti-linear Ar–ClBr geometry is also predicted. The bound state calculations are preformed to study intermolecular vibrational modes, rotational levels and average structures for the complex. Our transition frequencies, spectroscopic constants and average structures for all isotopomers of the collinear isomer agree well with experimental data. We have also provided pure rotational transitional frequencies for both nearly T-shaped and anti-linear isomers. These results are significant for further experimental investigations of the Ar–BrCl dimer.

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

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Tine N Vinther

Full Text Available An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic β-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 and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization to form the structural equivalent of the classical hexamer. The covalently linked dimer neither bound to the insulin receptor, nor induced a metabolic response in vitro. However, it was extremely thermodynamically stable and did not form amyloid fibrils when subjected to mechanical stress, underlining the importance of oligomerization for insulin stability.

Benzonitrile: Electron affinity, excited states, and anion solvation

Science.gov (United States)

Dixon, Andrew R.; Khuseynov, Dmitry; Sanov, Andrei

2015-10-01

We report a negative-ion photoelectron imaging study of benzonitrile and several of its hydrated, oxygenated, and homo-molecularly solvated cluster anions. The photodetachment from the unsolvated benzonitrile anion to the X ˜ 1 A 1 state of the neutral peaks at 58 ± 5 meV. This value is assigned as the vertical detachment energy (VDE) of the valence anion and the upper bound of adiabatic electron affinity (EA) of benzonitrile. The EA of the lowest excited electronic state of benzonitrile, a ˜ 3 A 1 , is determined as 3.41 ± 0.01 eV, corresponding to a 3.35 eV lower bound for the singlet-triplet splitting. The next excited state, the open-shell singlet A ˜ 1 A 1 , is found about an electron-volt above the triplet, with a VDE of 4.45 ± 0.01 eV. These results are in good agreement with ab initio calculations for neutral benzonitrile and its valence anion but do not preclude the existence of a dipole-bound state of similar energy and geometry. The step-wise and cumulative solvation energies of benzonitrile anions by several types of species were determined, including homo-molecular solvation by benzonitrile, hydration by 1-3 waters, oxygenation by 1-3 oxygen molecules, and mixed solvation by various combinations of O2, H2O, and benzonitrile. The plausible structures of the dimer anion of benzonitrile were examined using density functional theory and compared to the experimental observations. It is predicted that the dimer anion favors a stacked geometry capitalizing on the π-π interactions between the two partially charged benzonitrile moieties.

Improved anticancer effects of albumin-bound paclitaxel nanoparticle via augmentation of EPR effect and albumin-protein interactions using S-nitrosated human serum albumin dimer.

Science.gov (United States)

Kinoshita, Ryo; Ishima, Yu; Chuang, Victor T G; Nakamura, Hideaki; Fang, Jun; Watanabe, Hiroshi; Shimizu, Taro; Okuhira, Keiichiro; Ishida, Tatsuhiro; Maeda, Hiroshi; Otagiri, Masaki; Maruyama, Toru

2017-09-01

In the latest trend of anticancer chemotherapy research, there were many macromolecular anticancer drugs developed based on enhanced permeability and retention (EPR) effect, such as albumin bound paclitaxel nanoparticle (nab- PTX, also called Abraxane ® ). However, cancers with low vascular permeability posed a challenge for these EPR based therapeutic systems. Augmenting the intrinsic EPR effect with an intrinsic vascular modulator such as nitric oxide (NO) could be a promising strategy. S-nitrosated human serum albumin dimer (SNO-HSA Dimer) shown promising activity previously was evaluated for the synergistic effect when used as a pretreatment agent in nab-PTX therapy against various tumor models. In the high vascular permeability C26 murine colon cancer subcutaneous inoculation model, SNO-HSA Dimer enhanced tumor selectivity of nab-PTX, and attenuated myelosuppression. SNO-HSA Dimer also augmented the tumor growth inhibition of nab-PTX in low vascular permeability B16 murine melanoma subcutaneous inoculation model. Furthermore, nab-PTX therapy combined with SNO-HSA Dimer showed higher antitumor activity and improved survival rate of SUIT2 human pancreatic cancer orthotopic model. In conclusion, SNO-HSA Dimer could enhance the therapeutic effect of nab-PTX even in low vascular permeability or intractable pancreatic cancers. The possible underlying mechanisms of action of SNO-HSA Dimer were discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

VUV spectroscopy of rare gas van der Waals dimers

International Nuclear Information System (INIS)

Dehmer, P.M.; Pratt, S.T.

1982-01-01

We have undertaken a systematic study of the photoionization spectra of the homonuclear and heteronuclear rare gas dimers in order to better understand the nature of the bonding in the Rydberg states adnd ions of these molecules. We have obtained results for Ar 2 , Kr 2 , Xe 2 , NeAr, NeKr, NeXe, ArKr, ArXe, and KrXe. Of the remaining dimer species (Ne 2 and the Herare gas dimers), only Ne 2 has been studied using photoionization mass spectrometry. The results of the present series of experiments provide information both on the excited states of the neutral dimers and on the ground and excited states of the dimer ions. Using the data obtained in these measurements, we are able to compile for the first time a nearly complete list of ground state dissociation energies for the homonuclear and heteronuclear rare gas dimer ions. Somewhat less complete results are obtained for the excited states of these species. The observed trends in binding energy provide an excellent example of the systematic changes that occur as a result of changes in atomic orbital energies, polarizability, and internuclear distance, and these trends can be explained qualitatively in terms of simple molecular orbital theory

Hydrodynamic Torques and Rotations of Superparamagnetic Bead Dimers

Science.gov (United States)

Pease, Christopher; Etheridge, J.; Wijesinghe, H. S.; Pierce, C. J.; Prikockis, M. V.; Sooryakumar, R.

Chains of micro-magnetic particles are often rotated with external magnetic fields for many lab-on-a-chip technologies such as transporting beads or mixing fluids. These applications benefit from faster responses of the actuated particles. In a rotating magnetic field, the magnetization of superparamagnetic beads, created from embedded magnetic nano-particles within a polymer matrix, is largely characterized by induced dipoles mip along the direction of the field. In addition there is often a weak dipole mop that orients out-of-phase with the external rotating field. On a two-bead dimer, the simplest chain of beads, mop contributes a torque Γm in addition to the torque from mip. For dimers with beads unbound to each other, mop rotates individual beads which generate an additional hydrodynamic torque on the dimer. Whereas, mop directly torques bound dimers. Our results show that Γm significantly alters the average frequency-dependent dimer rotation rate for both bound and unbound monomers and, when mop exceeds a critical value, increases the maximum dimer rotation frequency. Models that include magnetic and hydrodynamics torques provide good agreement with the experimental findings over a range of field frequencies.

Laser isotope separation using selective inhibition and encouragement of dimer formation

International Nuclear Information System (INIS)

Kivel, B.

1979-01-01

Method and apparatus for inhibiting dimer formation of molecules of a selected isotope type in a cooled flow of gas to enhance the effectiveness of mass difference isotope separation techniques are described. Molecules in the flow containing atoms of the selected isotope type are selectively excited by infrared radiation in order to inhibit the formation of dimers and larger clusters of such molecules, while the molecules not containing atoms of the selected, excited type are encouraged to form dimers and higher order aggregates by the cooling of the gaseous flow. The molecules with the excited isotope will predominate in monomers and will constitute the enriched product stream, while the aggregated group comprising molecules having the unexcited isotope will predominate in dimers and larger clusters of molecules, forming the tails stream. The difference in diffusion coefficientts between particles of the excited and unexcited isotopes is enhanced by the greater mass differences resulting from aggregation of unexcited particles into dimers and larger clusters. Prior art separation techniques which exploit differences in isotopic diffusion rates will consequently exhibit enhanced enrichment per stage by the utilization of the present invention

Continuum emission of excited sodium dimer

International Nuclear Information System (INIS)

Pardo, A.; Poyato, J.M.L.; Alonso, J.I.; Rico, F.R.

1980-01-01

A study has been made of the behaviour of excited molecular sodium using high-power Ar + laser radiation. A continuum emission was observed in the red wavelength region. This emission was thought to be caused by the formation of excited triatomic molecules. Energy transfer was observed from excited molecules to atoms. (orig.)

MALDI Mass Spectral Imaging of Bile Acids Observed as Deprotonated Molecules and Proton-Bound Dimers from Mouse Liver Sections

Science.gov (United States)

Rzagalinski, Ignacy; Hainz, Nadine; Meier, Carola; Tschernig, Thomas; Volmer, Dietrich A.

2018-02-01

Bile acids (BAs) play two vital roles in living organisms, as they are involved in (1) the secretion of cholesterol from liver, and (2) the lipid digestion/absorption in the intestine. Abnormal bile acid synthesis or secretion can lead to severe liver disorders. Even though there is extensive literature on the mass spectrometric determination of BAs in biofluids and tissue homogenates, there are no reports on the spatial distribution in the biliary network of the liver. Here, we demonstrate the application of high mass resolution/mass accuracy matrix-assisted laser desorption/ionization (MALDI)-Fourier-transform ion cyclotron resonance (FTICR) to MS imaging (MSI) of BAs at high spatial resolutions (pixel size, 25 μm). The results show chemical heterogeneity of the mouse liver sections with a number of branching biliary and blood ducts. In addition to ion signals from deprotonation of the BA molecules, MALDI-MSI generated several further intense signals at larger m/z for the BAs. These signals were spatially co-localized with the deprotonated molecules and easily misinterpreted as additional products of BA biotransformations. In-depth analysis of accurate mass shifts and additional electrospray ionization and MALDI-FTICR experiments, however, confirmed them as proton-bound dimers. Interestingly, dimers of bile acids, but also unusual mixed dimers of different taurine-conjugated bile acids and free taurine, were identified. Since formation of these complexes will negatively influence signal intensities of the desired [M - H]- ions and significantly complicate mass spectral interpretations, two simple broadband techniques were proposed for non-selective dissociation of dimers that lead to increased signals for the deprotonated BAs. [Figure not available: see fulltext.

The steady-state and time-resolved photophysical properties of a dimeric indium phthalocyanine complex

International Nuclear Information System (INIS)

Chen Yu; Araki, Yasuyuki; Dini, Danilo; Liu Ying; Ito, Osamu; Fujitsuka, Mamoru

2006-01-01

The steady-state and time-resolved photophysical properties and some molecular orbital calculation results of a dimeric indium phthalocyanine complex with an indium-indium bond, i.e., [tBu 4 PcIn] 2 .2tmed, have been described. The results regarding triplet excited state lifetimes can be ascribed to strong intramolecular interactions existing only in the excited state of this dimer because no significant difference in the absorption spectra of the tBu 4 PcInCl monomer and the [tBu 4 PcIn] 2 .2tmed dimer is observed, suggesting that no ground-state interaction can be assessed. The deactivation processes of the excited singlet state of [tBu 4 PcIn] 2 .2tmed are apparently faster than that of μ-oxo-bridged PcIn dimer [tBu 4 PcIn] 2 O. Molecular orbital calculation on the PcIn dimer shows no node between two indium atoms was found in the HOMO - 2 of the PcIn-InPc dimer, suggesting that bonding electrons distribute between two indium atoms

Excitation of atomic nuclei and atoms by relativistic charge particles bound in a one-dimensional potential

International Nuclear Information System (INIS)

Almaliev, A.N.; Batkin, I.S.; Kopytin, I.V.

1987-01-01

The process of exciting atoms and atomic nuclei by relativistic electrons and positrons bound in a one-dimensional potential is investigated theoretically. It is shown that a pole corresponding to the emergence of a virtual photon on a bulk surface occurs in the matrix interaction element under definite kinematic relationships. It is obtained that the probability of the excitation process depends on the lifetime of the level being excited, the virtual photon, and the charged particle in a definite energetic state. An estimate of the magnitude of the excitation section of low-lying nuclear states yields a value exceeding by several orders the section obtained for charged particles in the absence of a binding potential

Stability of a nonlinear second order equation under parametric bounded noise excitation

International Nuclear Information System (INIS)

Wiebe, Richard; Xie, Wei-Chau

2016-01-01

The motivation for the following work is a structural column under dynamic axial loads with both deterministic (harmonic transmitted forces from the surrounding structure) and random (wind and/or earthquake) loading components. The bounded noise used herein is a sinusoid with an argument composed of a random (Wiener) process deviation about a mean frequency. By this approach, a noise parameter may be used to investigate the behavior through the spectrum from simple harmonic forcing, to a bounded random process with very little harmonic content. The stability of both the trivial and non-trivial stationary solutions of an axially-loaded column (which is modeled as a second order nonlinear equation) under parametric bounded noise excitation is investigated by use of Lyapunov exponents. Specifically the effect of noise magnitude, amplitude of the forcing, and damping on stability of a column is investigated. First order averaging is employed to obtain analytical approximations of the Lyapunov exponents of the trivial solution. For the non-trivial stationary solution however, the Lyapunov exponents are obtained via Monte Carlo simulation as the stability equations become analytically intractable. (paper)

Photoionization of helium dimers

International Nuclear Information System (INIS)

Havermeier, Tilo

2010-01-01

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.)

Proton-bound cluster ions in ion mobility spectrometry

Science.gov (United States)

Ewing, R. G.; Eiceman, G. A.; Stone, J. A.

1999-01-01

Gaseous oxygen and nitrogen bases, both singly and as binary mixtures, have been introduced into ion mobility spectrometers to study the appearance of protonated molecules, and proton-bound dimers and trimers. At ambient temperature it was possible to simultaneously observe, following the introduction of molecule A, comparable intensities of peaks ascribable to the reactant ion (H2O)nH+, the protonated molecule AH+ and AH+ H2O, and the symmetrical proton bound dimer A2H+. Mass spectral identification confirmed the identifications and also showed that the majority of the protonated molecules were hydrated and that the proton-bound dimers were hydrated to a much lesser extent. No significant peaks ascribable to proton-bound trimers were obtained no matter how high the sample concentration. Binary mixtures containing molecules A and B, in some cases gave not only the peaks unique to the individual compounds but also peaks due to asymmetrical proton bound dimers AHB+. Such ions were always present in the spectra of mixtures of oxygen bases but were not observed for several mixtures of oxygen and nitrogen bases. The dimers, which were not observable, notable for their low hydrogen bond strengths, must have decomposed in their passage from the ion source to the detector, i.e. in a time less than approximately 5 ms. When the temperature was lowered to -20 degrees C, trimers, both homogeneous and mixed, were observed with mixtures of alcohols. The importance of hydrogen bond energy, and hence operating temperature, in determining the degree of solvation of the ions that will be observed in an ion mobility spectrometer is stressed. The possibility is discussed that a displacement reaction involving ambient water plays a role in the dissociation.

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.

2007-07-01

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.)

Solvent effects on the excited-state double proton transfer mechanism in the 7-azaindole dimer: a TDDFT study with the polarizable continuum model.

Science.gov (United States)

Yu, Xue-Fang; Yamazaki, Shohei; Taketsugu, Tetsuya

2017-08-30

Solvent effects on the excited-state double proton transfer (ESDPT) mechanism in the 7-azaindole (7AI) dimer were investigated using the time-dependent density functional theory (TDDFT) method. Excited-state potential energy profiles along the reaction paths in a locally excited (LE) state and a charge transfer (CT) state were calculated using the polarizable continuum model (PCM) to include the solvent effect. A series of non-polar and polar solvents with different dielectric constants were used to examine the polarity effect on the ESDPT mechanism. The present results suggest that in a non-polar solvent and a polar solvent with a small dielectric constant, ESDPT follows a concerted mechanism, similar to the case in the gas phase. In a polar solvent with a relatively large dielectric constant, however, ESDPT is likely to follow a stepwise mechanism via a stable zwitterionic intermediate in the LE state on the adiabatic potential energy surface, although inclusion of zero-point vibrational energy (ZPE) corrections again suggests the concerted mechanism. In the meantime, the stepwise reaction path involving the CT state with neutral intermediates is also examined, and is found to be less competitive than the concerted or stepwise path in the LE state in both non-polar and polar solvents. The present study provides a new insight into the experimental controversy of the ESDPT mechanism of the 7AI dimer in a solution.

Excitation dynamics and relaxation in a molecular heterodimer

International Nuclear Information System (INIS)

Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

2012-01-01

Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: 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 molecular excitation energy gap, 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.

Inhomogeneous nuclear spin polarization induced by helicity-modulated optical excitation of fluorine-bound electron spins in ZnSe

Science.gov (United States)

Heisterkamp, F.; Greilich, A.; Zhukov, E. A.; Kirstein, E.; Kazimierczuk, T.; Korenev, V. L.; Yugova, I. A.; Yakovlev, D. R.; Pawlis, A.; Bayer, M.

2015-12-01

Optically induced nuclear spin polarization in a fluorine-doped ZnSe epilayer is studied by time-resolved Kerr rotation using resonant excitation of donor-bound excitons. Excitation with helicity-modulated laser pulses results in a transverse nuclear spin polarization, which is detected as a change of the Larmor precession frequency of the donor-bound electron spins. The frequency shift in dependence on the transverse magnetic field exhibits a pronounced dispersion-like shape with resonances at the fields of nuclear magnetic resonance of the constituent zinc and selenium isotopes. It is studied as a function of external parameters, particularly of constant and radio frequency external magnetic fields. The width of the resonance and its shape indicate a strong spatial inhomogeneity of the nuclear spin polarization in the vicinity of a fluorine donor. A mechanism of optically induced nuclear spin polarization is suggested based on the concept of resonant nuclear spin cooling driven by the inhomogeneous Knight field of the donor-bound electron.

Bound states and Cooper pairs of molecules in 2D optical lattices bilayer

Energy Technology Data Exchange (ETDEWEB)

Camacho-Guardian, A.; Dominguez-Castro, G.A.; Paredes, R. [Instituto de Fisica, Universidad Nacional Autonoma de Mexico (Mexico)

2016-08-15

We investigate the formation of Cooper pairs, bound dimers and the dimer-dimer elastic scattering of ultracold dipolar Fermi molecules confined in a 2D optical lattice bilayer configuration. While the energy and their associated bound states are determined in a variational way, the correlated two-molecule pair is addressed as in the original Cooper formulation. We demonstrate that the 2D lattice confinement favors the formation of zero center mass momentum bound states. Regarding the Cooper pairs binding energy, this depends on the molecule populations in each layer. Maximum binding energies occur for non-zero (zero) pair momentum when the Fermi system is polarized (unpolarized). We find an analytic expression for the dimer-dimer effective interaction in the deep BEC regime. The present analysis represents a route for addressing the BCS-BEC crossover in dipolar Fermi gases confined in 2D optical lattices within the current experimental panorama. (copyright 2016 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Molecular recognition of epothilones by microtubules and tubulin dimers revealed by biochemical and NMR approaches.

Science.gov (United States)

Canales, Angeles; Nieto, Lidia; Rodríguez-Salarichs, Javier; Sánchez-Murcia, Pedro A; Coderch, Claire; Cortés-Cabrera, Alvaro; Paterson, Ian; Carlomagno, Teresa; Gago, Federico; Andreu, José M; Altmann, Karl-Heinz; Jiménez-Barbero, Jesús; Díaz, J Fernando

2014-04-18

The binding of epothilones to dimeric tubulin and to microtubules has been studied by means of biochemical and NMR techniques. We have determined the binding constants of epothilone A (EpoA) and B (EpoB) to dimeric tubulin, which are 4 orders of magnitude lower than those for microtubules, and we have elucidated the conformation and binding epitopes of EpoA and EpoB when bound to tubulin dimers and microtubules in solution. The determined conformation of epothilones when bound to dimeric tubulin is similar to that found by X-ray crystallographic techniques for the binding of EpoA to the Tubulin/RB3/TTL complex; it is markedly different from that reported for EpoA bound to zinc-induced sheets obtained by electron crystallography. Likewise, only the X-ray structure of EpoA bound to the Tubulin/RB3/TTL complex at the luminal site, but not the electron crystallography structure, is compatible with the results obtained by STD on the binding epitope of EpoA bound to dimeric tubulin, thus confirming that the allosteric change (structuring of the M-loop) is the biochemical mechanism of induction of tubulin assembly by epothilones. TR-NOESY signals of EpoA bound to microtubules have been obtained, supporting the interaction with a transient binding site with a fast exchange rate (pore site), consistent with the notion that epothilones access the luminal site through the pore site, as has also been observed for taxanes. Finally, the differences in the tubulin binding affinities of a series of epothilone analogues has been quantitatively explained using the newly determined binding pose and the COMBINE methodology.

Quantum-statistical mechanics of an atom-dimer mixture: Lee-Yang cluster expansion approach

International Nuclear Information System (INIS)

Ohkuma, Takahiro; Ueda, Masahito

2006-01-01

We use the Lee-Yang cluster expansion method to study quantum-statistical properties of a mixture of interconvertible atoms and dimers, where the dimers form in a two-body bound state of the atoms. We point out an infinite series of cluster diagrams whose summation leads to the Bose-Einstein condensation of the dimers below a critical temperature. Our theory captures some important features of a cold atom-dimer mixture such as interconversion of atoms and dimers and properties of the mixture at the unitarity limit

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)

1996-12-31

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.

Relative stabilities and the spectral signatures of stacked and hydrogen-bonded dimers of serotonin

Science.gov (United States)

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

2015-10-01

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.

Magnetic Excitations in Cu2Fe2Ge4O13

International Nuclear Information System (INIS)

Masuda, Takatsugu; Zheludev, Andrey I.; Sales, Brian C.; Imai, S.; Uchinokura, K.

2005-01-01

Magnetic excitations in the cooperative ordered state in a weakly coupled Fe chains and Cu dimers compound Cu 2 Fe 2 Ge 4 O 13 is studied by thermal neutron scattering technique. We show that the low energy excitations up to 10 meV in wide q range are well described by spin wave theory of weakly coupled Fe chains. In higher energy range a narrow band excitation that can be associated with Cu dimers is observed at ℎω-24 meV. Both types of excitations can be understood by treating the weak coupling between Fe chains and Cu dimers at the level of Mean Field/Random Phase Approximation.

Magnetic excitations in (VO)HPO4· 1/2 H2O

International Nuclear Information System (INIS)

Garrett, A.W.; Nagler, S.E.; Tennant, D.A.

1997-01-01

The magnetic excitations of an antiferromagnetic spin dimer system, (VO)HPO 4 · 1/2 H 2 O, are examined using inelastic neutron scattering. A dispersionless mode is found, consistent with expectations for a dimer excitation. The intensity variation of the mode reveals a V 4+ - V 4+ dimer separation of 4.43 angstrom, almost 50% larger than the originally expected length

Excitations and possible bound states in the S = 1/2 alternating chain compound (VO)2P2O7

International Nuclear Information System (INIS)

Tennant, D.A.; Nagler, S.E.; Sales, B.C.

1997-01-01

Magnetic excitations in an array of (VO) 2 P 2 O 7 single crystals have been measured using inelastic neutron scattering. Until now, (VO) 2 P 2 O 7 has been thought of as a two-leg antiferromagnetic Heisenberg spin ladder with chains running in the a-direction. The present results show unequivocally that (VO) 2 P 2 O 7 is best described as an alternating spin-chain directed along the crystallographic b-direction. In addition to the expected magnon with magnetic zone-center energy gap Δ = 3.1 meV, a second excitation is observed at an energy just below 2Δ. The higher mode may be a triplet two-magnon bound state. Numerical results in support of bound modes are presented

Highly excited bound-state resonances of short-range inverse power-law potentials

Energy Technology Data Exchange (ETDEWEB)

Hod, Shahar [The Ruppin Academic Center, Emeq Hefer (Israel); The Hadassah Academic College, Jerusalem (Israel)

2017-11-15

We study analytically the radial Schroedinger equation with long-range attractive potentials whose asymptotic behaviors are dominated by inverse power-law tails of the form V(r) = -β{sub n}r{sup -n} with n > 2. In particular, assuming that the effective radial potential is characterized by a short-range infinitely repulsive core of radius R, we derive a compact analytical formula for the threshold energy E{sub l}{sup max} = E{sub l}{sup max}(n, β{sub n}, R), which characterizes the most weakly bound-state resonance (the most excited energy level) of the quantum system. (orig.)

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

2011-01-01

rate was clearly higher than the measured new particle formation rate at similar to 1.5 nmsuggesting that the rate limiting step for the nucleation takes place after the dimerization step. The quantum chemical calculations suggested that even in the ultraclean conditions there exist (a) stabilizing...... 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....

Dissociative recombination of the weakly bound NO-dimer cation: Cross sections and three-body dynamics

NARCIS (Netherlands)

Petrignani, A.; Andersson, P.U.; Pettersson, J.B.C.; Thomas, R.; Hellberg, F.; Ehlerding, A.; Larsson, M.; Zande, W.J. van der

2005-01-01

Dissociative recombination (DR) of the dimer ion (NO)(2)(+) has been studied at the heavy-ion storage ring CRYRING at the Manne Siegbahn Laboratory, Stockholm. The experiments were aimed at determining details on the strongly enhanced thermal rate coefficient for the dimer, interpreting the

Alignment and Imaging of the CS2 Dimer Inside Helium Nanodroplets

Science.gov (United States)

Pickering, James D.; Shepperson, Benjamin; Hübschmann, Bjarke A. K.; Thorning, Frederik; Stapelfeldt, Henrik

2018-03-01

The carbon disulphide (CS2) dimer is formed inside He nanodroplets and identified using fs laser-induced Coulomb explosion, by observing the CS2+ ion recoil velocity. It is then shown that a 160 ps moderately intense laser pulse can align the dimer in advantageous spatial orientations which allow us to determine the cross-shaped structure of the dimer by analysis of the correlations between the emission angles of the nascent CS2+ and S+ ions, following the explosion process. Our method will enable fs time-resolved structural imaging of weakly bound molecular complexes during conformational isomerization, including formation of exciplexes.

Contribution of water dimer absorption to the millimeter and far infrared atmospheric water continuum

Science.gov (United States)

Scribano, Yohann; Leforestier, Claude

2007-06-01

We present a rigorous calculation of the contribution of water dimers to the absorption coefficient α(ν¯,T ) in the millimeter and far infrared domains, over a wide range (276-310K) of temperatures. This calculation relies on the explicit consideration of all possible transitions within the entire rovibrational bound state manifold of the dimer. The water dimer is described by the flexible 12-dimensional potential energy surface previously fitted to far IR transitions [C. Leforestier et al., J. Chem. Phys. 117, 8710 (2002)], and which was recently further validated by the good agreement obtained for the calculated equilibrium constant Kp(T) with experimental data [Y. Scribano et al., J. Phys. Chem. A. 110, 5411 (2006)]. Transition dipole matrix elements were computed between all rovibrational states up to an excitation energy of 750cm-1, and J =K=5 rotational quantum numbers. It was shown by explicit calculations that these matrix elements could be extrapolated to much higher J values (J=30). Transitions to vibrational states located higher in energy were obtained from interpolation of computed matrix elements between a set of initial states spanning the 0-750cm-1 range and all vibrational states up to the dissociation limit (˜1200cm-1). We compare our calculations with available experimental measurements of the water continuum absorption in the considered range. It appears that water dimers account for an important fraction of the observed continuum absorption in the millimeter region (0-10cm-1). As frequency increases, their relative contribution decreases, becoming small (˜3%) at the highest frequency considered ν¯=944cm-1.

Artificial light harvesting by dimerized Möbius ring

Science.gov (United States)

Xu, Lei; Gong, Z. R.; Tao, Ming-Jie; Ai, Qing

2018-04-01

We theoretically study artificial light harvesting by a Möbius ring. When the donors in the ring are dimerized, the energies of the donor ring are split into two subbands. Because of the nontrivial Möbius boundary condition, both the photon and acceptor are coupled to all collective-excitation modes in the donor ring. Therefore, the quantum dynamics in the light harvesting is subtly influenced by dimerization in the Möbius ring. It is discovered that energy transfer is more efficient in a dimerized ring than that in an equally spaced ring. This discovery is also confirmed by a calculation with the perturbation theory, which is equivalent to the Wigner-Weisskopf approximation. Our findings may be beneficial to the optimal design of artificial light harvesting.

Pair Interaction of Catalytical Sphere Dimers in Chemically Active Media

Directory of Open Access Journals (Sweden)

Jing-Min Shi

2018-01-01

Full Text Available We study the pair dynamics of two self-propelled sphere dimers in the chemically active medium in which a cubic autocatalytic chemical reaction takes place. Concentration gradient around the dimer, created by reactions occurring on the catalytic sphere surface and responsible for the self-propulsion, is greatly influenced by the chemical activities of the environment. Consequently, the pair dynamics of two dimers mediated by the concentration field are affected. In the particle-based mesoscopic simulation, we combine molecular dynamics (MD for potential interactions and reactive multiparticle collision dynamics (RMPC for solvent flow and bulk reactions. Our results indicate three different configurations between a pair of dimers after the collision, i.e., two possible scenarios of bound dimer pairs and one unbound dimer pair. A phase diagram is sketched as a function of the rate coefficients of the environment reactions. Since the pair interactions are the basic elements of larger scale systems, we believe the results may shed light on the understanding of the collective dynamics.

Chloroplast Preproteins Bind to the Dimer Interface of the Toc159 Receptor during Import1[OPEN

Science.gov (United States)

Chen, Lih-Jen; Yeh, Yi-Hung; Hsiao, Chwan-Deng

2017-01-01

Most chloroplast proteins are synthesized in the cytosol as higher molecular weight preproteins and imported via the translocons in the outer (TOC) and inner (TIC) envelope membranes of chloroplasts. Toc159 functions as a primary receptor and directly binds preproteins through its dimeric GTPase domain. As a first step toward a molecular understanding of how Toc159 mediates preprotein import, we mapped the preprotein-binding regions on the Toc159 GTPase domain (Toc159G) of pea (Pisum sativum) using cleavage by bound preproteins conjugated with the artificial protease FeBABE and cysteine-cysteine cross-linking. Our results show that residues at the dimer interface and the switch II region of Toc159G are in close proximity to preproteins. The mature portion of preproteins was observed preferentially at the dimer interface, whereas the transit peptide was found at both regions equally. Chloroplasts from transgenic plants expressing engineered Toc159 with a cysteine placed at the dimer interface showed increased cross-linking to bound preproteins. Our data suggest that, during preprotein import, the Toc159G dimer disengages and the dimer interface contacts translocating preproteins, which is consistent with a model in which conformational changes induced by dimer-monomer conversion in Toc159 play a direct role in facilitating preprotein import. PMID:28250068

Photoionization of helium dimers; Photoionisation von Heliumdimeren

Energy Technology Data Exchange (ETDEWEB)

Havermeier, Tilo

2010-06-09

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.)

Excited, bound and resonant positron-atom systems

International Nuclear Information System (INIS)

Bromley, M W J; Mitroy, J

2010-01-01

Calculations have demonstrated that eleven neutral atoms can bind positrons, while many more can bind positronium. This is a short review of recent progress made in understanding some of the underlying mechanisms. The emphasis here being on configuration interaction calculations with excited state configurations. These have demonstrated the existence of a 2 P o excited state of e + Ca, which consists predominantly of a positronium cluster orbiting the Ca + ion in the L = 1 partial wave. Preliminary results are presented of excited state positron binding to a model alkali atom, where the excited 1 P o states are stable over a limited region. Implications for the unnatural parity, 2,4 S o , states of PsH, LiPs, NaPs and KPs are also discussed. The e + Mg, e + Cu, e + Zn and e + Cd systems show a lack of a 2 P o excited state, each instead possessing a low-energy p-wave shape resonance of varying strength.

Micrococcus radiodurans surface exonuclease. Dimer to monomer conversion by ionizing radiation-generated aqueous free radicals

Energy Technology Data Exchange (ETDEWEB)

Mitchel, R E.J.

1980-01-01

Micrococcus radiodurans possesses an exonuclease firmly bound to a middle cell wall membrane layer. Aqueous OH/sup -/ radicals generated chemically or by ionizing radiation cause the immediate release of this enzyme into the surrounding medium. The enzyme is located in a hydrophobic site and can also be released by aqueous n-butanol. When extracted by this solvent it is a non-covalently linked dimer and has a molecular weight of 260,000 as determined by gel filtration. When released by radiation generated OH/sup -/ radicals, the enzyme initially appears in solution as the dimer but is rapidly split by further aqueous radical attack into two 130,000 molecular weight subunits. Hydroxyl radicals are most effective but reducing radicals are also able to monomerize the enzyme. Only the released dimer enzyme is subject to free radical monomerization. Bound dimer enzyme is not split prior to release. No detectable loss of activity or change in catalytic properties accompanies the free radical cleavage of the enzyme. Both subunits of the dimer enzyme possess a tightly bound metal ion (probably Ca/sup 2 +/) required for activity. The monomer but not the dimer enzyme will bind to an anion exchanger. The monomer is susceptible to loss of its metal ion, and consequent inactivation, when exposed to the exchanger in the absence of Ca/sup 2 +/. Besides providing information on some of the immediate non-lethal effects of ionizing radiation, the behavior of this enzyme system demonstrates a potential cellular mechanism by which internally or externally generated free radicals could be utilized by the cell to control various enzymic reactions.

Pair condensation and bound states in fermionic systems

International Nuclear Information System (INIS)

Sedrakian, Armen; Clark, John W.

2006-01-01

We study the finite temperature-density phase diagram of an attractive fermionic system that supports two-body (dimer) and three-body (trimer) bound states in free space. Using interactions characteristic for nuclear systems, we obtain the critical temperature T c2 for the superfluid phase transition and the limiting temperature T c3 for the extinction of trimers. The phase diagram features a Cooper-pair condensate in the high-density, low-temperature domain which, with decreasing density, crosses over to a Bose condensate of strongly bound dimers. The high-temperature, low-density domain is populated by trimers whose binding energy decreases toward the density-temperature domain occupied by the superfluid and vanishes at a critical temperature T c3 >T c2

Excited, bound and resonant positron-atom systems

Energy Technology Data Exchange (ETDEWEB)

Bromley, M W J [Department of Physics and Computational Science Research Center, San Diego State University, San Diego CA 92182 (United States); Mitroy, J, E-mail: mbromley@physics.sdsu.ed [ARC Centre for Antimatter-Matter Studies and Faculty of Education, Health and Science, Charles Darwin University, Darwin NT 0909 (Australia)

2010-01-01

Calculations have demonstrated that eleven neutral atoms can bind positrons, while many more can bind positronium. This is a short review of recent progress made in understanding some of the underlying mechanisms. The emphasis here being on configuration interaction calculations with excited state configurations. These have demonstrated the existence of a {sup 2}P{sup o} excited state of e{sup +}Ca, which consists predominantly of a positronium cluster orbiting the Ca{sup +} ion in the L = 1 partial wave. Preliminary results are presented of excited state positron binding to a model alkali atom, where the excited {sup 1}P{sup o} states are stable over a limited region. Implications for the unnatural parity, {sup 2,4}S{sup o}, states of PsH, LiPs, NaPs and KPs are also discussed. The e{sup +}Mg, e{sup +}Cu, e{sup +}Zn and e{sup +}Cd systems show a lack of a {sup 2}P{sup o} excited state, each instead possessing a low-energy p-wave shape resonance of varying strength.

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

KAUST Repository

Kim, Jeong Joo

2016-04-09

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.

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

KAUST Repository

Kim, Jeong  Joo; Lorenz, Robin; Arold, Stefan T.; Reger, Albert  S.; Sankaran, Banumathi; Casteel, Darren  E.; Herberg, Friedrich  W.; Kim, Choel

2016-01-01

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.

LOCALIZATION OF POLYSOME-BOUND ALBUMIN AND SERINE DEHYDRATASE IN RAT LIVER CELL FRACTIONS

Science.gov (United States)

Ikehara, Yukio; Pitot, Henry C.

1973-01-01

The polysomes involved in albumin and serine dehydratase synthesis were identified and localized by the binding to rat liver polysomes of anti-rat serum albumin and anti-serine dehydratase [125I]Fab dimer and monomer. Techniques were developed for the isolation of undegraded free and membrane-bound polysomes and for the preparation of [125I]Fab monomers and dimers from the IgG obtained from the antisera to the two proteins, rat serum albumin and serine dehydratase. The distribution of anti-rat serum albumin [125I]Fab dimer in the polysome profile is in accordance with the size of polysomes that are expected to be synthesizing albumin. By direct precipitation, it has been demonstrated that nascent chains isolated from the membrane-bound polysomes by puromycin were precipitated by anti-rat serum albumin-IgG at a level of 5–6 times those released from free polysomes. Anti-rat serum albumin-[125I]Fab dimer reacted with membrane-bound polysomes almost exclusively compared to the binding of nonimmune, control [125I]Fab dimer; a significant degree of binding of anti-rat serum albumin-[125I]Fab to free polysomes was also obtained. The [125I]Fab dimer made from normal control rabbit serum does not react with polysomes from liver at all and this preparation will not interact with polysomes extracted from tissues that do not synthesize rat serum albumin. Both anti-serine dehydratase-[125I]Fab monomer and dimer react with free and bound polysomes from livers of animals fed a chow diet or those fed a high 90% protein diet and given glucagon. In the latter instance, however, it is clear that the majority of the binding occurs to the bound polysomes. Furthermore, the specificity of this reaction may be further shown by the use of kidney polysomes that do not normally synthesize serine dehydratase. When these latter polysomes are isolated, even after the addition of crude and purified serine dehydratase, no reaction with anti-serine dehydratase-Fab fragments could be

Van der Waals bond in dimers: H2Ne, H2Ar, H2Kr

International Nuclear Information System (INIS)

Waaijer, M.

1981-01-01

The H 2 -inert gas dimers H 2 X, and particularly H 2 Ne, H 2 Ar and H 2 Kr, form the subject of this thesis and are loosely bound van der Waals complexes, which is reflected in the low number of bound states and the small anisotropic interaction. The H 2 X dimers studied are formed in a supersonic nozzle expansion, in which the internal energy is converted into the macroscopic flow energy, establishing an internal temperature drop to 3 K, which favours dimer formation. Because of this cooling the H 2 X dimers relax to the lowest rotational states. The hyperfine transitions have been measured using magnetic beam resonance and yield information about the isotropic as well as the anisotropic intermolecular potential in the range between the classical turning points and in the adjacent part of the repulsive branch. The sensitivity of the method is very high and slight changes in the intermolecular potential cause significant effects. The analysis of the measured hyperfine transitions incorporates all interacting states of the molecule, bound as well as unbound (continuum) states. For H 2 Ne, which is the best studied H 2 -inert gas system from the experimental point of view, the author succeeded in establishing an intermolecular potential, that provides a solid ground for comparison with future ab initio calculations. (Auth.)

Investigation of the antiferromagnetic - ferromagnetic dimer chain compound BaCu{sub 2}V{sub 2}O{sub 8} at zero and finite temperatures

Energy Technology Data Exchange (ETDEWEB)

Klyushina, Ekaterina; Lake, Bella [Helmholtz-Zentrum Berlin fuer Materialien und Energie (Germany); Institut fuer Festkoerperphysik, Technische Universitaet Berlin (Germany); Tiegel, Alexander; Manmana, Salvatore [Georg-August-Universitaet Goettingen (Germany); Islam, Nazmul; Klemke, Bastian [Helmholtz-Zentrum Berlin fuer Materialien und Energie (Germany); Park, Jitae [Heinz Maier-Leibnitz Zentrum, TU Muenchen, Garching (Germany); Honecker, Andreas [Universite de Cergy-Pontoise (France)

2016-07-01

Highly dimerized quantum magnets have attracted a great deal of attention in the recently due to the unconventional temperature behavior of their magnetic excitations. Here we present our investigations of the highly dimerized antiferromagnet-ferromagnetic 1D chain BaCu{sub 2}V{sub 2}O{sub 8} both at base and at finite temperatures. The single crystal inelastic neutron scattering measurements at base temperature reveal that there are two excitation branches which disperse along the L direction over the energy range of 36-46 meV. The comparison with DMRG simulations indicates that the antiferromagnetic dimers are coupled ferromagnetically along the c axis. The line shape of the excitations at the dispersion minima was found to become asymmetry with increasing temperature. Thus unconventional thermal behavior also exists in dimer compounds with ferromagnetic interdimer coupling.

Visualization of multipolar longitudinal and transversal surface plasmon modes in nanowire dimers.

Science.gov (United States)

Alber, Ina; Sigle, Wilfried; Müller, Sven; Neumann, Reinhard; Picht, Oliver; Rauber, Markus; van Aken, Peter A; Toimil-Molares, Maria Eugenia

2011-12-27

We study the transversal and longitudinal localized surface plasmon resonances in single nanowires and nanowire dimers excited by the fast traveling electron beam in a transmission electron microscope equipped with high-resolution electron energy-loss spectroscopy. Bright and dark longitudinal modes up to the fifth order are resolved on individual metallic nanowires. On nanowire dimers, mode splitting into bonding and antibonding is measured up to the third order for several dimers with various aspect ratio and controlled gap size. We observe that the electric field maxima of the bonding modes are shifted toward the gap, while the electric field maxima of the antibonding modes are shifted toward the dimer ends. Finally, we observe that the transversal mode is not detected in the region of the dimer gap and decays away from the rod more rapidly than the longitudinal modes.

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)

2012-12-28

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.

Parametric excitation electromagnetic radiation in a bounded non-equilibrium plasma

International Nuclear Information System (INIS)

Balakirev, V.A.; Tolstoluzhskij, A.P.

1981-01-01

An excitation mechanism of electromagnetic radiation in a bounded plasma-beam system which is based on the process of induced scattering of electron beam-strengthened high-frequency wave (HF) of a plasma waveguide with an ion-sound wave, is investigated. It is shown that the process under investigation is an effective mechanism of electromagnetic radiation production. Up to 73 % of the beam power is trabsformed to the electromagnetic radiation under the conditions considered. As the frequency of the irradiated wave is close to the plasma frequency it can vary within wide limits by the change in plasma density. It is noted that the necessary condition of electromagnetic radiation production in the mechanism under consideration has the form of inequality ωsub(l)-ωsub(s)/(ksub(l)-ksub(s)>c (ωsub(l) - frequency of HF wave, ωsub(s)- frequency of ion-sound wave) and is less rigid as compared with the synchronism conditions for three-wave resonant interaction of proper oscillations. Therefore, the considered induced scattering process is less sensitive to a possible inhomogeneity of plasma density [ru

Adsorption, mobility, and dimerization of benzaldehyde on Pt(111)

DEFF Research Database (Denmark)

Rasmussen, Anton Michael Havelund; Hammer, Bjørk

2012-01-01

to have low energy barriers. Aggregation of molecules in dimers bound by aryl C–H⋯O hydrogen bonds is investigated, and specific configurations are found to be up to 0.15 eV more favorable than optimally configured, separated adsorbates. The binding is significantly stronger than what is found for gas...

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.

Perturbation expansion theory corrected from basis set superposition error. I. Locally projected excited orbitals and single excitations.

Science.gov (United States)

Nagata, Takeshi; Iwata, Suehiro

2004-02-22

The locally projected self-consistent field molecular orbital method for molecular interaction (LP SCF MI) is reformulated for multifragment systems. For the perturbation expansion, two types of the local excited orbitals are defined; one is fully local in the basis set on a fragment, and the other has to be partially delocalized to the basis sets on the other fragments. The perturbation expansion calculations only within single excitations (LP SE MP2) are tested for water dimer, hydrogen fluoride dimer, and colinear symmetric ArM+ Ar (M = Na and K). The calculated binding energies of LP SE MP2 are all close to the corresponding counterpoise corrected SCF binding energy. By adding the single excitations, the deficiency in LP SCF MI is thus removed. The results suggest that the exclusion of the charge-transfer effects in LP SCF MI might indeed be the cause of the underestimation for the binding energy. (c) 2004 American Institute of Physics.

The (6-4) Dimeric Lesion as a DNA Photosensitizer

OpenAIRE

Vendrell Criado, Victoria; Rodríguez Muñiz, Gemma María; Lhiaubet ., Virginie Lyria; Cuquerella Alabort, Maria Consuelo; Miranda Alonso, Miguel Ángel

2016-01-01

[EN] Based on our previous investigations into the photophysical properties of the 5-methyl-2-pyrimidone (Pyo) chromophore, we now extend our studies to the photobehavior of the dimeric (6-4) thymine photoproducts (6-4 PP) to evaluate their capability to act as instrinsic DNA photosensitizers. The lesion presents significant absorption in the UVB/UVA region, weak fluorescence emission, a singlet-excited-state energy of approximately 351 kJ mol(-1), and a triplet-excited-state energy of 297 kJ...

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

International Nuclear Information System (INIS)

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H.; Prodromou, Chrisostomos

2015-01-01

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90) 2 –Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

Energy Technology Data Exchange (ETDEWEB)

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H., E-mail: laurence.pearl@sussex.ac.uk; Prodromou, Chrisostomos, E-mail: laurence.pearl@sussex.ac.uk [University of Sussex, Falmer, Brighton BN1 9RQ (United Kingdom)

2015-05-01

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90){sub 2}–Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes.

Asymmetric monometallic nanorod nanoparticle dimer and related compositions and methods

KAUST Repository

Han, Yu

2016-03-31

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.

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

Science.gov (United States)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

Excitation and recombination of donor-acceptor pairs in ZnTe

International Nuclear Information System (INIS)

Nakashima, S.; Yasuda, S.

1979-01-01

The photoluminescence spectra and its excitation spectra of the donor-acceptor pairs are observed in ZnTe crystals doped with Li and As in the region below the bandgap energy. The relaxation of electrons and holes into the first excited state of d-a pairs is studied for the three excitation processes: (1) bound-to-bound transitions, (2) bound-to-free transitions, and (3) free-to-free transitions. It is concluded that most of the electrons and holes at the excited states of each impurity level are relaxed rapidly into their ground states before the occurrence of the recombination involving the excited states. For the excitation process (2), conduction electrons are preferentially trapped by positively charged pairs. The redistribution of bound holes by hopping is suggested to explain the broad d-a emission band observed for the bound-to-free excitation for very distant pairs. (author)

Fano resonances in heterogeneous dimers of silicon and gold nanospheres

Science.gov (United States)

Zhao, Qian; Yang, Zhong-Jian; He, Jun

2018-06-01

We theoretically investigate the optical properties of dimers consisting of a gold nanosphere and a silicon nanosphere. The absorption spectrum of the gold sphere in the dimer can be significantly altered and exhibits a pronounced Fano profile. Analytical Mie theory and numerical simulations show that the Fano profile is induced by constructive and destructive interference between the incident electric field and the electric field of the magnetic dipole mode of the silicon sphere in a narrow wavelength range. The effects of the silicon sphere size, distance between the two spheres, and excitation configuration on the optical responses of the dimers are studied. Our study reveals the coherent feature of the electric fields of magnetic dipole modes in dielectric nanostructures and the strong interactions of the coherent fields with other nanophotonic structures.

Dimerization in the Grb7 Protein

OpenAIRE

Peterson, Tabitha A.; Benallie, Renee L.; Bradford, Andrew M.; Pias, Sally C.; Yazzie, Jaron.; Lor, Siamee N.; Haulsee, Zachary M.; Park, Chad K.; Johnson, Dennis L.; Rohrschneider, Larry R.; Spuches, Anne.; Lyons, Barbara A.

2012-01-01

In previous studies, we showed that the tyrosine phosphorylation state of growth factor receptor–bound protein 7 (Grb7) affects its ability to bind to the transcription regulator FHL2 and the cortactin-interacting protein, human HS-1-associated protein-1. Here, we present results describing the importance of dimerization in the Grb7–Src homology 2 (SH2) domain in terms of its structural integrity and the ability to bind phosphorylated tyrosine peptide ligands. A tyrosine phosphorylation-mimic...

Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences

International Nuclear Information System (INIS)

Ai Yuejie; Zhang Feng; Cui Ganglong; Fang Weihai; Luo Yi

2010-01-01

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 1 ππ* 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.

Photo-physical properties of dimers formed by tri-aryl pyrylium salts: experimental and theoretical study

International Nuclear Information System (INIS)

Lampre, Isabelle

1996-01-01

This research thesis reports the study of dimers formed in solution by aggregation of tri-aryl pyrylium salts, in order to establish a direct correlation between properties and electronic structure of components, on the one hand, and molecular pattern, on the other hand. The author adopted a multidisciplinary approach by using experimental techniques and calculations based on the excitonic theory and methods of quantum chemistry. First, the properties of the first excited states of cationic chromophores have been studied (characterisation of electronic transitions, relaxation at the singlet excited state, formation of triplet state). Then, the author analysed dimerisation processes and showed that each dimer is formed by two pairs of ions. She discusses some original optical properties of dimers. The geometry of dimers is theoretically determined by minimising the system interaction potential energy. Electronic transitions are then determined as linear combinations of transitions of two monomers. Properties are thus calculated and are in agreement with those deduced from spectral analysis. The experimentally noticed polarisation change and large Stokes displacement are then explained in terms of emission for a localised state on a chromophore [fr

cis elements and trans-acting factors involved in dimer formation of murine leukemia virus RNA.

Science.gov (United States)

Prats, A C; Roy, C; Wang, P A; Erard, M; Housset, V; Gabus, C; Paoletti, C; Darlix, J L

1990-02-01

The genetic material of all retroviruses examined so far consists of two identical RNA molecules joined at their 5' ends by the dimer linkage structure (DLS). Since the precise location of the DLS as well as the mechanism and role(s) of RNA dimerization remain unclear, we analyzed the dimerization process of Moloney murine leukemia virus (MoMuLV) genomic RNA. For this purpose we derived an in vitro model for RNA dimerization. By using this model, murine leukemia virus RNA was shown to form dimeric molecules. Deletion mutagenesis in the 620-nucleotide leader of MoMuLV RNA showed that the dimer promoting sequences are located within the encapsidation element Psi between positions 215 and 420. Furthermore, hybridization assays in which DNA oligomers were used to probe monomer and dimer forms of MoMuLV RNA indicated that the DLS probably maps between positions 280 and 330 from the RNA 5' end. Also, retroviral nucleocapsid protein was shown to catalyze dimerization of MoMuLV RNA and to be tightly bound to genomic dimer RNA in virions. These results suggest that MoMuLV RNA dimerization and encapsidation are probably controlled by the same cis element, Psi, and trans-acting factor, nucleocapsid protein, and thus might be linked during virion formation.

Spectroscopic features of dimer and dangling bond E' centres in amorphous silica

International Nuclear Information System (INIS)

Mukhopadhyay, Sanghamitra; Sushko, Peter V; Mashkov, Vladimir A; Shluger, Alexander L

2005-01-01

We performed first-principle embedded cluster calculations of the hyperfine parameters, g-tensors and optical excitation energies for the dimer and back-projected configurations of the E' centre in amorphous silica. The optical transition energies of these defects are calculated for the first time. We predict a strong optical transition at about 6.3 eV for the dimer configuration and a relatively weak transition at 5.6 eV for the back-projected configuration of the E' centre. These predictions could be used for further experimental identification of these centres. Our results support the dimer model of the E' δ centre, and for the first time provide a full range of spectroscopic parameters for the back-projected configuration of the E' centre in amorphous silica

Modulation of BCR Signaling by the Induced Dimerization of Receptor-Associated SYK

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Mark L. Westbroek

2017-12-01

Full Text Available Clustering of the B cell antigen receptor (BCR by polyvalent antigens is transmitted through the SYK tyrosine kinase to the activation of multiple intracellular pathways that determine the physiological consequences of receptor engagement. To explore factors that modulate the quantity and quality of signals sent by the crosslinked BCR, we developed a novel chemical mediator of dimerization to induce clustering of receptor-associated SYK. To accomplish this, we fused SYK with E. coli dihydrofolate reductase (eDHFR, which binds the small molecule trimethoprim (TMP with high affinity and selectivity and synthesized a dimer of TMP with a flexible linker. The TMP dimer is able to induce the aggregation of eDHFR-linked SYK in live cells. The induced dimerization of SYK bound to the BCR differentially regulates the activation of downstream transcription factors, promoting the activation of Nuclear Factor of Activated T cells (NFAT without affecting the activation of NFκB. The dimerization of SYK enhances the duration but not the amplitude of calcium mobilization by enhancing the extent and duration of its interaction with the crosslinked BCR at the plasma membrane.

Van der Waals potential and vibrational energy levels of the ground state radon dimer

Science.gov (United States)

Sheng, Xiaowei; Qian, Shifeng; Hu, Fengfei

2017-08-01

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.

Braneworld black holes and entropy bounds

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Y. Heydarzade

2018-01-01

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.

Excitation mechanism in the photoisomerization of a surface-bound azobenzene derivative: Role of the metallic substrate

Science.gov (United States)

Hagen, Sebastian; Kate, Peter; Leyssner, Felix; Nandi, Dhananjay; Wolf, Martin; Tegeder, Petra

2008-10-01

Two-photon photoemission spectroscopy is employed to elucidate the electronic structure and the excitation mechanism in the photoinduced isomerization of the molecular switch tetra-tert-butyl-azobenzene (TBA) adsorbed on Au(111). Our results demonstrate that the optical excitation and the mechanism of molecular switching at a metal surface is completely different compared to the corresponding process for the free molecule. In contrast to direct (intramolecular) excitation operative in the isomerization in the liquid phase, the conformational change in the surface-bound TBA is driven by a substrate-mediated charge transfer process. We find that photoexcitation above a threshold hν ≈2.2 eV leads to hole formation in the Au d-band followed by a hole transfer to the highest occupied molecular orbital of TBA. This transiently formed positive ion resonance subsequently results in a conformational change. The photon energy dependent photoisomerization cross section exhibit an unusual shape for a photochemical reaction of an adsorbate on a metal surface. It shows a thresholdlike behavior below hν ≈2.2 eV and above hν ≈4.4 eV. These thresholds correspond to the minimum energy required to create single or multiple hot holes in the Au d-bands, respectively. This study provides important new insights into the use of light to control the structure and function of molecular switches in direct contact with metal electrodes.

Excitation mechanism in the photoisomerization of a surface-bound azobenzene derivative: Role of the metallic substrate

International Nuclear Information System (INIS)

Hagen, Sebastian; Kate, Peter; Leyssner, Felix; Nandi, Dhananjay; Wolf, Martin; Tegeder, Petra

2008-01-01

Two-photon photoemission spectroscopy is employed to elucidate the electronic structure and the excitation mechanism in the photoinduced isomerization of the molecular switch tetra-tert-butyl-azobenzene (TBA) adsorbed on Au(111). Our results demonstrate that the optical excitation and the mechanism of molecular switching at a metal surface is completely different compared to the corresponding process for the free molecule. In contrast to direct (intramolecular) excitation operative in the isomerization in the liquid phase, the conformational change in the surface-bound TBA is driven by a substrate-mediated charge transfer process. We find that photoexcitation above a threshold hν≅2.2 eV leads to hole formation in the Au d-band followed by a hole transfer to the highest occupied molecular orbital of TBA. This transiently formed positive ion resonance subsequently results in a conformational change. The photon energy dependent photoisomerization cross section exhibit an unusual shape for a photochemical reaction of an adsorbate on a metal surface. It shows a thresholdlike behavior below hν≅2.2 eV and above hν≅4.4 eV. These thresholds correspond to the minimum energy required to create single or multiple hot holes in the Au d-bands, respectively. This study provides important new insights into the use of light to control the structure and function of molecular switches in direct contact with metal electrodes.

The (6-4) Dimeric Lesion as a DNA Photosensitizer.

Science.gov (United States)

Vendrell-Criado, Victoria; Rodríguez-Muñiz, Gemma M; Lhiaubet-Vallet, Virginie; Cuquerella, M Consuelo; Miranda, Miguel A

2016-07-04

Based on our previous investigations into the photophysical properties of the 5-methyl-2-pyrimidone (Pyo) chromophore, we now extend our studies to the photobehavior of the dimeric (6-4) thymine photoproducts (6-4 PP) to evaluate their capability to act as instrinsic DNA photosensitizers. The lesion presents significant absorption in the UVB/UVA region, weak fluorescence emission, a singlet-excited-state energy of approximately 351 kJ mol(-1) , and a triplet-excited-state energy of 297 kJ mol(-1) . Its triplet transient absorption has a maximum at 420-440 nm, a lifetime of around 7 μs, and a high formation quantum yield, ΦISC =0.86. This species is efficiently quenched by thymidine. Its DNA photosensitizing properties are demonstrated by a series of experiments run on a pBR322 plasmid. The lesion photoinduces both single-strand breaks and the formation of cyclobutane thymine dimers. Altogether, these results show that, the substitution of the pyrimidone ring at C4 by a 5-hydroxy-5,6-dihydrothymine does not cancel out the photosensitization properties of the chromophore. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

How Does Thymine DNA Survive Ultrafast Dimerization Damage?

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Hongjuan Wang

2016-12-01

Full Text Available The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction takes place on a picosecond time scale along barrierless or low barrier singlet/triplet pathways. However, the observed dimerization quantum yield in different thymine multimer is considerable lower than might be expected. A reasonable explanation is required to understand why thymine in DNA is able to survive ultrafast dimerization damage. In this work, accurate quantum calculations based on the combined CASPT2//CASSCF/AMBER method were conducted to map the excited state relaxation pathways of the thymine monomer in aqueous solution and of the thymine oligomer in DNA. A monomer-like decay pathway, induced by the twisting of the methyl group, is found to provide a bypass channel to ensure the photostability of thymine in single-stranded oligomers. This fast relaxation path is regulated by the conical intersection between the bright SCT(1ππ* state with the intra-base charge transfer character and the ground state to remove the excess excitation energy, thereby achieving the ground-state recovery with high efficiency.

Single-Molecule Rotational Switch on a Dangling Bond Dimer Bearing.

Science.gov (United States)

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

2016-09-27

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.

Relativistic and Non-Relativistic Electronic Molecular-Structure Calculations for Dimers of 4p-, 5p-, and 6p-Block Elements

DEFF Research Database (Denmark)

Hofener, S.; Ahlrichs, R.; Knecht, S.

2012-01-01

We report results of non-relativistic and two-component relativistic single-reference coupled-cluster with single and double and perturbative triple excitations [CCSD(T)] treatments for the 4p-block dimers Ga2 to Br2, the 5p-block dimers In2 to I2, and their atoms. Extended basis sets up...

Frenkel and Charge-Transfer Excitations in Donor-acceptor Complexes from Many-Body Green's Functions Theory.

Science.gov (United States)

Baumeier, Björn; Andrienko, Denis; Rohlfing, Michael

2012-08-14

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.

Dynamic analysis and reliability assessment of structures with uncertain-but-bounded parameters under stochastic process excitations

International Nuclear Information System (INIS)

Do, Duy Minh; Gao, Wei; Song, Chongmin; Tangaramvong, Sawekchai

2014-01-01

This paper presents the non-deterministic dynamic analysis and reliability assessment of structures with uncertain-but-bounded parameters under stochastic process excitations. Random ground acceleration from earthquake motion is adopted to illustrate the stochastic process force. The exact change ranges of natural frequencies, random vibration displacement and stress responses of structures are investigated under the interval analysis framework. Formulations for structural reliability are developed considering the safe boundary and structural random vibration responses as interval parameters. An improved particle swarm optimization algorithm, namely randomised lower sequence initialized high-order nonlinear particle swarm optimization algorithm, is employed to capture the better bounds of structural dynamic characteristics, random vibration responses and reliability. Three numerical examples are used to demonstrate the presented method for interval random vibration analysis and reliability assessment of structures. The accuracy of the results obtained by the presented method is verified by the randomised Quasi-Monte Carlo simulation method (QMCSM) and direct Monte Carlo simulation method (MCSM). - Highlights: • Interval uncertainty is introduced into structural random vibration responses. • Interval dynamic reliability assessments of structures are implemented. • Boundaries of structural dynamic response and reliability are achieved

Gas-phase isotope fractionation factor for the proton-bound dimer of the ethoxide

International Nuclear Information System (INIS)

Ellenberger, M.R.; Farneth, W.E.; Dixon, D.A.

1981-01-01

The gas-phase isotope fractionation factor, phi/sub gp/, for A 2 L - where A = EtO and L = H or D has been measured by using ion cyclotron resonance spectroscopy. Two approaches to the formation of the A 2 L - dimers are presented. The value for phi/sub gp/ is 0.46 +- 0.1. This low value for phi/sub gp/ is consistent with motion of a proton in a potential with a small central maximum or no maximum

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

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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.

Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

Energy Technology Data Exchange (ETDEWEB)

Teplova, Marianna; Farazi, Thalia A.; Tuschl, Thomas; Patel, Dinshaw J.

2015-09-08

RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutationsin vivo.

Prospects for transferring 87Rb84Sr dimers to the rovibrational ground state based on calculated molecular structures

Science.gov (United States)

Chen, Tao; Zhu, Shaobing; Li, Xiaolin; Qian, Jun; Wang, Yuzhu

2014-06-01

Using fitted model potential curves of the ground and lowest three excited states yielded by the relativistic Kramers-restricted multireference configuration interaction method with 19 electrons correlated, we theoretically investigate the rovibrational properties including the number of vibrational state and diagonally distributed Franck-Condon factors for a 87Rb84Sr molecule. Benefiting from a turning point at about v'=20 for the Franck-Condon factors between the ground state and spin-orbit 2(Ω=1/2) excited state, we choose |2(Ω=1/2),v'=21,J'=1> as the intermediate state in the three-level model to theoretically analyze the possibility of performing stimulated Raman adiabatic passage to transfer weakly bound RbSr molecules to the rovibrational ground state. With 1550 nm pump laser (2 W/cm2) and 1342 nm dump laser (10 mW/cm2) employed and appropriate settings of pulse time length (about 300 μs), we have formalistically achieved a round-trip transfer efficiency of 60%, namely 77% for one-way transfer. The results demonstrate the possibility of producing polar 87Rb84Sr molecules efficiently in a submicrokelvin regime, and further provide promising directions for future theoretical and experimental studies on alkali-alkaline(rare)-earth dimers.

Effect of serotonin on the yield of UV-induced thymine dimers in DNA

International Nuclear Information System (INIS)

Frajkin, G.Ya.; Strakhovskaya, M.G.; Ivanova, Eh.V.

1985-01-01

Using fluorescence method serotonin interaction with DNA is studied and bond constant Ksub(c)=4.2x10 4 M -1 is defined. It is shown that bound serotonin reduces yield of UV-induced thymine dimers. Value of efficient distance of protective serotonin effect constituting part of DNA chain of 4 base pairs, is determined

Liquid crystal dimers

CERN Document Server

Kumar Pal, Santanu

2017-01-01

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.

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

Science.gov (United States)

Correia, Manuel; Neves-Petersen, Maria Teresa; Jeppesen, Per Bendix; Gregersen, Søren; Petersen, Steffen B

2012-01-01

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 in protein

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

Bound states in weakly disordered spin ladders

Energy Technology Data Exchange (ETDEWEB)

Arlego, M. [Departamento de Fisica, Universidad Nacional de La Plata, CC 67 (1900) La Plata (Argentina)]. E-mail: arlego@venus.fisica.unlp.edu.ar; Brenig, W. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Cabra, D.C. [Laboratoire de Physique Theorique, Universite Louis Pasteur Strasbourg (France); Heidrich-Meisner, F. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Honecker, A. [Institut fuer Theoretische Physik, Technische Universitaet Braunschweig (Germany); Rossini, G. [Departamento de Fisica, Universidad Nacional de La Plata, CC 67 (1900) La Plata (Argentina)

2005-04-30

We study the appearance of bound states in the spin gap of spin-12 ladders induced by weak bond disorder. Starting from the strong-coupling limit, i.e., the limit of weakly coupled dimers, we perform a projection on the single-triplet subspace and derive the position of bound states for the single impurity problem of one modified coupling as well as for small impurity clusters. The case of a finite concentration of impurities is treated with the coherent-potential approximation (CPA) in the strong-coupling limit and compared with numerical results. Further, we analyze the details in the structure of the density of states and relate their origin to the influence of impurity clusters.

Dark-matter bound states from Feynman diagrams

NARCIS (Netherlands)

Petraki, K.; Postma, M.; Wiechers, M.

2015-01-01

If dark matter couples directly to a light force mediator, then it may form bound states in the early universe and in the non-relativistic environment of haloes today. In this work, we establish a field-theoretic framework for the computation of bound-state formation cross-sections, de-excitation

New Insights into Molecular Organization of Human Neuraminidase-1: Transmembrane Topology and Dimerization Ability

Science.gov (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

2016-12-01

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.

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: jiangdu@ucsd.edu [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)

2014-02-15

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

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

International Nuclear Information System (INIS)

Li, Shihong; Chang, Eric Y.; Chung, Christine B.; Bae, Won C.; Du, Jiang; Hua, Yanqing; Zhou, Yi

2014-01-01

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 * s and/or relative fractions of short and long T2 * s. Results: For all bone samples UTE T2 * signal decay showed bicomponent behavior. A higher short T2 * 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 * 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 * 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 * 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 * s and relative fractions can be assessed using UTE bicomponent

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.)

2010-10-22

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.

Modelling Ca2+ bound Troponin in Excitation Contraction Coupling

Directory of Open Access Journals (Sweden)

Henry G. Zot

2016-09-01

Full Text Available To explain disparate decay rates of cytosolic Ca2+ and structural changes in the thin filaments during a twitch, we model the time course of Ca2+ bound troponin (Tn resulting from the free Ca2+ transient of fast skeletal muscle. In fibers stretched beyond overlap, the decay of Ca2+ as measured by a change in fluo 3 fluorescence is significantly slower than the intensity decay of the meridional 1/38.5 nm-1 reflection of Tn; this is not simply explained by considering only the Ca2+ binding properties of Tn alone (Matsuo, T., Iwamoto, H., and Yagi, N. (2010. Biophys. J. 99, 193-200. We apply a comprehensive model that includes the known Ca2+ binding properties of Tn in the context of the thin filament with and without cycling crossbridges. Calculations based on the model predict that the transient of Ca2+ bound Tn correlates with either the fluo 3 time course in muscle with overlapping thin and thick filaments or the intensity of the meridional 1/38.5 nm-1 reflection in overstretched muscle. Hence, cycling crossbridges delay the dissociation of Ca2+ from Tn. Correlation with the fluo 3 fluorescence change is not causal given that the transient of Ca2+ bound Tn depends on sarcomere length, whereas the fluo-3 fluorescence change does not. Transient positions of tropomyosin calculated from the time course of Ca2+ bound Tn are in reasonable agreement with the transient of measured perturbations of the Tn repeat in overlap and non-overlap muscle preparations.

The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.

Science.gov (United States)

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

2016-03-02

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.

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

Science.gov (United States)

Jankowski, Aleksander; Szczurek, Ewa; Jauch, Ralf; Tiuryn, Jerzy; Prabhakar, Shyam

2013-01-01

The binding of transcription factors (TFs) to their specific motifs in genomic regulatory regions is commonly studied in isolation. However, in order to elucidate the mechanisms of transcriptional regulation, it is essential to determine which TFs bind DNA cooperatively as dimers and to infer the precise nature of these interactions. So far, only a small number of such dimeric complexes are known. Here, we present an algorithm for predicting cell-type–specific TF–TF dimerization on DNA on a large scale, using DNase I hypersensitivity data from 78 human cell lines. We represented the universe of possible TF complexes by their corresponding motif complexes, and analyzed their occurrence at cell-type–specific DNase I hypersensitive sites. Based on ∼1.4 billion tests for motif complex enrichment, we predicted 603 highly significant cell-type–specific TF dimers, the vast majority of which are novel. Our predictions included 76% (19/25) of the known dimeric complexes and showed significant overlap with an experimental database of protein–protein interactions. They were also independently supported by evolutionary conservation, as well as quantitative variation in DNase I digestion patterns. Notably, the known and predicted TF dimers were almost always highly compact and rigidly spaced, suggesting that TFs dimerize in close proximity to their partners, which results in strict constraints on the structure of the DNA-bound complex. Overall, our results indicate that chromatin openness profiles are highly predictive of cell-type–specific TF–TF interactions. Moreover, cooperative TF dimerization seems to be a widespread phenomenon, with multiple TF complexes predicted in most cell types. PMID:23554463

Electron-beam-excited gas laser research

International Nuclear Information System (INIS)

Johnson, A.W.; Gerardo, J.B.; Patterson, E.L.; Gerber, R.A.; Rice, J.K.; Bingham, F.W.

1975-01-01

Net energy gain in laser fusion places requirements on the laser that are not realized by any existing laser. Utilization of relativistic electron beams (REB's), a relatively new source for the excitation of gas laser media, may lead to new lasers that could satisfy these requirements. Already REB's have been utilized to excite gas laser media and produce gas lasers that have not been produced as successfully any other way. Electron-beam-excitation has produced electronic-transition dimer lasers that have not yet been produced by any other excitation scheme (for example, Xe 2 / sup *(1)/, Kr:O(2 1 S)/sup 2/, KrF/sup *(3)/). In addition, REB's have initiated chemical reactions to produce HF laser radiation with unique and promising results. Relativistic-electron-beam gas-laser research is continuing to lead to new lasers with unique properties. Results of work carried out at Sandia Laboratories in this pioneering effort of electron-beam-excited-gas lasers are reviewed. (U.S.)

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: tolan@bu.edu [Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215 (United States); Allen, Karen N., E-mail: tolan@bu.edu [Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118-2394 (United States)

2008-05-01

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.

Internal energy selection in vacuum ultraviolet photoionization of ethanol and ethanol dimers

Science.gov (United States)

Bodi, Andras

2013-10-01

Internal energy selected ethanol monomer and ethanol dimer ions were prepared by threshold photoionization of a supersonic molecular beam seeded with ethanol. The dissociative photoionization processes of the monomer, the lowest-energy CH3-loss channel of the dimer, and the fragmentation of larger clusters were found to be disjunct from the ionization onset to about 12 eV, which made it possible to determine the 0 K appearance energy of C-C bond breaking in the H-donor unit of the ethanol dimer cation as 9.719 ± 0.004 eV. This reaction energy is used together with ab initio calculations in a thermochemical cycle to determine the binding energy change from the neutral ethanol dimer to a protonated ethanol-formaldehyde adduct. The cycle also shows general agreement between experiment, theory, and previously published enthalpies of formation. The role of the initial ionization site, or rather the initial photoion state, is also discussed based on the dimer breakdown diagram and excited state calculations. There is no evidence for isolated state behavior, and the ethanol dimer dissociative photoionization processes appear to be governed by statistical theory and the ground electronic state of the ion. In the monomer breakdown diagram, the smoothly changing branching ratio between H and CH3 loss is at odds with rate theory predictions, and shows that none of the currently employed few-parameter rate models, appropriate for experimental rate curve fitting, yields a correct description for this process in the experimental energy range.

Electronic energy transfer through non-adiabatic vibrational-electronic resonance. I. Theory for a dimer

Science.gov (United States)

Tiwari, Vivek; Peters, William K.; Jonas, David M.

2017-10-01

Non-adiabatic vibrational-electronic resonance in the excited electronic states of natural photosynthetic antennas drastically alters the adiabatic framework, in which electronic energy transfer has been conventionally studied, and suggests the possibility of exploiting non-adiabatic dynamics for directed energy transfer. Here, a generalized dimer model incorporates asymmetries between pigments, coupling to the environment, and the doubly excited state relevant for nonlinear spectroscopy. For this generalized dimer model, the vibrational tuning vector that drives energy transfer is derived and connected to decoherence between singly excited states. A correlation vector is connected to decoherence between the ground state and the doubly excited state. Optical decoherence between the ground and singly excited states involves linear combinations of the correlation and tuning vectors. Excitonic coupling modifies the tuning vector. The correlation and tuning vectors are not always orthogonal, and both can be asymmetric under pigment exchange, which affects energy transfer. For equal pigment vibrational frequencies, the nonadiabatic tuning vector becomes an anti-correlated delocalized linear combination of intramolecular vibrations of the two pigments, and the nonadiabatic energy transfer dynamics become separable. With exchange symmetry, the correlation and tuning vectors become delocalized intramolecular vibrations that are symmetric and antisymmetric under pigment exchange. Diabatic criteria for vibrational-excitonic resonance demonstrate that anti-correlated vibrations increase the range and speed of vibronically resonant energy transfer (the Golden Rule rate is a factor of 2 faster). A partial trace analysis shows that vibronic decoherence for a vibrational-excitonic resonance between two excitons is slower than their purely excitonic decoherence.

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.

2012-01-01

An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers...... 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...... and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization...

The two-state dimer receptor model: a general model for receptor dimers.

Science.gov (United States)

Franco, Rafael; Casadó, Vicent; Mallol, Josefa; Ferrada, Carla; Ferré, Sergi; Fuxe, Kjell; Cortés, Antoni; Ciruela, Francisco; Lluis, Carmen; Canela, Enric I

2006-06-01

Nonlinear Scatchard plots are often found for agonist binding to G-protein-coupled receptors. Because there is clear evidence of receptor dimerization, these nonlinear Scatchard plots can reflect cooperativity on agonist binding to the two binding sites in the dimer. According to this, the "two-state dimer receptor model" has been recently derived. In this article, the performance of the model has been analyzed in fitting data of agonist binding to A(1) adenosine receptors, which are an example of receptor displaying concave downward Scatchard plots. Analysis of agonist/antagonist competition data for dopamine D(1) receptors using the two-state dimer receptor model has also been performed. Although fitting to the two-state dimer receptor model was similar to the fitting to the "two-independent-site receptor model", the former is simpler, and a discrimination test selects the two-state dimer receptor model as the best. This model was also very robust in fitting data of estrogen binding to the estrogen receptor, for which Scatchard plots are concave upward. On the one hand, the model would predict the already demonstrated existence of estrogen receptor dimers. On the other hand, the model would predict that concave upward Scatchard plots reflect positive cooperativity, which can be neither predicted nor explained by assuming the existence of two different affinity states. In summary, the two-state dimer receptor model is good for fitting data of binding to dimeric receptors displaying either linear, concave upward, or concave downward Scatchard plots.

On the geometry dependence of molecular dimer spectra with an application to aggregates of perylene bisimide

International Nuclear Information System (INIS)

Seibt, J.; Marquetand, P.; Engel, Volker; Chen, Z.; Dehm, V.; Wuerthner, F.

2006-01-01

We study spectroscopic properties of molecular dimers coupled by dipole-dipole interactions within the framework of time-dependent quantum mechanics. A systematic variation of the dimer geometry allows to establish relationships between the latter and structures in the absorption spectrum. The theoretical model is constructed with the purpose to characterize the changes in absorption and emission properties arising upon aggregation of perylene bisimides. Measured and calculated spectra are compared, thereby addressing the question if a simple exciton model is capable to describe excited state properties of nanoaggregates of these molecules

Crystal Structure of Ripk4 Reveals Dimerization-Dependent Kinase Activity.

Science.gov (United States)

Huang, Christine S; Oberbeck, Nina; Hsiao, Yi-Chun; Liu, Peter; Johnson, Adam R; Dixit, Vishva M; Hymowitz, Sarah G

2018-05-01

Receptor-interacting protein kinase 4 (RIPK4) is a highly conserved regulator of epidermal differentiation. Members of the RIPK family possess a common kinase domain as well as unique accessory domains that likely dictate subcellular localization and substrate preferences. Mutations in human RIPK4 manifest as Bartsocas-Papas syndrome (BPS), a genetic disorder characterized by severe craniofacial and limb abnormalities. We describe the structure of the murine Ripk4 (MmRipk4) kinase domain, in ATP- and inhibitor-bound forms. The crystallographic dimer of MmRipk4 is similar to those of RIPK2 and BRAF, and we show that the intact dimeric entity is required for MmRipk4 catalytic activity through a series of engineered mutations and cell-based assays. We also assess the impact of BPS mutations on protein structure and activity to elucidate the molecular origins of the disease. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

2012-01-01

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...

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

NARCIS (Netherlands)

Bloemsma, E. A.; Knoester, J.

2012-01-01

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

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

NARCIS (Netherlands)

Geethalakshmi, K R; Ruipérez, Fernando; Knecht, Stefan; Ugalde, Jesus M.; Morse, Michael D.; Infante, Ivan

2012-01-01

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

Photomonomerization of pyrimidine dimers by indoles and proteins

Energy Technology Data Exchange (ETDEWEB)

Chen, J.; Huang, C.W.; Hinman, L.; Gordon, M.P.; Deranleau, D.A.

1976-01-01

Model systems for the study of photoreactivation have been developed that utilize a variety of indole derivatives. These systems can split uracil cis-syn cyclobutadipyrimidine, either free or in RNA, when irradiated at wavelengths absorbed only by the indole moiety. The ability of indole compounds to split dimers is closely related to their electronic properties. Those of high electron-donor capacity such as indole, 3-methylindole, indole-3-acetic acid, 5-hydroxytryptophan and tryptophan are good photosensitizers, with efficacy in that order. Indoles with electron-withdrawing substituents such as indole-3-carboxylic acid, indole-3-aldehyde and oxindole are inactive in the monomerization reaction. These findings support the proposed mechanism that the photosensitized monomerization occurs as a result of electron transfer from the excited indole molecules to the pyrimidine bases. Proteins containing fully exposed tryptophan residues (chicken egg white lysozyme and bovine diisopropylphosphoryltrypsin) also cause the splitting of the /sup 14/C-labeled dimers under the same conditions. In the case of lysozyme the quantum yield of monomerization is similar to that of free tryptophan. Much of the monomerization ability of lysozyme was lost after the solvent-available tryptophan had been oxidized by treatment with N-bromosuccinimide. Bovine pancreatic ribonuclease A, a protein devoid of tryptophan, failed to exhibit photosensitized monomerization of uracil dimers. The biological implication of these reactions involving a protein with an exposed tryptophan residue is discussed. Although indoles are able to split the dimers in RNA, they fail to photoreactivate uv-damaged TMV-RNA. Indole-3-acetic acid, 3-methylindole and 5-hydroxytryptophan rapidly inactive viral RNA when irradiated at 313 nm, possibly because of side reactions.

Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease.

Science.gov (United States)

Gable, Jonathan E; Lee, Gregory M; Acker, Timothy M; Hulce, Kaitlin R; Gonzalez, Eric R; Schweigler, Patrick; Melkko, Samu; Farady, Christopher J; Craik, Charles S

2016-04-19

Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Calculating the mean time to capture for tethered ligands and its effect on the chemical equilibrium of bound ligand pairs.

Science.gov (United States)

Shen, Lu; Decker, Caitlin G; Maynard, Heather D; Levine, Alex J

2016-09-01

We present here the calculation of the mean time to capture of a tethered ligand to the receptor. This calculation is then used to determine the shift in the partitioning between (1) free, (2) singly bound, and (3) doubly bound ligands in chemical equilibrium as a function of the length of the tether. These calculations are used in the research article Fibroblast Growth Factor 2 Dimer with Superagonist in vitro Activity Improves Granulation Tissue Formation During Wound Healing (Decker et al., in press [1]) to explain quantitatively how changes in polymeric linker length in the ligand dimers modifies the efficacy of these molecules relative to that of free ligands.

Parity lifetime of bound states in a proximitized semiconductor nanowire

DEFF Research Database (Denmark)

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

2015-01-01

Quasiparticle excitations can compromise the performance of superconducting devices, causing high frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic...... 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 Counting for Excited Bands of the Fractional Quantum Hall Effect: Exclusion Rules for Bound Excitons

Science.gov (United States)

Coimbatore Balram, Ajit; Wójs, Arkadiusz; Jain, Jainendra

2014-03-01

Exact diagonalization studies have revealed that the energy spectrum of interacting electrons in the lowest Landau level splits, non-perturbatively, into bands. The theory of nearly free composite fermions (CFs) has been shown to be valid for the lowest band, and thus to capture the low temperature physics, but it over-predicts the number of states for the excited bands. We explain the state counting of higher bands in terms of composite fermions with an infinitely strong short range interaction between a CF particle and a CF hole. This interaction, the form of which we derive from the microscopic CF theory, eliminates configurations containing certain tightly bound CF excitons. With this modification, the CF theory reproduces, for all well-defined excited bands, an exact counting for ν > 1 / 3 , and an almost exact counting for ν The resulting insight clarifies that the corrections to the nearly free CF theory are not thermodynamically significant at sufficiently low temperatures, thus providing a microscopic explanation for why it has proved successful for the analysis of the various properties of the CF Fermi sea. NSF grants DMR-1005536 and DMR-0820404, Polish NCN grant 2011/01/B/ST3/04504 and EU Marie Curie Grant PCIG09-GA-2011-294186, Research Computing and Cyberinfrastructure, PSU and Wroclaw Centre for Networking and Supercomputing

The dynamics of a polariton dimer in a disordered coupled array of cavities

Science.gov (United States)

Aiyejina, Abuenameh; Andrews, Roger

2018-03-01

We investigate the effect of disorder in the laser intensity on the dynamics of dark-state polaritons in an array of 20 cavities, each containing an ensemble of four-level atoms that is described by a Bose-Hubbard Hamiltonian. We examine the evolution of the polariton number in the cavities starting from a state with either one or two polaritons in one of the cavities. For the case of a single polariton without disorder in the laser intensity, we calculate the wavefunction of the polariton and find that it disperses away from the initial cavity with time. The addition of disorder results in minimal suppression of the dispersal of the wavefunction. In the case of two polaritons with an on-site repulsion to hopping strength ratio of 20, we find that the polaritons form a repulsively bound state or dimer. Without disorder the dimer wavefunction disperses similarly to the single polariton wavefunction but over a longer time period. The addition of sufficiently strong disorder results in localization of the polariton dimer. The localization length is found to be described by a power law with exponent - 1.31. We also find that we can localise the dimer at any given time by switching on the disorder.

Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization.

Science.gov (United States)

Liber, Miran; Tomov, Toma E; Tsukanov, Roman; Berger, Yaron; Popov, Mary; Khara, Dinesh C; Nir, Eyal

2018-06-01

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the "sticky end" and "weaving welding" attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self-dimerization of the origami monomers, likely via blunt-end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

2017-01-01

during the first hour after i.v. injection. The Tat-N-dimer suppressed stimulation-evoked synaptic activity by 2-20%, while cortical blood flow and cerebral oxygen metabolic (CMRO2) responses were preserved. During cortical spreading depression, the Tat-N-dimer reduced the average amplitude...... 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...

Microscopic observation of magnon bound states and their dynamics.

Science.gov (United States)

Fukuhara, Takeshi; Schauß, Peter; Endres, Manuel; Hild, Sebastian; Cheneau, Marc; Bloch, Immanuel; Gross, Christian

2013-10-03

The existence of bound states of elementary spin waves (magnons) in one-dimensional quantum magnets was predicted almost 80 years ago. Identifying signatures of magnon bound states has so far remained the subject of intense theoretical research, and their detection has proved challenging for experiments. Ultracold atoms offer an ideal setting in which to find such bound states by tracking the spin dynamics with single-spin and single-site resolution following a local excitation. Here we use in situ correlation measurements to observe two-magnon bound states directly in a one-dimensional Heisenberg spin chain comprising ultracold bosonic atoms in an optical lattice. We observe the quantum dynamics of free and bound magnon states through time-resolved measurements of two spin impurities. The increased effective mass of the compound magnon state results in slower spin dynamics as compared to single-magnon excitations. We also determine the decay time of bound magnons, which is probably limited by scattering on thermal fluctuations in the system. Our results provide a new way of studying fundamental properties of quantum magnets and, more generally, properties of interacting impurities in quantum many-body systems.

Collective spin wave and phonon excitations in ferromagnetic organic polymers

International Nuclear Information System (INIS)

Leong, Jit-Liang; Sun, Shih-Jye

2013-01-01

We proposed a model to investigate the properties of a conductive and ferromagnetic organic-polymer (OCP), which contains two collective excitations—spin wave and phonon—competing with each other; namely, the spin wave excitation accompanies the electron–phonon (e–ph) interactions in the conductive and ferromagnetic OCP. The ferromagnetism of the OCP is induced from the conductive carriers which couple with the phonon to become polarons. Due to the competition between both excitations, the Curie temperature (T C ) is sensitively suppressed by the e–ph interaction. In addition, an optimal T C with a small e–ph interaction exists in a specific density of conduction carrier, yet is contrary to the large e–ph interaction case. Furthermore, the dimerization, i.e. the atomic displacement induced from the e–ph interactions, increases with the strength of the e–ph interaction and decreases upon reaching the maximum dimerization. (paper)

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

Science.gov (United States)

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

2006-07-07

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.

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides

International Nuclear Information System (INIS)

Sener, Melih; Hsin, Jen; Trabuco, Leonardo G.; Villa, Elizabeth; Qian, Pu; Hunter, C. Neil; Schulten, Klaus

2009-01-01

The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter (Rba.) sphaeroides form membrane-bending dimeric complexes together with the polypeptide PufX. We present a structural model for these RC-LH1-PufX dimeric complexes constructed using the molecular dynamics flexible fitting method based on an EM density map. The arrangement of the LH1 BChls displays a distortion near the proposed location of the PufX polypeptide. The resulting atomic model for BChl arrays is used to compute the excitonic properties of the dimeric RC-LH1 complex. A comparison is presented between the structural and excitonic features of the S-shaped dimeric BChl array of Rba. sphaeroides and the circular BChl arrangement found in other purple bacteria

Relativistic and Non-Relativistic Electronic Molecular-Structure Calculations for Dimers of 4p-, 5p-, and 6p-Block Elements

NARCIS (Netherlands)

Hoefener, S.; Ahlrichs, R.; Knecht, S.; Visscher, L.

2012-01-01

We report results of non-relativistic and two-component relativistic single-reference coupled-cluster with single and double and perturbative triple excitations [CCSD(T)] treatments for the 4p-block dimers Ga

Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1.

Science.gov (United States)

Darlix, J L; Gabus, C; Nugeyre, M T; Clavel, F; Barré-Sinoussi, F

1990-12-05

The retroviral genome consists of two identical RNA molecules joined at their 5' ends by the Dimer Linkage Structure (DLS). To study the mechanism of dimerization and the DLS of HIV-1 RNA, large amounts of bona fide HIV-1 RNA and of mutants have been synthesized in vitro. We report that HIV-1 RNA forms dimeric molecules and that viral nucleocapsid (NC) protein NCp15 greatly activates dimerization. Deletion mutagenesis in the RNA 5' 1333 nucleotides indicated that a small domain of 100 nucleotides, located between positions 311 to 415 from the 5' end, is necessary and sufficient to promote HIV-1 RNA dimerization. This dimerization domain encompasses an encapsidation element located between the 5' splice donor site and initiator AUG of gag and shows little sequence variations in different strains of HIV-1. Furthermore, cross-linking analysis of the interactions between NC and HIV-1 RNA (311 to 415) locates a major contact site in the encapsidation element of HIV-1 RNA. The genomic RNA dimer is tightly associated with nucleocapsid protein molecules in avian and murine retroviruses, and this ribonucleoprotein structure is believed to be the template for reverse transcription. Genomic RNA-protein interactions have been analyzed in human immunodeficiency virus (HIV) virions and results showed that NC protein molecules are tightly bound to the genomic RNA dimer. Since retroviral RNA dimerization and packaging appear to be under the control of the same cis element, the encapsidation sequences, and trans-acting factor, the NC protein, they are probably related events in the course of virion assembly.

Two-nucleon bound states in quenched lattice QCD

International Nuclear Information System (INIS)

Yamazaki, T.; Kuramashi, Y.; Ukawa, A.

2011-01-01

We address the issue of bound state in the two-nucleon system in lattice QCD. Our study is made in the quenched approximation at the lattice spacing of a=0.128 fm with a heavy quark mass corresponding to m π =0.8 GeV. To distinguish a bound state from an attractive scattering state, we investigate the volume dependence of the energy difference between the ground state and the free two-nucleon state by changing the spatial extent of the lattice from 3.1 fm to 12.3 fm. A finite energy difference left in the infinite spatial volume limit leads us to the conclusion that the measured ground states for not only spin triplet but also singlet channels are bounded. Furthermore the existence of the bound state is confirmed by investigating the properties of the energy for the first excited state obtained by a 2x2 diagonalization method. The scattering lengths for both channels are evaluated by applying the finite volume formula derived by Luescher to the energy of the first excited states.

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA

Science.gov (United States)

Kringle, Loni; Sawaya, Nicolas P. D.; Widom, Julia; Adams, Carson; Raymer, Michael G.; Aspuru-Guzik, Alán; Marcus, Andrew H.

2018-02-01

Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the polarized collective excitations of excitonically coupled cyanine dimers (Cy3)2 that are rigidly positioned within the opposing sugar-phosphate backbones of the double-stranded region of a double-stranded (ds)-single-stranded (ss) DNA fork construct. We show that the exciton-coupling strength of the (Cy3)2-DNA construct can be systematically varied with temperature below the ds-ss DNA denaturation transition. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the (Cy3)2 dimer, as well as the degree of static disorder experienced by the Cy3 monomer and the (Cy3)2 dimer probe locally within their respective DNA duplex environments. The properties of the (Cy3)2-DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein-DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled bio-molecular arrays.

Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

International Nuclear Information System (INIS)

Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

2014-01-01

Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair

Unfolding the Quantum Nature of Proton Bound Symmetric Dimers of (MeOH)2H+ and (Me2O)2H+: a Theoretical Study

Science.gov (United States)

Tan, Jake Acedera; Kuo, Jer-Lai

2014-06-01

A proton under a tug of war between two competing Lewis bases is a common motif in biological systems and proton transfer processes. Over the past decades, model compounds for such motifs can be prepared by delicate stoichiometric control of salt solutions. Unfortunately, condensed phase studies, which aims to identify the key vibrational signatures are complicated to analyze. As a result, gas-phase studies do provide promising insights on the behavior of the shared proton. This study attempts to understand the quantum nature of the shared proton under theoretical paradigms. Proton bound symmetric dimers of (MeOH)2H+ and (Me2O)2H+ are chosen as the model compounds. The simulation is performed using Density Functional Theory (DFT) at the B3LYP level with 6-311+G(d,p) as the basis set. It was found out that stretching mode of shared proton couples with several other normal modes and its corresponding oscillator strength do distribute to other normal modes. J.R. Roscioli, L.R. McCunn and M.A. Johnson. Science 2007, 316, 249 T.E. DeCoursey. Physiol. Rev., 2003, 83, 475 E.S. Stoyanov. Psys. Chem. Phys., 2000,2,1137

Accurate determination of the binding energy of the formic acid dimer: The importance of geometry relaxation

Science.gov (United States)

Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

2014-02-01

The formic acid dimer in its C2h-symmetrical cyclic form is stabilized by two equivalent H-bonds. The currently accepted interaction energy is 18.75 kcal/mol whereas the experimental binding energy D0 value is only 14.22 ±0.12 kcal/mol [F. Kollipost, R. W. Larsen, A. V. Domanskaya, M. Nörenberg, and M. A. Suhm, J. Chem. Phys. 136, 151101 (2012)]. Calculation of the binding energies De and D0 at the CCSD(T) (Coupled Cluster with Single and Double excitations and perturbative Triple excitations)/CBS (Complete Basis Set) level of theory, utilizing CCSD(T)/CBS geometries and the frequencies of the dimer and monomer, reveals that there is a 3.2 kcal/mol difference between interaction energy and binding energy De, which results from (i) not relaxing the geometry of the monomers upon dissociation of the dimer and (ii) approximating CCSD(T) correlation effects with MP2. The most accurate CCSD(T)/CBS values obtained in this work are De = 15.55 and D0 = 14.32 kcal/mol where the latter binding energy differs from the experimental value by 0.1 kcal/mol. The necessity of employing augmented VQZ and VPZ calculations and relaxing monomer geometries of H-bonded complexes upon dissociation to obtain reliable binding energies is emphasized.

Theory and simulations of adhesion receptor dimerization on membrane surfaces.

Science.gov (United States)

Wu, Yinghao; Honig, Barry; Ben-Shaul, Avinoam

2013-03-19

The equilibrium constants of trans and cis dimerization of membrane bound (2D) and freely moving (3D) adhesion receptors are expressed and compared using elementary statistical-thermodynamics. Both processes are mediated by the binding of extracellular subdomains whose range of motion in the 2D environment is reduced upon dimerization, defining a thin reaction shell where dimer formation and dissociation take place. We show that the ratio between the 2D and 3D equilibrium constants can be expressed as a product of individual factors describing, respectively, the spatial ranges of motions of the adhesive domains, and their rotational freedom within the reaction shell. The results predicted by the theory are compared to those obtained from a novel, to our knowledge, dynamical simulations methodology, whereby pairs of receptors perform realistic translational, internal, and rotational motions in 2D and 3D. We use cadherins as our model system. The theory and simulations explain how the strength of cis and trans interactions of adhesive receptors are affected both by their presence in the constrained intermembrane space and by the 2D environment of membrane surfaces. Our work provides fundamental insights as to the mechanism of lateral clustering of adhesion receptors after cell-cell contact and, more generally, to the formation of lateral microclusters of proteins on cell surfaces. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

2014-07-23

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.

Characterization of ellagitannins, gallotannins, and bound proanthocyanidins from California almond (Prunus dulcis) varieties.

Science.gov (United States)

Xie, Liyang; Roto, Anna V; Bolling, Bradley W

2012-12-12

Extractable and bound proanthocyanidins and hydrolyzable tannins were characterized in Nonpareil, Carmel, and Butte almond varieties from California, with n = 3 samples/variety. Bound proanthocyanidins were recovered from extracted defatted almond residue by hydrolysis with 4 N sodium hydroxide and represented 3-21% of the total proanthocyanidin content among varieties. The bound proanthocyanidins were recovered primarily as monomers and dimers. In contrast, acid hydrolysis of extracted almond residue did not yield bound proanthocyanidins. Hydrolyzable tannins were characterized in aqueous acetone extracts of defatted almond using two-dimensional TLC and further quantitated by HPLC following acid hydrolysis. Almond hydrolyzable tannin content was 54.7 ± 2.3 mg ellagic acid and 27.4 ± 7.3 mg gallic acid per 100 g almond among varieties. The tannin contents of Nonpareil, Carmel, and Butte almond varieties were not significantly different. Thus, bound proanthocyanidins and hydrolyzable tannins significantly contribute to almond polyphenol content.

Sigma- versus Pi-Dimerization Modes of Triangulene.

Science.gov (United States)

Mou, Zhongyu; Kertesz, Miklos

2018-04-20

We show that the diradicaloid triangulene, a graphene nano-flake molecule, can aggregate in a variety of dimerization modes. We found by density functional theory modeling a number of triangulene dimers including six doubly bonded σ-dimers in addition to the previously reported six pancake bonded π-dimer isomers. The σ-dimers display a wide range of stabilities: the interaction energy of the most stable σ-dimer is -25.17 kcal mol -1 . Besides the doubly bonded σ-dimers with closed shell ground states, we also found an open-shell singly σ-bonded diradicaloid dimer. We found an interesting isomerization route between a doubly bonded σ-dimer, a singly bonded σ-dimer with a low-lying triplet state and two π-bonded dimers with low-lying quintet states. Derivatives of triangulene, trioxo-triangulenes (TOTs) have been previously characterized experimentally. Here, we show the reasons why so far only the π-dimer but not the σ-dimer was experimentally observed for all TOTs. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optical nonlinearity and bistability in the bound exciton energy range of CdS

International Nuclear Information System (INIS)

Hoenig, T.; Gutowski, J.

1988-01-01

Under high excitation conditions thick CdS samples show pronounced broad-band nonlinear transmission in the bound exciton region and up to a wavelength of about 515 nm at cryo-temperatures. This behavior is only explainable in a model based on impurity neutralization and bound exciton creation. The suitability of these nonlinearities to yield optical bistability will be shown. Bistable operation is investigated in dependence of crystal thickness, impurity concentration, excitation density, wavelength, and temperature. A strong correlation to acceptor-bound exciton generation is obtained, and the explanation of this bistable operation fits well with that of the above mentioned transmission behavior. (author)

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†

Science.gov (United States)

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

2013-01-01

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

Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization.

Science.gov (United States)

Tachikawa, Hiroto

2017-06-30

Reactions of water dimer cation (H2O)2+ following ionization have been investigated by means of a direct ab initio molecular dynamics method. In particular, the effects of zero point vibration and zero point energy (ZPE) on the reaction mechanism were considered in this work. Trajectories were run on two electronic potential energy surfaces (PESs) of (H2O)2+: ground state ( 2 A″-like state) and the first excited state ( 2 A'-like state). All trajectories on the ground-state PES lead to the proton-transferred product: H 2 O + (Wd)-H 2 O(Wa) → OH(Wd)-H 3 O + (Wa), where Wd and Wa refer to the proton donor and acceptor water molecules, respectively. Time of proton transfer (PT) varied widely from 15 to 40 fs (average time of PT = 30.9 fs). The trajectories on the excited-state PES gave two products: an intermediate complex with a face-to-face structure (H 2 O-OH 2 ) + and a PT product. However, the proton was transferred to the opposite direction, and the reverse PT was found on the excited-state PES: H 2 O(Wd)-H 2 O + (Wa) → H 3 O + (Wd)-OH(Wa). This difference occurred because the ionizing water molecule in the dimer switched between the ground and excited states. The reaction mechanism of (H2O)2+ and the effects of ZPE are discussed on the basis of the results. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Extracting dimer structures from simulations of organic-based materials using QM/MM methods

Energy Technology Data Exchange (ETDEWEB)

Pérez-Jiménez, A.J., E-mail: aj.perez@ua.es; Sancho-García, J.C., E-mail: jc.sancho@ua.es

2015-09-28

Highlights: • DFT geometries of isolated dimers in organic crystals differ from experimental ones. • This can be corrected using QM/MM geometry optimizations. • The QM = B3LYP–D3(ZD)/cc-pVDZ and MM = GAFF combination works reasonably well. - Abstract: The functionality of weakly bound organic materials, either in Nanoelectronics or in Materials Science, is known to be strongly affected by their morphology. Theoretical predictions of the underlying structure–property relationships are frequently based on calculations performed on isolated dimers, but the optimized structure of the latter may significantly differ from experimental data even when dispersion-corrected methods are used for it. Here, we address this problem on two organic crystals, namely coronene and 5,6,11,12-tetrachlorotetracene, concluding that it is caused by the absence of the surrounding monomers present in the crystal, and that it can be efficiently cured when the dimer is embedded into a general Quantum Mechanics/Molecular Mechanics (QM/MM) geometry optimization scheme. We also investigate how the size of the MM region affects the results. These findings may be helpful for the simulation of the morphology of active materials in crystalline or glassy samples.

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.

1982-05-01

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.

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

International Nuclear Information System (INIS)

Goble, J.H. Jr.

1982-05-01

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 + , HeNe + , NaAr, and Ar 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( 3 P 2 ) + Ca + h nu → Ar + Ca + (5p 2 P/sub J/) + e - 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( 3 P 2 ) + Ca → Ar + Ca + (4p 2 P/sub J/) + e - a surprisingly large cross section of 6.7 x 10 3 A 2 is estimated

Crossover from bound to free states in plasmas

International Nuclear Information System (INIS)

Lankin, Alexander V; Norman, Genri E

2009-01-01

A self-consistent joint description of free and weakly bound electron states in strongly coupled plasmas is presented. The existence of two problems is emphasized. The first one is a well-known restriction of the number of atomic excited states. Another one is a description of the smooth crossover from bound pair electron-ion excited states to collective excitations of free electrons. The fluctuation approach is developed to study the spectrum domain intermediate between low-lying excited atoms and free electron continuous energy levels. The molecular dynamics method is applied to study the plasma model since the method is able to distinguish all kinds of fluctuations. The electron-ion interaction is described by the temperature-independent cut-off Coulomb potential. The diagnostics of pair electron-ion fluctuations is developed. The concept of pair fluctuations elucidates the smooth vanishing of atomic states near the ionization limit. The approach suggested removes the artificial break of the electron state density at the ionization limit: atomic state density divergent at the negative energy side and free electron state density starting from zero density at the positive energy side

Preparation and characterization of dimeric and tetrameric clusters of molybdenum and tungsten

Energy Technology Data Exchange (ETDEWEB)

Ryan, T.R.

1981-10-01

The cyclo-addition of two Mo/sub 2/Cl/sub 4/(P(C/sub 6/H/sub 5/)/sub 3/)/sub 2/(CH/sub 3/OH)/sub 2/ molecules has produced a new type of tetrameric molybdenum cluster, Mo/sub 4/Cl/sub 8/L/sub 4/. Structural characterization of this dimer revealed weak molybdenum-methanol bonding which was consistent with the observed reactivity of the compound. New synthetic methods were devised for the preparation of Mo/sub 4/X/sub 8/L/sub 4/ clusters where X = Cl, Br, I and L = PR/sub 3/, Po/sub 3/, RCN, CH/sub 3/OH. A scheme for the metal-metal bonding in these clusters was presented which was in agreement with the known structural features of Mo/sub 4/Cl/sub 8/(PR/sub 3/)/sub 4/, R = C/sub 2/H/sub 5/, n-C/sub 4/H/sub 9/. The preparation of the analogous W/sub 4/Cl/sub 8/(PR/sub 3/)/sub 4/ cluster from WCl/sub 4/ was accomplished by application of techniques used in the molybdenum syntheses. The single crystal x-ray structure revealed slight differences from the molybdenum analog which were rationalized in terms of the known behavior in dimeric tungsten and molybdenum species. The attempted preparation of a tetrameric tungsten cluster from W/sub 2/(mhp)/sub 4/ was unsuccessful (mhp = anion of 2-methyl-6-hydroxypyridine). Instead, the new tungsten dimer, W/sub 2/Cl/sub 2/(mhp)/sub 3/, was isolated which possessed a metal-metal bond order of 3.5. The x-ray crystal structure of the dimer revealed that the chlorine atoms were situated cis, one bound to each tungsten. Cyclic voltammetry showed that the compound could be reversibly reduced, presumably to a W/sub 2//sup 4 +/ dimer containing a quadruple metal-metal bond.

Do bound color octet states of liberated quarks exist

International Nuclear Information System (INIS)

Lipkin, H.J.

1979-01-01

In models where quarks are liberated and color can be excited, the three-quark color-octet state is shown to be unbound and unstable against breakup into free quarks and diquarks. The signature for color excitation in deep inelastic processes will not be a bound three-quark state which decays electromagnetically but a final state containing free quarks. (author)

2-Ethynylpyridine dimers

DEFF Research Database (Denmark)

Bakarić, Danijela; Spanget-Larsen, Jens

2018-01-01

are used to study possible 2-EP dimer structures as well as their distribution in an inert solvent such as tetrachloroethene. Experimentally, the ≡C–H stretching vibration of the 2-EPmonomer absorbs close to 3300 cm−1, whereas a broad band withmaximum around 3215 cm−1 emerges as the concentration rises...... model with counterpoise correction predict that the two most stable dimers are of the pi-stacked variety, closely followed by dimers with intermolecular ≡C–H···N hydrogen bonding; the predicted red shifts of the ≡C–H stretching wavenumbers due to hydrogen bonding are in the range 54 – 120 cm–1...

Electronic excitations in fast ion-solid collisions

International Nuclear Information System (INIS)

Burgdoerfer, J.

1990-01-01

We review recent developments in the study of electronic excitation of projectiles in fast ion-solid collisions. Our focus will be primarily on theory but experimental advances will also be discussed. Topics include the evidence for velocity-dependent thresholds for the existence of bound states, wake-field effects on excited states, the electronic excitation of channeled projectiles, transport phenomena, and the interaction of highly charged ions with surfaces. 44 refs., 14 figs

Phase diagram study of a dimerized spin-S zig–zag ladder

International Nuclear Information System (INIS)

Matera, J M; Lamas, C A

2014-01-01

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. (paper)

Structure of alanine racemase from Oenococcus oeni with bound pyridoxal 5′-phosphate

International Nuclear Information System (INIS)

Palani, Kandavelu; Burley, Stephen K.; Swaminathan, Subramanyam

2012-01-01

Alanine racemase from O. oeni exists as a dimer in the crystal structure. Both monomers contribute to the two active sites present, one for each monomer. The crystal structure of alanine racemase from Oenococcus oeni has been determined at 1.7 Å resolution using the single-wavelength anomalous dispersion (SAD) method and selenium-labelled protein. The protein exists as a symmetric dimer in the crystal, with both protomers contributing to the two active sites. Pyridoxal 5′-phosphate, a cofactor, is bound to each monomer and forms a Schiff base with Lys39. Structural comparison of alanine racemase from O. oeni (Alr) with homologous family members revealed similar domain organization and cofactor binding

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

KAUST Repository

Luo, Jie

2015-01-21

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.

Water dimers in the atmosphere III: equilibrium constant from a flexible potential.

Science.gov (United States)

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

2006-04-27

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.

Bound states in strongly correlated magnetic and electronic systems

International Nuclear Information System (INIS)

Trebst, S.

2002-02-01

A novel strong coupling expansion method to calculate two-particle spectra of quantum lattice models is developed. The technique can be used to study bosonic and fermionic models and in principle it can be applied to systems in any dimension. A number of strongly correlated magnetic and electronic systems are examined including the two-leg spin-half Heisenberg ladder, the dimerized Heisenberg chain with a frustrating next-nearest neighbor interaction, coupled Heisenberg ladders, and the one-dimensional Kondo lattice model. In the various models distinct bound states are found below the two-particle continuum. Quantitative calculations of the dispersion, coherence length and binding energy of these bound states are used to describe spectroscopic experiments on (Ca,La) 14 Cu 24 O 41 and NaV 2 O 5 . (orig.)

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.

Science.gov (United States)

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

2013-07-16

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

Excitation equilibria in plasmas; a classification

International Nuclear Information System (INIS)

Mullen, J.A.M. van der

1990-01-01

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.)

Rubidium dimers in paraffin-coated cells

International Nuclear Information System (INIS)

Acosta, V M; Windes, D; Corsini, E; Ledbetter, M P; Karaulanov, T; Budker, D; Jarmola, A; Auzinsh, M; Rangwala, S A; Jackson Kimball, D F

2010-01-01

Measurements were made to determine the density of rubidium dimer vapor in paraffin-coated cells. The number density of dimers and atoms in similar paraffin-coated and uncoated cells was measured by optical spectroscopy. Due to the relatively low melting point of paraffin, a limited temperature range of 43-80 0 C was explored, with the lower end corresponding to a dimer density of less than 10 7 cm -3 . With 1 min integration time, a sensitivity to dimer number density of better than 10 6 cm -3 was achieved. No significant difference in dimer density between the cells was observed.

Ab initio and matrix isolation study of the acetylene-furan dimer

International Nuclear Information System (INIS)

Sanchez-Garcia, Elsa; Mardyukov, Artur; Tekin, Adem; Crespo-Otero, Rachel; Montero, Luis A.; Sander, Wolfram; Jansen, Georg

2008-01-01

Five acetylene-furan dimer structures are identified using ab initio calculations at the second-order Moller-Plesset (MP2) level of theory. The structures are stabilized by two basic types of intermolecular interactions: the CH...O and the CH...π interaction. The CH...π interaction appears in two variants, depending on which molecule provides the hydrogen atom and which molecule the π system. The MP2 results indicate that the CH...π interaction between one of the hydrogen atoms of acetylene and the π system of furan as found in structure A is the strongest interaction, followed by the in-plane CH...O interaction in the second most stable acetylene-furan dimer structure B. A matrix isolation study shows the acetylene-furan dimer to exist in an argon matrix, but likely rather as structure B than as A. High level coupled cluster calculations with up to triple excitations (CCSD(T)) yield the interaction energy of structure A as about -2.4 kcal/mol in the complete basis set limit and find structure B to be nearly isoenergetic with -2.3 kcal/mol. This is confirmed in calculations employing the density functional theory combined with symmetry adapted intermolecular perturbation theory (DFT-SAPT) approach yielding interaction energies of -2.3 and -2.0 kcal/mol for A and B, respectively. DFT-SAPT also helps to understand the importance of the electrostatic, induction and dispersion interaction energies and their respective exchange counterparts for the stability of the various acetylene-furan dimer structures. The CH...O and CH...π interactions are furthermore analyzed with the help of the atoms in molecules (AIM) theory

The majority of lipoprotein lipase in plasma is bound to remnant lipoproteins: A new definition of remnant lipoproteins.

Science.gov (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

2016-10-01

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.

Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.

Science.gov (United States)

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2017-06-07

We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH 2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

Structure and energetics of InN and GaN dimers

Science.gov (United States)

Šimová, Lucia; Tzeli, Demeter; Urban, Miroslav; Černušák, Ivan; Theodorakopoulos, Giannoula; Petsalakis, Ioannis D.

2008-06-01

Large-scale mapping of various dimers of indium nitride and gallium nitride in singlet and triplet electronic states is reported. Second-order perturbation theory with Møller-Plesset partitioning of the Hamiltonian (MP2) and coupled-cluster with single and double excitations corrected for the triple excitations (CCSD(T)) are used for the geometry determinations and evaluation of excitation and dissociation energies. For gallium and nitrogen we have used the singly augmented correlation-consistent triple-zeta basis set (aug-cc-pVTZ), for indium we have used the aug-cc-pVTZ-pseudopotential basis set. The dissociation energies are corrected for basis set superposition error (BBSE) including geometrical relaxation of the monomers. We compare and discuss the similarities and dissimilarities in the structural patterns and energetics of both groups of isomers, including the effect of the BSSE. Our computations show that there are not only different ground states for In 2N 2 and Ga 2N 2 but also different numbers of stable stationary points on their potential energy surface. We compare our results with the molecular data published so far for these systems.

Structure and energetics of InN and GaN dimers

International Nuclear Information System (INIS)

Simova, Lucia; Tzeli, Demeter; Urban, Miroslav; Cernusak, Ivan; Theodorakopoulos, Giannoula; Petsalakis, Ioannis D.

2008-01-01

Large-scale mapping of various dimers of indium nitride and gallium nitride in singlet and triplet electronic states is reported. Second-order perturbation theory with Moller-Plesset partitioning of the Hamiltonian (MP2) and coupled-cluster with single and double excitations corrected for the triple excitations (CCSD(T)) are used for the geometry determinations and evaluation of excitation and dissociation energies. For gallium and nitrogen we have used the singly augmented correlation-consistent triple-zeta basis set (aug-cc-pVTZ), for indium we have used the aug-cc-pVTZ-pseudopotential basis set. The dissociation energies are corrected for basis set superposition error (BBSE) including geometrical relaxation of the monomers. We compare and discuss the similarities and dissimilarities in the structural patterns and energetics of both groups of isomers, including the effect of the BSSE. Our computations show that there are not only different ground states for In 2 N 2 and Ga 2 N 2 but also different numbers of stable stationary points on their potential energy surface. We compare our results with the molecular data published so far for these systems

Optical studies of multiply excited states

International Nuclear Information System (INIS)

Mannervik, S.

1989-01-01

Optical studies of multiply-excited states are reviewed with emphasis on emission spectroscopy. From optical measurements, properties such as excitation energies, lifetimes and autoionization widths can be determined with high accuracy, which constitutes a challenge for modern computational methods. This article mainly covers work on two-, three- and four-electron systems, but also sodium-like quartet systems. Furthermore, some comments are given on bound multiply-excited states in negative ions. Fine structure effects on transition wavelengths and lifetimes (autoionization) are discussed. In particular, the most recent experimental and theoretical studies of multiply-excited states are covered. Some remaining problems, which require further attention, are discussed in more detail. (orig.) With 228 refs

Real time observation of the excimer formation dynamics of a gas phase benzene dimer by picosecond pump-probe spectroscopy.

Science.gov (United States)

Miyazaki, Mitsuhiko; Fujii, Masaaki

2015-10-21

We observed the real-time excimer (EXC) formation dynamics of a gas phase benzene dimer (Bz2) cluster after photo-excitation to the S1 state by applying an ionization detected picosecond transient absorption method for probing the visible EXC absorption for the first time. The time evolution of the EXC absorption from the S1 0(0) level shows a rise that is well fitted by a single exponential function with a time constant of 18 ± 2 ps. The structure of the Bz dimer has a T-shaped structure in the ground electronic state, and that in the EXC state is a parallel sandwich (SW) structure. Thus, the observed rise time corresponds to the structural change from the T to the SW structures, which directly shows the EXC formation. On the other hand, the EXC formation after excitation of the S1 6(1) vibrational level of the stem site showed a faster rise of the time constant of 10 ± 2 ps. Supposing equilibrium between the EXC and the local excited states, it followed that the intramolecular vibrational energy redistribution rate of the 6(1) level is largely enhanced and becomes faster than the EXC formation reaction.

Mixed dimers, ch. 7

International Nuclear Information System (INIS)

Deursen, A.P.J. van; Reuss, J.

1976-01-01

An attempt has been made to detect mixed dimers in nozzle beams of mixtures; NeAr and HeNe dimers were observed with sufficient intensity to determine the total collision cross section. A similar attempt for H 2 Ar was partially hampered by the circumstance that the corresponding HAr + ion must be detected on the wing of the thousand times larger Ar + peak. The search for H 2 He, H 2 Ne and HeAr dimers was not successful, due to masking ion peaks, H 5 + for HHe + , 21 Ne + for H 20 Ne + , and CO 2 + for HeAr + . (Auth.)

Dimers at Ge/Si(001) surfaces: Ge coverage dependent quenching, reactivation of flip-flop motion, and interaction with dimer vacancy lines

International Nuclear Information System (INIS)

Hirayama, H.; Mizuno, H.; Yoshida, R.

2002-01-01

We studied Ge coverage (θ Ge ) dependent quenching, reactivation of the flip-flop motion, and interaction with dimer vacancy lines (DVLs) of dimers on Ge/Si(001) surfaces using a scanning tunneling microscope (STM) combined with a molecular beam epitaxy apparatus. Deposition of ∼0.3 ML (monolayer) Ge quenched the flip-flop motion, making all dimers asymmetric. Further deposition introduced DVLs at θ Ge ≥∼0.5 ML, and symmetric dimer domains appeared again locally at θ≥1.5 ML. High-resolution STM images indicated that asymmetric dimer rows always invert their phase in alternation with buckled dimer's up-end at the DVLs. Low-temperature STM images indicated that the symmetric dimer domains were due to flip-flopping of asymmetric dimers activated by large θ Ge at room temperature. The symmetric dimer domains extended along the dimer rows over the DVLs due to the phase correlation

Comparison of clinical probability-adjusted D-dimer and age-adjusted D-dimer interpretation to exclude venous thromboembolism.

Science.gov (United States)

Takach Lapner, Sarah; Julian, Jim A; Linkins, Lori-Ann; Bates, Shannon; Kearon, Clive

2017-10-05

Two new strategies for interpreting D-dimer results have been proposed: i) using a progressively higher D-dimer threshold with increasing age (age-adjusted strategy) and ii) using a D-dimer threshold in patients with low clinical probability that is twice the threshold used in patients with moderate clinical probability (clinical probability-adjusted strategy). Our objective was to compare the diagnostic accuracy of age-adjusted and clinical probability-adjusted D-dimer interpretation in patients with a low or moderate clinical probability of venous thromboembolism (VTE). We performed a retrospective analysis of clinical data and blood samples from two prospective studies. We compared the negative predictive value (NPV) for VTE, and the proportion of patients with a negative D-dimer result, using two D-dimer interpretation strategies: the age-adjusted strategy, which uses a progressively higher D-dimer threshold with increasing age over 50 years (age in years × 10 µg/L FEU); and the clinical probability-adjusted strategy which uses a D-dimer threshold of 1000 µg/L FEU in patients with low clinical probability and 500 µg/L FEU in patients with moderate clinical probability. A total of 1649 outpatients with low or moderate clinical probability for a first suspected deep vein thrombosis or pulmonary embolism were included. The NPV of both the clinical probability-adjusted strategy (99.7 %) and the age-adjusted strategy (99.6 %) were similar. However, the proportion of patients with a negative result was greater with the clinical probability-adjusted strategy (56.1 % vs, 50.9 %; difference 5.2 %; 95 % CI 3.5 % to 6.8 %). These findings suggest that clinical probability-adjusted D-dimer interpretation is a better way of interpreting D-dimer results compared to age-adjusted interpretation.

Magnetic excitations and exchange interactions in the spin-gap system TlCuCl sub 3

CERN Document Server

Oosawa, A; Kato, T; Kakurai, K; Müller, M; Mikeska, H J

2002-01-01

The magnetic excitations from the gapped ground state in TlCuCl sub 3 have been investigated by means of inelastic neutron scattering experiments. The excitation data were collected along four different directions in the a sup * -c sup * plane. A well-defined single magnetic excitation mode was observed. The lowest excitation occurs at Q=(h,0,l) with integer h and odd l, as observed in KCuCl sub 3. The dispersion relations were analyzed by the cluster-series expansion up to the sixth order, so that the individual exchange interactions were evaluated. It was demonstrated that TlCuCl sub 3 is a strongly coupled spin-dimer system. (orig.)

Electric field dependence of the total excimer luminescence of xenon excited below the atomic ionization limit

International Nuclear Information System (INIS)

Anon.

1987-01-01

In the spectral region of interest (i.e., 11.1 eV ≤ h nu ≤ 11.9 eV), the photoionization yield of electrons from excited-state dimers of xenon, increases monotonically to relatively high values (e.g., Y(11.7 eV) = 0.43 electrons/absorbed photon). It is also known however, that the luminescence intensity excited by photons in this region is quite high, even at low pressures. These two observations can be reconciled only by assuming that one of the processes leading to excimer luminescence involves dimer-ion + electron recombination. If this assumption is correct, application of an electric field, with concomitant collection of the free charges generated by the incident photons, should lead to a decrease in luminescence intensity; moreover, this decrease should follow the energy dependence of the photoionization yield function. The present report demonstrates experimentally that this is indeed the case. Such experiments combining luminescence and electric fields were made, until now, only by high-energy excitation. In this case the deconvolution of the various decay channels is hardly possible

Prompt and delayed excitation and photolysis of cesium dimers

International Nuclear Information System (INIS)

Davanloo, F.; Collins, C.B.; Inamdar, A.S.; Mehendale, N.Y.; Nagvi, A.S.

1984-01-01

In this work a time-delayed, double resonance technique was used for the study of the state selective photolysis of Cs 2 excited in the yellow range of visible wavelengths. Particular attention being placed on the production of the fine structure components of the 5 2 D and 6 2 P states of Cs and upon the lifetimes of the product populations in the cesium vapor. A quantitative model was constructed to fit the data and rate coefficients were extracted for processes tending to attenuate the product state selectivity. Reported here is what appears to be the first value for the fine-structure mixing cross section for Cs(5 2 D5/2 → 5 2 D 3 /sub 3/2/) of 17 A 2 +-50%, close to the geometric cross section

Excited nuclei fragmentation

International Nuclear Information System (INIS)

Ngo, C.

1986-11-01

Experimental indications leading to the thought of a very excited nucleus fragmentation are resumed. Theoretical approaches are briefly described; they are used to explain the phenomenon in showing off they are based on a minimum information principle. This model is based on time dependent Thomas-Fermi calculation which allows the mean field effect description, and with a site-bound percolation model which allows the fluctuation description [fr

Universal bounds in even-spin CFTs

Energy Technology Data Exchange (ETDEWEB)

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

2015-12-01

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.

Understanding the influence of low-frequency vibrations on the hydrogen bonds of acetic acid and acetamide dimers.

Science.gov (United States)

Copeland, Christopher; Menon, Omkaran; Majumdar, D; Roszak, Szczepan; Leszczynski, Jerzy

2017-09-20

Low-frequency vibrations coupled to high-frequency modes are known to influence the hydrogen bond strengths in a weakly interacting dimer. In this context, various acetic acid and acetamide dimers were analyzed using Møller-Plesset second-order perturbation (MP2) and density functional theory (DFT)-based approaches with explicit anharmonicity corrections. The computed low-frequency fundamentals as well as the high-frequency modes, which were found to be related to hydrogen bonding (OH/NH stretching modes), were analyzed and their computed intensities were correlated with their hydrogen-bond strengths/binding energies. There are similarities in the nature of eight low-frequency fundamentals of these two dimers, and the in-plane bending and stretch-bend fundamentals of the different dimers of these two species (in this low-frequency region) have specific roles in their relative stability order. The computed linear correlations were further verified against the results from coupled cluster calculations including triple excitation (CCSD(T)), Gaussian-G4 (G4), Gaussian-G2-MP2 (G2MP2) and complete basis set (CBS-QB3) methods of high accuracy energy calculations. As a consequence of such linear correlations, an additive property of local fragment energies (responsible for hydrogen bonding) was found to be a valid approximation to predict the binding energies of such dimers and the idea was found to be extendable to the other homologues of these acids/amides.

Anti-cooperative supramolecular polymerization: a new K2-K model applied to the self-assembly of perylene bisimide dye proceeding via well-defined hydrogen-bonded dimers.

Science.gov (United States)

Gershberg, Jana; Fennel, Franziska; Rehm, Thomas H; Lochbrunner, Stefan; Würthner, Frank

2016-03-01

A perylene bisimide dye bearing amide functionalities at the imide positions derived from amino acid l-alanine and a dialkoxy-substituted benzyl amine self-assembles into tightly bound dimers by π-π-stacking and hydrogen bonding in chloroform. In less polar or unpolar solvents like toluene and methylcyclohexane, and in their mixtures, these dimers further self-assemble into extended oligomeric aggregates in an anti-cooperative process in which even numbered aggregates are highly favoured. The stepwise transition from dimers into oligomers can not be properly described by conventional K 2 - K model, and thus a new K 2 - K aggregation model has been developed, which interpretes the present anti-cooperative supramolecular polymerization more appropriately. The newly developed K 2 - K model will be useful to describe self-assembly processes of a plethora of other π-conjugated molecules that are characterized by a favored dimer species.

D-dimers (DD) in CVST.

Science.gov (United States)

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

2017-06-01

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.

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

Directory of Open Access Journals (Sweden)

Lin Chien-Hung

2011-01-01

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.

Structural basis for the cooperative DNA recognition by Smad4 MH1 dimers

Science.gov (United States)

Baburajendran, Nithya; Jauch, Ralf; Tan, Clara Yueh Zhen; Narasimhan, Kamesh; Kolatkar, Prasanna R.

2011-01-01

Smad proteins form multimeric complexes consisting of the ‘common partner’ Smad4 and receptor regulated R-Smads on clustered DNA binding sites. Deciphering how pathway specific Smad complexes multimerize on DNA to regulate gene expression is critical for a better understanding of the cis-regulatory logic of TGF-β and BMP signaling. To this end, we solved the crystal structure of the dimeric Smad4 MH1 domain bound to a palindromic Smad binding element. Surprisingly, the Smad4 MH1 forms a constitutive dimer on the SBE DNA without exhibiting any direct protein–protein interactions suggesting a DNA mediated indirect readout mechanism. However, the R-Smads Smad1, Smad2 and Smad3 homodimerize with substantially decreased efficiency despite pronounced structural similarities to Smad4. Therefore, intricate variations in the DNA structure induced by different Smads and/or variant energetic profiles likely contribute to their propensity to dimerize on DNA. Indeed, competitive binding assays revealed that the Smad4/R-Smad heterodimers predominate under equilibrium conditions while R-Smad homodimers are least favored. Together, we present the structural basis for DNA recognition by Smad4 and demonstrate that Smad4 constitutively homo- and heterodimerizes on DNA in contrast to its R-Smad partner proteins by a mechanism independent of direct protein contacts. PMID:21724602

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.

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

2011-01-01

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....

Radiation from an excited vortex in the Abelian Higgs model

Science.gov (United States)

Arodź, H.; Hadasz, L.

1996-09-01

An excited vortex in the Abelian Higgs model is investigated with the help of a polynomial approximation. The excitation consists of the longitudinal component of a vector field trapped by the vortex. The energy and profile of the excitation as well as its back reaction on the vortex are found in the case of small κ. It turns out that the width of the excited vortex oscillates in time. Moreover, the vector field has a radiative long range component. Also, an upper bound on the amplitude of the excitation is found.

Aspects of Majorana Bound States in One-Dimensional Systems with and without Time-Reversal Symmetry

DEFF Research Database (Denmark)

Wölms, Konrad Udo Hannes

In recent years there has been a lot of interest in topological phases of matter. Unlike conventional phases of matter, topological phases are not distinguished by symmetries, but by so-called topological invariants which have more subtle physical implications. It comes therefore as no surprise...... phase the edge excitations are called Majorana bound states and they are interesting in themselves. There has been a lot of eort in detecting Majorana bound states in the lab. One reason is that these excitations provide evidence that a system is indeed in a topological phase. It is therefore required...... to have unambiguous experimental evidence for the presence Majorana bound states, which in turn requires a good theoretical understanding of the physics associated with Majorana bound states. In particular for the most common experimental methods that are used to study them, the signature of Majorana...

Neutron scattering study of two-magnon states in the quantum magnet copper nitrate

DEFF Research Database (Denmark)

Tennant, D.A.; Broholm, C.; Reich, D.H.

2003-01-01

We report measurements of the two-magnon states in a dimerized antiferromagnetic chain material, copper nitrate [Cu(NO3)(2).2.5D(2)O]. Using inelastic neutron scattering we have measured the one- and two-magnon excitation spectra in a large single crystal. The data are in excellent agreement...... with a perturbative expansion of the alternating Heisenberg Hamiltonian from the strongly dimerized limit. The expansion predicts a two-magnon bound state for qsimilar to(2n+1)pid which is consistent with the neutron scattering data....

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

Energy Technology Data Exchange (ETDEWEB)

Kalugina, Yulia N., E-mail: kalugina@phys.tsu.ru [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)

2014-06-21

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.

Stochastic optimization-based study of dimerization kinetics

Indian Academy of Sciences (India)

To this end, we study dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and ... optimization; dimerization kinetics; sensitivity analysis; stochastic simulation ... tion in large molecules and clusters, or the design ..... An unbiased strategy of allocating.

Radiation from an excited vortex in the Abelian Higgs model

International Nuclear Information System (INIS)

Arodz, H.; Hadasz, L.

1996-01-01

An excited vortex in the Abelian Higgs model is investigated with the help of a polynomial approximation. The excitation consists of the longitudinal component of a vector field trapped by the vortex. The energy and profile of the excitation as well as its back reaction on the vortex are found in the case of small κ. It turns out that the width of the excited vortex oscillates in time. Moreover, the vector field has a radiative long range component. Also, an upper bound on the amplitude of the excitation is found. copyright 1996 The American Physical Society

Data supporting beta-amyloid dimer structural transitions and protein–lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

Directory of Open Access Journals (Sweden)

Sara Y. Cheng

2016-06-01

Full Text Available This data article supports the research article entitled “Maximally Asymmetric Transbilayer Distribution of Anionic Lipids Alters the Structure and interaction with Lipids of an Amyloidogenic Protein Dimer Bound to the Membrane Surface” [1]. We describe supporting data on the binding kinetics, time evolution of secondary structure, and residue-contact maps of a surface-absorbed beta-amyloid dimer protein on different membrane surfaces. We further demonstrate the sorting of annular and non-annular regions of the protein/lipid bilayer simulation systems, and the correlation of lipid-number mismatch and surface area per lipid mismatch of asymmetric lipid membranes.

Dark excitations in monolayer transition metal dichalcogenides

DEFF Research Database (Denmark)

Deilmann, Thorsten; Thygesen, Kristian Sommer

2017-01-01

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...

Retroviral RNA Dimerization: From Structure to Functions

Directory of Open Access Journals (Sweden)

Noé Dubois

2018-03-01

Full Text Available The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA molecules of positive polarity. The dimerization process allows two gRNA molecules to be non-covalently linked together through intermolecular base-pairing. This step is critical for the viral life cycle and is highly conserved among retroviruses with the exception of spumaretroviruses. Furthermore, packaging of two gRNA copies into viral particles presents an important evolutionary advantage for immune system evasion and drug resistance. Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are now at hand. This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV…, the mechanisms of RNA dimer formation and functional implications in the retroviral cycle.

Push-and-stick mechanism for charged and excited small cluster emission under ion bombardment

International Nuclear Information System (INIS)

Bitensky, I.S.; Parilis, E.S.; Wojciechowski, I.A.

1992-01-01

The mechanism for the formation, excitation and ionization of small clusters emitted under ion bombardment is discussed. It is shown that the increased degree of ionization for the transition metal dimers, trimers and tetramers can be explained by the existence of an additional effective channel for their formation, namely the associative ionization process. A simple estimate shows that the sticking together of a fast cascade atom and the pushed out surface atom is 30-40 times more effective for dimer formation, than the recombination of two fast atoms. This push-and-stick mechanism of cluster formation could also be effective for the formation of trimers and tetramers. (orig.)

Fractional excitations in the square-lattice quantum antiferromagnet

DEFF Research Database (Denmark)

Piazza, B. Dalla; Mourigal, M.; Christensen, Niels Bech

2015-01-01

-projected trial wavefunctions. The excitation continuum is accounted for by the existence of spatially extended pairs of fractional S=1/2 quasiparticles, 2D analogues of 1D spinons. Away from the anomalous wavevector, these fractional excitations are bound and form conventional magnons. Our results establish...... the existence of fractional quasiparticles in the high-energy spectrum of a quasi-two-dimensional antiferromagnet, even in the absence of frustration....

Search for quasi bound η mesons

International Nuclear Information System (INIS)

Machner, H

2015-01-01

The search for a quasi bound η meson in atomic nuclei is reviewed. This tentative state is studied theoretically as well as experimentally. The theory starts from elastic η nucleon scattering which is derived from production data within some models. From this interaction the η nucleus interaction is derived. Model calculations predict binding energies and widths of the quasi bound state. Another method is to derive the η nucleus interaction from excitation functions of η production experiments. The s wave interaction is extracted from such data via final state interaction (FSI) theorem. We give the derivation of s wave amplitudes in partial wave expansion and in helicity amplitudes and their relation to observables. Different experiments extracting the FSI are discussed as are production experiments. So far only three experiments give evidence for the existence of the quasi bound state: a pion double charge exchange experiment, an effective mass measurement, and a transfer reaction at recoil free kinematics with observation of the decay of the state. (topical review)

Resonant and nonresonant transfer and excitation in Si11+ + He collisions

International Nuclear Information System (INIS)

Clark, M.W.

1988-01-01

For many years now, dielectronic recombination (DR) has been discussed as a possible energy loss mechanism in high temperature plasmas (e.g. stars). The process is basically the inverse Auger process and involves the capture of a free electron by an ion and the simultaneous excitation of an inner shell electron of the ion producing a doubly excited state. The DR process also includes the radiative deexcitation of the ion and hence represents an energy loss from the plasma since the plasma is essentially transparent to the photons. If, instead of a free electron, an electron that is weakly bound to an atom is captured and an inner shell electron of the ion is excited, the same excited states are produced as in DR. Because the bound electrons have a momentum distribution (Compton profile), individual doubly excited states cannot, in general, be observed in this case. This new process has been called Resonant Transfer and Excitation (RTE). There is also a competing mechanism for RTE in which excitation occurs via the interaction between a projectile ion electron and a target nucleus and the capture occurs because of the interaction of the projectile nucleus and a target electron. This competing mechanism has been termed Nonresonant Transfer and Excitation (NTE) Measurements have been performed to measure RTE and NTE cross sections. A discussion of the theory, methods, and results is included

Statistical transmutation in doped quantum dimer models.

Science.gov (United States)

Lamas, C A; Ralko, A; Cabra, D C; Poilblanc, D; Pujol, P

2012-07-06

We prove a "statistical transmutation" symmetry of doped quantum dimer models on the square, triangular, and kagome lattices: the energy spectrum is invariant under a simultaneous change of statistics (i.e., bosonic into fermionic or vice versa) of the holes and of the signs of all the dimer resonance loops. This exact transformation enables us to define the duality equivalence between doped quantum dimer Hamiltonians and provides the analytic framework to analyze dynamical statistical transmutations. We investigate numerically the doping of the triangular quantum dimer model with special focus on the topological Z(2) dimer liquid. Doping leads to four (instead of two for the square lattice) inequivalent families of Hamiltonians. Competition between phase separation, superfluidity, supersolidity, and fermionic phases is investigated in the four families.

Ab initio configuration interaction description of excitation energy transfer between closely packed molecules

International Nuclear Information System (INIS)

Fink, R.F.; Pfister, J.; Schneider, A.; Zhao, H.; Engels, B.

2008-01-01

We present new, generally applicable protocols for the computation of the coupling parameter, J, of excitation energy transfer with quantum chemical ab initio methods. The protocols allow to select the degree of approximation and computational demand such that they are applicable for realistic systems and still allow to control the quality of the approach. We demonstrate the capabilities of the different protocols using the CO dimer as a first example. Correlation effects are found to scale J by a factor of about 0.7 which is in good agreement to earlier results obtained for the ethene dimer. The various levels of the protocol allow to assess the influence of ionic configurations and the polarisation within the dimer. Further, the interplay between the Foerster and Dexter contribution to J is investigated. The computations also show error compensation within approximations that are widely used for extended systems as in particular the transition density cube method

Ab initio configuration interaction description of excitation energy transfer between closely packed molecules

Energy Technology Data Exchange (ETDEWEB)

Fink, R.F. [University of Wuerzburg, Institute of Organic Chemistry, Am Hubland, D-97074 Wuerzburg (Germany)], E-mail: reinhold.fink@rub.de; Pfister, J.; Schneider, A.; Zhao, H.; Engels, B. [University of Wuerzburg, Institute of Organic Chemistry, Am Hubland, D-97074 Wuerzburg (Germany)

2008-01-29

We present new, generally applicable protocols for the computation of the coupling parameter, J, of excitation energy transfer with quantum chemical ab initio methods. The protocols allow to select the degree of approximation and computational demand such that they are applicable for realistic systems and still allow to control the quality of the approach. We demonstrate the capabilities of the different protocols using the CO dimer as a first example. Correlation effects are found to scale J by a factor of about 0.7 which is in good agreement to earlier results obtained for the ethene dimer. The various levels of the protocol allow to assess the influence of ionic configurations and the polarisation within the dimer. Further, the interplay between the Foerster and Dexter contribution to J is investigated. The computations also show error compensation within approximations that are widely used for extended systems as in particular the transition density cube method.

Strain mediated interaction of adatom dimers

OpenAIRE

Kappus, Wolfgang

2013-01-01

An earlier model for substrate strain mediated interactions between monomer adatoms is extended to the interaction of monomers with dimers and the interaction of dimers. While monomers (sitting on high symmetric sites) are supposed to create isotropic stress on the substrate, dimers would create anisotropic stress caused by stretching their bond. Resulting interactions are strongly angle dependent and also reflect the elastic anisotropy of the substrate. The applicability of a continuum elast...

Electron excitation of alkali atoms

International Nuclear Information System (INIS)

Ormonde, S.

1979-02-01

The development and testing of a synthesized close-coupling effective model potential ten-channel electron-atom scattering code and some preliminary calculations of resonances in cross sections for the excitation of excited states of potassium by low energy electrons are described. The main results obtained are: identification of 1 S and 1 D structures in excitation cross sections below the 5 2 S threshold of neutral potassium; indications of additional structures - 1 P and 1 D between the 5 2 S and 5 2 D thresholds; and a suggested explanation of anomalously high interstate-electron impact excitation cross sections inferred from experiments on potassium-seeded plasmas. The effective potential model imbedded in the code can be used to simulate any atomic system that can be approximated by a single bound electron outside an ionic core. All that is needed is a set of effective potential parameters--experimental or theoretical. With minor modifications the code could be adapted to calculations of electron scattering by two-electron systems

New ab initio adiabatic potential energy surfaces and bound state calculations for the singlet ground X˜ 1A1 and excited C˜ 1B2(21A') states of SO2

Science.gov (United States)

Kłos, Jacek; Alexander, Millard H.; Kumar, Praveen; Poirier, Bill; Jiang, Bin; Guo, Hua

2016-05-01

We report new and more accurate adiabatic potential energy surfaces (PESs) for the ground X˜ 1A1 and electronically excited C˜ 1B2(21A') states of the SO2 molecule. Ab initio points are calculated using the explicitly correlated internally contracted multi-reference configuration interaction (icMRCI-F12) method. A second less accurate PES for the ground X ˜ state is also calculated using an explicitly correlated single-reference coupled-cluster method with single, double, and non-iterative triple excitations [CCSD(T)-F12]. With these new three-dimensional PESs, we determine energies of the vibrational bound states and compare these values to existing literature data and experiment.

Vibrational circular dichroism of a 2,5-diketopiperazine (DKP) peptide: Evidence for dimer formation in cyclo LL or LD diphenylalanine in the solid state.

Science.gov (United States)

Pérez-Mellor, Ariel; Zehnacker, Anne

2017-02-01

The diastereomer diketopiperazine (DKP) peptides built on phenylalanine, namely, cyclo diphenylalanine LPhe-LPhe and LPhe-DPhe, were studied in the solid phase by vibrational circular dichroism (VCD) coupled to quantum chemical calculations. The unit structure of cyclo LPhe-LPhe in KBr pellets is a dimer bridged by two strong NH…O hydrogen bonds. The intense bisignate signature in the CO stretch region is interpreted in terms of two contributions arising from the free COs of the dimer and the antisymmetrical combination of the bound COs. In contrast, cyclo LPhe-DPhe shows no VCD signal in relation to its symmetric nature. © 2017 Wiley Periodicals, Inc.

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

OpenAIRE

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

2002-01-01

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.

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

Science.gov (United States)

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

2002-08-19

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.

Kinetic simulation on collisional bounded plasma

International Nuclear Information System (INIS)

Zhu, S.P.; Sato, Tetsuya; Tomita, Yukihiro; Hatori, Tadatsugu

1998-01-01

A self-consistent kinetic simulation model on collisional bounded plasma is presented. The electric field is given by solving Poisson equation and collisions among particles (including charged particles and neutral particles) are included. The excitation and ionization of neutral particle, and recombination are also contained in the present model. The formation of potential structure near a boundary for a discharge system was used as an application of this model. (author)

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: udayaditya.sen@saha.ac.in

2014-07-18

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.

The a-Type K = 0 Microwave Spectrum of the Methanol Dimer

Science.gov (United States)

Lovas, F. J.; Belov, S. P.; Tretyakov, M. Y.; Stahl, W.; Suenram, R. D.

1995-04-01

The rotational spectrum of (CH3OH)2 has been observed in the region 4-22 GHz with pulsed-beam Fabry-Perot cavity Fourier-transform microwave spectrometers at NIST and at the University of Kiel. Each a-type R(J), Ka = 0 transition is split into 15 states by tunneling motions for (CH3OH)2, (13CH3OH)2, (CH3OD)2, (CD3OH)2, and (CD3OH)2. The preliminary analysis of the methyl internal rotation presented here was guided by the previously developed multidimensional tunneling theory which predicts 16 tunneling components for each R(J) transition from 25 distinct tunneling motions. Several isotopically mixed dimers of methanol have also been measured, namely 13CH3OH, CH3OD, CD3OH, and CD3OD bound to 12CH3OH. Since the hydrogen bond interchange motion (which converts a donor into an acceptor) would produce a new and less favorable conformation from an energy viewpoint, it does not occur and only 10 tunneling components are observed for these mixed dimers. The structure of the complex is similar to that of water dimer with a hydrogen bond distance of 2.035 Å and a tilt of the acceptor methanol of 84° from the O-H-O axis. The effective barrier to internal rotation for the donor methyl group of (CH3OH)2 is ν3 = 183.0 cm-1 and is one-half of the value for the methanol monomer (370 cm-1), while the barrier to internal rotation of the acceptor methyl group is 120 cm-1.

Lower bounds on scintillation detector timing performance

International Nuclear Information System (INIS)

Clinthorne, N.H.; Rogers, W.L.; Hero, A.O. III.; Petrick, N.A.

1990-01-01

Fundamental method-independent limits on the timing performance of scintillation detectors are useful for identifying regimes in which either present timing methods are nearly optimal or where a considerable performance gain might be realized using better pulse processing techniques. Several types of lower bounds on mean-squared timing error (MSE) performance have been developed and applied to scintillation detectors. The simple Cramer-Rao (CR) bound can be useful in determining the limiting MSE for scintillators having a relatively high rate of photon problction such as BaF 2 and NaI(Tl); however, it tends to overestimate the achievalbe performance for scintillators with lower rates such as BGO. For this reason, alternative bounds have been developed using rate-distortion theory or by assuming that the conversion of energy to scintillation light must pass through excited states which have exponential lifetime densities. The bounds are functions of the mean scintillation pulse shape, the scintillation intensity, and photodetector characteristics; they are simple to evaluate and can be used to conveniently assess the limiting timing performance of scintillation detectors. (orig.)

Selective amine catalysed steroidal dimerization

Indian Academy of Sciences (India)

of cholesterol is the formation of a green colour in concentrated sulphuric acid, and this was shown to be due to a polyenyl steroidal dimer carbocation.7–9 Many dimeric and oligomeric steroids exhibit interesting micellular, detergent and liquid crystal behaviour.10,11. Most of the steroidal dimmers are also well-known.

Emergent low-energy bound states in the two-orbital Hubbard model

Science.gov (United States)

Núñez-Fernández, Y.; Kotliar, G.; Hallberg, K.

2018-03-01

A repulsive Coulomb interaction between electrons in different orbitals in correlated materials can give rise to bound quasiparticle states. We study the nonhybridized two-orbital Hubbard model with intra- (inter)orbital interaction U (U12) and different bandwidths using an improved dynamical mean-field theory numerical technique which leads to reliable spectra on the real energy axis directly at zero temperature. We find that a finite density of states at the Fermi energy in one band is correlated with the emergence of well-defined quasiparticle states at excited energies Δ =U -U12 in the other band. These excitations are interband holon-doublon bound states. At the symmetric point U =U12 , the quasiparticle peaks are located at the Fermi energy, leading to a simultaneous and continuous Mott transition settling a long-standing controversy.

Tunneling dynamics of double proton transfer in formic acid and benzoic acid dimers

Science.gov (United States)

Smedarchina, Zorka; Fernández-Ramos, Antonio; Siebrand, Willem

2005-04-01

Direct dynamics calculations based on instanton techniques are reported of tunneling splittings due to double proton transfer in formic and benzoic acid dimers. The results are used to assign the observed splittings to levels for which the authors of the high-resolution spectra could not provide a definitive assignment. In both cases the splitting is shown to be due mainly to the zero-point level rather than to the vibrationally or electronically excited level whose spectrum was investigated. This leads to zero-point splittings of 375MHz for (DCOOH)2 and 1107MHz for the benzoic acid dimer. Thus, contrary to earlier calculations, it is found that the splitting is considerably larger in the benzoic than in the formic acid dimer. The calculations are extended to solid benzoic acid where the asymmetry of the proton-transfer potential induced by the crystal can be overcome by suitable doping. This has allowed direct measurement of the interactions responsible for double proton transfer, which were found to be much larger than those in the isolated dimer. To account for this observation both static and dynamic effects of the crystal forces on the intradimer hydrogen bonds are included in the calculations. The same methodology, extended to higher temperatures, is used to calculate rate constants for HH, HD, and DD transfers in neat benzoic acid crystals. The results are in good agreement with reported experimental rate constants measured by NMR relaxometry and, if allowance is made for small structural changes induced by doping, with the transfer matrix elements observed in doped crystals. Hence the method used allows a unified description of tunneling splittings in the gas phase and in doped crystals as well as of transfer rates in neat crystals.

Small-angle X-ray scattering analysis reveals the ATP-bound monomeric state of the ATPase domain from the homodimeric MutL endonuclease, a GHKL phosphotransferase superfamily protein.

Science.gov (United States)

Iino, Hitoshi; Hikima, Takaaki; Nishida, Yuya; Yamamoto, Masaki; Kuramitsu, Seiki; Fukui, Kenji

2015-05-01

DNA mismatch repair is an excision system that removes mismatched bases chiefly generated by replication errors. In this system, MutL endonucleases direct the excision reaction to the error-containing strand of the duplex by specifically incising the newly synthesized strand. Both bacterial homodimeric and eukaryotic heterodimeric MutL proteins belong to the GHKL ATPase/kinase superfamily that comprises the N-terminal ATPase and C-terminal dimerization regions. Generally, the GHKL proteins show large ATPase cycle-dependent conformational changes, including dimerization-coupled ATP binding of the N-terminal domain. Interestingly, the ATPase domain of human PMS2, a subunit of the MutL heterodimer, binds ATP without dimerization. The monomeric ATP-bound state of the domain has been thought to be characteristic of heterodimeric GHKL proteins. In this study, we characterized the ATP-bound state of the ATPase domain from the Aquifex aeolicus MutL endonuclease, which is a homodimeric GHKL protein unlike the eukaryotic MutL. Gel filtration, dynamic light scattering, and small-angle X-ray scattering analyses clearly showed that the domain binds ATP in a monomeric form despite its homodimeric nature. This indicates that the uncoupling of dimerization and ATP binding is a common feature among bacterial and eukaryotic MutL endonucleases, which we suggest is closely related to the molecular mechanisms underlying mismatch repair.

Pyrimidine dimer formation and repair in human skin

International Nuclear Information System (INIS)

Sutherland, B.M.; Harber, L.C.; Kochevar, I.E.

1980-01-01

Cyclobutyl pyrimidine dimers have been detected in the DNA of human skin following in vivo irradiation with suberythermal doses of ultraviolet (UV) radiation from FS-20 sun lamp fluorescent tubes. Dimers were assayed by treatment of extracted DNA with Micrococus luteus UV-specific endonuclease, alkaline agarose electrophoresis, and ethidum bromide staining. This technique, in contrast to conventional dimer assays, can be used with nonradioactive DNA and is optimal at low UV light doses. These data suggest that some dimer disappearance by excision repair occurs within 20 min of UV irradiation and that photoreactivation of dimers can make a contribution to the total repair process

Adventures in holographic dimer models

International Nuclear Information System (INIS)

Kachru, Shamit; Karch, Andreas; Yaida, Sho

2011-01-01

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.

Dynamic interplay between adhesive and lateral E-cadherin dimers

DEFF Research Database (Denmark)

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

2002-01-01

M. The disappearance of adhesive dimers was counterbalanced by an increase in Trp156-dependent lateral dimers. Increasing the calcium concentration to a normal level rapidly restored the original balance between adhesive and lateral dimers. We also present evidence that E-cadherin dimers in vivo have a short lifetime...

Plasmonic nanospherical dimers for color pixels

KAUST Repository

Alrasheed, Salma

2018-04-20

Display technologies are evolving more toward higher resolution and miniaturization. Plasmonic color pixels can offer solutions to realize such technologies due to their sharp resonances and selective scattering and absorption at particular wavelengths. Metal nanosphere dimers are capable of supporting plasmon resonances that can be tuned to span the entire visible spectrum. In this article, we demonstrate numerically bright color pixels that are highly polarized and broadly tuned using periodic arrays of metal nanosphere dimers on a glass substrate. We show that it is possible to obtain RGB pixels in the reflection mode. The longitudinal plasmon resonance of nanosphere dimers along the axis of the dimer is the main contributor to the color of the pixel, while far-field diffractive coupling further enhances and tunes the plasmon resonance. The computational method used is the finite-difference time-domain method. The advantages of this approach include simplicity of the design, bright coloration, and highly polarized function. In addition, we show that it is possible to obtain different colors by varying the angle of incidence, the periodicity, the size of the dimer, the gap, and the substrate thickness.

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

2003-11-15

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)

Universal extra dimensions and Kaluza-Klein bound states

International Nuclear Information System (INIS)

Carone, Christopher D.; Conroy, Justin M.; Sher, Marc; Turan, Ismail

2004-01-01

We study the bound states of the Kaluza-Klein (KK) excitations of quarks in certain models of universal extra dimensions. Such bound states may be detected at future lepton colliders in the cross section for the pair production of KK quarks near threshold. For typical values of model parameters, we find that 'KK quarkonia' have widths in the 10-100 MeV range, and production cross sections of the order of a few picobarns for the lightest resonances. Two body decays of the constituent KK quarks lead to distinctive experimental signatures. We point out that such KK resonances may be discovered before any of the higher KK modes

Age-Adjusted D-Dimer in the Prediction of Pulmonary Embolism: Does a Normal Age-Adjusted D-Dimer Rule Out PE?

Directory of Open Access Journals (Sweden)

Jacob Ortiz

2017-01-01

Full Text Available Risk assessment for pulmonary embolism (PE currently relies on physician judgment, clinical decision rules (CDR, and D-dimer testing. There is still controversy regarding the role of D-dimer testing in low or intermediate risk patients. The objective of the study was to define the role of clinical decision rules and D-dimer testing in patients suspected of having a PE. Records of 894 patients referred for computed tomography pulmonary angiography (CTPA at a University medical center were analyzed. The clinical decision rules overall had an ROC of approximately 0.70, while signs of DVT had the highest ROC (0.80. A low probability CDR coupled with a negative age-adjusted D-dimer largely excluded PE. The negative predictive value (NPV of an intermediate CDR was 86–89%, while the addition of a negative D-dimer resulted in NPVs of 94%. Thus, in patients suspected of having a PE, a low or intermediate CDR does not exclude PE; however, in patients with an intermediate CDR, a normal age-adjusted D-dimer increases the NPV.

Peptides Interfering 3A Protein Dimerization Decrease FMDV Multiplication.

Directory of Open Access Journals (Sweden)

Mónica González-Magaldi

Full Text Available Nonstructural protein 3A is involved in relevant functions in foot-and-mouth disease virus (FMDV replication. FMDV 3A can form homodimers and preservation of the two hydrophobic α-helices (α1 and α2 that stabilize the dimer interface is essential for virus replication. In this work, small peptides mimicking residues involved in the dimer interface were used to interfere with dimerization and thus gain insight on its biological function. The dimer interface peptides α1, α2 and that spanning the two hydrophobic α-helices, α12, impaired in vitro dimer formation of a peptide containing the two α-helices, this effect being higher with peptide α12. To assess the effect of dimer inhibition in cultured cells, the interfering peptides were N-terminally fused to a heptaarginine (R7 sequence to favor their intracellular translocation. Thus, when fused to R7, interference peptides (100 μM were able to inhibit dimerization of transiently expressed 3A, the higher inhibitions being found with peptides α1 and α12. The 3A dimerization impairment exerted by the peptides correlated with significant, specific reductions in the viral yield recovered from peptide-treated FMDV infected cells. In this case, α2 was the only peptide producing significant reductions at concentrations lower than 100 μM. Thus, dimer interface peptides constitute a tool to understand the structure-function relationship of this viral protein and point to 3A dimerization as a potential antiviral target.

-CH2- lengthening of the internucleotide linkage in the ApA dimer can improve its conformational compatibility with its natural polynucleotide counterpart

Science.gov (United States)

Hanu, J.; Barvík, I.; Ruszová-Chmelová, K.; ŠtÆpánek, J.; Turpin, P.-Y.; Bok, J.; Rosenberg, I.; Petrová-Endová, M.

2001-01-01

The complete family of ApA phosphonate analogues with the internucleotide linkage elongated by insertion of a -CH2- group was prepared and the hybridisation and structural properties of its members in interaction with polyuridylic acid were investigated using an original 2D Raman approach. Except for the conformationally restricted ACHpA(2′3′endo-5′) modification, all of the isopolar, non-isosteric analogues form triplex-like complexes with poly(rU) at room temperature, in which two polymer strands are bound by Watson–Crick and Hoogsteen bonds to a central pseudostrand consisting of a ‘chain’ of A-dimers. For all of these dimers, the overall conformation of the triplexes was found to be similar according to their extracted Raman spectra. A simple semi-empirical model was introduced to explain the observed dependency of the efficiency of triplex formation on the adenine concentration. Apparently, for most of the modifications studied, the creation of a stable complex at room temperature requires the formation of a central pseudostrand, consisting of several adenine dimers. Molecular dynamics calculations were finally performed to interpret the differences in ‘cooperative’ behaviour between the different dimers studied. The results indicate that the exceptional properties of the ApCH2A(3′-5′) dimer could be caused by the 3D conformational compatibility of this modified linkage with the second (Hoogsteen) poly(rU) strand. PMID:11812852

Understanding the effects of packing and chemical terminations on the optical excitations of azobenzene-functionalized self-assembled monolayers

Science.gov (United States)

Cocchi, Caterina; Draxl, Claudia

2017-10-01

In a first-principles study based on many-body perturbation theory, we analyze the optical excitations of azobenzene-functionalized self-assembled monolayers (SAMs) with increasing packing density and different terminations, considering for comparison the corresponding gas-phase molecules and dimers. Intermolecular coupling increases with the density of the chromophores independently of the functional groups. The intense π → π* resonance that triggers photo-isomerization is present in the spectra of isolated dimers and diluted SAMs, but it is almost completely washed out in tightly packed architectures. Intermolecular coupling is partially inhibited by mixing differently functionalized azobenzene derivatives, in particular when large groups are involved. In this way, the excitation band inducing the photo-isomerization process is partially preserved and the effects of dense packing partly counterbalanced. Our results suggest that a tailored design of azobenzene-functionalized SAMs which optimizes the interplay between the packing density of the chromophores and their termination can lead to significant improvements in the photo-switching efficiency of these systems.

Generalized Bethe-Negele inequalities for excited states in muonic atoms

International Nuclear Information System (INIS)

Klarsfeld, S.

1976-11-01

Rigorous upper and lower bounds are derived for the Bethe logarithms in excited states of muonic atoms. Comparison with previous empirical estimates shows that the latter are inadequate in certain cases

Rotational spectrum and structure of the carbonyl sulfide-trifluoromethane weakly bound dimer.

Science.gov (United States)

Serafin, Michal M; Peebles, Sean A

2006-11-02

Pure rotational spectra of five isotopomers of the 1:1 weakly bound complex formed between carbonyl sulfide and trifluoromethane (TFM) have been measured using Fourier transform microwave spectroscopy. The experimental rotational constants and dipole moment components are consistent with a structure of C(s) symmetry in which the dipole moment vectors of OCS and HCF(3) are aligned antiparallel and at an angle of about 40 degrees and with a center of mass separation of 3.965(26) A. The derived H...O distance is 2.90(5) A, which is up to 0.6 A longer than is seen in other similar TFM complexes exhibiting C-H...O interactions. Ab initio calculations at the MP2/6-311++G(2d,2p) level give a structure with rotational constants that are in reasonable agreement with those of the normal isotopic species.

Excitation spectrum of ferromagnetic xxz-chains

International Nuclear Information System (INIS)

Schneider, T.; Stoll, E.

1983-01-01

In the history of xxz-Heisenberg spin chains, understanding of the dynamic form factors (DFF) is much less advanced. In this paper the DFF of ferromagnetic xxz chains as a tool to probe and interpret excitation spectrum is reviewed. The Isingheisenberg chain, and the Planar-Heisenberg chain (where HF approximations become exact) are studied. The results provide instructive connections between spin systems, interacting fermions and bosons. Various new aspects--thermally induced bound state effects in terms of central peaks in DFF for Isinglike xxz chains; the possibility to observe bound states in S /SUB zz/ (q,w) accessible by neutron scattering techniques, in the planar system--are found

Theory of nuclear excitation by electron capture for heavy ions

International Nuclear Information System (INIS)

Palffy, Adriana; Scheid, Werner; Harman, Zoltan

2006-01-01

We investigate the resonant process of nuclear excitation by electron capture (NEEC), in which a continuum electron is captured into a bound state of an ion with the simultaneous excitation of the nucleus. In order to derive the cross section a Feshbach projection operator formalism is introduced. Nuclear states and transitions are described by a nuclear collective model and making use of experimental data. Transition rates and total cross sections for NEEC followed by the radiative decay of the excited nucleus are calculated for various heavy-ion collision systems

Ab initio investigation on the valence and dipole-bound states of CNa - and SiNa -

Science.gov (United States)

Kalcher, Josef; Sax, Alexander F.

2000-08-01

CNa - and SiNa - have been studied by the CAS-ACPF method. The 3Σ- ground states have binding energies of 5420 and 7517 cm -1, respectively. The 5Σ- excited states are 494 and 1551 cm -1 above the respective ground states. The 1Δ , 3Π , and 1Π valence-excited states for SiNa - should be at least metastable. CNa - and SiNa - possess dipole-bound 5Σ- and 3Σ- states. Binding energies of these states in CNa - are 217 and 236 cm -1, respectively. SiNa - has two stable 5Σ- dipole-bound states, whose binding energies are 246 and 118 cm -1, respectively.

Bound-bound transitions in the emission spectra of Ba+-He excimer

Science.gov (United States)

Moroshkin, P.; Kono, K.

2016-05-01

We present an experimental and theoretical study of the emission and absorption spectra of the Ba+ ions and Ba+*He excimer quasimolecules in the cryogenic Ba-He plasma. We observe several spectral features in the emission spectrum, which we assign to the electronic transitions between bound states of the excimer correlating to the 6 2P3 /2 and 5 2D3 /2 ,5 /2 states of Ba+. The resulting Ba+(5 2DJ) He is a metastable electronically excited complex with orbital angular momentum L =2 , thus expanding the family of known metal-helium quasimolecules. It might be suitable for high-resolution spectroscopic studies and for the search for new polyatomic exciplex structures.

Mahler Measure, Eisenstein Series and Dimers

NARCIS (Netherlands)

Stienstra, J.

2007-01-01

This note reveals a mysterious link between the partition function of certain dimer models on 2-dimensional tori and the L-function of their spectral curves. It also relates the partition function in certain families of dimer models to Eisenstein series. http://www.arxiv.org/abs/math.NT/0502197

Effects of Dimers on Cooperation in the Spatial Prisoner's Dilemma Game

International Nuclear Information System (INIS)

Li Haihong; Cheng Hongyan; Dai Qionglin; Ju Ping; Yang Junzhong; Zhang Mei

2011-01-01

We investigate the evolutionary prisoner's dilemma game in structured populations by introducing dimers, which are defined as that two players in each dimer always hold a same strategy. We find that influences of dimers on cooperation depend on the type of dimers and the population structure. For those dimers in which players interact with each other, the cooperation level increases with the number of dimers though the cooperation improvement level depends on the type of network structures. On the other hand, the dimers, in which there are not mutual interactions, will not do any good to the cooperation level in a single community, but interestingly, will improve the cooperation level in a population with two communities. We explore the relationship between dimers and self-interactions and find that the effects of dimers are similar to that of self-interactions. Also, we find that the dimers, which are established over two communities in a multi-community network, act as one type of interaction through which information between communities is communicated by the requirement that two players in a dimer hold a same strategy. (general)

Her4 and Her2/neu tyrosine kinase domains dimerize and activate in a reconstituted in vitro system.

Science.gov (United States)

Monsey, John; Shen, Wei; Schlesinger, Paul; Bose, Ron

2010-03-05

Her4 (ErbB-4) and Her2/neu (ErbB-2) are receptor-tyrosine kinases belonging to the epidermal growth factor receptor (EGFR) family. Crystal structures of EGFR and Her4 kinase domains demonstrate kinase dimerization and activation through an allosteric mechanism. The kinase domains form an asymmetric dimer, where the C-lobe surface of one monomer contacts the N-lobe of the other monomer. EGFR kinase dimerization and activation in vitro was previously reported using a nickel-chelating lipid-liposome system, and we now apply this system to all other members of the EGFR family. Polyhistidine-tagged Her4, Her2/neu, and Her3 kinase domains are bound to these nickel-liposomes and are brought to high local concentration, mimicking what happens to full-length receptors in vivo following ligand binding. Addition of nickel-liposomes to Her4 kinase domain results in 40-fold activation in kinase activity and marked enhancement of C-terminal tail autophosphorylation. Activation of Her4 shows a sigmoidal dependence on kinase concentration, consistent with a cooperative process requiring kinase dimerization. Her2/neu kinase activity is also activated by nickel-liposomes, and is increased further by heterodimerization with Her3 or Her4. The ability of Her3 and Her4 to heterodimerize and activate other family members is studied in vitro. Her3 kinase domain readily activates Her2/neu but is a poor activator of Her4, which differs from the prediction made by the asymmetric dimer model. Mutation of Her3 residues (952)ENI(954) to the corresponding sequence in Her4 enhanced the ability of Her3 to activate Her4, demonstrating that sequence differences on the C-lobe surface influence the heterodimerization and activation of ErbB kinase domains.

Semi-active control of a cable-stayed bridge under multiple-support excitations.

Science.gov (United States)

Dai, Ze-Bing; Huang, Jin-Zhi; Wang, Hong-Xia

2004-03-01

This paper presents a semi-active strategy for seismic protection of a benchmark cable-stayed bridge with consideration of multiple-support excitations. In this control strategy, Magnetorheological (MR) dampers are proposed as control devices, a LQG-clipped-optimal control algorithm is employed. An active control strategy, shown in previous researches to perform well at controlling the benchmark bridge when uniform earthquake motion was assumed, is also used in this study to control this benchmark bridge with consideration of multiple-support excitations. The performance of active control system is compared to that of the presented semi-active control strategy. Because the MR fluid damper is a controllable energy- dissipation device that cannot add mechanical energy to the structural system, the proposed control strategy is fail-safe in that bounded-input, bounded-output stability of the controlled structure is guaranteed. The numerical results demonstrated that the performance of the presented control design is nearly the same as that of the active control system; and that the MR dampers can effectively be used to control seismically excited cable-stayed bridges with multiple-support excitations.

Influence of Magnetic Ordering between Cr Adatoms on the Yu-Shiba-Rusinov States of the β -Bi2Pd Superconductor

Science.gov (United States)

Choi, Deung-Jang; Fernández, Carlos García; Herrera, Edwin; Rubio-Verdú, Carmen; Ugeda, Miguel M.; Guillamón, Isabel; Suderow, Hermann; Pascual, José Ignacio; Lorente, Nicolás

2018-04-01

We show that the magnetic ordering of coupled atomic dimers on a superconductor is revealed by their intragap spectral features. Chromium atoms on the superconductor β -Bi2Pd surface display Yu-Shiba-Rusinov bound states, detected as pairs of intragap excitations in tunneling spectra. By means of atomic manipulation with a scanning tunneling microscope's tip, we form Cr dimers with different arrangements and find that their intragap features appear either shifted or split with respect to single atoms. These spectral variations are associated with the magnetic coupling, ferromagnetic or antiferromagnetic, of the dimer, as confirmed by density functional theory simulations. The striking qualitative differences between the observed tunneling spectra prove that intragap Shiba states are extremely sensitive to the magnetic ordering on the atomic scale.

Kinetics of DNA tile dimerization.

Science.gov (United States)

Jiang, Shuoxing; Yan, Hao; Liu, Yan

2014-06-24

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

Dimers in Piecewise Temperleyan Domains

Science.gov (United States)

Russkikh, Marianna

2018-03-01

We study the large-scale behavior of the height function in the dimer model on the square lattice. Richard Kenyon has shown that the fluctuations of the height function on Temperleyan discretizations of a planar domain converge in the scaling limit (as the mesh size tends to zero) to the Gaussian Free Field with Dirichlet boundary conditions. We extend Kenyon's result to a more general class of discretizations. Moreover, we introduce a new factorization of the coupling function of the double-dimer model into two discrete holomorphic functions, which are similar to discrete fermions defined in Smirnov (Proceedings of the international congress of mathematicians (ICM), Madrid, Spain, 2006; Ann Math (2) 172:1435-1467, 2010). For Temperleyan discretizations with appropriate boundary modifications, the results of Kenyon imply that the expectation of the double-dimer height function converges to a harmonic function in the scaling limit. We use the above factorization to extend this result to the class of all polygonal discretizations, that are not necessarily Temperleyan. Furthermore, we show that, quite surprisingly, the expectation of the double-dimer height function in the Temperleyan case is exactly discrete harmonic (for an appropriate choice of Laplacian) even before taking the scaling limit.

Detection of rhodopsin dimerization in situ by PIE-FCCS, a time-resolved fluorescence spectroscopy.

Science.gov (United States)

Smith, Adam W

2015-01-01

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

Dimer-based model for heptaspanning membrane receptors.

Science.gov (United States)

Franco, Rafael; Casadó, Vicent; Mallol, Josefa; Ferré, Sergi; Fuxe, Kjell; Cortés, Antonio; Ciruela, Francisco; Lluis, Carmen; Canela, Enric I

2005-07-01

The existence of intramembrane receptor-receptor interactions for heptaspanning membrane receptors is now fully accepted, but a model considering dimers as the basic unit that binds to two ligand molecules is lacking. Here, we propose a two-state-dimer model in which the ligand-induced conformational changes from one component of the dimer are communicated to the other. Our model predicts cooperativity in binding, which is relevant because the other current models fail to address this phenomenon satisfactorily. Our two-state-dimer model also predicts the variety of responses elicited by full or partial agonists, neutral antagonists and inverse agonists. This model can aid our understanding of the operation of heptaspanning receptors and receptor channels, and, potentially, be important for improving the treatment of cardiovascular, neurological and neuropsychyatric diseases.

Gutzwiller approach for elementary excitations in S = 1 antiferromagnetic chains

International Nuclear Information System (INIS)

Liu, Zheng-Xin; Zhou, Yi; Ng, Tai-Kai

2014-01-01

In a previous paper (Liu et al 2012 Phys. Rev. B 85 195144), a variational Monte Carlo method (based on Gutzwiller projected states) was generalized to S = 1 systems. This method provided very good trial ground states for the gapped phases of an S = 1 bilinear-biquadratic (BLBQ) Heisenberg chain. In this paper, we extend the approach to study the low-lying elementary excitations in S = 1 chains. We calculate the one-magnon and two-magnon excitation spectra of the BLBQ Heisenberg chain and the results agree very well with recent data in the literature. In our approach, the difference of the excitation spectrum between the Haldane phase and the dimer phase (such as the even/odd size effect) can be understood from their different topologies of the corresponding mean field theory. We especially study the Takhtajan–Babujian critical point. Despite the fact that the ‘elementary excitations’ are spin-1 magnons, which are different from the spin-1/2 spinons in Bethe solution, we show that the excitation spectrum, critical exponent (η=0.74) and central charge (c = 1.45) calculated from our theory agree well with the Bethe ansatz solution and conformal field theory predictions. (paper)

Plasmid DNA linearization in the antibacterial action of a new fluorescent Ag nanoparticle-paracetamol dimer composite

Science.gov (United States)

Sahoo, Amaresh Kumar; Sk, Md Palashuddin; Ghosh, Siddhartha Sankar; Chattopadhyay, Arun

2011-10-01

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

Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems.

Science.gov (United States)

Fujita, Takatoshi; Mochizuki, Yuji

2018-04-19

We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems; in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.

Detection of cyclobutane thymine dimers in DNA of human cells with monoclonal antibodies raised against a thymine dimer-containing tetranucleotide

Energy Technology Data Exchange (ETDEWEB)

Roza, L; Wulp, K.J.M. van der; MacFarlane, S J; Lohman, P H.M.; Baan, R A

1988-11-01

A hybrid cell line (hybridoma) has been isolated after fusion between mouse-plasmacytoma cells and spleen cells from mice immunized with a thymine dimer-containing tetranucleotide coupled to a carrier protein. Monoclonal antibodies produced by this hybridoma were characterized by testing the effect of various inhibitors in a competitive enzyme-linked immunosorbent assay (ELISA). The antibodies have a high specificity for thymine dimers in single-stranded DNA or poly(dT), but do not bind UV-irradiated d(TpC)/sub 5/. Less binding is observed with short thymine dimer-containing sequences. In vitro treatment of UV-irradiated DNA with photoreactivating enzyme in the presence of light, or with Micrococcus luteus UV-endonuclease results in disappearance of antigenicity. Antibody-binding to DNA isolated from UV-irradiated human fibroblasts (at 254 nm) is linear with dose. Removal of thymine dimers in these cells during a post-irradiation incubation, as detected with the antibodies, is fast initially but the rate rapidly decreases (about 50% residual dimers at 20 h after 10 J/m/sup 2/). The induction of thymine dimers in human skin irradiated with low doses of UV-B, too, was demonstrated immunochemically, by ELISA as well as by quantitative immunofluorescence microscopy.

Applications of the infinite momentum method to quantum electrodynamics and bound state problem

International Nuclear Information System (INIS)

Brodsky, S.J.

1973-01-01

It is shown that the infinite momentum method is a valid and useful calculational alternative to standard perturbation theory methods. The most exciting future applications may be in bound state problems in quantum electrodynamics

Adsorption of dimeric surfactants in lamellar silicates

Energy Technology Data Exchange (ETDEWEB)

Balcerzak, Mateusz; Pietralik, Zuzanna [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland); Domka, Ludwik [Department of Metalorganic Chemistry, Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznań (Poland); Skrzypczak, Andrzej [Institute of Chemical Technology, Poznań University of Technology, Berdychowo 4, 60-965 Poznań (Poland); Kozak, Maciej, E-mail: mkozak@amu.edu.pl [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland)

2015-12-01

Highlights: • The intercalation of dimeric surfactants changed the morphology of MMT samples. • XRD indicated structures formed by surfactant molecules in interlayer space. • The four-step thermal decomposition of dimeric surfactant, confirms intercalation. - Abstract: The adsorption of different types of cationic surfactants in lamellar silicates changes their surface character from hydrophilic to hydrophobic. This study was undertaken to obtain lamellar silicates modified by a series of novel dimeric (gemini) surfactants of different length alkyl chains and to characterise these organophilised materials. Synthetic sodium montmorillonite SOMASIF® ME 100 (M) and enriched bentonite of natural origin (Nanoclay – hydrophilic bentonite®) were organophilised with dimeric (gemini) surfactants (1,1′-(1,4-butanediyl)bis(alkoxymethyl)imidazolium dichlorides). As a result of surfactant molecule adsorption in interlamellar space, the d-spacing (d{sub 001}) increased from 0.97 nm (for the anhydrous structure) to 2.04 nm. A Fourier transform infrared spectroscopy (FTIR) analysis of the modified systems reveals bands assigned to the stretching vibrations of the CH{sub 2} and CH{sub 3} groups and the scissoring vibrations of the NH group from the structure of the dimeric surfactants. Thermogravimetric (TG) and derivative thermogravimetric (DTG) studies imply a four-stage process of surfactant decomposition. Scanning electron microscopy (SEM) images provide information on the influence of dimeric surfactant intercalation into the silicate structures. Particles of the modified systems show a tendency toward the formation of irregularly shaped agglomerates.

D-dimer Test

Science.gov (United States)

... 1997). Taber's Cyclopedic Medical Dictionary. F.A. Davis Company, Philadelphia, PA [18th Edition]. Pagana, Kathleen D. & Pagana, ... www.itxm.org . Titus, K. (2003 January). Identity crisis persists: which D-dimer? CAP Today , In the ...

Molecular mechanics calculations on cobalt phthalocyanine dimers

NARCIS (Netherlands)

Heuts, J.P.A.; Schipper, E.T.W.M.; Piet, P.; German, A.L.

1995-01-01

In order to obtain insight into the structure of cobalt phthalocyanine dimers, molecular mechanics calculations were performed on dimeric cobalt phthalocyanine species. Molecular mechanics calculations are first presented on monomeric cobalt(II) phthalocyanine. Using the Tripos force field for the

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

2016-04-20

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.

Technique for description of nonrotational excited states in a semiphenomenological nuclear theory

International Nuclear Information System (INIS)

Krutov, V.A.

1985-01-01

A non-standard technique for microscopic description of excited nonrotational states is considered; it is suitable for inseparable force application. Besides, an additional binding operator, mixing quasi-particle excitations and E1-resonance states, is considered. Instead of the standard technique of state ''collectivization'' of the random phase approximation type it is used the so-called ''method of bound amplitudes''

Revealing the Dimeric Crystal and Solution Structure of β-Lactoglobulin at pH 4 and Its pH and Salt Dependent Monomer–Dimer Equilibrium

DEFF Research Database (Denmark)

Khan, Sanaullah; Ipsen, Richard; Almdal, Kristoffer

2018-01-01

The dimeric structure of bovine β-lactoglobulin A (BLGA) at pH 4.0 was solved to 2.0 Å resolution. Fitting the BLGA pH 4.0 structure to SAXS data at low ionic strength (goodness of fit R-factor = 3.6%) verified the dimeric state in solution. Analysis of the monomer–dimer equilibrium at varying pH...... and ionic strength by SAXS and scattering modeling showed that BLGA is dimeric at pH 3.0 and 4.0, shifting toward a monomer at pH 2.2, 2.6, and 7.0 yielding monomer/dimer ratios of 80/20%, 50/50%, and 25/75%, respectively. BLGA remained a dimer at pH 3.0 and 4.0 in 50–150 mM NaCl, whereas the electrostatic...... shielding raised the dimer content at pH 2.2, 2.6, and 7.0, i.e., below and above the pI. Overall, the findings provide new insights into the molecular characteristics of BLGA relevant for dairy product formulations and for various biotechnological and pharmaceutical applications....

Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

Directory of Open Access Journals (Sweden)

Yijin Liu

2015-12-01

Full Text Available We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.

Dynamics of dimer and z spin component fluctuations in spin-1/2 XY chain

Directory of Open Access Journals (Sweden)

P.Hlushak

2005-01-01

Full Text Available One-dimensional quantum spin-1/2 XY models admit the rigorous analysis not only of their static properties (i.e. the thermodynamic quantities and the equal-time spin correlation functions but also of their dynamic properties (i.e. the different-time spin correlation functions, the dynamic susceptibilities, the dynamic structure factors. This becomes possible after exploiting the Jordan-Wigner transformation which reduces the spin model to a model of spinless noninteracting fermions. A number of dynamic quantities (e.g. related to transverse spin operator or dimer operator fluctuations are entirely determined by two-fermion excitations and can be examined in much detail.

Anisotropic plasmon-coupling dimerization of a pair of spherical electron gases

International Nuclear Information System (INIS)

Gumbs, Godfrey; Iurov, Andrii; Balassis, Antonios; Huang, Danhong

2014-01-01

We have discovered a novel feature in the plasmon excitations for a pair of Coulomb-coupled non-concentric spherical two-dimensional electron gases (S2DEGs). Our results show that the plasmon excitations for such pairs depend on the orientation with respect to the external electromagnetic probe field. The origin of this anisotropy of the inter-sphere Coulomb interaction is due to the directional asymmetry of the electrostatic coupling of electrons in excited states which depend on both the angular momentum quantum number L and its projection M on the axis of quantization taken as the probe E-field direction. We demonstrate the anisotropic inter-sphere Coulomb coupling in space and present semi-analytic results in the random-phase approximation both perpendicular and parallel to the axis of quantization. For the incidence of light with a finite orbital or spin angular momentum, the magnetic field generated from an induced oscillating electric dipole on one sphere can couple to an induced magnetic dipole on another sphere in a way that is dependent on whether the direction is parallel or perpendicular to the probe E field. Such an effect from the plasmon spatial correlation is expected to be experimentally observable by employing circularly polarized light or a helical light beam for incidence. The S2DEG serves as a simple model for fullerenes as well as metallic dimers, when the energy bands are far apart. (paper)

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 ...

Manipulation of Squeezed Two-Phonon Bound States using Femtosecond Laser Pulses

Directory of Open Access Journals (Sweden)

Nakamura Kazutaka G.

2013-03-01

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.

Electronically excited and ionized states in condensed phase: Theory and applications

Science.gov (United States)

Sadybekov, Arman

Predictive modeling of chemical processes in silico is a goal of XXI century. While robust and accurate methods exist for ground-state properties, reliable methods for excited states are still lacking and require further development. Electronically exited states are formed by interactions of matter with light and are responsible for key processes in solar energy harvesting, vision, artificial sensors, and photovoltaic applications. The greatest challenge to overcome on our way to a quantitative description of light-induced processes is accurate inclusion of the effect of the environment on excited states. All above mentioned processes occur in solution or solid state. Yet, there are few methodologies to study excited states in condensed phase. Application of highly accurate and robust methods, such as equation-of-motion coupled-cluster theory EOM-CC, is limited by a high computational cost and scaling precluding full quantum mechanical treatment of the entire system. In this thesis we present successful application of the EOM-CC family of methods to studies of excited states in liquid phase and build hierarchy of models for inclusion of the solvent effects. In the first part of the thesis we show that a simple gasphase model is sufficient to quantitatively analyze excited states in liquid benzene, while the latter part emphasizes the importance of explicit treatment of the solvent molecules in the case of glycine in water solution. In chapter 2, we use a simple dimer model to describe exciton formation in liquid and solid benzene. We show that sampling of dimer structures extracted from the liquid benzene is sufficient to correctly predict exited-state properties of the liquid. Our calculations explain experimentally observed features, which helped to understand the mechanism of the excimer formation in liquid benzene. Furthermore, we shed light on the difference between dimer configurations in the first solvation shell of liquid benzene and in unit cell of solid

Through space and through bridge channels of charge transfer at p-n nano-junctions: A DFT study

Energy Technology Data Exchange (ETDEWEB)

Dandu, Naveen [Department of Chemistry and Biochemistry, NDSU, Fargo, ND 58108 (United States); Tretiak, Sergei [Theoretical Division, Center for Nonlinear Studies (CNLS) and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, 57069, NM 87454 (United States); Kilina, Svetlana [Department of Chemistry and Biochemistry, NDSU, Fargo, ND 58108 (United States); Kilin, Dmitri, E-mail: Dmitri.Kilin@ndsu.edu [Department of Chemistry and Biochemistry, NDSU, Fargo, ND 58108 (United States)

2016-12-20

Highlights: • Properties of interacting QDs depend on the fashion of interaction: through-bond or through-space. • The disconnected and undoped dimer models shows FÓ§rster band formation. • Dimer models with some doping exhibit degenerate charge-transfer excitons. • p- and n-doped qds shows polarization at the interface. • A photoexcitation polarizes p-n interface, in relation to phototovoltaic effect. - Abstract: Details of charge density distribution at p-n nano interface are analyzed with density functional theory techniques using model system of dimers of doped silicon quantum dots interacting through bond and through space. Spatial distributions of transition densities between the ground and excited states suggest the character of essential electronic excitations, which have a FÓ§rster, bound, unbound, or charge transfer character. A redistribution of electronic density from n-impurities to p-impurities results in a ground state polarization and creates an offset of energies of the bands localized on p-doped quantum dot and the bands localized on n-doped quantum dot. Although impurities contribute very few orbitals to the total density, a ground state charge redistribution and polarization are both responsible for the presence of a large number of charge transfer excitations involving solely silicon orbitals.

Dualism of Sensitivity and Selectivity of Porphyrin Dimers in Electroanalysis.

Science.gov (United States)

Lisak, Grzegorz; Tamaki, Takashi; Ogawa, Takuji

2017-04-04

This work uncovers the application of porphyrin dimers for the use in electroanalysis, such as potentiometric determination of ions. It also puts in question a current perception of an occurrence of the super-Nernstian response, as a result of the possible dimerization of single porphyrins within an ion-selective membrane. To study that, four various porphyrin dimers were used as ionophores, namely, freebase-freebase, Zn-Zn, Zn-freebase, and freebase-Zn. Since the Zn-freebase and freebase-Zn porphyrin dimers carried both anion- and cation-sensitive porphyrin units, their application in ISEs was utilized in both anion- and cation-sensitive sensors. With respect to the lipophilic salt added, both porphyrins dimers were found anion- and cation-sensitive. This allowed using a single molecule as novel type of versatile ionophore (anion- and cation-selective), simply by varying the membrane composition. All anion-sensitive sensors were perchlorate-sensitive, while the cation-selective sensors were silver-sensitive. The selectivity of the sensors depended primarily on the porphyrin dimers in the ion-selective membrane. Furthermore, the selectivity of cation-sensitive dimer based sensors was found significantly superior to the ones measured for the single porphyrin unit based sensors (precursors of the porphyrin dimers). Thus, the dimerization of single porphyrins may actually be a factor to increase or modulate porphyrin selectivity. Moreover, in the case of cation-sensitive sensors, the selectivity vastly depended on the order of porphyrin units in the dimer. This opens a new approach of regulating and adjusting sensitivity and selectivity of the sensor through the application of complex porphyrin systems with more than one porphyrin units with mix sensitive porphyrins.

Factors associated with D-dimer levels in HIV-infected individuals

DEFF Research Database (Denmark)

Borges, Alvaro H; O'Connor, Jemma L; Phillips, Andrew N

2014-01-01

BACKGROUND: Higher plasma D-dimer levels are strong predictors of mortality in HIV+ individuals. The factors associated with D-dimer levels during HIV infection, however, remain poorly understood. METHODS: In this cross-sectional study, participants in three randomized controlled trials...... with measured D-dimer levels were included (N = 9,848). Factors associated with D-dimer were identified by linear regression. Covariates investigated were: age, gender, race, body mass index, nadir and baseline CD4+ count, plasma HIV RNA levels, markers of inflammation (C-reactive protein [CRP], interleukin-6...... viruses, was positively correlated with D-dimer. Other factors independently associated with higher D-dimer levels were black race, higher plasma HIV RNA levels, being off ART at baseline, and increased levels of CRP, IL-6 and cystatin C. In contrast, higher baseline CD4+ counts and higher high...

Mechanism for Controlling the Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease

Energy Technology Data Exchange (ETDEWEB)

Shi,J.; Sivaraman, J.; Song, J.

2008-01-01

Unlike 3C protease, the severe acute respiratory syndrome coronavirus (SARS-CoV) 3C-like protease (3CLpro) is only enzymatically active as a homodimer and its catalysis is under extensive regulation by the unique extra domain. Despite intense studies, two puzzles still remain: (i) how the dimer-monomer switch is controlled and (ii) why dimerization is absolutely required for catalysis. Here we report the monomeric crystal structure of the SARS-CoV 3CLpro mutant R298A at a resolution of 1.75 Angstroms . Detailed analysis reveals that Arg298 serves as a key component for maintaining dimerization, and consequently, its mutation will trigger a cooperative switch from a dimer to a monomer. The monomeric enzyme is irreversibly inactivated because its catalytic machinery is frozen in the collapsed state, characteristic of the formation of a short 310-helix from an active-site loop. Remarkably, dimerization appears to be coupled to catalysis in 3CLpro through the use of overlapped residues for two networks, one for dimerization and another for the catalysis.

Accurate calculations of bound rovibrational states for argon trimer

Energy Technology Data Exchange (ETDEWEB)

Brandon, Drew; Poirier, Bill [Department of Chemistry and Biochemistry, and Department of Physics, Texas Tech University, Box 41061, Lubbock, Texas 79409-1061 (United States)

2014-07-21

This work presents a comprehensive quantum dynamics calculation of the bound rovibrational eigenstates of argon trimer (Ar{sub 3}), using the ScalIT suite of parallel codes. The Ar{sub 3} rovibrational energy levels are computed to a very high level of accuracy (10{sup −3} cm{sup −1} or better), and up to the highest rotational and vibrational excitations for which bound states exist. For many of these rovibrational states, wavefunctions are also computed. Rare gas clusters such as Ar{sub 3} are interesting because the interatomic interactions manifest through long-range van der Waals forces, rather than through covalent chemical bonding. As a consequence, they exhibit strong Coriolis coupling between the rotational and vibrational degrees of freedom, as well as highly delocalized states, all of which renders accurate quantum dynamical calculation difficult. Moreover, with its (comparatively) deep potential well and heavy masses, Ar{sub 3} is an especially challenging rare gas trimer case. There are a great many rovibrational eigenstates to compute, and a very high density of states. Consequently, very few previous rovibrational state calculations for Ar{sub 3} may be found in the current literature—and only for the lowest-lying rotational excitations.

Computational Insight Into the Structural Organization of Full-Length Toll-Like Receptor 4 Dimer in a Model Phospholipid Bilayer

Directory of Open Access Journals (Sweden)

Mahesh Chandra Patra

2018-03-01

Full Text Available Toll-like receptors (TLRs are a unique category of pattern recognition receptors that recognize distinct pathogenic components, often utilizing the same set of downstream adaptors. Specific molecular features of extracellular, transmembrane (TM, and cytoplasmic domains of TLRs are crucial for coordinating the complex, innate immune signaling pathway. Here, we constructed a full-length structural model of TLR4—a widely studied member of the interleukin-1 receptor/TLR superfamily—using homology modeling, protein–protein docking, and molecular dynamics simulations to understand the differential domain organization of TLR4 in a membrane-aqueous environment. Results showed that each functional domain of the membrane-bound TLR4 displayed several structural transitions that are biophysically essential for plasma membrane integration. Specifically, the extracellular and cytoplasmic domains were partially immersed in the upper and lower leaflets of the membrane bilayer. Meanwhile, TM domains tilted considerably to overcome the hydrophobic mismatch with the bilayer core. Our analysis indicates an alternate dimerization or a potential oligomerization interface of TLR4-TM. Moreover, the helical properties of an isolated TM dimer partly agree with that of the full-length receptor. Furthermore, membrane-absorbed or solvent-exposed surfaces of the toll/interleukin-1 receptor domain are consistent with previous X-ray crystallography and biochemical studies. Collectively, we provided a complete structural model of membrane-bound TLR4 that strengthens our current understanding of the complex mechanism of receptor activation and adaptor recruitment in the innate immune signaling pathway.

Study of molybdenum(VI) dimerization equilibrium in strongly acidic medium

International Nuclear Information System (INIS)

Esbelin, E.

2000-01-01

Molybdenum (VI) was investigated spectro-photometrically in non complexing and strongly acidic medium for the first time by Krumenacker. Cationic species of molybdenum were identified by electrophoresis on cellulose paper in highly acidic solutions. From these early results using absorption spectrophotometry, Krumenacker postulated the condensation of molybdenum in this medium. He studied the polymeric species by measuring diffusion coefficients and identified the polymeric form as a dimer. He described the system by equations (1) and (2). Cruywagen later added two equations (3) and (4) to supplement the description of the system. The aim of this work was to re-examine the conditional dimerization equilibrium between the various species of molybdenum(VI) in strongly acid medium by focussing on the influence of the medium. All Mo solution concentrations were analyzed by ICP-AES. Absorbance of the solutions were measured with a VARIAN model CARY5 spectrophotometer in double beam mode with air as reference; blank solutions contained all reagents except molybdenum. The quartz cell path length was 1 mm. The dimerization of monomeric molybdenum(VI) was investigated spectro-photometrically at perchloric acid concentrations of 0.5, 1.0, 2.0 and 3 M at 25 deg C. Two absorption bands at 215 and 245 nm were observed and attributed to monomeric and dimeric forms respectively. The variations in the conditional molar absorption coefficient of molybdenum with total molybdenum(VI) concentration is indicative of several molybdenum forms involved in the total absorbance. Dimerization equilibrium is defined by equation (5). By using the additivity of absorbance and mass conservation of molybdenum, a descriptive equation of the 'spectrochemical' system is developed. This equation is linearized into two forms (6) et (7). From them, two refinement methods were used to estimate the conditional dimerization constant K' d for various medium concentrations. This numerical procedure offers

Laser-induced nonsequential double ionization at and above the recollision-excitation-tunneling threshold

International Nuclear Information System (INIS)

Shaaran, T.; Figueira de Morisson Faria, C.; Nygren, M. T.

2010-01-01

We perform a rigorous, semianalytic study of the recollision excitation with subsequent tunneling ionization (RESI) mechanism in laser-induced nonsequential double ionization (NSDI), based on the strong-field approximation. We show that the shapes of the electron momentum distributions carry information about the bound state with which the first electron collides, the bound state to which the second electron is excited, and the type of electron-electron interaction. Furthermore, one may define a driving-field intensity threshold for the RESI physical mechanism. At the threshold, the kinetic energy of the first electron, upon return, is just sufficient to excite the second electron. We compute the distributions for helium and argon in the threshold and above-threshold intensity regimes. In the latter case, we relate our findings to existing experiments. The electron momentum distributions encountered are symmetric with respect to all quadrants of the plane spanned by the momentum components parallel to the laser-field polarization, instead of concentrating on only the second and fourth quadrants. The above-mentioned momentum constraints, together with the strong dependence of the distributions on the bound states involved, may be important for singling out the RESI mechanism in actual physical situations and using NSDI in ultrafast imaging.

Structural insights into lipid-dependent reversible dimerization of human GLTP

International Nuclear Information System (INIS)

Samygina, Valeria R.; Ochoa-Lizarralde, Borja; Popov, Alexander N.; Cabo-Bilbao, Aintzane; Goni-de-Cerio, Felipe; Molotkovsky, Julian G.; Patel, Dinshaw J.; Brown, Rhoderick E.; Malinina, Lucy

2013-01-01

It is shown that dimerization is promoted by glycolipid binding to human GLTP. The importance of dimer flexibility in wild-type protein is manifested by point mutation that ‘locks’ the dimer while diversifying ligand/protein adaptations. Human glycolipid transfer protein (hsGLTP) forms the prototypical GLTP fold and is characterized by a broad transfer selectivity for glycosphingolipids (GSLs). The GLTP mutation D48V near the ‘portal entrance’ of the glycolipid binding site has recently been shown to enhance selectivity for sulfatides (SFs) containing a long acyl chain. Here, nine novel crystal structures of hsGLTP and the SF-selective mutant complexed with short-acyl-chain monoSF and diSF in different crystal forms are reported in order to elucidate the potential functional roles of lipid-mediated homodimerization. In all crystal forms, the hsGLTP–SF complexes displayed homodimeric structures supported by similarly organized intermolecular interactions. The dimerization interface always involved the lipid sphingosine chain, the protein C-terminus (C-end) and α-helices 6 and 2, but the D48V mutant displayed a ‘locked’ dimer conformation compared with the hinge-like flexibility of wild-type dimers. Differences in contact angles, areas and residues at the dimer interfaces in the ‘flexible’ and ‘locked’ dimers revealed a potentially important role of the dimeric structure in the C-end conformation of hsGLTP and in the precise positioning of the key residue of the glycolipid recognition centre, His140. ΔY207 and ΔC-end deletion mutants, in which the C-end is shifted or truncated, showed an almost complete loss of transfer activity. The new structural insights suggest that ligand-dependent reversible dimerization plays a role in the function of human GLTP

The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis.

Science.gov (United States)

Sasaki, Hiroshi; Kubota, Keiko; Lee, Woo C; Ohtsuka, Jun; Kojima, Masaki; Iwata, So; Nakagawa, Atsushi; Takahashi, Kenji; Tanokura, Masaru

2012-07-01

Aspergilloglutamic peptidase from Aspergillus niger var. macrosporus (AGP) is one of the so-called pepstatin-insensitive acid endopeptidases, which are distinct from the well-studied aspartic peptidases. Among the known homologues of the glutamic peptidases, AGP is a unique two-chain enzyme with a light chain and a heavy chain bound non-covalently with each other, and thus is an interesting target for protein structure-function relationship studies. In this article, we report the crystal structure of a dimeric form of the enzyme at a resolution of 1.6 Å. This form has a unique structure in which the C-terminal region of the light chain of one of the molecules binds to the active site cleft of the other molecule like a part of a substrate. This form mimics the enzyme-activation product complex produced upon autoproteolysis, and provides a structural clue that could help to clarify the activation mechanism. This type of dimeric structure of a peptidase is here reported for the first time.

Association of atoms into universal dimers using an oscillating magnetic field.

Science.gov (United States)

Langmack, Christian; Smith, D Hudson; Braaten, Eric

2015-03-13

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.

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.

2008-01-01

  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...

Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state.

Science.gov (United States)

Nyblom, Maria; Poulsen, Hanne; Gourdon, Pontus; Reinhard, Linda; Andersson, Magnus; Lindahl, Erik; Fedosova, Natalya; Nissen, Poul

2013-10-04

The Na(+), K(+)-adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na(+) and K(+) across the plasma membrane--a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K(+)-bound or ouabain-blocked forms. We present the crystal structure of a Na(+)-bound Na(+), K(+)-ATPase as determined at 4.3 Å resolution. Compared with the K(+)-bound form, large conformational changes are observed in the α subunit whereas the β and γ subunit structures are maintained. The locations of the three Na(+) sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na(+) from IIIb through IIIa, followed by exchange of Na(+) for K(+) at sites I and II, is suggested.

Multiple regions of Harvey sarcoma virus RNA can dimerize in vitro.

Science.gov (United States)

Feng, Y X; Fu, W; Winter, A J; Levin, J G; Rein, A

1995-04-01

Retroviruses contain a dimeric RNA consisting of two identical molecules of plus-strand genomic RNA. The structure of the linkage between the two monomers is not known, but they are believed to be joined near their 5' ends. Darlix and coworkers have reported that transcripts of retroviral RNA sequences can dimerize spontaneously in vitro (see, for example, E. Bieth, C. Gabus, and J. L. Darlix, Nucleic Acids Res. 18:119-127, 1990). As one approach to identification of sequences which might participate in the linkage, we have mapped sequences derived from the 5' 378 bases of Harvey sarcoma virus (HaSV) RNA which can dimerize in vitro. We found that at least three distinct regions, consisting of nucleotides 37 to 229, 205 to 272, and 271 to 378, can form these dimers. Two of these regions contain nucleotides 205 to 226; computer analysis suggests that this region can form a stem-loop with an inverted repeat in the loop. We propose that this hypothetical structure is involved in dimer formation by these two transcripts. We also compared the thermal stabilities of each of these dimers with that of HaSV viral RNA. Dimers of nucleotides 37 to 229 and 205 to 272 both exhibited melting temperatures near that of viral RNA, while dimers of nucleotides 271 to 378 are quite unstable. We also found that dimers of nucleotides 37 to 378 formed at 37 degrees C are less thermostable than dimers of the same RNA formed at 55 degrees C. It seems possible that bases from all of these regions participate in the dimer linkage present in viral RNA.

Kinetics of thymine dimer excision in ultraviolet-irradiated human cells

International Nuclear Information System (INIS)

Ehmann, U.K.; Cook, K.H.; Friedberg, E.C.

1978-01-01

We have investigated the kinetics of the loss of thymine dimers from the acid-insoluble fraction of several ultraviolet (uv)-irradiated cultured human cell lines. Our results show that uv fluences between 10 and 40 J/m 2 produce an average of 21 to 85 x 10 5 thymine dimers per cell and an eventual maximal loss per cell of 12 to 20 x 10 5 thymine dimers. The time for half-maximal loss of dimers ranged from 12 to 22 h after uv irradiation. In contrast, the time for half-maximal repair synthesis of DNA measured by autoradiography was 4.5 h. This figure agrees well with reported half-maximal repair synthesis times, which range from 0.5 to 3.6 h based on our analysis. The discrepancy in the kinetics of the loss of thymine dimers from DNA and repair synthesis is discussed in terms of possible molecular mechanisms of thymine dimer excision in vivo and in terms of possible experimental artifacts

Role of cyclobutane dimers in UV-denaturation of DNA

International Nuclear Information System (INIS)

Zavil'gel'skij, G.B.; Zuev, A.V.

1978-01-01

UV irradiation of double-stranded DNA produces local denatured regions. The evidence presented indicates that these single-stranded regions arise from photoproducts other than pyrimidine dimers. The irradiation of T2 DNA at 8x10 4 erg/mm 2 (254 nm) produces 6-8% thymine dimers, amd Tsub(mel) drops by 12-14 deg C, accompanied by a significant broadening of the transition profile. The kinetics of denatured region formation and lowering Tsub(mel) corresponds to that of formation of crosslinkages and differs markedly from the kinetics of formation of cyclobutane pyrimidine dimers. Treatment of UV-irradiated DNA with light in the presence of yeast photoreactivating enzyme monomerizes almost all thymine dimers but does not change the Tsub(mel). Local denatured regions are detected in UV-irradiated DNA and are absent from AcPhM-sensibilized DNA, which contains 20-25% thymine dimers, as determined by the accridine orange fluorescence technique. S1 nuclease from Aspergillis oryzae produces single-strand breaks in UV-irradiated DNA of phage PM2 but is not active on AcPhM-treated PM2 DNA, which contains about 50 thymine dimers. It is supposed that the formation of a cyclobutane dimer only weakens the hydrogen bonds in the AT base pair rather than breaks them. Local denatured regions are thought to arise from the accumulation in UV-irradiated DNA (254 nm) of the sufficient number of photoproducts with impaired ability to base pairing

Localization of Dirac-like excitations in graphene in the presence of smooth inhomogeneous magnetic fields.

Science.gov (United States)

Roy, Pratim; Ghosh, Tarun Kanti; Bhattacharya, Kaushik

2012-02-08

The present paper discusses magnetic confinement of the Dirac excitations in graphene in the presence of inhomogeneous magnetic fields. In the first case a magnetic field directed along the z axis whose magnitude is proportional to 1/r is chosen. In the next case we choose a more realistic magnetic field which does not blow up at the origin and gradually fades away from the origin. The magnetic fields chosen do not have any finite/infinite discontinuity for finite values of the radial coordinate. The novelty of the two magnetic fields is related to the equations which are used to find the excited spectra of the excitations. It turns out that the bound state solutions of the two-dimensional hydrogen atom problem are related to the spectra of graphene excitations in the presence of the 1/r (inverse-radial) magnetic field. For the other magnetic field profile one can use the knowledge of the bound state spectrum of a two-dimensional cutoff Coulomb potential to dictate the excitation spectra of graphene. The spectrum of the graphene excitations in the presence of the inverse-radial magnetic field can be exactly solved while the other case cannot be. In the later case we give the localized solutions of the zero-energy states in graphene.

Family C 7TM receptor dimerization and activation

DEFF Research Database (Denmark)

Bonde, Marie Mi; Sheikh, Søren P; Hansen, Jakob Lerche

2006-01-01

The family C seven transmembrane (7TM) receptors constitutes a small and especially well characterized subfamily of the large 7TM receptor superfamily. Approximately 50% of current prescription drugs target 7TM receptors, this biologically important family represents the largest class of drug...... 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.......-targets today. It is well established that family C 7TM receptors form homo- or hetero-dimers on the cell surface of living cells. The large extra-cellular domains (ECD) have been crystallized as a dimer in the presence and absence of agonist. Upon agonist binding, the dimeric ECD undergoes large conformational...

Ab initio theoretical calculations of the electronic excitation energies of small water clusters.

Science.gov (United States)

Tachikawa, Hiroto; Yabushita, Akihiro; Kawasaki, Masahiro

2011-12-14

A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.

Characterization of oxygen dimer-enriched silicon detectors

CERN Document Server

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

2005-01-01

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.

First observation of bound excited states in the A/Z = 3 nucleus 15B

International Nuclear Information System (INIS)

Dobradi, Zs.; Sohler, D.; Azaiez, F.

2004-01-01

Complete text of publication follows. Structure of strongly neutron rich nuclei, especially of those lying close to the neutron drip line came into the focus of interest. Among others, the structure of neutron rich Boron isotopes also attracted attention in the last decade. The nuclei 15 B, 17 B and 19 B are particle stable, while the isotopes with even mass number are unstable against neutron emission. Even the neutron rich Boron isotopes with odd mass number have a low neutron binding energy, which is a sign of their weakly bound nature. As a common effect of the weak binding and of the large neutron excess, neutron skin or halo can also develop already in the isotope 15 B with A/Z = 3. Structure of the nucleus 15 B has been investigated by in-beam γ-spectroscopic study of the 9 Be + 36 S fragmentation reaction at GANIL, France. The emerging fragments were identified by use of a standard ΔE-time-of-fight technique with help of the SPEG spectrograph. γ-ray energies, intensities and γγ coincidences have been measured in coincidence with the projectile like fragments by 74 BaF 2 detectors of the Chateau de crystal. On the basis of the γ-spectroscopic information the level scheme presented in Figure 1 was constructed. The level scheme is shown together with the results of di rent model calculations. The common in predictions of these models is that all of them suggest a ground state band with the spin sequence 3/2 - , 5/2 - and 7/2 - , as well as a 1/2 - state, which involves a proton single particle excitation. The shell model calculations (SM) predict similar moments of inertia, strongly different from that of the antisymmetrized molecular dynamics calculations (AMD). The experimentally observed states can be assigned to the members of the rotational band on the basis of their decay properties. The experimental results confirm the predictions of the shell model. (author)

Dimeric Surfactants: Promising Ingredients of Cosmetics and Toiletries

Directory of Open Access Journals (Sweden)

Naveen Kumar

2013-11-01

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.

The dimerization of the yeast cytochrome bc1 complex is an early event and is independent of Rip1.

Science.gov (United States)

Conte, Annalea; Papa, Benedetta; Ferramosca, Alessandra; Zara, Vincenzo

2015-05-01

In Saccharomyces cerevisiae the mature cytochrome bc1 complex exists as an obligate homo-dimer in which each monomer consists of ten distinct protein subunits inserted into or bound to the inner mitochondrial membrane. Among them, the Rieske iron-sulfur protein (Rip1), besides its catalytic role in electron transfer, may be implicated in the bc1 complex dimerization. Indeed, Rip1 has the globular domain containing the catalytic center in one monomer while the transmembrane helix interacts with the adjacent monomer. In addition, the lack of Rip1 leads to the accumulation of an immature bc1 intermediate, only loosely associated with cytochrome c oxidase. In this study we have investigated the biogenesis of the yeast cytochrome bc1 complex using epitope tagged proteins to purify native assembly intermediates. We showed that the dimerization process is an early event during bc1 complex biogenesis and that the presence of Rip1, differently from previous proposals, is not essential for this process. We also investigated the multi-step model of bc1 assembly thereby lending further support to the existence of bona fide subcomplexes during bc1 maturation in the inner mitochondrial membrane. Finally, a new model of cytochrome bc1 complex assembly, in which distinct intermediates sequentially interact during bc1 maturation, has been proposed. Copyright © 2015 Elsevier B.V. All rights reserved.

2νββ decay of 76Ge into excited states with GERDA phase I

Science.gov (United States)

GERDA Collaboration; Agostini, M.; Allardt, M.; Bakalyarov, A. M.; Balata, M.; Barabanov, I.; Barros, N.; Baudis, L.; Bauer, C.; Becerici-Schmidt, N.; Bellotti, E.; Belogurov, S.; Belyaev, S. T.; Benato, G.; Bettini, A.; Bezrukov, L.; Bode, T.; Borowicz, D.; Brudanin, V.; Brugnera, R.; Budjáš, D.; Caldwell, A.; Cattadori, C.; Chernogorov, A.; D'Andrea, V.; Demidova, E. V.; di Vacri, A.; Domula, A.; Doroshkevich, E.; Egorov, V.; Falkenstein, R.; Fedorova, O.; Freund, K.; Frodyma, N.; Gangapshev, A.; Garfagnini, A.; Gooch, C.; Grabmayr, P.; Gurentsov, V.; Gusev, K.; Hegai, A.; Heisel, M.; Hemmer, S.; Heusser, G.; Hofmann, W.; Hult, M.; Inzhechik, L. V.; Janicskó Csáthy, J.; Jochum, J.; Junker, M.; Kazalov, V.; Kihm, T.; Kirpichnikov, I. V.; Kirsch, A.; Klimenko, A.; Knöpfle, K. T.; Kochetov, O.; Kornoukhov, V. N.; Kuzminov, V. V.; Laubenstein, M.; Lazzaro, A.; Lebedev, V. I.; Lehnert, B.; Liao, H. Y.; Lindner, M.; Lippi, I.; Lubashevskiy, A.; Lubsandorzhiev, B.; Lutter, G.; Macolino, C.; Majorovits, B.; Maneschg, W.; Medinaceli, E.; Mi, Y.; Misiaszek, M.; Moseev, P.; Nemchenok, I.; Palioselitis, D.; Panas, K.; Pandola, L.; Pelczar, K.; Pullia, A.; Riboldi, S.; Rumyantseva, N.; Sada, C.; Salathe, M.; Schmitt, C.; Schneider, B.; Schreiner, J.; Schulz, O.; Schwingenheuer, B.; Schönert, S.; Schütz, A.-K.; Selivanenko, O.; Shirchenko, M.; Simgen, H.; Smolnikov, A.; Stanco, L.; Stepaniuk, M.; Ur, C. A.; Vanhoefer, L.; Vasenko, A. A.; Veresnikova, A.; von Sturm, K.; Wagner, V.; Walter, M.; Wegmann, A.; Wester, T.; Wilsenach, H.; Wojcik, M.; Yanovich, E.; Zavarise, P.; Zhitnikov, I.; Zhukov, S. V.; Zinatulina, D.; Zuber, K.; Zuzel, G.

2015-11-01

Two neutrino double beta decay of {}76{Ge} to excited states of {}76{Se} has been studied using data from Phase I of the GERDA experiment. An array composed of up to 14 germanium detectors including detectors that have been isotopically enriched in {}76{Ge} was deployed in liquid argon. The analysis of various possible transitions to excited final states is based on coincidence events between pairs of detectors where a de-excitation γ ray is detected in one detector and the two electrons in the other. No signal has been observed and an event counting profile likelihood analysis has been used to determine Frequentist 90% C.L. bounds for three transitions: {0}{{g}.{{s}}.}+-{2}1+: {T}1/22ν \\gt 1.6× {10}23 yr, {0}{{g}.{{s}}.}+-{0}1+: {T}1/22ν \\gt 3.7× {10}23 yr and {0}{{g}.{{s}}.}+-{2}2+: {T}1/22ν \\gt 2.3× {10}23 yr. These bounds are more than two orders of magnitude larger than those reported previously. Bayesian 90% credibility bounds were extracted and used to exclude several models for the {0}{{g}.{{s}}.}+-{0}1+ transition.

Monitoring orientation and dynamics of membrane-bound melittin utilizing dansyl fluorescence.

Science.gov (United States)

Haldar, Sourav; Raghuraman, H; Chattopadhyay, Amitabha

2008-11-06

Melittin is a cationic hemolytic peptide isolated from the European honey bee, Apis mellifera. In spite of a number of studies, there is no consensus regarding the orientation of melittin in membranes. In this study, we used a melittin analogue that is covalently labeled at its amino terminal (Gly-1) with the environment-sensitive 1-dimethylamino-5-sulfonylnaphthalene (dansyl) group to obtain information regarding the orientation and dynamics of the amino terminal region of membrane-bound melittin. Our results show that the dansyl group in Dns-melittin exhibits red edge excitation shift in vesicles of 1,2-dioleoyl-sn-glycero-3-phosphocholine, implying its localization in a motionally restricted region of the membrane. This is further supported by wavelength-dependent anisotropy and lifetime changes and time-resolved emission spectra characterized by dynamic Stokes shift, which indicates relatively slow solvent relaxation in the excited state. Membrane penetration depth analysis using the parallax method shows that the dansyl group is localized at a depth of approximately 18 A from the center of the bilayer in membrane-bound Dns-melittin. Further analysis of dansyl and tryptophan depths in Dns-melittin shows that the tilt angle between the helix axis of membrane-bound melittin and the bilayer normal is approximately 70 degrees. Our results therefore suggest that melittin adopts a pseudoparallel orientation in DOPC membranes at low concentration.

Two Populations Mean-Field Monomer-Dimer Model

Science.gov (United States)

Alberici, Diego; Mingione, Emanuele

2018-04-01

A two populations mean-field monomer-dimer model including both hard-core and attractive interactions between dimers is considered. The pressure density in the thermodynamic limit is proved to satisfy a variational principle. A detailed analysis is made in the limit of one population is much smaller than the other and a ferromagnetic mean-field phase transition is found.

Evaluation of Serum D-dimer Levels in Children with Pneumonia

Directory of Open Access Journals (Sweden)

Nilgün Selçuk Duru

2016-03-01

Full Text Available Aim: The aim of this study was to investigate the relationship of plasma D-dimer levels with duration of hospitalization and radiological and laboratory findings in patients with pneumonia. Methods: Forty-seven patients with pneumonia (31 boys and 16 girls, mean age: 4.2±4.7 years were included in the study. The patients were divided into two groups according to duration of hospitalization and three groups according to radiological findings. D-dimer and other laboratory findings were compared between the groups. Results: The mean serum D-dimer level was 1333.5±1364.4 ng/L. There was no statistically significant difference in D-dimer, leukocyte, erythrocyte sedimentation rate (ESR and C-reactive protein (CRP between the groups divided according to duration of hospitalization. In addition, there was no statistically difference in D-dimer levels between the groups divided according to radiological findings. Age, percentage of neutrophils, ESR and fibrinogen levels were higher in patients with lobar pneumonia when compared with the other groups and CRP level was higher in lobar pneumonia group when compared to interstitial pneumonia group. D-dimer levels were negatively correlated with age and positively correlated with ESR, CRP, and fibrinogen. Conclusion: In our study, D-dimer levels were high in patient with pneumonia. Further studies with a larger number of patients are necessary to determine the role of D-dimer levels as an acutephase reactant in patients with pneumonia

Electron transfer reactions induced by the triplet state of thiacarbocyanine dimers

International Nuclear Information System (INIS)

Chibisov, Alexander K.; Slavnova, Tatyana D.; Goerner, Helmut

2004-01-01

The photoinduced electron transfer between either cationic 5,5 ' -dichloro-3,3 ' ,9-triethylthiacarbocyanine (1) or a structurally similar anionic dye (2) and appropriate donors, e.g. ascorbic acid, and acceptors, e.g. methyl viologen, was studied by ns-laser photolysis. In aqueous solution the dyes in the ground state are present as an equilibrated mixture of dimers and monomers, whereas the triplet state is mainly populated from dimers. The triplet states of both dimers and monomers are quenched by electron donors or acceptors and the rate constant for quenching is generally 2-4 times higher for dimers than for monomers. The kinetics of triplet decay and radical formation and decay as a result of primary and secondary electron transfer were analyzed. While the one-electron reduced dimer decays due to back reactions, the one-electron oxidized dimer rapidly dissociates into the monomer and the monomeric dye radical. For the dimeric dye/donor/acceptor systems the primary photoinduced electron transfer occurs either from the donor or to the acceptor yielding the dimeric dye radicals. The one-electron reduced dimer can be efficiently oxidized by acceptors, e.g. the rate constant for reaction of the dimeric dye radical of 1 with methyl viologen (photoreductive pathway of sensitization) is 1.6x10 9 M -1 s -1 . The photooxidative pathway of sensitization is more complicated; after dissociation of the dimeric dye radical, the monomeric dye radical is reduced in a secondary electron transfer from ascorbic acid, e.g. with a rate constant of 1x10 9 M -1 s -1 for 2, yielding the monomer. On increasing the donor concentration the photooxidative pathway of sensitization is switched to a photoreductive one

Tunneling anisotropic magnetoresistance via molecular π orbitals of Pb dimers

Science.gov (United States)

Schöneberg, Johannes; Ferriani, Paolo; Heinze, Stefan; Weismann, Alexander; Berndt, Richard

2018-01-01

Pb dimers on a ferromagnetic surface are shown to exhibit large tunneling anisotropic magnetoresistance (TAMR) due to molecular π orbitals. Dimers oriented differently with respect to the magnetization directions of a ferromagnetic Fe double layer on W(110) were made with a scanning tunneling microscope. Depending on the dimer orientations, TAMR is absent or as large as 20% at the Fermi level. General arguments and first-principles calculations show that mixing of molecular orbitals due to spin-orbit coupling, which leads to TAMR, is maximal when the magnetization is oriented parallel to the dimer axis.

Crystal structure of inhibitor of growth 4 (ING4) dimerization domain reveals functional organization of ING family of chromatin-binding proteins.

Science.gov (United States)

Culurgioni, Simone; Muñoz, Inés G; Moreno, Alberto; Palacios, Alicia; Villate, Maider; Palmero, Ignacio; Montoya, Guillermo; Blanco, Francisco J

2012-03-30

The protein ING4 binds to histone H3 trimethylated at Lys-4 (H3K4me3) through its C-terminal plant homeodomain, thus recruiting the HBO1 histone acetyltransferase complex to target promoters. The structure of the plant homeodomain finger bound to an H3K4me3 peptide has been described, as well as the disorder and flexibility in the ING4 central region. We report the crystal structure of the ING4 N-terminal domain, which shows an antiparallel coiled-coil homodimer with each protomer folded into a helix-loop-helix structure. This arrangement suggests that ING4 can bind simultaneously two histone tails on the same or different nucleosomes. Dimerization has a direct impact on ING4 tumor suppressor activity because monomeric mutants lose the ability to induce apoptosis after genotoxic stress. Homology modeling based on the ING4 structure suggests that other ING dimers may also exist.

From Soil to Structure, a Novel Dimeric β-Glucosidase Belonging to Glycoside Hydrolase Family 3 Isolated from Compost Using Metagenomic Analysis

Science.gov (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.

2013-01-01

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. PMID:23580647

Crystal structure of product-bound complex of UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3.

Science.gov (United States)

Pampa, K J; Lokanath, N K; Girish, T U; Kunishima, N; Rai, V R

2014-10-24

UDP-N-acetyl-d-mannosamine dehydrogenase (UDP-d-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-d-mannosamine (UDP-d-ManNAc) to Uridine-diphospho-N-acetyl-d-mannosaminuronic acid (UDP-d-ManNAcA) through twofold oxidation of NAD(+). In order to reveal the structural features of the Pyrococcus horikoshii UDP-d-ManNAcADH, we have determined the crystal structure of the product-bound enzyme by X-ray diffraction to resolution of 1.55Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-d-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed. Copyright © 2014 Elsevier Inc. All rights reserved.

Low-pressure appraoch to the formation and study of exciplex systems

International Nuclear Information System (INIS)

Sanzone, G.

1977-11-01

Studies on the formation and properties of new materials for high-energy, gas-phase lasers are described. Attention is directed mainly to systems having bound excited states but unbound ground states. An important class of such excimer/exciplex systems has a van der Waals dimer/oligomer as its ground state. This research attempts to probe the relative rates of electron pumping of excited-state manifolds and the preferentially pumped vibronic states within each manifold. Reactive quenching of emission, resonant self-absorption of laser emissions, and collision- and noncollision-induced intersystem crossing are also considered. 11 figures, 2 tables

Subsurface dimerization in III-V semiconductor (001) surfaces

DEFF Research Database (Denmark)

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

2001-01-01

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....

The water dimer II: Theoretical investigations

Energy Technology Data Exchange (ETDEWEB)

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

2018-03-29

As the archetype of hydrogen bonding between water molecules, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the theoretical advances using electronic structure methods pertaining to the structure, hydrogen bonding and vibrational spectroscopy of the water dimer as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interaction in clusters and liquid water.

Role of Feshbach resonances in enhancing the production of deeply bound ultracold LiRb molecules with laser pulses

Science.gov (United States)

Gacesa, Marko; Ghosal, Subhas; Côté, Robin

2010-03-01

We investigate the possibility of forming deeply bound LiRb molecules in a two-color photoassociation experiment. Ultracold ^6Li and ^87Rb atoms colliding in the vicinity of a magnetic Feshbach resonance are photoassociated into an excited electronic state. A wavepacket is then formed by exciting a few vibrational levels of the excited state and allowed to propagate. We calculate the time-dependent overlaps between the wave packet and the lowest vibrational levels of the ground state. After the optimal overlap is obtained we use the second laser pulse to dump the wave packet and efficiently populate the deeply bound ro-vibrational levels of ^6Li^87Rb in the ground state. The resulting combination of Feshbach-optimized photoassociation (FOPA) with the time-dependent pump-dump approach will produce a large number of stable ultracold molecules in the ground state. This technique is general and applicable to other systems.

In Situ Structural Characterization of Ferric Iron Dimers in Aqueous Solutions

DEFF Research Database (Denmark)

Zhu, Mengqiang; Puls, Brendan W.; Frandsen, Cathrine

2013-01-01

The structure of ferric iron (Fe3+) dimers in aqueous solutions has long been debated. In this work, we have determined the dimer structure in situ in aqueous solutions using extended X-ray absorption fine structure (EXAFS) spectroscopy. An Fe K-edge EXAFS analysis of 0.2 M ferric nitrate solutions...... at pH 1.28–1.81 identified a Fe–Fe distance at ∼3.6 Å, strongly indicating that the dimers take the μ-oxo form. The EXAFS analysis also indicates two short Fe–O bonds at ∼1.80 Å and ten long Fe–O bonds at ∼2.08 Å, consistent with the μ-oxo dimer structure. The scattering from the Fe–Fe paths interferes...... confirmed by Mössbauer analyses of analogous quick frozen solutions. This work also explores the electronic structure and the relative stability of the μ-oxo dimer in a comparison to the dihydroxo dimer using density function theory (DFT) calculations. The identification of such dimers in aqueous solutions...

Effects of breakup of weakly bound projectile and neutron transfer on fusion reactions around Coulomb barrier

International Nuclear Information System (INIS)

Lin, C.J.; Zhang, H.Q.; Yang, F.; Ruan, M.; Liu, Z.H.; Wu, Y.W.; Wu, X.K.; Zhou, P.; Zhang, C.L.; Zhang, G.L.; An, G.P.; Jia, H.M.; Xu, X.X.

2007-01-01

The excitation functions of quasielastic and elastic scattering at backward angles have been measured for the systems of 16 O+ 152 Sm, 6,7 Li+ 208 Pb and 32 S+ 90,96 Zr. The barrier distributions are extracted from these measured excitation functions and compared with the corresponding fusion barrier distributions. Except some details, the barrier distributions derived from the data of fusion and quasielastic/elastic scattering are almost the same for the tightly bound reaction systems. For the reaction systems with weakly bound projectile, the barrier distributions extracted from quasielastic scattering are obviously different from the fusion barrier distributions. However, the barrier distributions extracted from the excitation functions of the quasielastic scattering plus breakup are almost the same as the one extracted from the complete fusion data. This result means that barrier distribution not only bears the information of nuclear structures but also contains the knowledge of reaction mechanisms. Our results show that the complete fusion of the weakly bound projectile with heavy target is suppressed at the above barrier energies as compared with the model predictions. In addition, the measured barrier distribution of 32 S+ 96 Zr is broaden and extends to lower energy than in the case of 32 S+ 90 Zr due to the coupling of neutron transfer with positive Q-values, which result in a significant enhancement of fusion cross sections at the subbarrier energies

Synthesis and Isotope Effects on the Excited State Properties of NN Bound Complexes

NARCIS (Netherlands)

Soman, Suraj; Younis, Hamid M.; Browne, Wesley R.; Vos, Johannes G.; Pryce, Mary T.

2017-01-01

A versatile approach to the preparation of [Ir(LL)(2)Cl-2](PF6) type complexes is reported, in which LL is an (NN)-N- bound polypyridyl ligand [X(2)bpy, X(2)phen, where X = H-, CH3-, (CH3)(3)C-, or phenyl-, and bpy = 2,2-bipyridyl, phen = 1,10-phenanthroline] as well as their deuterated analogues.

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains.

Science.gov (United States)

Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S E; Prabhakar, Shyam; Jauch, Ralf

2015-05-27

The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins.

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

Science.gov (United States)

Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S. E.; Prabhakar, Shyam; Jauch, Ralf

2015-01-01

The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins. PMID:26013289

Fermionic bound states in distinct kinklike backgrounds

Energy Technology Data Exchange (ETDEWEB)

Bazeia, D. [Universidade Federal da Paraiba, Departamento de Fisica, Joao Pessoa, Paraiba (Brazil); Mohammadi, A. [Universidade Federal de Campina Grande, Departamento de Fisica, Caixa Postal 10071, Campina Grande, Paraiba (Brazil)

2017-04-15

This work deals with fermions in the background of distinct localized structures in the two-dimensional spacetime. Although the structures have a similar topological character, which is responsible for the appearance of fractionally charged excitations, we want to investigate how the geometric deformations that appear in the localized structures contribute to the change in the physical properties of the fermionic bound states. We investigate the two-kink and compact kinklike backgrounds, and we consider two distinct boson-fermion interactions, one motivated by supersymmetry and the other described by the standard Yukawa coupling. (orig.)

NLIE of Dirichlet sine-Gordon model for boundary bound states

International Nuclear Information System (INIS)

Ahn, Changrim; Bajnok, Zoltan; Palla, Laszlo; Ravanini, Francesco

2008-01-01

We investigate boundary bound states of sine-Gordon model on the finite-size strip with Dirichlet boundary conditions. For the purpose we derive the nonlinear integral equation (NLIE) for the boundary excited states from the Bethe ansatz equation of the inhomogeneous XXZ spin 1/2 chain with boundary imaginary roots discovered by Saleur and Skorik. Taking a large volume (IR) limit we calculate boundary energies, boundary reflection factors and boundary Luescher corrections and compare with the excited boundary states of the Dirichlet sine-Gordon model first considered by Dorey and Mattsson. We also consider the short distance limit and relate the IR scattering data with that of the UV conformal field theory

Topological triplon modes and bound states in a Shastry-Sutherland magnet

Science.gov (United States)

McClarty, P. A.; Krüger, F.; Guidi, T.; Parker, S. F.; Refson, K.; Parker, A. W.; Prabhakaran, D.; Coldea, R.

2017-08-01

The twin discoveries of the quantum Hall effect, in the 1980s, and of topological band insulators, in the 2000s, were landmarks in physics that enriched our view of the electronic properties of solids. In a nutshell, these discoveries have taught us that quantum mechanical wavefunctions in crystalline solids may carry nontrivial topological invariants which have ramifications for the observable physics. One of the side effects of the recent topological insulator revolution has been that such physics is much more widespread than was appreciated ten years ago. For example, while topological insulators were originally studied in the context of electron wavefunctions, recent work has initiated a hunt for topological insulators in bosonic systems: in photonic crystals, in the vibrational modes of crystals, and in the excitations of ordered magnets. Using inelastic neutron scattering along with theoretical calculations, we demonstrate that, in a weak magnetic field, the dimerized quantum magnet SrCu2(BO3)2 is a bosonic topological insulator with topologically protected chiral edge modes of triplon excitations.

Spin-polarized spin excitation spectroscopy

International Nuclear Information System (INIS)

Loth, Sebastian; Lutz, Christopher P; Heinrich, Andreas J

2010-01-01

We report on the spin dependence of elastic and inelastic electron tunneling through transition metal atoms. Mn, Fe and Cu atoms were deposited onto a monolayer of Cu 2 N on Cu(100) and individually addressed with the probe tip of a scanning tunneling microscope. Electrons tunneling between the tip and the substrate exchange energy and spin angular momentum with the surface-bound magnetic atoms. The conservation of energy during the tunneling process results in a distinct onset threshold voltage above which the tunneling electrons create spin excitations in the Mn and Fe atoms. Here we show that the additional conservation of spin angular momentum leads to different cross-sections for spin excitations depending on the relative alignment of the surface spin and the spin of the tunneling electron. For this purpose, we developed a technique for measuring the same local spin with a spin-polarized and a non-spin-polarized tip by exchanging the last apex atom of the probe tip between different transition metal atoms. We derive a quantitative model describing the observed excitation cross-sections on the basis of an exchange scattering process.

An excited-state approach within full configuration interaction quantum Monte Carlo

International Nuclear Information System (INIS)

Blunt, N. S.; Smart, Simon D.; Booth, George H.; Alavi, Ali

2015-01-01

We present a new approach to calculate excited states with the full configuration interaction quantum Monte Carlo (FCIQMC) method. The approach uses a Gram-Schmidt procedure, instantaneously applied to the stochastically evolving distributions of walkers, to orthogonalize higher energy states against lower energy ones. It can thus be used to study several of the lowest-energy states of a system within the same symmetry. This additional step is particularly simple and computationally inexpensive, requiring only a small change to the underlying FCIQMC algorithm. No trial wave functions or partitioning of the space is needed. The approach should allow excited states to be studied for systems similar to those accessible to the ground-state method due to a comparable computational cost. As a first application, we consider the carbon dimer in basis sets up to quadruple-zeta quality and compare to existing results where available

Radiation chemistry of aromatic dimer radical cations

International Nuclear Information System (INIS)

Okamoto, Kazumasa; Tagawa, Seiichi

2009-01-01

π-π Interactions of aromatic molecules are paid attention much in many fields, especially biology, chemistry, and applied physics, represented as protein, DNA, electron donor-accepter complexes, charge transfers, and self assembly molecules. Aromatic molecules including benzene rings are the simplest case to study the π-π interactions. To interpret the charge resonance (CR) structure in the dimer radical cations, spectroscopic and ESR methods have been carried out. The spectroscopic study on the dimer radical ion of molecules with two chromophores would be profitable to identify the electronic and configurational properties. In this article, dynamics of the dimer radical cation of benzenes, polystyrenes, and resist polymers is described on the basis of direct observation of CR band by the nanosecond pulse radiolysis and low temperature γ-radiolysis methods. (author)

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

2011-12-31

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.

Energy transfer and electron transfer in dimers and polymers of porphyrin and phthalocyanines: from the liquid phase to Langmuir-Blodgett films

International Nuclear Information System (INIS)

Lipskier, Jean-Francois

1991-01-01

The understanding of phenomena of photo-induced transfer of energy and of electron between chromophores belonging to a same supra-molecular entity is necessary for the design and fabrication of molecule devices performing the conversion of a light signal into electric signal or chemical potential. As porphyrin oligomers and phthalocyanine oligomers are examples of interest for the systematic study of parameters governing these processes, the first part of this research thesis addresses the study of dimers and trimers bound by covalent bridges. The second part addresses the study of physical-chemical properties of complexes bound by the Van der Waals interaction as well as by the Coulomb attraction. An extension to Langmuir-Blodgett films is proposed, and the properties of complexes organised in thin films according to this methodology are compared with those of their homologues in solution [fr

Charge-resonance excitations in symmetric molecules - Comparison of linear response DFT with CC3 for the excited states of a model dimer

DEFF Research Database (Denmark)

Kuhlman, Thomas Scheby; Mikkelsen, Kurt V.; Møller, Klaus Braagaard

2009-01-01

to a reference CC3 calculation revealing a better description of the excited states by CAM-B3LYP than that of B3LYP. The Λ parameter introduced by Peach et al. [M.J.G. Peach, P. Benfield, T. Helgaker, D.J. Tozer, J. Chem. Phys. 128 (2008) 044118] does not always reveal the problematic charge-resonance states...

Analysis of hepatitis C virus RNA dimerization and core–RNA interactions

Science.gov (United States)

Ivanyi-Nagy, Roland; Kanevsky, Igor; Gabus, Caroline; Lavergne, Jean-Pierre; Ficheux, Damien; Penin, François; Fossé, Philippe; Darlix, Jean-Luc

2006-01-01

The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3′-untranslated region (3′-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623–2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3′-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus. PMID:16707664

Analysis of hepatitis C virus RNA dimerization and core-RNA interactions.

Science.gov (United States)

Ivanyi-Nagy, Roland; Kanevsky, Igor; Gabus, Caroline; Lavergne, Jean-Pierre; Ficheux, Damien; Penin, François; Fossé, Philippe; Darlix, Jean-Luc

2006-01-01

The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3'-untranslated region (3'-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623-2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3'-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus.

Depletion of the excited state population in negative ions using laser photodetachment in a gas-filled RF quadrupole ion guide

Energy Technology Data Exchange (ETDEWEB)

Lindahl, A O; Hanstorp, D [Department of Physics, University of Gothenburg, SE-412 96 Gothenburg (Sweden); Forstner, O [VERA Laboratory, Faculty of Physics, Universitaet Wien, Vienna (Austria); Gibson, N D [Department of Physics and Astronomy, Denison University, Granville, OH 43023 (United States); Gottwald, T; Wendt, K [Institut fuer Physik, Johannes Gutenberg-Universitaet, Mainz, 55099 Mainz (Germany); Havener, C C; Liu, Y, E-mail: Dag.Hanstorp@physics.gu.s [Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6368 (United States)

2010-06-14

The depopulation of excited states in beams of negatively charged carbon and silicon ions was demonstrated using collisional detachment and laser photodetachment in a radio-frequency quadrupole ion guide filled with helium. The high-lying, loosely bound {sup 2}D excited state in C{sup -} was completely depleted through collisional detachment alone, which was quantitatively determined within 6%. For Si{sup -} the combined signal from the population in the {sup 2}P and {sup 2}D excited states was only partly depleted through collisions in the cooler. The loosely bound {sup 2}P state was likely to be completely depopulated, and the more tightly bound {sup 2}D state was partly depopulated through collisions. 98(2)% of the remaining {sup 2}D population was removed by photodetachment in the cooler using less than 2 W laser power. The total reduction of the excited population in Si{sup -}, including collisional detachment and photodetachment, was estimated to be 99(1)%. Employing this novel technique to produce a pure ground state negative ion beam offers possibilities of enhancing selectivity, as well as accuracy, in high-precision experiments on atomic as well as molecular negative ions.

Quantum dissipative dynamics and decoherence of dimers on helium droplets

International Nuclear Information System (INIS)

Schlesinger, Martin

2011-01-01

In this thesis, quantum dynamical simulations are performed in order to describe the vibrational motion of diatomic molecules in a highly quantum environment, so-called helium droplets. We aim to reproduce and explain experimental findings which were obtained from dimers on helium droplets. Nanometer-sized helium droplets contain several thousands of 4 He atoms. They serve as a host for embedded atoms or molecules and provide an ultracold ''refrigerator'' for them. Spectroscopy of molecules in or on these droplets reveals information on both the molecule and the helium environment. The droplets are known to be in the superfluid He II phase. Superfluidity in nanoscale systems is a steadily growing field of research. Spectra obtained from full quantum simulations for the unperturbed dimer show deviations from measurements with dimers on helium droplets. These deviations result from the influence of the helium environment on the dimer dynamics. In this work, a well-established quantum optical master equation is used in order to describe the dimer dynamics effectively. The master equation allows to describe damping fully quantum mechanically. By employing that equation in the quantum dynamical simulation, one can study the role of dissipation and decoherence in dimers on helium droplets. The effective description allows to explain experiments with Rb 2 dimers on helium droplets. Here, we identify vibrational damping and associated decoherence as the main explanation for the experimental results. The relation between decoherence and dissipation in Morse-like systems at zero temperature is studied in more detail. The dissipative model is also used to investigate experiments with K 2 dimers on helium droplets. However, by comparing numerical simulations with experimental data, one finds that further mechanisms are active. Here, a good agreement is obtained through accounting for rapid desorption of dimers. We find that decoherence occurs in the electronic manifold of the

Photon Propagation through Linearly Active Dimers

Directory of Open Access Journals (Sweden)

José Delfino Huerta Morales

2017-06-01

Full Text Available We provide an analytic propagator for non-Hermitian dimers showing linear gain or losses in the quantum regime. In particular, we focus on experimentally feasible realizations of the PT -symmetric dimer and provide their mean photon number and second order two-point correlation. We study the propagation of vacuum, single photon spatially-separable, and two-photon spatially-entangled states. We show that each configuration produces a particular signature that might signal their possible uses as photon switches, semi-classical intensity-tunable sources, or spatially entangled sources to mention a few possible applications.

Mutability of bacteriophage M13 by ultraviolet light: role of pyrimidine dimers

International Nuclear Information System (INIS)

Schaaper, R.M.; Glickman, B.W.

1982-01-01

The role of pyrimidine dimers in mutagenesis by ultraviolet light was examined by measuring the UV-induced reversion of six different bacteriophage M13 amber mutants for which the neighboring DNA sequences are known. The mutational response at amber (TAG) codons preceded by a guanine or adenine (where no pyrimidine dimer can be formed) were compared with those preceded by thymine or cytosine (where dimer formation is possible). Equivalent levels of UV-induced mutagenesis were observed at both kinds of sites. This observation demonstrates that there is no requirement for a pyrimidine dimer directly at the site of UV-induced mutation in this single-stranded DNA phage. UV irradiation of the phage was also performed in the presence of Ag + ions, which specifically sensitize the DNA to dimer formation. The two methods of irradiation, when compared at equal survival levels (and presumably equal dimer frequencies), produced equivalent frequencies of reversion of the amber phage. We believe these results indicate that while the presence of pyrimidine dimers may be a prerequisite for UV mutagenesis, the actual mutagenic event can occur at a site some distance removed from a dimer. (orig.)

Fiber optic D dimer biosensor

Science.gov (United States)

Glass, Robert S.; Grant, Sheila A.

1999-01-01

A fiber optic sensor for D dimer (a fibrinolytic product) can be used in vivo (e.g., in catheter-based procedures) for the diagnosis and treatment of stroke-related conditions in humans. Stroke is the third leading cause of death in the United States. It has been estimated that strokes and stroke-related disorders cost Americans between $15-30 billion annually. Relatively recently, new medical procedures have been developed for the treatment of stroke. These endovascular procedures rely upon the use of microcatheters. These procedures could be facilitated with this sensor for D dimer integrated with a microcatheter for the diagnosis of clot type, and as an indicator of the effectiveness, or end-point of thrombolytic therapy.

Singlet fission in pentacene dimers

Science.gov (United States)

Zirzlmeier, Johannes; Lehnherr, Dan; Coto, Pedro B.; Chernick, Erin T.; Casillas, Rubén; Basel, Bettina S.; Thoss, Michael; Tykwinski, Rik R.; Guldi, Dirk M.

2015-01-01

Singlet fission (SF) has the potential to supersede the traditional solar energy conversion scheme by means of boosting the photon-to-current conversion efficiencies beyond the 30% Shockley–Queisser limit. Here, we show unambiguous and compelling evidence for unprecedented intramolecular SF within regioisomeric pentacene dimers in room-temperature solutions, with observed triplet quantum yields reaching as high as 156 ± 5%. Whereas previous studies have shown that the collision of a photoexcited chromophore with a ground-state chromophore can give rise to SF, here we demonstrate that the proximity and sufficient coupling through bond or space in pentacene dimers is enough to induce intramolecular SF where two triplets are generated on one molecule. PMID:25858954

Optical properties of electrically connected plasmonic nanoantenna dimer arrays

Science.gov (United States)

Zimmerman, Darin T.; Borst, Benjamin D.; Carrick, Cassandra J.; Lent, Joseph M.; Wambold, Raymond A.; Weisel, Gary J.; Willis, Brian G.

2018-02-01

We fabricate electrically connected gold nanoantenna arrays of homodimers and heterodimers on silica substrates and present a systematic study of their optical properties. Electrically connected arrays of plasmonic nanoantennas make possible the realization of novel photonic devices, including optical sensors and rectifiers. Although the plasmonic response of unconnected arrays has been studied extensively, the present study shows that the inclusion of nanowire connections modifies the device response significantly. After presenting experimental measurements of optical extinction for unconnected dimer arrays, we compare these to measurements of dimers that are interconnected by gold nanowire "busbars." The connected devices show the familiar dipole response associated with the unconnected dimers but also show a second localized surface plasmon resonance (LSPR) that we refer to as the "coupled-busbar mode." Our experimental study also demonstrates that the placement of the nanowire along the antenna modifies the LSPR. Using finite-difference time-domain simulations, we confirm the experimental results and investigate the variation of dimer gap and spacing. Changing the dimer gap in connected devices has a significantly smaller effect on the dipole response than it does in unconnected devices. On the other hand, both LSPR modes respond strongly to changing the spacing between devices in the direction along the interconnecting wires. We also give results for the variation of E-field strength in the dimer gap, which will be important for any working sensor or rectenna device.

Metal membrane with dimer slots as a universal polarizer

Science.gov (United States)

Zhukovsky, Sergej; Zalkovskij, Maksim; Malureanu, Radu; Kremers, Christian; Chigrin, Dmitry; Tang, Peter T.; Jepsen, Peter U.; Lavrinenko, Andrei V.

2014-03-01

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 electromagnetic response of an arbitrary dimer based on the Green functions approach. The theory confirms that a great variety of polarization properties, such as birefringence, chirality and elliptical dichroism, can be achieved in a metal layer with such slot-dimer patterning (i.e. in a metasurface). Optical properties of the metasurface can be extensively tuned by varying the geometry (shape and dimensions) of the dimer, for example, by adjusting the sizes and mutual placement of the slots (e.g. inter-slot distance and alignment angle). Three basic shapes of dimers are analyzed: II-shaped (parallel slots), V-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 UV lithography with subsequent Ni growth. Such metasurfaces were characterized using time-domain THz spectroscopy. The samples exhibit pronounced optical activity (500 degrees per wavelength) and high transmission: even though the slots cover only 4.3 % of the total membrane area the amplitude transmission reaches 0.67 at the resonance frequency 0.56 THz.

Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA: identification of a putative ligand binding pocket at the dimeric interface

Directory of Open Access Journals (Sweden)

Chittori Sagar

2012-10-01

Full Text Available Abstract Background Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA and phosphotransacetylase (Pta, key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism. Results Here we report kinetic characterization of S. typhimurium AckA (StAckA and structures of its unliganded (Form-I, 2.70 Å resolution and citrate-bound (Form-II, 1.90 Å resolution forms. The enzyme showed broad substrate specificity with kcat/Km in the order of acetate > propionate > formate. Further, the Km for acetyl-phosphate was significantly lower than for acetate and the enzyme could catalyze the reverse reaction (i.e. ATP synthesis more efficiently. ATP and Mg2+ could be substituted by other nucleoside 5′-triphosphates (GTP, UTP and CTP and divalent cations (Mn2+ and Co2+, respectively. Form-I StAckA represents the first structural report of an unliganded AckA. StAckA protomer consists of two domains with characteristic βββαβαβα topology of ASKHA superfamily of proteins. These domains adopt an intermediate conformation compared to that of open and closed forms of ligand-bound Methanosarcina thermophila AckA (MtAckA. Spectroscopic and structural analyses of StAckA further suggested occurrence of inter-domain motion upon ligand-binding. Unexpectedly, Form-II StAckA structure showed a drastic change in the conformation of residues 230–300 compared to that of Form-I. Further investigation revealed electron density corresponding to a citrate molecule in a pocket located at the dimeric interface of Form-II StAckA. Interestingly, a similar dimeric interface pocket lined with largely conserved residues could be identified in Form-I StAckA as well as in other enzymes homologous to AckA suggesting that ligand binding at this pocket may influence the function of these

Analytical study of avian reticuloendotheliosis virus dimeric RNA generated in vivo and in vitro.

Science.gov (United States)

Darlix, J L; Gabus, C; Allain, B

1992-12-01

The retroviral genome consists of two identical RNA molecules associated at their 5' ends by a stable structure called the dimer linkage structure. The dimer linkage structure, while maintaining the dimer state of the retroviral genome, might also be involved in packaging and reverse transcription, as well as recombination during proviral DNA synthesis. To study the dimer structure of the retroviral genome and the mechanism of dimerization, we analyzed features of the dimeric genome of reticuloendotheliosis virus (REV) type A and identified elements required for its dimerization. Here we report that the REV dimeric genome extracted from virions and infected cells, as well as that synthesized in vitro, is more resistant to heat denaturation than avian sarcoma and leukemia virus, murine leukemia virus, or human immunodeficiency virus type 1 dimeric RNA. The minimal domain required to form a stable REV RNA dimer in vitro was found to map between positions 268 and 452 (KpnI and SalI sites), thus corresponding to the E encapsidation sequence (J. E. Embretson and H. M. Temin, J. Virol. 61:2675-2683, 1987). In addition, both the 5' and 3' halves of E are necessary in cis for RNA dimerization and the extent of RNA dimerization is influenced by viral sequences flanking E. Rapid and efficient dimerization of REV RNA containing gag sequences in addition to the E sequences and annealing of replication primer tRNA(Pro) to the primer-binding site necessitate the nucleocapsid protein.

Dynamic nuclear polarization of membrane proteins: covalently bound spin-labels at protein–protein interfaces

International Nuclear Information System (INIS)

Wylie, Benjamin J.; Dzikovski, Boris G.; Pawsey, Shane; Caporini, Marc; Rosay, Melanie; Freed, Jack H.; McDermott, Ann E.

2015-01-01

We demonstrate that dynamic nuclear polarization of membrane proteins in lipid bilayers may be achieved using a novel polarizing agent: pairs of spin labels covalently bound to a protein of interest interacting at an intermolecular interaction surface. For gramicidin A, nitroxide tags attached to the N-terminal intermolecular interface region become proximal only when bimolecular channels forms in the membrane. We obtained signal enhancements of sixfold for the dimeric protein. The enhancement effect was comparable to that of a doubly tagged sample of gramicidin C, with intramolecular spin pairs. This approach could be a powerful and selective means for signal enhancement in membrane proteins, and for recognizing intermolecular interfaces

Excitation-energy-dependent resonances in x-ray emissions under near-threshold electron excitation of the Ce 3d and 4d levels

International Nuclear Information System (INIS)

Chamberlain, M.B.; Baun, W.L.

1975-01-01

Soft x-ray appearance potential spectra of the 3d and 4d levels of polycrystalline cerium metal are reported in this paper. Resonant x-ray emissions are observed when the electron-excitation energy sweeps through the ionization energies of the 3d and 4d levels. The resonant x rays excited at the 3d-level onsets are considerably more intense, and are excited at a lower electron-excitation energy than the 3d-series characteristic x rays. In the neighborhood of the 4d-electron thresholds, four line-like structures extend to approx.8 eV below the 4d-electron binding energies, while two broad and more intense structures occur above the 4d onsets, with the largest one reaching a peak intensity at 12 eV above the 4d thresholds. The resonant emissions apparently arise from the decay of threshold-excited states which are bound to the inner vacancy and have core configurations nd 9 4f 3 , (n=3,4). The exchange interaction between the three 4f electrons and the respective d-orbital vacancy spreads the 4d-threshold structures over a 20 eV range of excitation energies and the 3d-threshold structures over a much smaller range

Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism.

Science.gov (United States)

Marquet, R; Baudin, F; Gabus, C; Darlix, J L; Mougel, M; Ehresmann, C; Ehresmann, B

1991-05-11

The retroviral genome consists of two identical RNA molecules joined close to their 5' ends by the dimer linkage structure. Recent findings indicated that retroviral RNA dimerization and encapsidation are probably related events during virion assembly. We studied the cation-induced dimerization of HIV-1 RNA and results indicate that all in vitro generated HIV-1 RNAs containing a 100 nucleotide domain downstream from the 5' splice site are able to dimerize. RNA dimerization depends on the concentration of RNA, mono- and multivalent cations, the size of the monovalent cation, temperature, and pH. Up to 75% of HIV-1 RNA is dimeric in the presence of spermidine. HIV-1 RNA dimer is fairly resistant to denaturing agents and unaffected by intercalating drugs. Antisense HIV-1 RNA does not dimerize but heterodimers can be formed between HIV-1 RNA and either MoMuLV or RSV RNA. Therefore retroviral RNA dimerization probably does not simply proceed through mechanisms involving Watson-Crick base-pairing. Neither adenine and cytosine protonation, nor quartets containing only guanines appear to determine the stability of the HIV-1 RNA dimer, while quartets involving both adenine(s) and guanine(s) could account for our results. A consensus sequence PuGGAPuA found in the putative dimerization-encapsidation region of all retroviral genomes examined may participate in the dimerization process.

Excitonic Behavior of Rhodamine Dimers: A Single-Molecule Study

NARCIS (Netherlands)

Hernando Campos, J.; van der Schaaf, Martijn; van Dijk, E.M.H.P.; Sauer, Markus; Garcia Parajo, M.F.; van Hulst, N.F.

2003-01-01

The optical behavior of a dimer of tetramethylrhodamine-5-isothiocyanate has been investigated by means of single-molecule measurements. Bulk absorption and fluorescence spectra show the existence of two populations of the dimer molecule that exhibit distinct excitonic interactions (strong and weak

2-Ethynylpyridine dimers: IR spectroscopic and computational study

Science.gov (United States)

Bakarić, Danijela; Spanget-Larsen, Jens

2018-04-01

2-ethynylpyridine (2-EP) presents a multifunctional system capable of participation in hydrogen-bonded complexes utilizing hydrogen bond donating (tbnd Csbnd H, Aryl-H) and hydrogen bond accepting functions (N-atom, Ctbnd C and pyridine π-systems). In this work, IR spectroscopy and theoretical calculations are used to study possible 2-EP dimer structures as well as their distribution in an inert solvent such as tetrachloroethene. Experimentally, the tbnd Csbnd H stretching vibration of the 2-EP monomer absorbs close to 3300 cm-1, whereas a broad band with maximum around 3215 cm-1 emerges as the concentration rises, indicating the formation of hydrogen-bonded complexes involving the tbnd Csbnd H moiety. The Ctbnd C stretching vibration of monomer 2-EP close to 2120 cm-1 is, using derivative spectroscopy, resolved from the signals of the dimer complexes with maximum around 2112 cm-1. Quantum chemical calculations using the B3LYP + D3 model with counterpoise correction predict that the two most stable dimers are of the π-stacked variety, closely followed by dimers with intermolecular tbnd Csbnd H⋯N hydrogen bonding; the predicted red shifts of the tbnd Csbnd H stretching wavenumbers due to hydrogen bonding are in the range 54-120 cm-1. No species with obvious hydrogen bonding involving the Ctbnd C or pyridine π-systems as acceptors are predicted. Dimerization constant at 25 °C is estimated to be K2 = 0.13 ± 0.01 mol-1 dm3.

Recent results on fusion and direct reactions with weakly bound stable nuclei

International Nuclear Information System (INIS)

Shrivastava, A.

2011-01-01

Recent measurements of fusion and direct reactions in case of weakly bound stable nuclei at extreme sub-barrier energies using a sensitive off beam technique are presented. First section deals with deep sub-barrier fusion cross-section measurement for 67 Li + 198 Pt followed by the study of fragment capture reaction of 7 Li + 198 Pt. Deviation in the slope of the fusion excitation function, as observed in case of medium heavy systems, is absent in the present asymmetric systems at these low energies. This study shows the absence of fusion hindrance, suggesting modifications in models that explain deep sub-barrier fusion data to incorporate weakly bound asymmetric systems

Experimental and theoretical study of bound and quasibound states of Ce{sup -}

Energy Technology Data Exchange (ETDEWEB)

Walter, C. W.; Gibson, N. D.; Li, Y.-G.; Matyas, D. J.; Alton, R. M.; Lou, S. E.; Field, R. L. III; Hanstorp, D.; Pan, Lin; Beck, Donald R. [Department of Physics and Astronomy, Denison University, Granville, Ohio 43023 (United States); Department of Physics, University of Gothenburg, SE-412 96 Gothenburg (Sweden); Department of Physics, Michigan Technological University, Houghton, Michigan 49931 (United States)

2011-09-15

The negative ion of cerium is investigated experimentally with tunable infrared laser photodetachment spectroscopy and theoretically with relativistic configuration interaction in the continuum formalism. The relative cross section for neutral atom production is measured with a crossed ion-beam-laser-beam apparatus over the photon energy range of 0.54-0.75 eV. A rich resonance spectrum is revealed near the threshold with, at least, 12 peaks observed due to transitions from bound states of Ce{sup -} to either bound or quasibound excited states of the negative ion. Theoretical calculations of the photodetachment cross sections enable identification of the transitions responsible for the measured peaks. Two of the peaks are due to electric dipole-allowed bound-bound transitions in Ce{sup -}, making cerium only the second atomic negative ion that has been demonstrated to support multiple bound states of opposite parity. In addition, combining the experimental data with the theoretical analysis determines the electron affinity of cerium to be 0.628(10) eV and the fine structure splitting of the ground state of Ce{sup -} ({sup 4} H{sub 7/2}-{sup 4} H{sub 9/2}) to be 0.097 75(4) eV.

Two-magnon bound state causes ultrafast thermally induced magnetisation switching

Science.gov (United States)

Barker, J.; Atxitia, U.; Ostler, T. A.; Hovorka, O.; Chubykalo-Fesenko, O.; Chantrell, R. W.

2013-01-01

There has been much interest recently in the discovery of thermally induced magnetisation switching using femtosecond laser excitation, where a ferrimagnetic system can be switched deterministically without an applied magnetic field. Experimental results suggest that the reversal occurs due to intrinsic material properties, but so far the microscopic mechanism responsible for reversal has not been identified. Using computational and analytic methods we show that the switching is caused by the excitation of two-magnon bound states, the properties of which are dependent on material factors. This discovery allows us to accurately predict the onset of switching and the identification of this mechanism will allow new classes of materials to be identified or designed for memory devices in the THz regime. PMID:24253110

Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

Science.gov (United States)

de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin

2016-01-01

Abstract Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein–RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA–RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins. PMID:27131381

Modeling of Inelastic Collisions in a Multifluid Plasma: Excitation and Deexcitation (Preprint)

Science.gov (United States)

2015-06-01

interaction. We use superscripts (en), (ei) and ( xd ) to denote electron-neutral, electron-ion (Coulomb), and excitation/dexcitation (as a whole...for each bound-bound transition and summed over all transitions to yield the total rates: K( xd ) = me ∑ ℓ ∑ u>ℓ ( κ↑(u|ℓ)nlne + κ ↓ (ℓ|u)nune ) (70a) J... xd ) = ∑ ℓ ∑ u>ℓ ( j↑(u|ℓ)nlne + j ↓ (ℓ|u)nune ) (70b) Based on the total frictional and thermal resistance coefficients, we can extract average

Exact Solution of a Generalized Nonlinear Schrodinger Equation Dimer

DEFF Research Database (Denmark)

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

1998-01-01

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...... differential equation....

Formation of thymine containing dimers in skin exposed to ultraviolet radiation

Energy Technology Data Exchange (ETDEWEB)

Johnson, B E [Dundee Univ. (UK)

1978-01-01

Nuclear DNA appears to be the major molecular target for the inhibitory, mutagenic and lethal effects of ultraviolet radiation on cells in culture. Cyclobutyl dimers between adjacent pyrimidine bases, the major photochemical lesions for these effects in prokaryotes, also play a part in UVR effects on eukaryotes cells. Pyrimidine dimers have been isolated from in vivo UV-irradiated guinea pig and mouse skin. The wavelength dependence for dimer induction is similar to that for acute skin reactions but no direct causal relationship has been established. Sunlight UVR may induce dimers in skin DNA. Excision of dimers from mouse skin in vivo is deficient as it is for most rodent cells in culture; human cell excision is efficient and the difficulties in interpretation of UV-carcinogenesis results with mice in terms of human skin cancer are therefore increased.

The induction and repair of cyclobutane thymidine dimers in human skin

International Nuclear Information System (INIS)

Roza, L.; Erasmus Univ., Rotterdam; Vermeulen, W.; Schans, G.P. van der; Lohman, P.H.M.

1987-01-01

The most important detrimental effect of ultraviolet radiation (UV) on the living cell, so far known, is the induction of damage in the DNA. The major photoproducts induced in DNA by UV-C (200-280 nm) and UV-B (280-315 nm) are the cyclobutane-type pyrimidine dimers, which have been implicated in UV-induced mutagenesis and carcinogenesis. Dimer lesions in DNA of cells may be repaired in the dark by a multi-enzyme process (excision repair), or via a light dependent enzymatic reaction known as photoreactivation (phr) which is specific for pyrimidine dimers. Although phr has been found to occur in a wide range of organisms, studies on the presence of phr in mammalian cells have yielded conflicting results. To investigate repair of pyrimidine dimers in human skin cells irradiated in vivo, a specific and sensitive detection method was developed based on a monoclonal antibody directed against thymidine dimers. Application together with a fluorescent immunostaining permits the direct detection of thymidine dimers in human skin cells. The method is used in studies aimed at a better understanding of the role of these lesions in the process of carcinogenesis. A report is given on the isolation and characterization of the antibodies, and their application in a study on the induction of pyrimidine dimers in human skin and on photorepair in cultured cells. 10 refs.; 2 figs

Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

Energy Technology Data Exchange (ETDEWEB)

Chen, Chuanying; Beck, Brian W.; Krause, Kurt; Weksberg, Tiffany E.; Pettitt, Bernard M.

2007-02-15

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

Two-Dimensional Electronic Spectroscopy of Benzene, Phenol, and Their Dimer: An Efficient First-Principles Simulation Protocol.

Science.gov (United States)

Nenov, Artur; Mukamel, Shaul; Garavelli, Marco; Rivalta, Ivan

2015-08-11

First-principles simulations of two-dimensional electronic spectroscopy in the ultraviolet region (2DUV) require computationally demanding multiconfigurational approaches that can resolve doubly excited and charge transfer states, the spectroscopic fingerprints of coupled UV-active chromophores. Here, we propose an efficient approach to reduce the computational cost of accurate simulations of 2DUV spectra of benzene, phenol, and their dimer (i.e., the minimal models for studying electronic coupling of UV-chromophores in proteins). We first establish the multiconfigurational recipe with the highest accuracy by comparison with experimental data, providing reference gas-phase transition energies and dipole moments that can be used to construct exciton Hamiltonians involving high-lying excited states. We show that by reducing the active spaces and the number of configuration state functions within restricted active space schemes, the computational cost can be significantly decreased without loss of accuracy in predicting 2DUV spectra. The proposed recipe has been successfully tested on a realistic model proteic system in water. Accounting for line broadening due to thermal and solvent-induced fluctuations allows for direct comparison with experiments.

Quantitative Experimental Determination of Primer-Dimer Formation Risk by Free-Solution Conjugate Electrophoresis

Science.gov (United States)

Desmarais, Samantha M.; Leitner, Thomas; Barron, Annelise E.

2012-01-01

DNA barcodes are short, unique ssDNA primers that “mark” individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis (FSCE) approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer-barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 basepairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive basepairs formed, yet non-consecutive basepairs did not create stable dimers even when 20 out of 30 possible basepairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation. PMID:22331820

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

CERN Multimedia

2002-01-01

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.

99mTcO(MAG2-3G3-dimer): a new integrin αvβ3-targeted SPECT radiotracer with high tumor uptake and favorable pharmacokinetics

International Nuclear Information System (INIS)

Shi, Jiyun; Wang, Lijun; Kim, Young-Seung; Zhai, Shizhen; Liu, Shuang; Jia, Bing; Wang, Fan

2009-01-01

This report presents the synthesis of a cyclic RGD dimer conjugate, MAG 2 -G 3 -E[G 3 -c(RGDfK)] 2 (MAG 2 -3G 3 -dimer, G 3 = Gly-Gly-Gly, MAG 2 = S-benzoyl mercaptoacetylglycylglycyl), and evaluation of its 99m Tc complex, 99m TcO(MAG 2 -3G 3 -dimer), as a new radiotracer for imaging the tumor integrin α v β 3 expression. An in vitro displacement assay was used to determine the integrin α v β 3 binding affinity of MAG 2 -3G 3 -dimer against 125 I-c(RGDyK) bound to U87MG human glioma cells. The athymic nude mice bearing U87MG glioma xenografts were used for biodistribution and planar imaging studies. We found that (1) MAG 2 is such a highly effective bifunctional chelator that 99m TcO(MAG 2 -3G 3 -dimer) can be prepared in high yield (radiochemical purity >95%) and with high specific activity (∝5 Ci/μmol) using a kit formulation; (2) 99m TcO(MAG 2 -3G 3 -dimer) has very high solution stability in the kit matrix; and (3) 99m TcO(MAG 2 -3G 3 -dimer) has very fast clearance kinetics from the intestine, liver, and kidneys. Among the 99m Tc-labeled cyclic RGD peptides evaluated in the xenografted U87MG glioma models, 99m TcO(MAG 2 -3G 3 -dimer) has the best pharmacokinetics and tumor to background ratios (tumor/liver = 4.29 ± 1.00 at 30 min postinjection and 8.29 ± 1.50 at 120 min postinjection; tumor/kidney = 1.16 ± 0.19 at 30 min postinjection and 2.49 ± 0.25 at 120 min postinjection). Planar imaging studies showed that tumors in the glioma-bearing mice administered with 99m TcO(MAG 2 -3G 3 -dimer) can be visualized with excellent contrast as early as 15 min postinjection. 99m TcO(MAG 2 -3G 3 -dimer) was able to maintain its chemical integrity in kidneys (>80% intact) and liver (>95% intact) over the 2-h period. However, there was significant metabolism (>50% of the injected radioactivity) detected in both urine and feces samples. 99m TcO(MAG 2 -3G 3 -dimer) is a very attractive radiotracer for early detection of integrin α v β 3 -positive tumors and has

Instability of hot electroweak theory: Bounds on mH and mt

International Nuclear Information System (INIS)

Arnold, P.; Vokos, S.

1991-01-01

The electroweak vacuum need not be absolutely stable. For certain top-quark and Higgs-boson masses in the minimal standard model, it is instead metastable with a lifetime exceeding the present age of the Universe. The decay of our vacuum may be nucleated at low temperature by quantum tunneling or at high temperature by thermal excitation. We show that the requirement that the vacuum survive the high temperatures of the early Universe places the strongest constraints from vacuum stability on the top-quark and Higgs-boson masses in the minimal standard model. If a single Higgs boson is found experimentally, these constraints may place an upper bound on the scale of new physics beyond the minimal standard model. In contrast with other work, we examine temperatures very large compared to the scale of weak symmetry restoration and find much stronger bounds. We also present a simple analytic approximation that directly relates the bounds to the running coupling constants of the minimal standard model

Designer interface peptide grafts target estrogen receptor alpha dimerization

International Nuclear Information System (INIS)

Chakraborty, S.; Asare, B.K.; Biswas, P.K.; Rajnarayanan, R.V.

2016-01-01

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

Tricriticality for dimeric Coulomb molecular crystals in ground state

Science.gov (United States)

Travěnec, Igor; Šamaj, Ladislav

2017-12-01

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

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: pbiswas@tougaloo.edu [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Rajnarayanan, R.V., E-mail: rajendra@buffalo.edu [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States)

2016-09-09

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

Low-pressure approach to the formation and study of exciplex systems

International Nuclear Information System (INIS)

Sanzone, G.

1977-10-01

Studies on the formation and properties of new materials for high-energy, gas-phase lasers are described. Attention is directed mainly to systems having bound excited states but unbound ground states. An important class of such excimer/exciplex systems has a van der Waals dimer/oligomer as its ground state. This research attempts to probe the relative rates of electron pumping of excited-state manifolds and the preferentially pumped vibronic states within each manifold. Reactive quenching of emission, resonant self-absorption of laser emissions, and collision- and noncollision-induced intersystem crossing are also considered. Lists of personnel and facilities are included. 8 figures, 2 tables

Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers.

Science.gov (United States)

Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek; Faber, Rasmus; Lacerda, Evanildo G; Sauer, Stephan P A

2016-02-05

Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [CCSD(T)] calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr, and the AQZP basis set for Xe. For the dimers also, zero-point vibrational (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. © 2015 Wiley Periodicals, Inc.

Pump-probe study of the formation of rubidium molecules by ultrafast photoassociation of ultracold atoms

Science.gov (United States)

McCabe, David J.; England, Duncan G.; Martay, Hugo E. L.; Friedman, Melissa E.; Petrovic, Jovana; Dimova, Emiliya; Chatel, Béatrice; Walmsley, Ian A.

2009-09-01

An experimental pump-probe study of the photoassociative creation of translationally ultracold rubidium molecules is presented together with numerical simulations of the process. The formation of loosely bound excited-state dimers is observed as a first step toward a fully coherent pump-dump approach to the stabilization of Rb2 into its lowest ground vibrational states. The population that contributes to the pump-probe process is characterized and found to be distinct from a background population of preassociated molecules.

Dimerization of the voltage-sensing phosphatase controls its voltage-sensing and catalytic activity.

Science.gov (United States)

Rayaprolu, Vamseedhar; Royal, Perrine; Stengel, Karen; Sandoz, Guillaume; Kohout, Susy C

2018-05-07

Multimerization is a key characteristic of most voltage-sensing proteins. The main exception was thought to be the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP). In this study, we show that multimerization is also critical for Ci-VSP function. Using coimmunoprecipitation and single-molecule pull-down, we find that Ci-VSP stoichiometry is flexible. It exists as both monomers and dimers, with dimers favored at higher concentrations. We show strong dimerization via the voltage-sensing domain (VSD) and weak dimerization via the phosphatase domain. Using voltage-clamp fluorometry, we also find that VSDs cooperate to lower the voltage dependence of activation, thus favoring the activation of Ci-VSP. Finally, using activity assays, we find that dimerization alters Ci-VSP substrate specificity such that only dimeric Ci-VSP is able to dephosphorylate the 3-phosphate from PI(3,4,5)P 3 or PI(3,4)P 2 Our results indicate that dimerization plays a significant role in Ci-VSP function. © 2018 Rayaprolu et al.

Changes in fibrin D-dimer, fibrinogen, and protein S during pregnancy

DEFF Research Database (Denmark)

Hansen, Anette Tarp; Andreasen, Birgitte Horst; Salvig, Jannie Dalby

2010-01-01

Background. Pregnancy is a hypercoagulable state with a 5- to 10- fold higher risk of venous thromboembolism. Existing reference intervals for fibrin D-dimer (D-dimer), functional fibrinogen (fibrinogen) and protein S, free antigen (protein S) are based on non-pregnant patients and reference...... intervals for pregnant patients are warranted. Objectives. The aim of the present study was to contribute to the establishment of reference intervals for D-dimer, fibrinogen and protein S during pregnancy and to discuss the use of the analyses during pregnancy. Methods. We included 55 healthy pregnant women...... in gestational week 11–17, with normal current pregnancy. Blood samples were collected in gestational weeks 11–17, 21–27 and 34–37. The three plasma parameters D-dimer, fibrinogen and protein S were analysed by STA-R Evolution®. Results. A significant rise in D-dimer was found from first to second trimester (p...

Risk of deep venous thrombosis (DVT) in bedridden or wheelchair-bound multiple sclerosis patients: a prospective study.

Science.gov (United States)

Arpaia, G; Bavera, P M; Caputo, D; Mendozzi, L; Cavarretta, R; Agus, G B; Milani, M; Ippolito, E; Cimminiello, C

2010-04-01

Multiple sclerosis (MS) often causes progressive loss of mobility, leading to limb paralysis. Venous and lymphatic stasis is a risk condition for venous thromboembolism (VTE). There is, however, no data on the frequency of VTE complicating the progression of MS. The aim of this study was to assess the frequency of deep vein thrombosis (DVT) in patients with late-stage MS attending a neurology center for rehabilitation. A total of 132 patients with MS were enrolled, 87 women and 45 men, mean age 58+/-11 years. The disease had started on average 18.7 years before; patients reported 9.6 hours bedridden per day or 14.3 hours wheelchair-bound. Only 25 patients reported a residual ability to walk alone or with help. Lower limb edema was present in 113 patients, bilateral in 41 cases. At admission all patients underwent extended compression ultrasonography. Their plasma D-dimer levels were measured. No antithrombotic prophylaxis was given. DVT was found in 58 patients (43.9%); 32 had a history of VTE. Forty of these patients (69%) had chronic lower limb edema, in 19 cases bilateral. D-dimer levels in the DVT patients were significantly higher than in patients without DVT (553+/-678 vs. 261+/-152 ng/mL, p=0.0112, Mann-Whitney Test). Nearly half the DVT patients (26, 45%) had high D-dimer levels (701+/-684 ng/mL). Of the 74 patients without DVT, 48 had normal D-dimer (193.37+/-67.28 ng/mL) and 26 high (387.61+/-187.42 ng/mL). The frequency of DVT in late-stage MS may be over 40%. The long history of the disease means the onset of each episode cannot be established with certainty. A number of patients with positive CUS findings had negative D-dimer values, suggesting a VTE event in the past. However, the level of DVT risk in this series should lead physicians to consider the systematic application of long-term preventive measures. (c) 2009 Elsevier Ltd. All rights reserved.

Observation of the a3Σu+-Χ1Σg+ system of calcium dimer

International Nuclear Information System (INIS)

Gondal, M.A.; Khan, M.A.; Rais, M.H.

1998-01-01

The authors report the observation of collision-induced spectra of calcium dimer in the 680-692 nm region. The spectra were recorded after resonant laser excitation of 4s4p 3 P 1 state of atomic calcium. Here the upper state a 3 Σ u + is populated through collisions. The same spectra were reproduced in a low-current glow discharge in calcium vapor. The assignment of the observed spectral lines was carried out by applying the Dunham-type analysis and the spectra were assigned to the a 3 Σ u + -Χ 1 Σ g + transition of Ca 2 . The existence of a a 3 Σ u + state with v 00 =13850±1 cm -1 and ω e ∼37.6 cm -1 is confirmed

Radiation-induced tetramer-to-dimer transition of Escherichia coli lactose repressor

International Nuclear Information System (INIS)

Goffinont, S.; Davidkova, M.; Spotheim-Maurizot, M.

2009-01-01

The wild type lactose repressor of Escherichia coli is a tetrameric protein formed by two identical dimers. They are associated via a C-terminal 4-helix bundle (called tetramerization domain) whose stability is ensured by the interaction of leucine zipper motifs. Upon in vitro γ-irradiation the repressor losses its ability to bind the operator DNA sequence due to damage of its DNA-binding domains. Using an engineered dimeric repressor for comparison, we show here that irradiation induces also the change of repressor oligomerisation state from tetramer to dimer. The splitting of the tetramer into dimers can result from the oxidation of the leucine residues of the tetramerization domain.

Is the anomalous effect an experimental evidence for the excitation of new exotic states in heavy-ion collisions

International Nuclear Information System (INIS)

Ion, D.B.; Ion, R.; Topor Pop, V.

1984-10-01

Lower bound on the mean free path of the projectile fragments from the relativistic heavy ion collisions are drived using generalized Rarita-Schwed's theorems. These bounds are compared with the experimental data on the anomalous mean free path observed in recent experiments. The near saturation of these bounds provide a specific interpretation of the anomalous effects as an experimental evidence for the excitation of those extreme nuclear states which saturate the limits of the convetional nuclear physics. (authors)

D-dimer: a useful tool in gauging optimal duration of oral anticoagulant therapy?

Directory of Open Access Journals (Sweden)

M. Silingardi

2013-05-01

Full Text Available BACKGROUND AND AIM OF THE STUDY Optimal duration of oral anticoagulant therapy (OAT in idiopathic venous thromboembolism (VTE is unknown. Indefinite OAT carries an unacceptable risk of major bleeding and prospective studies have demonstrated that OAT is no longer protective after its withdrawal. How to identify the patients at risk for recurrence? D-dimer is a marker of thrombin activity. Early prospective studies showed that elevated D-dimer levels after anticoagulation had a highly predictive value for a recurrent episode. Does D-dimer assay have a role in gauging the appropriate duration of anticoagulant therapy? The PROLONG study tries to answer this question. METHOD D-dimer assay was performed one month after stopping anticoagulation. Patiens with normal D-dimer levels did not resume anticoagulation while patients with elevated D-dimer levels were randomized to discontinue or resume anticoagulation. Study end-points was the composite of recurrent VTE and major bleeding during an average follow-up of 1.4 years. RESULTS The rate of recurrence is significantly higher in patients with elevated D-dimer levels who discontinued anticoagulation. Resuming anticoagulation in this cohort of patients markedly reduces recurrent events without increasing major bleeding. DISCUSSION AND CONCLUSIONS PROLONG study is provocative, because D-dimer assay is simple, thus not requiring dedicated laboratory facilities. D-dimer test has otherwise high sensitivity but low specificity in VTE diagnosis. Aspecifically elevated D-dimer levels are available in the elderly and the majority of patients included in the study were > 65 years old, thus introducing a possible selection bias. Nonetheless the results of the study are useful for the clinician. Prolongation of vitamin K antagonists in patients with elevated D-dimer levels one month after discontinuation of OAT for a first unprovoked episode of VTE results in a favourable risk-benefit relationship. Probably this

Dimer and String Formation during Low Temperature Silicon Deposition on Si(100)

DEFF Research Database (Denmark)

Smith, A. P.; Jonsson, Hannes

1996-01-01

We present theoretical results based on density functional theory and kinetic Monte Carlo simulations of silicon deposition and address observations made in recently reported low temperature scanning tunneling microscopy studies. A mechanism is presented which explains dimer formation on top...... of the substrate's dimer rows at 160 K and up to room temperature, while between-row dimers and longer strings of adatoms (''diluted dimer rows'') form at higher temperature. A crossover occurs at around room temperature between two different mechanisms for adatom diffusion in our model....

A discotic triphenylene dimer as organic hole transporting material for electroluminescence devices

International Nuclear Information System (INIS)

Mao Huaxiang; He Zhiqun; Wang Junling; Zhang Chunxiu; Xie, Ping; Zhang Rongben

2007-01-01

A triphenylene dimer, an intermediate between a discotic triphenylene molecule and the macromolecule, had been prepared by linking together two triphenylene units via phenylene carbamate linkages, which was formed through a reaction between one 1,4-phenylene diisocyanate and two hydroxyl end groups on flexible substituents of triphenylenes. The dimer exhibited good film-forming property. Its temperature-dependent phase transitions were investigated using differential scanning calorimetry and polarized optical microscopy. Room temperature microstructure of the dimer was analyzed by X-ray diffraction. Charge mobility of the triphenylene dimer was also measured. Our preliminary result using the materials in a sandwich light-emitting device is reported here. It demonstrates that the triphenylene dimer is a promising candidate as a hole transporting material

D-dimer as marker for microcirculatory failure: correlation with LOD and APACHE II scores.

Science.gov (United States)

Angstwurm, Matthias W A; Reininger, Armin J; Spannagl, Michael

2004-01-01

The relevance of plasma d-dimer levels as marker for morbidity and organ dysfunction in severely ill patients is largely unknown. In a prospective study we determined d-dimer plasma levels of 800 unselected patients at admission to our intensive care unit. In 91% of the patients' samples d-dimer levels were elevated, in some patients up to several hundredfold as compared to normal values. The highest mean d-dimer values were present in the patient group with thromboembolic diseases, and particularly in non-survivors of pulmonary embolism. In patients with circulatory impairment (r=0.794) and in patients with infections (r=0.487) a statistically significant correlation was present between d-dimer levels and the APACHE II score (P<0.001). The logistic organ dysfunction score (LOD, P<0.001) correlated with d-dimer levels only in patients with circulatory impairment (r=0.474). On the contrary, patients without circulatory impairment demonstrated no correlation of d-dimer levels to the APACHE II or LOD score. Taking all patients together, no correlations of d-dimer levels with single organ failure or with indicators of infection could be detected. In conclusion, d-dimer plasma levels strongly correlated with the severity of the disease and organ dysfunction in patients with circulatory impairment or infections suggesting that elevated d-dimer levels may reflect the extent of microcirculatory failure. Thus, a therapeutic strategy to improve the microcirculation in such patients may be monitored using d-dimer plasma levels.

Dimerization of the Glucan Phosphatase Laforin Requires the Participation of Cysteine 329

Science.gov (United States)

Sánchez-Martín, Pablo; Raththagala, Madushi; Bridges, Travis M.; Husodo, Satrio; Gentry, Matthew S.; Sanz, Pascual; Romá-Mateo, Carlos

2013-01-01

Laforin, encoded by a gene that is mutated in Lafora Disease (LD, OMIM 254780), is a modular protein composed of a carbohydrate-binding module and a dual-specificity phosphatase domain. Laforin is the founding member of the glucan-phosphatase family and regulates the levels of phosphate present in glycogen. Multiple reports have described the capability of laforin to form dimers, although the function of these dimers and their relationship with LD remains unclear. Recent evidence suggests that laforin dimerization depends on redox conditions, suggesting that disulfide bonds are involved in laforin dimerization. Using site-directed mutagenesis we constructed laforin mutants in which individual cysteine residues were replaced by serine and then tested the ability of each protein to dimerize using recombinant protein as well as a mammalian cell culture assay. Laforin-Cys329Ser was the only Cys/Ser mutant unable to form dimers in both assays. We also generated a laforin truncation lacking the last three amino acids, laforin-Cys329X, and this truncation also failed to dimerize. Interestingly, laforin-Cys329Ser and laforin-Cys329X were able to bind glucans, and maintained wild type phosphatase activity against both exogenous and biologically relevant substrates. Furthermore, laforin-Cys329Ser was fully capable of participating in the ubiquitination process driven by a laforin-malin complex. These results suggest that dimerization is not required for laforin phosphatase activity, glucan binding, or for the formation of a functional laforin-malin complex. Cumulatively, these results suggest that cysteine 329 is specifically involved in the dimerization process of laforin. Therefore, the C329S mutant constitutes a valuable tool to analyze the physiological implications of laforin’s oligomerization. PMID:23922729

Iminodiacetic acid as bifunctional linker for dimerization of cyclic RGD peptides

International Nuclear Information System (INIS)

Xu, Dong; Zhao, Zuo-Quan; Chen, Shu-Ting; Yang, Yong; Fang, Wei; Liu, Shuang

2017-01-01

Introduction: In this study, I2P-RGD 2 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 99m Tc-labeled dimeric cyclic RGD peptides. Methods: HYNIC-I2P-RGD 2 was prepared by reacting I2P-RGD 2 with HYNIC-OSu in the presence of diisopropylethylamine, and was evaluated for its α v β 3 binding affinity against 125 I-echistatin bound to U87MG glioma cells. 99m Tc-I2P-RGD 2 was prepared with high specific activity (~185 GBq/μmol). The athymic nude mice bearing U87MG glioma xenografts were used to evaluate its biodistribution properties and image quality in comparison with those of 99m Tc-3P-RGD 2 . Results: The IC 50 value for HYNIC-I2P-RGD 2 was determined to be 39 ± 6 nM, which was very close to that (IC 50 = 33 ± 5 nM) of HYNIC-3P-RGD 2 . Replacing glutamic acid with iminodiacetic acid had little impact on α v β 3 binding affinity of cyclic RGD peptides. 99m Tc-I2P-RGD 2 and 99m Tc-3P-RGD 2 shared similar tumor uptake values over the 2 h period, and its α v β 3 -specificity was demonstrated by a blocking experiment. The uptake of 99m Tc-I2P-RGD 2 was significantly lower than 99m Tc-3P-RGD 2 in the liver and kidneys. The U87MG glioma tumors were visualized by SPECT with excellent contrast using both 99m Tc-I2P-RGD 2 and 99m Tc-3P-RGD 2 . Conclusion: Iminodiacetic acid is an excellent bifunctional linker for dimerization of cyclic RGD peptides. Bifunctional linkers have significant impact on the excretion kinetics of 99m Tc radiotracers. Because of its lower liver uptake and better tumor/liver ratios, 99m Tc-I2P-RGD 2 may have advantages over 99m Tc-3P-RGD 2 for diagnosis of tumors in chest region. -- Graphical abstract: This report presents novel approach for dimerization of cyclic RGD peptides using iminodiacetic acid as a

An accurate and linear-scaling method for calculating charge-transfer excitation energies and diabatic couplings

Energy Technology Data Exchange (ETDEWEB)

Pavanello, Michele [Department of Chemistry, Rutgers University, Newark, New Jersey 07102-1811 (United States); Van Voorhis, Troy [Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307 (United States); Visscher, Lucas [Amsterdam Center for Multiscale Modeling, VU University, De Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Neugebauer, Johannes [Theoretische Organische Chemie, Organisch-Chemisches Institut der Westfaelischen Wilhelms-Universitaet Muenster, Corrensstrasse 40, 48149 Muenster (Germany)

2013-02-07

Quantum-mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those charge transfer excitations that take place between non-covalently bound molecules. In particular, we present a method that scales linearly with the number of non-covalently bound molecules in the system and is based on a two-pronged approach: The molecular electronic structure of broken-symmetry charge-localized states is obtained with the frozen density embedding formulation of subsystem density-functional theory; subsequently, in a post-SCF calculation, the full-electron Hamiltonian and overlap matrix elements among the charge-localized states are evaluated with an algorithm which takes full advantage of the subsystem DFT density partitioning technique. The method is benchmarked against coupled-cluster calculations and achieves chemical accuracy for the systems considered for intermolecular separations ranging from hydrogen-bond distances to tens of Angstroms. Numerical examples are provided for molecular clusters comprised of up to 56 non-covalently bound molecules.

Strong Wilson polygons from the lodge of free and bound mesons

Energy Technology Data Exchange (ETDEWEB)

Bonini, Alfredo; Fioravanti, Davide [Sezione INFN di Bologna, Dipartimento di Fisica e Astronomia, Università di Bologna,Via Irnerio 46, 40126 Bologna (Italy); Piscaglia, Simone [Dipartimento di Fisica and INFN, Università di Torino,Via P. Giuria 1, 10125 Torino (Italy); Rossi, Marco [Dipartimento di Fisica dell’Università della Calabria and INFN, Gruppo collegato di Cosenza,Arcavacata di Rende, 87036 Cosenza (Italy)

2016-04-05

Previously predicted by the S-matrix bootstrap of the excitations over the GKP quantum vacuum, the appearance of a new particle at strong coupling — formed by one fermion and one anti-fermion — is here confirmed: this two-dimensional meson shows up, along with its infinite tower of bound states, while analysing the fermionic contributions to the Operator Product Expansion (collinear regime) of the Wilson null polygon loop. Moreover, its existence, free and bound, turns out to be a powerful idea in re-summing all the contributions (at large coupling) for a general n-gon (n≥6) to a Thermodynamic Bethe Ansatz, which is proven to be equivalent to the known one and suggests new structures for a special Y-system.

Dimer coverings on random multiple chains of planar honeycomb lattices

International Nuclear Information System (INIS)

Ren, Haizhen; Zhang, Fuji; Qian, Jianguo

2012-01-01

We study dimer coverings on random multiple chains. A multiple chain is a planar honeycomb lattice constructed by successively fusing copies of a ‘straight’ condensed hexagonal chain at the bottom of the previous one in two possible ways. A random multiple chain is then generated by admitting the Bernoulli distribution on the two types of fusing, which describes a zeroth-order Markov process. We determine the expectation of the number of the pure dimer coverings (perfect matchings) over the ensemble of random multiple chains by the transfer matrix approach. Our result shows that, with only two exceptions, the average of the logarithm of this expectation (i.e., the annealed entropy per dimer) is asymptotically nonzero when the fusing process goes to infinity and the length of the hexagonal chain is fixed, though it is zero when the fusing process and the length of the hexagonal chain go to infinity simultaneously. Some numerical results are provided to support our conclusion, from which we can see that the asymptotic behavior fits well to the theoretical results. We also apply the transfer matrix approach to the quenched entropy and reveal that the quenched entropy of random multiple chains has a close connection with the well-known Lyapunov exponent of random matrices. Using the theory of Lyapunov exponents we show that, for some random multiple chains, the quenched entropy per dimer is strictly smaller than the annealed one when the fusing process goes to infinity. Finally, we determine the expectation of the free energy per dimer over the ensemble of the random multiple chains in which the three types of dimers in different orientations are distinguished, and specify a series of non-random multiple chains whose free energy per dimer is asymptotically equal to this expectation. (paper)

A new D-dimer cutoff in bedridden hospitalized elderly patients.

Science.gov (United States)

Granziera, Serena; Rechichi, Alfonsina; De Rui, Marina; De Carlo, Paola; Bertozzo, Giulia; Marigo, Lucia; Nante, Giovanni; Manzato, Enzo

2013-03-01

Asymptomatic deep vein thrombosis (DVT) and pulmonary embolism are leading causes of morbidity following the hospitalization of elderly people. The diagnosis of DVT is supported by the D-dimer laboratory assay. The concentration of D-dimer increases in patients with DVT, but may be high in other conditions too (i.e. cancer, infections and inflammation). Old age coincides with a physiological increase in D-dimer values, and that is why D-dimer assay in the elderly is characteristically highly sensitive but scarcely specific. The aim of our study was to explore the reliability of different D-dimer cutoffs for the diagnosis of asymptomatic DVT in a population of bedridden hospitalized elderly patients. We studied 199 patients who were a mean 86.3 ± 6.7 years old. All participants underwent lower limb Doppler ultrasound (DUS) and D-dimer venous blood sampling on admission. In our cohort, the usual cutoff proved highly sensitive (100%), but its specificity was very poor (20.1%). To find a higher cutoff that could improve the method's specificity, we analyzed our data using a receiver operating characteristic curve analysis. The resulting D-dimer cutoff of 492 μg/l enabled us to retain the same sensitivity while improving the test's specificity to 39.1%, with a consequent improvement in its positive predictive value and accuracy. In addition to improving the method's reliability, this result may be helpful in clinical practice, in both medical wards and nursing homes. By adopting a cutoff of 492 μg/l, clinicians could significantly increase the proportion of older patients in whom DVT can be safely ruled out, reducing referrals for DUS and administration of heparin, with consequent clinical, practical and economic advantages.

Kinetics of the monomer-dimer reaction of yeast hexokinase PI.

Science.gov (United States)

Hoggett, J G; Kellett, G L

1992-10-15

Kinetic studies of the glucose-dependent monomer-dimer reaction of yeast hexokinase PI at pH 8.0 in the presence of 0.1 M-KCl have been carried out using the fluorescence temperature-jump technique. A slow-relaxation effect was observed which was attributed from its dependence on enzyme concentration to the monomer-dimer reaction; the reciprocal relaxation times tau-1 varied from 3 s-1 at low concentrations of glucose to 42 s-1 at saturating concentrations. Rate constants for association (kass.) and dissociation (kdiss.) were determined as a function of glucose concentration using values of the equilibrium association constant of the monomer-dimer reaction derived from sedimentation ultracentrifugation studies under similar conditions, and also from the dependence of tau-2 on enzyme concentration. kass. was almost independent of glucose concentration and its value (2 x 10(5) M-1.s-1) was close to that expected for a diffusion-controlled process. The influence of glucose on the monomer-dimer reaction is entirely due to effects on kdiss., which increases from 0.21 s-1 in the absence of glucose to 25 s-1 at saturating concentrations. The monomer and dimer forms of hexokinase have different affinities and Km values for glucose, and the results reported here imply that there may be a significant lag in the response of the monomer-dimer reaction to changes in glucose concentrations in vivo with consequent hysteretic effects on the hexokinase activity.

Structural features of the KPI domain control APP dimerization, trafficking, and processing.

Science.gov (United States)

Ben Khalifa, Naouel; Tyteca, Donatienne; Marinangeli, Claudia; Depuydt, Mathieu; Collet, Jean-François; Courtoy, Pierre J; Renauld, Jean-Christophe; Constantinescu, Stefan; Octave, Jean-Noël; Kienlen-Campard, Pascal

2012-02-01

The two major isoforms of human APP, APP695 and APP751, differ by the presence of a Kunitz-type protease inhibitor (KPI) domain in the extracellular region. APP processing and function is thought to be regulated by homodimerization. We used bimolecular fluorescence complementation (BiFC) to study dimerization of different APP isoforms and mutants. APP751 was found to form significantly more homodimers than APP695. Mutation of dimerization motifs in the TM domain did not affect fluorescence complementation, but native folding of KPI is critical for APP751 homodimerization. APP751 and APP695 dimers were mostly localized at steady state in the Golgi region, suggesting that most of the APP751 and 695 dimers are in the secretory pathway. Mutation of the KPI led to the retention of the APP homodimers in the endoplasmic reticulum. We finally showed that APP751 is more efficiently processed through the nonamyloidogenic pathway than APP695. These findings provide new insight on the particular role of KPI domain in APP dimerization. The correlation observed between dimerization, subcellular localization, and processing suggests that dimerization acts as an efficient regulator of APP trafficking in the secretory compartments that has major consequences on its processing.

Unique self-assembly properties of a bridge-shaped protein dimer with quantum dots

International Nuclear Information System (INIS)

Wang, Jianhao; Jiang, Pengju; Gao, Liqian; Yu, Yongsheng; Lu, Yao; Qiu, Lin; Wang, Cheli; Xia, Jiang

2013-01-01

How protein–protein interaction affects protein–nanoparticle self-assembly is the key to the understanding of biomolecular coating of nanoparticle in biological fluids. However, the relationship between protein shape and its interaction with nanoparticles is still under-exploited because of lack of a well-conceived binding system and a method to detect the subtle change in the protein–nanoparticle assemblies. Noticing this unresolved need, we cloned and expressed a His-tagged SpeA protein that adopts a bridge-shaped dimer structure, and utilized a high-resolution capillary electrophoresis method to monitor assembly formation between the protein and quantum dots (QDs, 5 nm in diameter). We observed that the bridge-shaped structure rendered a low SpeA:QD stoichiometry at saturation. Also, close monitoring of imidazole (Im) displacement of surface-bound protein revealed a unique two-step process. High-concentration Im could displace surface-bound SpeA protein and form a transient QD–protein intermediate, through a kinetically controlled displacement process. An affinity-driven equilibrium step then followed, resulting in re-assembling of the QD–protein complex in about 1 h. Through a temporarily formed intermediate, Im causes a rearrangement of His-tagged proteins on the surface. Thus, our work showcases that the synergistic interplay between QD–His-tag interaction and protein–protein interaction can result in unique properties of protein–nanoparticle assembly for the first time

Unique self-assembly properties of a bridge-shaped protein dimer with quantum dots

Science.gov (United States)

Wang, Jianhao; Jiang, Pengju; Gao, Liqian; Yu, Yongsheng; Lu, Yao; Qiu, Lin; Wang, Cheli; Xia, Jiang

2013-09-01

How protein-protein interaction affects protein-nanoparticle self-assembly is the key to the understanding of biomolecular coating of nanoparticle in biological fluids. However, the relationship between protein shape and its interaction with nanoparticles is still under-exploited because of lack of a well-conceived binding system and a method to detect the subtle change in the protein-nanoparticle assemblies. Noticing this unresolved need, we cloned and expressed a His-tagged SpeA protein that adopts a bridge-shaped dimer structure, and utilized a high-resolution capillary electrophoresis method to monitor assembly formation between the protein and quantum dots (QDs, 5 nm in diameter). We observed that the bridge-shaped structure rendered a low SpeA:QD stoichiometry at saturation. Also, close monitoring of imidazole (Im) displacement of surface-bound protein revealed a unique two-step process. High-concentration Im could displace surface-bound SpeA protein and form a transient QD-protein intermediate, through a kinetically controlled displacement process. An affinity-driven equilibrium step then followed, resulting in re-assembling of the QD-protein complex in about 1 h. Through a temporarily formed intermediate, Im causes a rearrangement of His-tagged proteins on the surface. Thus, our work showcases that the synergistic interplay between QD-His-tag interaction and protein-protein interaction can result in unique properties of protein-nanoparticle assembly for the first time.

On the asymptotics of dimers on tori

OpenAIRE

Kenyon, Richard W.; Sun, Nike; Wilson, David B.

2013-01-01

We study asymptotics of the dimer model on large toric graphs. Let $\\mathbb L$ be a weighted $\\mathbb{Z}^2$-periodic planar graph, and let $\\mathbb{Z}^2 E$ be a large-index sublattice of $\\mathbb{Z}^2$. For $\\mathbb L$ bipartite we show that the dimer partition function on the quotient $\\mathbb{L}/(\\mathbb{Z}^2 E)$ has the asymptotic expansion $\\exp[A f_0 + \\text{fsc} + o(1)]$, where $A$ is the area of $\\mathbb{L}/(\\mathbb{Z}^2 E)$, $f_0$ is the free energy density in the bulk, and $\\text{fsc...

On the diffusion and self-trapping of surface dimers

Science.gov (United States)

Kappus, W.

1982-03-01

The theory of elastic interactions between surface atoms which are caused by substrate strains is applied to the interaction of dimers on the (211) surface of tungsten. From the comparison of theoretical and experimental interactions which were derived from the diffusion behaviour of dimers, conclusions are drawn on the nature of the adatom-substrate bond.

Photoemission from excited states in rare gas solids by combining synchrotronradiation with a laser

International Nuclear Information System (INIS)

Bernstorff, S.

1984-09-01

A new spectroscopic method has been developed to study excited states in rare gas solids: Excitons and conductionband-states are populated by synchrotron radiation (photon energy hw SR =5 - 30 eV). Subsequently electrons from these bound or conduction band-states are excited above the vacuum level of the solid by a pulsed dye laser (hw L =1.9 - 3.7 eV). This experimental technique was applied to solid Xe, Kr, Ar and Ne. (orig./GSCH)

Dislocations and vacancies in two-dimensional mixed crystals of spheres and dimers

KAUST Repository

Gerbode, Sharon J.

2010-10-15

In colloidal crystals of spheres, dislocation motion is unrestricted. On the other hand, recent studies of relaxation in crystals of colloidal dimer particles have demonstrated that the dislocation dynamics in such crystals are reminiscent of glassy systems. The observed glassy dynamics arise as a result of dislocation cages formed by certain dimer orientations. In the current study, we use experiments and simulations to investigate the transition that arises when a pure sphere crystal is doped with an increasing concentration of dimers. Specifically, we focus on both dislocation caging and vacancy motion. Interestingly, we find that any nonzero fraction of dimers introduces finite dislocation cages, suggesting that glassy dynamics are present for any mixed crystal. However, we have also identified a vacancy-mediated uncaging mechanism for releasing dislocations from their cages. This mechanism is dependent on vacancy diffusion, which slows by orders of magnitude as the dimer concentration is increased. We propose that in mixed crystals with low dimer concentrations vacancy diffusion is fast enough to uncage dislocations and delay the onset of glassy dislocation dynamics. © 2010 The American Physical Society.

Dislocations and vacancies in two-dimensional mixed crystals of spheres and dimers

KAUST Repository

Gerbode, Sharon J.; Ong, Desmond C.; Liddell, Chekesha M.; Cohen, Itai

2010-01-01

In colloidal crystals of spheres, dislocation motion is unrestricted. On the other hand, recent studies of relaxation in crystals of colloidal dimer particles have demonstrated that the dislocation dynamics in such crystals are reminiscent of glassy systems. The observed glassy dynamics arise as a result of dislocation cages formed by certain dimer orientations. In the current study, we use experiments and simulations to investigate the transition that arises when a pure sphere crystal is doped with an increasing concentration of dimers. Specifically, we focus on both dislocation caging and vacancy motion. Interestingly, we find that any nonzero fraction of dimers introduces finite dislocation cages, suggesting that glassy dynamics are present for any mixed crystal. However, we have also identified a vacancy-mediated uncaging mechanism for releasing dislocations from their cages. This mechanism is dependent on vacancy diffusion, which slows by orders of magnitude as the dimer concentration is increased. We propose that in mixed crystals with low dimer concentrations vacancy diffusion is fast enough to uncage dislocations and delay the onset of glassy dislocation dynamics. © 2010 The American Physical Society.

Low-valent low-coordinated manganese(I) ion dimer: a temperature dependent W-band EPR study.

Science.gov (United States)

Sorace, Lorenzo; Golze, Christian; Gatteschi, Dante; Bencini, Alessandro; Roesky, Herbert W; Chai, Jianfang; Stückl, A Claudia

2006-01-09

W-Band EPR spectra of [[HC(CMeNAr)(2)]Mn](2) (Ar = 2,6-(i)Pr(2)C(6)H(3)) have been measured at different temperatures. The spectra show a behavior which is typical for an antiferromagnetically coupled dimer with excited states populating upon increasing temperature. By following the intensity variation of the different features of the spectra with temperature, we attributed different groups of resonances to the S = 1, 2, and 3 states of the dimer. Their corresponding spin Hamiltonian parameters were derived from simulations. The zero-field-splitting parameters measured in this way were D(S=1) = 1.57 cm(-1) and E(S=1) = 0.064 cm(-1), D(S=2) = 0.266 cm(-1) and E(S=2) = 0.0045 cm(-1), and D(S=3) = 0.075 cm(-1) and E(S=3) = 0. On the basis of the molecular structure of the system, we could estimate that zero-field splitting (ZFS) is the result of anisotropic exchange and single-ion anisotropic contributions of similar magnitude (|D| approximately 0.2 cm(-1)). These results allow a deeper insight into the electronic structure of the Mn(I) centers in low-coordination environments, further supporting the electronic structure of Mn(I) to be 4s(1)3d(5), as previously indicated by DFT calculations.

Effect of Optical Excitation Energy on the Red Luminescence of Eu(3+) in GaN

National Research Council Canada - National Science Library

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

2005-01-01

...)] transition 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...

Asymmetric monometallic nanorod nanoparticle dimer and related compositions and methods

KAUST Repository

Han, Yu; Huang, Jianfeng; Zhu, Yihan

2016-01-01

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

DFT Study of dimers of dimethyl sulfoxide in gas phase

Directory of Open Access Journals (Sweden)

Reza Fazaeli

2014-10-01

Full Text Available Density functional (DFT calculations at M05-2x/aug-cc-pVDZ level were used to analyze the interactions between dimethyl sulfoxide (DMSO dimers. The structures obtained have been ana-lyzed with the Atoms in Molecules (AIMs and Natural Bond Orbital (NBO methodologies. Four minima were located on the potential energy surface of the dimers. Three types of interac-tions are observed, CH•••O, CH•••S hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the sulfur atom. Stabilization energies of dimers including BSSE and ZPE are in the range 27–40 kJmol-1. The most stable conformers of dimers at DFT level is cyclic structure with antiparallel orientation of S=O groups pairing with three C–H∙∙∙O and a S∙∙∙O interactions.

Photoreactivation of pyrimidine dimers in the DNA of normal and xeroderma pigmentosum cells

International Nuclear Information System (INIS)

Sutherland, B.M.; Oliver, R.; Fuselier, C.O.; Sutherland, J.C.

1976-01-01

Photoproducts formed in the DNA of human cells irradiated with ultraviolet light (uv) were identified as cyclobutyl pyrimidine dimers by their chromatographic mobility, reversibility to monomers upon short wavelength uv irradiation, and comparison of the kinetics of this monomerization with that of authentic cis--syn thymine--thymine dimers prepared by irradiation of thymine in ice. The level of cellular photoreactivation of these dimers reflects the level of photoreactivating enzyme measured in cell extracts. Action spectra for cellular dimer photoreactivation in the xeroderma pigmentosum line XP12BE agree in range (300 nm to at least 577 nm) and maximum (near 400 nm) with that for photoreactivation by purified human photoreactivating enzyme. Normal human cells can also photoreactivate dimers in their DNA. The action spectrum for the cellular monomerization of dimers is similar to that for photoreactivation by the photoreactivating enzyme in extracts of normal human fibroblasts

A new probe of solvent accessibility of bound photosensitizers. 1. Ruthenium(II) and osmium(II) photosensitizers in sodium lauryl sulfate micelles

International Nuclear Information System (INIS)

Hauenstein, B.L. Jr.; Dressick, W.J.; Buell, S.L.; Demas, J.N.; DeGraff, B.A.

1983-01-01

A new method of measuring solvent accessibility of photosensitizers bound to organized media is presented. In particular, the solvent accessibility of a series of ruthenium(II) and osmium(II) photosensitizers bound to sodium lauryl sulfate micelles has been determined. The method takes advantage of the large solvent deuterium effect on the excited-state lifetimes of these complexes. The solvent accessibility of the bound complexes correlates with the hydrophobicity of the ligands. The potential application of this method to a variety of other systems is mentioned

Dimerization of 3He in 3He-4He mixture films

International Nuclear Information System (INIS)

Bashkin, E.

1994-01-01

3 He atoms dissolved in superfluid 4 He may form dimers ( 3 He) 2 in two-dimensional geometries. Dimer formation is studied in films of dilute 3 He- 4 He mixture. After designing a schematic 3 He- 3 He interaction potential, the dimer binding energy is calculated for various substrates. It is shown that 3 He impurity states localized near the substrate give rise to the highest magnitudes of the binding energy. (author). 32 refs., 6 figs.,; 1 tab

Testing the Nature of Kaluza-Klein Excitations at Future Lepton Colliders

International Nuclear Information System (INIS)

Rizzo, Thomas G.

1999-01-01

With one extra dimension, current high precision electroweak data constrain the masses of the first Kaluza-Klein excitations of the Standard Model gauge fields to lie above ≅ 4 TeV. States with masses not much larger than this should be observable at the LHC. However, even for first excitation masses close to this lower bound, the second set of excitations will be too heavy to be produced thus eliminating the possibility of realizing the cleanest signature for KK scenarios. Previous studies of heavy $Z'$ and $W'$ production in this mass range at the LHC have demonstrated that very little information can be obtained about their couplings to the conventional fermions given the limited available statistics and imply that the LHC cannot distinguish an ordinary $Z'$ from the degenerate pair of the first KK excitations of the γ and Z. In this paper we discuss the capability of lepton colliders with center of mass energies significantly below the excitation mass to resolve this ambiguity. In addition, we examine how direct measurements obtained on and near the top of the first excitation peak at lepton colliders can confirm these results. For more than one extra dimension we demonstrate that it is likely that the first KK excitation is too massive to be produced at the LHC

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity

International Nuclear Information System (INIS)

Shrestha, Utsab R.; Bhowmik, Debsindhu; Van Delinder, Kurt W.; Mamontov, Eugene; O’Neill, Hugh

2017-01-01

Here, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in a globular protein, human serum albumin (HSA), and taking advantage of the state-of-the-art inelastic X-ray scattering (IXS) technique. Such excitations demonstrate that the protein becomes softer upon thermal denaturation due to disruption of weak noncovalent bonds. On the other hand, no significant change in the local excitations is detected in ligand- (drugs) bound HSA compared to the ligand-free HSA. These results clearly suggest that the protein conformational flexibility and rigidity are balanced by the native protein structure for biological activity.

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity

Energy Technology Data Exchange (ETDEWEB)

Shrestha, Utsab R. [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy; Bhowmik, Debsindhu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computational Science and Engineering Division; Van Delinder, Kurt W. [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy; Mamontov, Eugene [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical and Engineering Materials Division; O’Neill, Hugh [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biology and Soft Matter Division; Zhang, Qiu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biology and Soft Matter Division; Alatas, Ahmet [Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source; Chu, Xiang-Qiang [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy

2017-01-12

Here, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in a globular protein, human serum albumin (HSA), and taking advantage of the state-of-the-art inelastic X-ray scattering (IXS) technique. Such excitations demonstrate that the protein becomes softer upon thermal denaturation due to disruption of weak noncovalent bonds. On the other hand, no significant change in the local excitations is detected in ligand- (drugs) bound HSA compared to the ligand-free HSA. These results clearly suggest that the protein conformational flexibility and rigidity are balanced by the native protein structure for biological activity.

Glycine transporter dimers: evidence for occurrence in the plasma membrane.

Science.gov (United States)

Bartholomäus, Ingo; Milan-Lobo, Laura; Nicke, Annette; Dutertre, Sébastien; Hastrup, Hanne; Jha, Alok; Gether, Ulrik; Sitte, Harald H; Betz, Heinrich; Eulenburg, Volker

2008-04-18

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 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 by fluorescence resonance energy transfer microscopy. Endoglycosidase treatment and surface biotinylation further revealed that complex-glycosylated GlyTs form dimers located at the cell surface. Furthermore, substitution of tryptophan 469 of GlyT2 by an arginine generated a transporter deficient in dimerization that was retained intracellulary. Based on these results and GlyT structures modeled by using the crystal structure of the bacterial homolog LeuT(Aa), as a template, residues located within the extracellular loop 3 and at the beginning of transmembrane domain 6 are proposed to contribute to the dimerization interface of GlyTs.

Accuracy of D-Dimers to Rule Out Venous Thromboembolism Events across Age Categories

Directory of Open Access Journals (Sweden)

G. Der Sahakian

2010-01-01

Full Text Available Background. Strategies combining pretest clinical assessment and D-dimers measurement efficiently and safely rule out venous thromboembolism events (VTE in low- and intermediate-risk patients. Objectives. As process of ageing is associated with altered concentrations of coagulation markers including an increase in D-dimers levels, we investigated whether D-dimers could reliably rule out VTE across age categories. Method. We prospectively assessed the test performance in 1,004 patients visiting the emergency department during the 6-month period with low or intermediate risk of VTE who also received additional diagnostic procedures. Results. 67 patients had VTE with D-dimers levels above the threshold, and 3 patients displayed D-dimers levels below the threshold. We observed that specificity of D-dimers test decreased in an age-dependent manner. However, sensitivity and negative predictive value remained at very high level in each age category including older patients. Conclusion. We conclude that, even though D-dimers level could provide numerous false positive results in elderly patients, its high sensitivity could reliably help physicians to exclude the diagnosis of VTE in every low- and intermediate-risk patient.

Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases†

Science.gov (United States)

Liang, JingXin; Nguyen, Quynh L.; Matsika, Spiridoula

2016-01-01

Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids’ structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process. PMID:23625036

Analysis of pyrimidine dimer content of isolated DNA by nuclease digestion

International Nuclear Information System (INIS)

Farland, W.H.; Sutherland, B.M.

1980-01-01

Isolated DNA is highly susceptible to degradation by exogenous nucleases. Complete digestion is possible with a number of well-characterized enzymes from a variety of sources. Treatment of DNA with a battery of enzymes including both phosphodiesterase and phosphatase activities yields a mixture of nucleosides and inorganic phosphate (P/sub i/) as a final product. Unlike native DNA, ultraviolet-irradiated DNA is resistant to complete digestion. Setlow et al. demonstrated that the structural changes in the DNA responsible for the nuclease resistance were the formation of cyclobutyl pyrimidine dimers, the major photoproduct in UV-irradiated DNA. Using venom phosphodiesterase, they demonstrated that UV irradiation of DNA affected both the rate and extent of enzymatic hydrolysis. In addition, it was demonstrated that the major nuclease-resistant product of this hydrolysis was an oligonucleotide containing dimerized pyrimidines. Treatment of the DNA to split the dimers, either photochemically or photoenzymatically, rendered the polymer more susceptible to hydrolysis by the phosphodiesterase. The specificity of photoreactivating enzyme for pyrimidine dimers lends support to the role of these structures in conferring nuclease resistance to UV-irradiated DNA. The nuclease resistance of DNA containing dimers has been the basis of several assays for the measurement of these photoproducts. Sutherland and Chamberlin reported the development of a rapid and sensitive assay for dimers in 32 P-labeled DNA

Investigation of split-off dimers on the Si(001)2x1 surface

International Nuclear Information System (INIS)

Schofield, S.R.; O'Brien, J.L.; Curson, N.J.; Simmons, M.Y.; Clark, R.G.

2002-01-01

Full text: A detailed knowledge of the nature of crystalline defects on the Si(001)2x1 surface is becoming increasingly important as more research effort is dedicated to producing atomic-scale electronic devices. Here we present high-resolution scanning tunnelling microscopy (STM) images and ab initio pseudopotential calculations of an unusual defect of the silicon (001) surface called the split-off dimer. In high-resolution filled-state images, split-off dimers appear as a pair of protrusions, in contrast to the surrounding surface dimers that appear as 'bean-shaped' protrusions. We show that π-bonding does not exist between the atoms of the split-off dimer, but instead, the dimer atoms form π-bonds with two second layer atoms as part of a tetramer bonding arrangement. We discuss the strain associated with split-off dimer defects and describe how this strain significantly affects the bonding arrangements and local density of states around these defects

A short autocomplementary sequence plays an essential role in avian sarcoma-leukosis virus RNA dimerization.

Science.gov (United States)

Fossé, P; Motté, N; Roumier, A; Gabus, C; Muriaux, D; Darlix, J L; Paoletti, J

1996-12-24

Retroviral genomes consist of two identical RNA molecules joined noncovalently near their 5'-ends. Recently, two models have been proposed for RNA dimer formation on the basis of results obtained in vitro with human immunodeficiency virus type 1 RNA and Moloney murine leukemia virus RNA. It was first proposed that viral RNA dimerizes by forming an interstrand quadruple helix with purine tetrads. The second model postulates that RNA dimerization is initiated by a loop-loop interaction between the two RNA molecules. In order to better characterize the dimerization process of retroviral genomic RNA, we analyzed the in vitro dimerization of avian sarcoma-leukosis virus (ASLV) RNA using different transcripts. We determined the requirements for heterodimer formation, the thermal dissociation of RNA dimers, and the influence of antisense DNA oligonucleotides on dimer formation. Our results strongly suggest that purine tetrads are not involved in dimer formation. Data show that an autocomplementary sequence located upstream from the splice donor site and within a major packaging signal plays a crucial role in ASLV RNA dimer formation in vitro. This sequence is able to form a stem-loop structure, and phylogenetic analysis reveals that it is conserved in 28 different avian sarcoma and leukosis viruses. These results suggest that dimerization of ASLV RNA is initiated by a loop-loop interaction between two RNA molecules and provide an additional argument for the ubiquity of the dimerization process via loop-loop interaction.

Unphosphorylated rhabdoviridae phosphoproteins form elongated dimers in solution.

Science.gov (United States)

Gerard, Francine C A; Ribeiro, Euripedes de Almeida; Albertini, Aurélie A V; Gutsche, Irina; Zaccai, Guiseppe; Ruigrok, Rob W H; Jamin, Marc

2007-09-11

The phosphoprotein (P) is an essential component of the replication machinery of rabies virus (RV) and vesicular stomatitis virus (VSV), and the oligomerization of P, potentially controlled by phosphorylation, is required for its function. Up to now the stoichiometry of phosphoprotein oligomers has been controversial. Size exclusion chromatography combined with detection by multiangle laser light scattering shows that the recombinant unphosphorylated phosphoproteins from VSV and from RV exist as dimers in solution. Hydrodynamic analysis indicates that the dimers are highly asymmetric, with a Stokes radius of 4.8-5.3 nm and a frictional ratio larger than 1.7. Small-angle neutron scattering experiments confirm the dimeric state and the asymmetry of the structure and yield a radius of gyration of about 5.3 nm and a cross-sectional radius of gyration of about 1.6-1.8 nm. Similar hydrodynamic properties and molecular dimensions were obtained with a variant of VSV phosphoprotein in which Ser60 and Thr62 are substituted by Asp residues and which has been reported previously to mimic phosphorylation by inducing oligomerization and activating transcription. Here, we show that this mutant also forms a dimer with hydrodynamic properties and molecular dimensions similar to those of the wild type protein. However, incubation at 30 degrees C for several hours induced self-assembly of both wild type and mutant proteins, leading to the formation of irregular filamentous structures.

Resolving the Spatial Structures of Bound Hole States in Black Phosphorus.

Science.gov (United States)

Qiu, Zhizhan; Fang, Hanyan; Carvalho, Alexandra; Rodin, A S; Liu, Yanpeng; Tan, Sherman J R; Telychko, Mykola; Lv, Pin; Su, Jie; Wang, Yewu; Castro Neto, A H; Lu, Jiong

2017-11-08

Understanding the local electronic properties of individual defects and dopants in black phosphorus (BP) is of great importance for both fundamental research and technological applications. Here, we employ low-temperature scanning tunnelling microscope (LT-STM) to probe the local electronic structures of single acceptors in BP. We demonstrate that the charge state of individual acceptors can be reversibly switched by controlling the tip-induced band bending. In addition, acceptor-related resonance features in the tunnelling spectra can be attributed to the formation of Rydberg-like bound hole states. The spatial mapping of the quantum bound states shows two distinct shapes evolving from an extended ellipse shape for the 1s ground state to a dumbbell shape for the 2p x excited state. The wave functions of bound hole states can be well-described using the hydrogen-like model with anisotropic effective mass, corroborated by our theoretical calculations. Our findings not only provide new insight into the many-body interactions around single dopants in this anisotropic two-dimensional material but also pave the way to the design of novel quantum devices.

Simulations of the dissociation of small helium clusters with ab initio molecular dynamics in electronically excited states

International Nuclear Information System (INIS)

Closser, Kristina D.; Head-Gordon, Martin; Gessner, Oliver

2014-01-01

The dynamics resulting from electronic excitations of helium clusters were explored using ab initio molecular dynamics. The simulations were performed with configuration interaction singles and adiabatic classical dynamics coupled to a state-following algorithm. 100 different configurations of He 7 were excited into the 2s and 2p manifold for a total of 2800 trajectories. While the most common outcome (90%) was complete fragmentation to 6 ground state atoms and 1 excited state atom, 3% of trajectories yielded bound, He 2 * , and <0.5% yielded an excited helium trimer. The nature of the dynamics, kinetic energy release, and connections to experiments are discussed

Three-photon laser spectroscopy of even-parity bound states of samarium atom

International Nuclear Information System (INIS)

Gomonaj, O.Yi.; Kudelich, O.Yi.

2002-01-01

The energy spectrum of highly-excited even-parity bound states of a Sm atom, lying in the energy range 34421.1 - 36031.8 cm -1 , is investigated using three-photon resonance-ionization spectroscopy. The energies and total momenta of 48 levels are determined. Eight new levels not observed before are discovered. Thirteen intense two-photon transitions, which can be used in the schemes of Sm atom effective photoionization, are observed

Covalent α-synuclein dimers: chemico-physical and aggregation properties.

Directory of Open Access Journals (Sweden)

Micaela Pivato

Full Text Available The aggregation of α-synuclein into amyloid fibrils constitutes a key step in the onset of Parkinson's disease. Amyloid fibrils of α-synuclein are the major component of Lewy bodies, histological hallmarks of the disease. Little is known about the mechanism of aggregation of α-synuclein. During this process, α-synuclein forms transient intermediates that are considered to be toxic species. The dimerization of α-synuclein could represent a rate-limiting step in the aggregation of the protein. Here, we analyzed four covalent dimers of α-synuclein, obtained by covalent link of the N-terms, C-terms, tandem cloning of two sequences and tandem juxtaposition in one protein of the 1-104 and 29-140 sequences. Their biophysical properties in solution were determined by CD, FT-IR and NMR spectroscopies. SDS-induced folding was also studied. The fibrils formation was analyzed by ThT and polarization fluorescence assays. Their morphology was investigated by TEM and AFM-based quantitative morphometric analysis. All dimers were found to be devoid of ordered secondary structure under physiological conditions and undergo α-helical transition upon interaction with SDS. All protein species are able to form amyloid-like fibrils. The reciprocal orientation of the α-synuclein monomers in the dimeric constructs affects the kinetics of the aggregation process and a scale of relative amyloidogenic propensity was determined. Structural investigations by FT IR spectroscopy, and proteolytic mapping of the fibril core did not evidence remarkable difference among the species, whereas morphological analyses showed that fibrils formed by dimers display a lower and diversified level of organization in comparison with α-synuclein fibrils. This study demonstrates that although α-synuclein dimerization does not imply the acquisition of a preferred conformation by the participating monomers, it can strongly affect the aggregation properties of the molecules. The results

Pyrimidine dimer sites associated with the daughter DNA strands in uv-irradiated human fibroblasts

Energy Technology Data Exchange (ETDEWEB)

Lehmann, A R; Kirk-Bell, S [Sussex Univ., Brighton (UK)

1978-03-01

Pyrimidine dimer sites associated with the newly-synthesized DNA were detected during post-replication repair of DNA in uv-irradiated human fibroblasts. These pyrimidine dimer sites were inferred from a decrease in the molecular weight of pulse-labelled DNA after treatment with an extract of Micrococcus luteus containing uv-specific endonuclease activity. In DNA synthesized immediately after irradiation, the frequency of these daughter strand dimer sites was 7 to 20% of that in the parental DNA. Such sites were found in fibroblasts from normal donors and from xeroderma pigmentosum patients (with defects in excision-repair or post-replication repair). They were excised from the DNA of normal cells. As the time between uv irradiation and pulse-labelling was increased, the frequency of dimer sites associated with the labelled DNA decreased. If the pulse-label was delivered 6 h after irradiation of normal cells or excision-defective xeroderma pigmentosum cells, no dimer sites were detected in the labelled DNA. It has usually been assumed that daughter-strand dimer sites were the result of recombinational exchanges. The assay procedure used in these experiments and in similar experiments of others did not distinguish between labelled DNA containing pyrimidine dimers within the labelled section, and labelled DNA which did not contain pyrimidine dimers but was attached to unlabelled DNA which did contain dimers. The latter structures would arise during normal replication immediately following uv irradiation of mammalian cells. Calculations are presented which suggest that a significant proportion and conceivably all of the dimer sites associated with the daughter strands may have arisen in this way, rather than from recombinational exchanges as has been generally assumed.

Pyrimidine dimer sites associated with the daughter DNA strands in UV-irradiated human fibroblasts

International Nuclear Information System (INIS)

Lehmann, A.R.; Kirk-Bell, S.

1978-01-01

Pyrimidine dimer sites associated with the newly-synthesized DNA were detected during post-replication repair of DNA in UV-irradiated human fibroblasts. These pyrimidine dimer sites were inferred from a decrease in the molecular weight of pulse-labelled DNA after treatment with an extract of Micrococcus luteus containing UV-specific endonuclease activity. In DNA synthesized immediately after irradiation the frequency of these daughter strand dimer sites was 7-20% of that in the parental DNA. Such sites were found in fibroblasts from normal donors and from xeroderma pigmentosum patients (with defects in excision-repair or post-replication repair). They were excised from the DNA of normal cells. As the time between UV-irradiation and pulse-labelling was increased, the frequency of dimer sites associated with the labelled DNA decreased. If the pulse-label was delivered 6 h after irradiation of normal cells or excision-defective xeroderma pigmentosum cells, no dimer sites were detected in the labelled DNA. It has usually been assumed that daughter-strand dimer sites were the result of recombinational exchanges. The assay procedure used in these experiments and in similar experiments of others did not distinguish between labelled DNA containing pyrimidine dimers within the labelled section, and labelled DNA which did not contain pyrimidine dimers but was attached to unlabelled DNA which did contain dimers. The latter structures would arise during normal replication immediately following UV-irradiation of mammalian cells. Calculations are presented which suggest that a significant proportion and conceivably all of the dimer sites associated with the daughter strands may have arisen in this way, rather than from recombinational exchanges as has been generally assumed. (author)

Single-molecule photobleaching reveals increased MET receptor dimerization upon ligand binding in intact cells

International Nuclear Information System (INIS)

Dietz, Marina S; Haße, Daniel; Ferraris, Davide M; Göhler, Antonia; Niemann, Hartmut H; Heilemann, Mike

2013-01-01

The human receptor tyrosine kinase MET and its ligand hepatocyte growth factor/scatter factor are essential during embryonic development and play an important role during cancer metastasis and tissue regeneration. In addition, it was found that MET is also relevant for infectious diseases and is the target of different bacteria, amongst them Listeria monocytogenes that induces bacterial uptake through the surface protein internalin B. Binding of ligand to the MET receptor is proposed to lead to receptor dimerization. However, it is also discussed whether preformed MET dimers exist on the cell membrane. To address these issues we used single-molecule fluorescence microscopy techniques. Our photobleaching experiments show that MET exists in dimers on the membrane of cells in the absence of ligand and that the proportion of MET dimers increases significantly upon ligand binding. Our results indicate that partially preformed MET dimers may play a role in ligand binding or MET signaling. The addition of the bacterial ligand internalin B leads to an increase of MET dimers which is in agreement with the model of ligand-induced dimerization of receptor tyrosine kinases.

Circuit lower bounds in bounded arithmetics

Czech Academy of Sciences Publication Activity Database

Pich, Ján

2015-01-01

Roč. 166, č. 1 (2015), s. 29-45 ISSN 0168-0072 R&D Projects: GA AV ČR IAA100190902 Keywords : bounded arithmetic * circuit lower bounds Subject RIV: BA - General Mathematics Impact factor: 0.582, year: 2015 http://www.sciencedirect.com/science/article/pii/S0168007214000888

Spin Quantum Tunneling via Entangled States in a Dimer of Exchange-Coupled Single-Molecule Magnets

Science.gov (United States)

Tiron, R.; Wernsdorfer, W.; Foguet-Albiol, D.; Aliaga-Alcalde, N.; Christou, G.

2003-11-01

A new family of supramolecular, antiferromagnetically exchange-coupled dimers of single-molecule magnets (SMMs) has recently been reported. Each SMM acts as a bias on its neighbor, shifting the quantum tunneling resonances of the individual SMMs. Hysteresis loop measurements on a single crystal of SMM dimers have now established quantum tunneling of the magnetization via entangled states of the dimer. This shows that the dimer really does behave as a quantum mechanically coupled dimer, and also allows the measurement of the longitudinal and transverse superexchange coupling constants.

Light activation of the LOV protein vivid generates a rapidly exchanging dimer.

Science.gov (United States)

Zoltowski, Brian D; Crane, Brian R

2008-07-08

The fungal photoreceptor Vivid (VVD) plays an important role in the adaptation of blue-light responses in Neurospora crassa. VVD, an FAD-binding LOV (light, oxygen, voltage) protein, couples light-induced cysteinyl adduct formation at the flavin ring to conformational changes in the N-terminal cap (Ncap) of the VVD PAS domain. Size-exclusion chromatography (SEC), equilibrium ultracentrifugation, and static and dynamic light scattering show that these conformational changes generate a rapidly exchanging VVD dimer, with an expanded hydrodynamic radius. A three-residue N-terminal beta-turn that assumes two different conformations in a crystal structure of a VVD C71V variant is essential for light-state dimerization. Residue substitutions at a critical hinge between the Ncap and PAS core can inhibit or enhance dimerization, whereas a Tyr to Trp substitution at the Ncap-PAS interface stabilizes the light-state dimer. Cross-linking through engineered disulfides indicates that the light-state dimer differs considerably from the dark-state dimer found in VVD crystal structures. These results verify the role of Ncap conformational changes in gating the photic response of N. crassa and indicate that LOV-LOV homo- or heterodimerization may be a mechanism for regulating light-activated gene expression.

Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus

DEFF Research Database (Denmark)

Lauritsen, Iben; Willemoës, Martin; Jensen, Kaj Frank

2011-01-01

CTP synthase catalyzes the last committed step in de novo pyrimidine-nucleotide biosynthesis. Active CTP synthase is a tetrameric enzyme composed of a dimer of dimers. The tetramer is favoured in the presence of the substrate nucleotides ATP and UTP; when saturated with nucleotide, the tetramer...... completely dominates the oligomeric state of the enzyme. Furthermore, phosphorylation has been shown to regulate the oligomeric states of the enzymes from yeast and human. The crystal structure of a dimeric form of CTP synthase from Sulfolobus solfataricus has been determined at 2.5 Å resolution...

The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs.

Science.gov (United States)

Raeber, Alexandra E; Wong, Bryan M

2015-05-12

We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.

Preparation of 177Lu-DOTA/DTPA-Bz-Cys-RGD dimer and biodistribution evaluation in normal mice

International Nuclear Information System (INIS)

Sheng Feng; Jia Bing; Wang Fan; He Weiwei; Liu Zhaofei; Zhao Huiyun

2008-01-01

177 Lu-DOTA-Bz-Cys-RGD dimer and 177 Lu-DTPA-Bz-Cys-RGD dimer were prepared, and the in vitro and in vivo properties were compared. TLC and HPLC show that the labeling yields of two radiolabeled compounds are more than 95% under optimal conditions (pH=5.0, reacting at 100 degree C for 15-20 min), and the two radiolabeled compounds show pretty good in vitro stability. HPLC analyses and lg P values reveal that lipophilicity of 177 Lu-DOTA-Bz-Cys- RGD dimer is higher than 177 Lu-DTPA-Bz-Cys-RGD dimer. The uptake of 177 Lu-DTPA-Bz-Cys- RGD dimer in other tissues is significantly higher than that of 177 Lu-DOTA-Bz-Cys-RGD dimer at 4 h postinjection, except for blood and spleen. The in vivo stability of 177 Lu-DOTA-Bz-Cys-RGD dimer is much better than 177 Lu-DTPA-Bz-Cys-RGD dimer. Bz-DOTA is an ideal bifunctional chelator for 177 Lu labeling of RGD dimer. (authors)

Adiabatic physics of an exchange-coupled spin-dimer system: Magnetocaloric effect, zero-point fluctuations, and possible two-dimensional universal behavior

International Nuclear Information System (INIS)

Brambleby, J.; Goddard, P. A.; Singleton, John; Jaime, Marcelo; Lancaster, T.

2017-01-01

We present the magnetic and thermal properties of the bosonic-superfluid phase in a spin-dimer network using both quasistatic and rapidly changing pulsed magnetic fields. The entropy derived from a heat-capacity study reveals that the pulsed-field measurements are strongly adiabatic in nature and are responsible for the onset of a significant magnetocaloric effect (MCE). In contrast to previous predictions we show that the MCE is not just confined to the critical regions, but occurs for all fields greater than zero at sufficiently low temperatures. We explain the MCE using a model of the thermal occupation of exchange-coupled dimer spin states and highlight that failure to take this effect into account inevitably leads to incorrect interpretations of experimental results. In addition, the heat capacity in our material is suggestive of an extraordinary contribution from zero-point fluctuations and appears to indicate universal behavior with different critical exponents at the two field-induced critical points. Finally, the data at the upper critical point, combined with the layered structure of the system, are consistent with a two-dimensional nature of spin excitations in the system.

Finite element (fem) Kohn-Sham density functional approach to lighter dimers

International Nuclear Information System (INIS)

Kolb, D.; Kopylow, A.V.; Duesterhoft, C.; Heinemann, D.

1998-01-01

The very accurate Finite Element Method has been employed for a comparative study of various combinations of frequently used exchange and correlation density functionals both local and non-local. We also investigated the properties of the Colle- Salvetti orbital functional in KLI approximation. All these studies were done for atoms and dimers of the sp-shell which exhibits a rich variety of system dependent properties. Moving through the sp-shell we compare binding energies, radii and vibrational frequencies for ground state and excited configurations and also compute potential energy surfaces (curves) as a function of internuclear distance. The dependency of total energies on occupation number variations of the Kohn-Sham orbitals provides inferences on polarisation and alignment. An interesting question is how to incorporate at least approximately non- relativistic strict physical conservation laws like spin S 2 and S z , angular momentum L 2 and L z and parity and how to allow for symmetry breaking necessary for the dissociation e.g. of N 2 . (Copyright (1998) World Scientific Publishing Co. Pte. Ltd)

Structure factors for the alternating Heisenberg chain

International Nuclear Information System (INIS)

Hamer, C.J.; Zheng, W.

2004-01-01

Full text: We develop a linked cluster method to calculate the spectral weights of many-particle excitations at zero temperature. The dynamical structure factor, which is measured in neutron scattering experiments, is expressed as a sum of 'exclusive' structure factors, each representing the contribution of a specific excited state. We apply these methods to the alternating Heisenberg chain, where complete wave-vector and frequency dependent spectral weights for one- and two-particle excitations (continuum and bound states) are calculated near the dimerized limit (λ = O). We also examine the variation of the spectral weights as the uniform chain (λ = 1) is approached. In agreement with Schmidt and Uhrig, we find that the spectral weight is dominated by 2-triplet states, even at λ 1, which implies that a description in terms of triplet-pair excitations remains a good quantitative description even for the uniform, undimerized chain

Time-resolved photon echoes from donor-bound excitons in ZnO epitaxial layers

Science.gov (United States)

Poltavtsev, S. V.; Kosarev, A. N.; Akimov, I. A.; Yakovlev, D. R.; Sadofev, S.; Puls, J.; Hoffmann, S. P.; Albert, M.; Meier, C.; Meier, T.; Bayer, M.

2017-07-01

The coherent optical response from 140 nm and 65 nm thick ZnO epitaxial layers is studied using four-wave-mixing spectroscopy with picosecond temporal resolution. Resonant excitation of neutral donor-bound excitons results in two-pulse and three-pulse photon echoes. For the donor-bound A exciton (D0XA ) at temperature of 1.8 K we evaluate optical coherence times T2=33 -50 ps corresponding to homogeneous line widths of 13 -19 μ eV , about two orders of magnitude smaller as compared with the inhomogeneous broadening of the optical transitions. The coherent dynamics is determined mainly by the population decay with time T1=30 -40 ps, while pure dephasing is negligible. Temperature increase leads to a significant shortening of T2 due to interaction with acoustic phonons. In contrast, the loss of coherence of the donor-bound B exciton (D0XB ) is significantly faster (T2=3.6 ps ) and governed by pure dephasing processes.

Towards first-principles calculation of electronic excitations in the ring of the protein-bound bacteriochlorophylls

Science.gov (United States)

Polyakov, Igor V.; Khrenova, Maria G.; Moskovsky, Alexander A.; Shabanov, Boris M.; Nemukhin, Alexander V.

2018-04-01

Modeling electronic excitation of bacteriochlorophyll (BChl) molecules in light-harvesting (LH) antennae from photosynthetic centers presents a challenge for the quantum theory. We report on a quantum chemical study of the ring of 32 BChl molecules from the bacterial core complex LH1-RC. Diagonal and off-diagonal elements of the excitonic Hamiltonian matrices are estimated in quantum chemical calculations of relevant fragments using the TD-DFT and CIS approaches. The deviation of the computed excitation energy of this BChl system from the experimental data related to the Qy band maximum of this LH1-RC complex is about 0.2 eV. We demonstrate that corrections due to improvement in modeling of an individual BChl molecule and due to contributions from the protein environment are in the range of the obtained discrepancy between theory and experiment. Differences between results of the excitonic model and direct quantum chemical calculations of BChl aggregates fall in the same range.

The Rate of Vitamin A Dimerization in Lipofuscinogenesis, Fundus Autofluorescence, Retinal Senescence and Degeneration.

Science.gov (United States)

Washington, Ilyas; Saad, Leonide

2016-01-01

One of the earliest events preceding several forms of retinal degeneration is the formation and accumulation of vitamin A dimers in the retinal pigment epithelium (RPE) and underlying Bruch's membrane (BM). Such degenerations include Stargardt disease, Best disease, forms of retinitis pigmentosa, and age-related macular degeneration (AMD). Since their discovery in the 1990's, dimers of vitamin A, have been postulated as chemical triggers driving retinal senescence and degeneration. There is evidence to suggest that the rate at which vitamin A dimerizes and the eye's response to the dimerization products may dictate the retina's lifespan. Here, we present outstanding questions, finding the answers to which may help to elucidate the role of vitamin A dimerization in retinal degeneration.

Gap solitons in a chain of split-ring resonator dimers

Energy Technology Data Exchange (ETDEWEB)

Cui, Wei-na, E-mail: cuiweinaa@163.com [Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094 (China); Li, Hong-xia, E-mail: hxli@njust.edu.cn [Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094 (China); Sun, Min [Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094 (China); Bu, Ling-bing [Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Key Laboratory for Aerosol-Cloud-Precipitation of China Meteorological Administration, Key Laboratory of Meteorological Disaster of Ministry of Education, Nanjing University of Information Science and Technology, Nanjing 210044 (China)

2017-06-21

Dynamics of a chain of split-ring resonator dimers with Kerr nonlinear interaction are investigated. A dimer is built as a pair of coupled split-ring resonators with different size. It is shown that the gap solitons with frequency lying in the gap exist due to the interaction of the discreteness and nonlinearity. Such localized structures are studied in the phase plane and analytical and numerical expressions are also obtained. - Highlights: • The coupling of the two modes is studied in the chain of split-ring resonator dimers with Kerr nonlinear interaction. • The evolution of the localized structures is studied in the phase plane. • This system supports gap solitons with the frequencies lying in the gap.

Thermal entanglement in an orthogonal dimer-plaquette chain with alternating Ising–Heisenberg coupling

International Nuclear Information System (INIS)

Paulinelli, H G; De Souza, S M; Rojas, Onofre

2013-01-01

In this paper we explore the entanglement in an orthogonal dimer-plaquette Ising–Heisenberg chain, assembled between plaquette edges, also known as orthogonal dimer plaquettes. The quantum entanglement properties involving an infinite chain structure are quite important, not only because the mathematical calculation is cumbersome but also because real materials are well represented by infinite chains. Using the local gauge symmetry of this model, we are able to map onto a simple spin-1 like Ising and spin-1/2 Heisenberg dimer model with single effective ion anisotropy. Thereafter this model can be solved using the decoration transformation and transfer matrix approach. First, we discuss the phase diagram at zero temperature of this model, where we find five ground states, one ferromagnetic, one antiferromagnetic, one triplet–triplet disordered and one triplet–singlet disordered phase, beside a dimer ferromagnetic–antiferromagnetic phase. In addition, we discuss the thermodynamic properties such as entropy, where we display the residual entropy. Furthermore, using the nearest site correlation function it is possible also to analyze the pairwise thermal entanglement for both orthogonal dimers. Additionally, we discuss the threshold temperature of the entangled region as a function of Hamiltonian parameters. We find a quite interesting thin reentrance threshold temperature for one of the dimers, and we also discuss the differences and similarities for both dimers. (paper)

Bounds on the vibrational energy that can be harvested from random base motion

Science.gov (United States)

Langley, R. S.

2015-03-01

This paper is concerned with the development of upper bounds on the energy harvesting performance of a general multi-degree-of-freedom nonlinear electromechanical system that is subjected to random base motion and secondary applied periodic forces. The secondary forces are applied with the aim of enhancing the energy harvested from the base motion, and they may constitute direct excitation, or they may produce parametric terms in the equations of motion. It is shown that when the base motion has white noise acceleration then the power input by the base is always πS0 M / 2 where S0 is the single sided spectral density of the acceleration, and M is the mass of the system. This implies that although the secondary forces may enhance the energy harvested by causing a larger fraction of the power input from the base to be harvested rather than dissipated, there is an upper limit on the power that can be harvested. Attention is then turned to narrow band excitation, and it is found that in the absence of secondary forces a bound can be derived for a single degree of freedom system with linear damping and arbitrary nonlinear stiffness. The upper bound on the power input by the base is πM max [ S (ω) ] / 2, where S (ω) is the single sided base acceleration spectrum. The validity of this result for more general systems is found to be related to the properties of the first Wiener kernel, and this issue is explored analytically and by numerical simulation.

Synthesis and Diels–Alder cycloaddition reaction of norbornadiene and benzonorbornadiene dimers

Directory of Open Access Journals (Sweden)

Bilal Nişancı

2009-08-01

Full Text Available Dimeric forms of norbornadiene and benzonorbornadiene were synthesized starting with known monobromide derivatives. The Diels–Alder cycloaddition reaction of dimers with TCNE and PTAD was investigated and new norbornenoid polycyclics were obtained. All compounds were characterized properly using NMR spectroscopy.

Theoretical Insights into a CO Dimerization Mechanism in CO2 Electroreduction.

Science.gov (United States)

Montoya, Joseph H; Shi, Chuan; Chan, Karen; Nørskov, Jens K

2015-06-04

In this work, we present DFT simulations that demonstrate the ability of Cu to catalyze CO dimerization in CO2 and CO electroreduction. We describe a previously unreported CO dimer configuration that is uniquely stabilized by a charged water layer on both Cu(111) and Cu(100). Without this charged water layer at the metal surface, the formation of the CO dimer is prohibitively endergonic. Our calculations also demonstrate that dimerization should have a lower activation barrier on Cu(100) than Cu(111), which, along with a more exergonic adsorption energy and a corresponding higher coverage of *CO, is consistent with experimental observations that Cu(100) has a high activity for C-C coupling at low overpotentials. We also demonstrate that this effect is present with cations other than H(+), a finding that is consistent with the experimentally observed pH independence of C2 formation on Cu.

Conformational study of the protegrin-1 (PG-1 dimer interaction with lipid bilayers and its effect

Directory of Open Access Journals (Sweden)

Nussinov Ruth

2007-04-01

Full Text Available Abstract Background Protegrin-1 (PG-1 is known as a potent antibiotic peptide; it prevents infection via an attack on the membrane surface of invading microorganisms. In the membrane, the peptide forms a pore/channel through oligomerization of multiple subunits. Recent experimental and computational studies have increasingly unraveled the molecular-level mechanisms underlying the interactions of the PG-1 β-sheet motifs with the membrane. The PG-1 dimer is important for the formation of oligomers, ordered aggregates, and for membrane damaging effects. Yet, experimentally, different dimeric behavior has been observed depending on the environment: antiparallel in the micelle environment, and parallel in the POPC bilayer. The experimental structure of the PG-1 dimer is currently unavailable. Results Although the β-sheet structures of the PG-1 dimer are less stable in the bulk water environment, the dimer interface is retained by two intermolecular hydrogen bonds. The formation of the dimer in the water environment implies that the pathway of the dimer invasion into the membrane can originate from the bulk region. In the initial contact with the membrane, both the antiparallel and parallel β-sheet conformations of the PG-1 dimer are well preserved at the amphipathic interface of the lipid bilayer. These β-sheet structures illustrate the conformations of PG-1 dimer in the early stage of the membrane attack. Here we observed that the activity of PG-1 β-sheets on the bilayer surface is strongly correlated with the dimer conformation. Our long-term goal is to provide a detailed mechanism of the membrane-disrupting effects by PG-1 β-sheets which are able to attack the membrane and eventually assemble into the ordered aggregates. Conclusion In order to understand the dimeric effects leading to membrane damage, extensive molecular dynamics (MD simulations were performed for the β-sheets of the PG-1 dimer in explicit water, salt, and lipid bilayers

How different is the borazine-acetylene dimer from the benzene-acetylene dimer? A matrix isolation infrared and ab initio quantum chemical study

Science.gov (United States)

Verma, Kanupriya; Viswanathan, K. S.; Majumder, Moumita; Sathyamurthy, N.

2017-11-01

The 1:1 dimer of borazine-acetylene has been studied for the first time, both experimentally and computationally. The borazine-acetylene dimer was trapped in Ar and N2 matrices, and studied using infrared spectroscopy. Our experiments clearly revealed two isomers of the borazine-acetylene complex, one in which the N-H of borazine interacted with the carbon of acetylene, and another in which the C-H of acetylene formed a hydrogen bond with a nitrogen atom of borazine. The formation of both isomers in the matrix was evidenced by shifts in the vibrational frequencies of the appropriate modes. Reassuringly, the experimental observations were corroborated by our computations using the second-order Møller-Plesset perturbation theoretic method and coupled-cluster singles, doubles and perturbative triples method in conjunction with different Dunning basis sets, which indicated both these isomers to be stable minima, with the N-HṡṡṡC complex being the global minimum. Atoms-in-molecules and energy decomposition analysis were also carried out for the different isomers of the dimer. These studies reveal that replacing the three C-C linkages in benzene with three B-N linkages in borazine modifies the interaction in the dimer sufficiently, to result in a different potential energy landscape for the borazine-acetylene system when compared with the benzene-acetylene system.

Breaking symmetry in the structure determination of (large) symmetric protein dimers

Energy Technology Data Exchange (ETDEWEB)

Gaponenko, Vadim; Altieri, Amanda S.; Li, Jess; Byrd, R. Andrew [National Cancer Institute, Structural Biophysics Laboratory (United States)], E-mail: rabyrd@ncifcrf.gov

2002-10-15

We demonstrate a novel methodology to disrupt the symmetry in the NMR spectra of homodimers. A paramagnetic probe is introduced sub-stoichiometrically to create an asymmetric system with the paramagnetic probe residing on only one monomer within the dimer. This creates sufficient magnetic anisotropy for resolution of symmetry-related overlapped resonances and, consequently, detection of pseudocontact shifts and residual dipolar couplings specific to each monomeric component. These pseudocontact shifts can be readily incorporated into existing structure refinement calculations and enable determination of monomer orientation within the dimeric protein. This methodology can be widely used for solution structure determination of symmetric dimers.

Substrate-Induced Dimerization of Engineered Monomeric Variants of Triosephosphate Isomerase from Trichomonas vaginalis.

Directory of Open Access Journals (Sweden)

Samuel Lara-Gonzalez

Full Text Available The dimeric nature of triosephosphate isomerases (TIMs is maintained by an extensive surface area interface of more than 1600 Å2. TIMs from Trichomonas vaginalis (TvTIM are held in their dimeric state by two mechanisms: a ball and socket interaction of residue 45 of one subunit that fits into the hydrophobic pocket of the complementary subunit and by swapping of loop 3 between subunits. TvTIMs differ from other TIMs in their unfolding energetics. In TvTIMs the energy necessary to unfold a monomer is greater than the energy necessary to dissociate the dimer. Herein we found that the character of residue I45 controls the dimer-monomer equilibrium in TvTIMs. Unfolding experiments employing monomeric and dimeric mutants led us to conclude that dimeric TvTIMs unfold following a four state model denaturation process whereas monomeric TvTIMs follow a three state model. In contrast to other monomeric TIMs, monomeric variants of TvTIM1 are stable and unexpectedly one of them (I45A is only 29-fold less active than wild-type TvTIM1. The high enzymatic activity of monomeric TvTIMs contrast with the marginal catalytic activity of diverse monomeric TIMs variants. The stability of the monomeric variants of TvTIM1 and the use of cross-linking and analytical ultracentrifugation experiments permit us to understand the differences between the catalytic activities of TvTIMs and other marginally active monomeric TIMs. As TvTIMs do not unfold upon dimer dissociation, herein we found that the high enzymatic activity of monomeric TvTIM variants is explained by the formation of catalytic dimeric competent species assisted by substrate binding.

Roughness effect on the efficiency of dimer antenna based biosensor

Directory of Open Access Journals (Sweden)

D. Barchiesi

2012-09-01

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.

Ising tricriticality in the extended Hubbard model with bond dimerization

Science.gov (United States)

Fehske, Holger; Ejima, Satoshi; Lange, Florian; Essler, Fabian H. L.

We explore the quantum phase transition between Peierls and charge-density-wave insulating states in the one-dimensional, half-filled, extended Hubbard model with explicit bond dimerization. We show that the critical line of the continuous Ising transition terminates at a tricritical point, belonging to the universality class of the tricritical Ising model with central charge c=7/10. Above this point, the quantum phase transition becomes first order. Employing a numerical matrix-product-state based (infinite) density-matrix renormalization group method we determine the ground-state phase diagram, the spin and two-particle charge excitations gaps, and the entanglement properties of the model with high precision. Performing a bosonization analysis we can derive a field description of the transition region in terms of a triple sine-Gordon model. This allows us to derive field theory predictions for the power-law (exponential) decay of the density-density (spin-spin) and bond-order-wave correlation functions, which are found to be in excellent agreement with our numerical results. This work was supported by Deutsche Forschungsgemeinschaft (Germany), SFB 652, project B5, and by the EPSRC under Grant No. EP/N01930X/1 (FHLE).

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

Science.gov (United States)

Verma, Vikash; Mallik, Leena; Hariadi, Rizal F.; Sivaramakrishnan, Sivaraj; Skiniotis, Georgios; Joglekar, Ajit P.

2015-01-01

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. PMID:26348722

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

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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.

Large enhancement of functional activity of active site-inhibited factor VIIa due to protein dimerization: insights into mechanism of assembly/disassembly from tissue factor.

Science.gov (United States)

Stone, Matthew D; Harvey, Stephen B; Martinez, Michael B; Bach, Ronald R; Nelsestuen, Gary L

2005-04-26

Active site-inhibited blood clotting factor VIIa (fVIIai) binds to tissue factor (TF), a cell surface receptor that is exposed upon injury and initiates the blood clotting cascade. FVIIai blocks binding of the corresponding enzyme (fVIIa) or zymogen (fVII) forms of factor VII and inhibits coagulation. Although several studies have suggested that fVIIai may have superior anticoagulation effects in vivo, a challenge for use of fVIIai is cost of production. This study reports the properties of dimeric forms of fVIIai that are cross-linked through their active sites. Dimeric wild-type fVIIai was at least 75-fold more effective than monomeric fVIIai in blocking fVIIa association with TF. The dimer of a mutant fVIIai with higher membrane affinity was 1600-fold more effective. Anticoagulation by any form of fVIIai differed substantially from agents such as heparin and showed a delayed mode of action. Coagulation proceeded normally for the first minutes, and inhibition increased as equilibrium binding was established. It is suggested that association of fVIIa(i) with TF in a collision-dependent reaction gives equal access of inhibitor and enzyme to TF. Assembly was not influenced by the higher affinity and slower dissociation of the dimer. As a result, anticoagulation was delayed until the reaction reached equilibrium. Properties of different dissociation experiments suggested that dissociation of fVIIai from TF occurred by a two-step mechanism. The first step was separation of TF-fVIIa(i) while both proteins remained bound to the membrane, and the second step was dissociation of the fVIIa(i) from the membrane. These results suggest novel actions of fVIIai that distinguish it from most of the anticoagulants that block later steps of the coagulation cascade.

Study of structural stability and damaging effect on membrane for four Aβ42 dimers.

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Wei Feng

Full Text Available Increasing evidence shows that Aβ oligomers are key pathogenic molecules in Alzheimer's disease. Among Aβ oligomers, dimer is the smallest aggregate and toxic unit. Therefore, understanding its structural and dynamic properties is quite useful to prevent the formation and toxicity of the Aβ oligomers. In this study, we performed molecular dynamic simulations on four Aβ42 dimers, 2NCb, CNNC, NCNC and NCCN, within the hydrated DPPC membrane. Four Aβ42 dimers differ in the arrangements of two Aβ42 peptides. This study aims to investigate the impact of aggregation pattern of two Aβ peptides on the structural stability of the Aβ42 dimer and its disruption to the biological membrane. The MD results demonstrate that the NCCN, CNNC and NCNC have the larger structural fluctuation at the N-terminus of Aβ42 peptide, where the β-strand structure converts into the coil structure. The loss of the N-terminal β-strand further impairs the aggregate ability of Aβ42 dimer. In addition, inserting Aβ42 dimer into the membrane can considerably decrease the average APL of DPPC membrane. Moreover this decrease effect is largely dependent on the distance to the location of Aβ42 dimer and its secondary structure forms. Based on the results, the 2NCb is considered as a stable dimeric unit for aggregating the larger Aβ42 oligomer, and has a potent ability to disrupt the membrane.

Perceptron Mistake Bounds

OpenAIRE

Mohri, Mehryar; Rostamizadeh, Afshin

2013-01-01

We present a brief survey of existing mistake bounds and introduce novel bounds for the Perceptron or the kernel Perceptron algorithm. Our novel bounds generalize beyond standard margin-loss type bounds, allow for any convex and Lipschitz loss function, and admit a very simple proof.

Alkane dimers interaction

DEFF Research Database (Denmark)

Ferrighi, Lara; Madsen, Georg Kent Hellerup; Hammer, Bjørk

2010-01-01

The interaction energies of a series of n-alkane dimers, from methane to decane, have been investigated with Density Functional Theory (DFT), using the MGGA-M06-L density functional. The results are compared both to the available wavefunction-based values as well as to dispersion corrected DFT...... values. The MGGA-M06-L density functional is a semi-local functional designed and has proven to provide accurate estimates of dispersion interactions for several systems at moderate computational cost. In the present application, it reproduces the trends obtained by the more expensive wavefunction...

Using dimers to measure biosignatures and atmospheric pressure for terrestrial exoplanets.

Science.gov (United States)

Misra, Amit; Meadows, Victoria; Claire, Mark; Crisp, Dave

2014-02-01

We present a new method to probe atmospheric pressure on Earth-like planets using (O2-O2) dimers in the near-infrared. We also show that dimer features could be the most readily detectable biosignatures for Earth-like atmospheres and may even be detectable in transit transmission with the James Webb Space Telescope (JWST). The absorption by dimers changes more rapidly with pressure and density than that of monomers and can therefore provide additional information about atmospheric pressures. By comparing the absorption strengths of rotational and vibrational features to the absorption strengths of dimer features, we show that in some cases it may be possible to estimate the pressure at the reflecting surface of a planet. This method is demonstrated by using the O2 A band and the 1.06 μm dimer feature, either in transmission or reflected spectra. It works best for planets around M dwarfs with atmospheric pressures between 0.1 and 10 bar and for O2 volume mixing ratios above 50% of Earth's present-day level. Furthermore, unlike observations of Rayleigh scattering, this method can be used at wavelengths longer than 0.6 μm and is therefore potentially applicable, although challenging, to near-term planet characterization missions such as JWST. We also performed detectability studies for JWST transit transmission spectroscopy and found that the 1.06 and 1.27 μm dimer features could be detectable (SNR>3) for an Earth analogue orbiting an M5V star at a distance of 5 pc. The detection of these features could provide a constraint on the atmospheric pressure of an exoplanet and serve as biosignatures for oxygenic photosynthesis. We calculated the required signal-to-noise ratios to detect and characterize O2 monomer and dimer features in direct imaging-reflected spectra and found that signal-to-noise ratios greater than 10 at a spectral resolving power of R=100 would be required.

Engineering of a novel Ca2+-regulated kinesin molecular motor using a calmodulin dimer linker

International Nuclear Information System (INIS)

Shishido, Hideki; Maruta, Shinsaku

2012-01-01

Highlights: ► Engineered kinesin–M13 and calmodulin involving single cysteine were prepared. ► CaM mutant was cross-linked to dimer by bifunctional thiol reactive reagent. ► Kinesin–M13 was dimerized via CaM dimer in the presence of calcium. ► Function of the engineered kinesin was regulated by a Ca 2+ -calmodulin dimer linker. -- Abstract: The kinesin–microtubule system holds great promise as a molecular shuttle device within biochips. However, one current barrier is that such shuttles do not have “on–off” control of their movement. Here we report the development of a novel molecular motor powered by an accelerator and brake system, using a kinesin monomer and a calmodulin (CaM) dimer. The kinesin monomer, K355, was fused with a CaM target peptide (M13 peptide) at the C-terminal part of the neck region (K355–M13). We also prepared CaM dimers using CaM mutants (Q3C), (R86C), or (A147C) and crosslinkers that react with cysteine residues. Following induction of K355–M13 dimerization with CaM dimers, we measured K355–M13 motility and found that it can be reversibly regulated in a Ca 2+ -dependent manner. We also found that velocities of K355–M13 varied depending on the type and crosslink position of the CaM dimer used; crosslink length also had a moderate effect on motility. These results suggest Ca 2+ -dependent dimerization of K355–M13 could be used as a novel molecular shuttle, equipped with an accelerator and brake system, for biochip applications.

Morphological and physiological retinal degeneration induced by intravenous delivery of vitamin A dimers in rabbits

Directory of Open Access Journals (Sweden)

Jackie Penn

2015-02-01

Full Text Available The eye uses vitamin A as a cofactor to sense light and, during this process, some vitamin A molecules dimerize, forming vitamin A dimers. A striking chemical signature of retinas undergoing degeneration in major eye diseases such as age-related macular degeneration (AMD and Stargardt disease is the accumulation of these dimers in the retinal pigment epithelium (RPE and Bruch’s membrane (BM. However, it is not known whether dimers of vitamin A are secondary symptoms or primary insults that drive degeneration. Here, we present a chromatography-free method to prepare gram quantities of the vitamin A dimer, A2E, and show that intravenous administration of A2E to the rabbit results in retinal degeneration. A2E-damaged photoreceptors and RPE cells triggered inflammation, induced remolding of the choroidal vasculature and triggered a decline in the retina’s response to light. Data suggest that vitamin A dimers are not bystanders, but can be primary drivers of retinal degeneration. Thus, preventing dimer formation could be a preemptive strategy to address serious forms of blindness.

Photoionization of furan from the ground and excited electronic states.

Science.gov (United States)

Ponzi, Aurora; Sapunar, Marin; Angeli, Celestino; Cimiraglia, Renzo; Došlić, Nađa; Decleva, Piero

2016-02-28

Here we present a comparative computational study of the photoionization of furan from the ground and the two lowest-lying excited electronic states. The study aims to assess the quality of the computational methods currently employed for treating bound and continuum states in photoionization. For the ionization from the ground electronic state, we show that the Dyson orbital approach combined with an accurate solution of the continuum one particle wave functions in a multicenter B-spline basis, at the density functional theory (DFT) level, provides cross sections and asymmetry parameters in excellent agreement with experimental data. On the contrary, when the Dyson orbitals approach is combined with the Coulomb and orthogonalized Coulomb treatments of the continuum, the results are qualitatively different. In excited electronic states, three electronic structure methods, TDDFT, ADC(2), and CASSCF, have been used for the computation of the Dyson orbitals, while the continuum was treated at the B-spline/DFT level. We show that photoionization observables are sensitive probes of the nature of the excited states as well as of the quality of excited state wave functions. This paves the way for applications in more complex situations such as time resolved photoionization spectroscopy.

Symmetry breaking and spectral considerations of the surprisingly floppy c-C3H radical and the related dipole-bound excited state of c-C3H-

Science.gov (United States)

Bassett, Matthew K.; Fortenberry, Ryan C.

2017-06-01

The C3H radical is believed to be prevalent throughout the interstellar medium and may be involved in the formation of polycyclic aromatic hydrocarbons. C3H exists as both a linear and a cyclic isomer. The C2 v cyclopropenylidenyl radical isomer was detected in the dark molecular cloud TMC-1, and the linear propenylidenyl radical isomer has been observed in various dark molecular clouds. Even though the c-C3H radical has been classified rotationally, the vibrational frequencies of this seemingly important interstellar molecule have never been directly observed. Established, highly accurate quartic force field methodologies are employed here to compute useful geometrical data, spectroscopic constants, and vibrational frequencies. The computed rotational constants are consistent with the experimental results. Consequently, the three a1 (ν1, ν2, and ν3) and one b1 (ν6) anharmonic vibrational frequencies at 3117.7 cm-1, 1564.3 cm-1, 1198.5 cm-1, and 826.7 cm-1, respectively, are reliable predictions for these, as of yet unseen, observables. Unfortunately, the two b2 fundamentals (ν4 and ν5) cannot be treated adequately in the current approach due to a flat and possible double-well potential described in detail herein. The dipole-bound excited state of the anion suffers from the same issues and may not even be bound. However, the trusted fundamental vibrational frequencies described for the neutral radical should not be affected by this deformity and are the first robustly produced for c-C3H. The insights gained here will also be applicable to other structures containing three-membered bare and exposed carbon rings that are surprisingly floppy in nature.

Dimerization inhibits the activity of receptor-like protein-tyrosine phosphatase-alpha

DEFF Research Database (Denmark)

Jiang, G; den Hertog, J; Su, J

1999-01-01

that dimerization can negatively regulate activity, through the interaction of an inhibitory 'wedge' on one monomer with the catalytic cleft of domain 1 in the other monomer. Here we show that dimerization inhibits the activity of a full-length RPTP in vivo. We generated stable disulphide-bonded full...

Detectability of H2-Ar and H2-Ne Dimers in Jovian Atmospheres

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Young-Key Minn

1997-12-01

Full Text Available The detection of jovian hydrogen-hydrogen dimers through the clear telluric 2-micron window(Kim et al. 1995, Trafton et al. 1997 suggests possibility to detect noble gases in the form of dimer with hydrogen in jovian atmospheres. Since noble gases do not have spectral structures in the infrared, it has been difficult to derive their abundances in the atmospheres of jovian planets. If there is a significant component of noble gases other than helium in the jovian atmospheres. it might be detected through its dimer spectrum with hydrogen molecule. The relatively sharp spectral structures of hydrogen-argon and hydrogen-neon dimers compared with those of hydrogen-hydrogen dimers are useful for the detection, if an adequate signal-to-noise (S/N is obtained. If we use a large telescope, such as the Keck telescope, with a long exposure time (>24 hours, then H2-Ar spectral structure may be detected.

Classical molecular dynamics simulation of weakly-bound projectile heavy-ion reactions

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Morker Mitul R.

2015-01-01

Full Text Available A 3-body classical molecular dynamics approach for heavy-ion reactions involving weakly bound projectiles is developed. In this approach a weakly bound projectile is constructed as a two-body cluster of the constituent tightly bound nuclei in a configuration corresponding to the observed breakup energy. This 3-body system with their individual nucleon configuration in their ground state is dynamically evolved for given initial conditions using the three-stage classical molecular dynamics approach (3S-CMD. Various levels of rigidbody constraints on the projectile constituents and the target are considered at appropriate stages. This 3-dimensional approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but internal excitations and breakup probabilities at distances close to the barrier also. Dynamical simulations of 6Li+209Bi show all the possible reaction mechanism like complete fusion, incomplete fusion, scattering and breakup scattering. Complete fusion cross sections of 6Li+209Bi and 7Li+209Bi reactions are calculated in this approach with systematic relaxations of the rigid-body constraints on one or more constituent nuclei.

Investigation of the 34S(p,γ)35Cl reaction and resonant absorption applied to the excitation of bound states

International Nuclear Information System (INIS)

Sparks, R.J.

1976-01-01

The yield curve of the reaction 34 S(p,γ) 35 Cl has been measured over the energy range Esub(p) = 1.95 - 2.91 MeV. Proton energies and strengths of 84 resonances are given. The decay schemes of 38 selected resonances have been studied, and for these branching ratios and spin limits are presented. Angular distributions have been measured at four 34 S(p,γ) 35 Cl resonances, at Esub(x) = 8.63, 8.64, 8.95 and 9.08 MeV, giving spin-parity assignments Jsup(π) = 7/2 - , (3/2,5/2), 3/2 + and 5/2, respectively. Spins and parities have been determined for bound states at Esub(x) = 3.92, 4.11, 4.85 and 5.16 MeV, as Jsup(π) = 3/2 + , 7/2 + , (1/2,3/2), 7/2 - , respectively. Branching and mixing ratios have been obtained for the decay of the states at Esub(x) = 3.92, 4.11, 4.35 and 5.16 MeV. Transition strengths are presented for the first three of these. A resonant absorption experiment at the Esub(p) = 2.79 MeV resonance gives for the resonance width GAMMA = 65 +- 20 eV, and also determines the partial widths GAMMAsub(γ), GAMMAsub(p) and GAMMAsub(p1). The level at 7064.3 +- 0.5 keV in 208 Pb has been excited in a resonant absorption experiment by Doppler shifted γ-radiation from the 34 S(p,γ) 35 Cl reaction at Esub(p) = 1974 keV. (Auth.)

Anion Photoelectron Spectroscopy of the Homogenous 2-Hydroxypyridine Dimer Electron Induced Proton Transfer System

Science.gov (United States)

Vlk, Alexandra; Stokes, Sarah; Wang, Yi; Hicks, Zachary; Zhang, Xinxing; Blando, Nicolas; Frock, Andrew; Marquez, Sara; Bowen, Kit; Bowen Lab JHU Team

Anion photoelectron spectroscopic (PES) and density functional theory (DFT) studies on the dimer anion of (2-hydroxypyridine)2-are reported. The experimentally measured vertical detachment energy (VDE) of 1.21eV compares well with the theoretically predicted values. The 2-hydroxypyridine anionic dimer system was investigated because of its resemblance to the nitrogenous heterocyclic pyrimidine nucleobases. Experimental and theoretical results show electron induced proton transfer (EIPT) in both the lactim and lactam homogeneous dimers. Upon electron attachment, the anion can serve as the intermediate between the two neutral dimers. A possible double proton transfer process can occur from the neutral (2-hydroxypyridine)2 to (2-pyridone)2 through the dimer anion. This potentially suggests an electron catalyzed double proton transfer mechanism of tautomerization. Research supported by the NSF Grant No. CHE-1360692.

Solution-dispersible Au nanocube dimers with greatly enhanced two-photon luminescence and SERS

Science.gov (United States)

Liu, Xiao-Li; Liang, Shan; Nan, Fan; Yang, Zhong-Jian; Yu, Xue-Feng; Zhou, Li; Hao, Zhong-Hua; Wang, Qu-Quan

2013-05-01

We report the synthesis of 43-nm diameter Au nanocube dimers by using Ag+ ions as competitive ligands to freeze l-cysteine-induced assembly process of the nanocubes to a desirable stage. Ascribed to the resonant interparticle coupling with an newly arising plasmon band at 710 nm and local field enhancement, the two-photon luminescence intensity of the Au nanocube dimers in solution was over 20 times stronger than that of the monomers in the wavelength range 555-620 nm. Furthermore, by coupling Raman tags onto the nanocube surface, a solution-based surface-enhanced Raman scattering (SERS) of the nanocube dimers had an enhancement factor of over 10 times compared to the isolated nanocubes. To sum up, with high stability in solution and attractive optical properties, the Au nanocube dimers have potential applications in in vivo bio-imaging and solution-based SERS.We report the synthesis of 43-nm diameter Au nanocube dimers by using Ag+ ions as competitive ligands to freeze l-cysteine-induced assembly process of the nanocubes to a desirable stage. Ascribed to the resonant interparticle coupling with an newly arising plasmon band at 710 nm and local field enhancement, the two-photon luminescence intensity of the Au nanocube dimers in solution was over 20 times stronger than that of the monomers in the wavelength range 555-620 nm. Furthermore, by coupling Raman tags onto the nanocube surface, a solution-based surface-enhanced Raman scattering (SERS) of the nanocube dimers had an enhancement factor of over 10 times compared to the isolated nanocubes. To sum up, with high stability in solution and attractive optical properties, the Au nanocube dimers have potential applications in in vivo bio-imaging and solution-based SERS. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr01170d

Synthesis and Dimerization Behavior of Five Metallophthalocyanines in Different Solvents

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Zhenhua Cheng

2014-01-01

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.

Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

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Lukas P. Feilen

2017-05-01

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.

Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction.

Science.gov (United States)

Feilen, Lukas P; Haubrich, Kevin; Strecker, Paul; Probst, Sabine; Eggert, Simone; Stier, Gunter; Sinning, Irmgard; Konietzko, Uwe; Kins, Stefan; Simon, Bernd; Wild, Klemens

2017-01-01

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.

FAK dimerization controls its kinase-dependent functions at focal adhesions

KAUST Repository

Brami-Cherrier, Karen; Gervasi, Nicolas; Arsenieva, Diana A.; Walkiewicz, Katarzyna; Boutterin, Marie Claude; Ortega, Á lvaro Darí o; Leonard, Paul G.; Seantier, Bastien; Gasmi, Laï la; Bouceba, Tahar; Kadaré , Gress; Girault -, Jean Antoine; Arold, Stefan T.

2014-01-01

Focal adhesion kinase (FAK) controls adhesion-dependent cell motility, survival, and proliferation. FAK has kinase-dependent and kinase-independent functions, both of which play major roles in embryogenesis and tumor invasiveness. The precise mechanisms of FAK activation are not known. Using x-ray crystallography, small angle x-ray scattering, and biochemical and functional analyses, we show that the key step for activation of FAK's kinase-dependent functions-autophosphorylation of tyrosine-397-requires site-specific dimerization of FAK. The dimers form via the association of the N-terminal FERM domain of FAK and are stabilized by an interaction between FERM and the C-terminal FAT domain. FAT binds to a basic motif on FERM that regulates co-activation and nuclear localization. FAK dimerization requires local enrichment, which occurs specifically at focal adhesions. Paxillin plays a dual role, by recruiting FAK to focal adhesions and by reinforcing the FAT:FERM interaction. Our results provide a structural and mechanistic framework to explain how FAK combines multiple stimuli into a site-specific function. The dimer interfaces we describe are promising targets for blocking FAK activation. © 2014 The Authors.

Tautomerization and Dimerization of 6,13-Disubstituted Derivatives of Pentacene.

Science.gov (United States)

Garcia-Borràs, Marc; Konishi, Akihito; Waterloo, Andreas; Liang, Yong; Cao, Yang; Hetzer, Constantin; Lehnherr, Dan; Hampel, Frank; Houk, Kendall N; Tykwinski, Rik R

2017-05-02

Two new 6,13-disubstituted pentacene derivatives, 1 c and 1 d, with alkyl and triisopropylsilylethynyl substitution have been synthesized and characterized experimentally and computationally. The alkyl substituted 1 c and 1 d represent the first 6-alkyl-substituted pentacene derivative where the fully aromatic species dominates over the corresponding tautomer. Indeed, no tautomerization product is found for either 1 c or 1 d upon heating or in the presence of catalytic amounts of acid. On the other hand, an unexpected dimer (3 c) is formed from 1 c. A plausible mechanism for this new dimerization process of the 6-methyl-substituted pentacene derivative 1 c is proposed, which involves first a bimolecular hydrogen atom transfer followed by an intramolecular [4+2] Diels-Alder cycloaddition. In the case of 6-butyl substitution, neither tautomerization nor dimerization is observed. Computations support the proposed 1 c dehydrodimerization pathway, explain why 1 d does not dimerize, and show the importance of the nature of the group at C-13 in controlling the relative stability of 6-alkyl-substituted pentacene tautomers. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

FAK dimerization controls its kinase-dependent functions at focal adhesions

KAUST Repository

Brami-Cherrier, Karen

2014-01-30

Focal adhesion kinase (FAK) controls adhesion-dependent cell motility, survival, and proliferation. FAK has kinase-dependent and kinase-independent functions, both of which play major roles in embryogenesis and tumor invasiveness. The precise mechanisms of FAK activation are not known. Using x-ray crystallography, small angle x-ray scattering, and biochemical and functional analyses, we show that the key step for activation of FAK\\'s kinase-dependent functions-autophosphorylation of tyrosine-397-requires site-specific dimerization of FAK. The dimers form via the association of the N-terminal FERM domain of FAK and are stabilized by an interaction between FERM and the C-terminal FAT domain. FAT binds to a basic motif on FERM that regulates co-activation and nuclear localization. FAK dimerization requires local enrichment, which occurs specifically at focal adhesions. Paxillin plays a dual role, by recruiting FAK to focal adhesions and by reinforcing the FAT:FERM interaction. Our results provide a structural and mechanistic framework to explain how FAK combines multiple stimuli into a site-specific function. The dimer interfaces we describe are promising targets for blocking FAK activation. © 2014 The Authors.

Controlled Patterning of Plasmonic Dimers by Using an Ultrathin Nanoporous Alumina Membrane as a Shadow Mask.

Science.gov (United States)

Hao, Qi; Huang, Hao; Fan, Xingce; Yin, Yin; Wang, Jiawei; Li, Wan; Qiu, Teng; Ma, Libo; Chu, Paul K; Schmidt, Oliver G

2017-10-18

We report on design and fabrication of patterned plasmonic dimer arrays by using an ultrathin anodic aluminum oxide (AAO) membrane as a shadow mask. This strategy allows for controllable fabrication of plasmonic dimers where the location, size, and orientation of each particle in the dimer pairs can be independently tuned. Particularly, plasmonic dimers with ultrasmall nanogaps down to the sub-10 nm scale as well as a large dimer density up to 1.0 × 10 10 cm -2 are fabricated over a centimeter-sized area. The plasmonic dimers exhibit significant surface-enhanced Raman scattering (SERS) enhancement with a polarization-dependent behavior, which is well interpreted by finite-difference time-domain (FDTD) simulations. Our results reveal a facile approach for controllable fabrication of large-area dimer arrays, which is of fundamental interest for plasmon-based applications in surface-enhanced spectroscopy, biochemical sensing, and optoelectronics.

Plasma D-dimer concentration in patients with systemic sclerosis

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Montagnana Martina

2006-01-01

Full Text Available Abstract Background Systemic sclerosis (SSc is an autoimmune disorder of the connective tissue characterized by widespread vascular lesions and fibrosis. Little is known so far on the activation of the hemostatic and fibrinolytic systems in SSc, and most preliminary evidences are discordant. Methods To verify whether SSc patients might display a prothrombotic condition, plasma D-dimer was assessed in 28 consecutive SSc patients and in 33 control subjects, matched for age, sex and environmental habit. Results and discussion When compared to healthy controls, geometric mean and 95% confidence interval (IC95% of plasma D-dimer were significantly increased in SSc patients (362 ng/mL, IC 95%: 361–363 ng/mL vs 229 ng/mL, IC95%: 228–231 ng/mL, p = 0.005. After stratifying SSc patients according to disease subset, no significant differences were observed between those with limited cutaneous pattern and controls, whereas patients with diffuse cutaneous pattern displayed substantially increased values. No correlation was found between plasma D-dimer concentration and age, sex, autoantibody pattern, serum creatinine, erythrosedimentation rate, nailfold videocapillaroscopic pattern and pulmonary involvement. Conclusion We demonstrated that SSc patients with diffuse subset are characterized by increased plasma D-dimer values, reflecting a potential activation of both the hemostatic and fibrinolytic cascades, which might finally predispose these patients to thrombotic complications.

Quantitation of pyrimidine dimers in DNA from UVB-irradiated alfalfa (Medicago sativa L.) seedlings

International Nuclear Information System (INIS)

Quaite, F.E.; Sutherland, B.M.; Sutherland, J.C.

1991-01-01

Depletion of stratospheric ozone will increase the solar ultraviolet radiation in the range from 290-320 nm (UVB) that reaches the surface of the earth, placing an increased UV burden on exposed organisms. One consequence of increased UVB may be decreased productivity of crop plants. A principal lesion caused by UV in DNA is the cyclobutyl pyrimidine dimer. We have adapted a method for measuring these dimers in nanogram quantities of non-radioactive DNA for use in UV-irradiated plants. We find that biologically relevant doses of broad band UVB radiation induce easily detectable frequencies of pyrimidine dimers in the DNA of irradiated alfalfa sprout leaves and that the dose response for dimer formation is linear up to doses of at least 690 J/m 2 . We also find easily measurable frequencies of dimers in the leaves of seedlings grown in glass filtered sunlight but not exposed to additional UVB, suggesting that significant number of dimers are formed in plants exposed to normal sunlight. 27 refs., 3 figs., 1 tab

Selective reflection of resonance radiation from excited media

International Nuclear Information System (INIS)

Veklenko, B.A.; Gusarov, R.B.; Sherkunov, Yu.B.

1998-01-01

According to quantum electrodynamics, the cross section for resonant scattering of radiation on an aggregate of excited atoms can be written as a sum of positive definite terms. This type of structure is not consistent with the Fresnel formulas for the reflection coefficient of radiation from thermally excited media. The difference shows up on a macroscopic level and indicates that semiclassical radiation theory cannot be used. A study of the correlation between elastic scattering and stimulated emission processes clarifies the reason for the discrepancies. The resulting singularities require summing of Feynman diagrams which appear beginning in the sixth order of perturbation theory. A lower bound estimate for the reflection coefficient from a plane layer is given, including processes which violate the statistics of radiation. The contribution of stimulated emission processes caused by the initially scattered photon are examined specifically. An experiment is proposed which would settle the choice of theories

Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly.

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David J Bray

Full Text Available Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1 the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2 new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3 evidence for tri-subdomain partitioning in the head and tail domains; and, (4 identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general.

Zak phase and band inversion in dimerized one-dimensional locally resonant metamaterials

Science.gov (United States)

Zhu, Weiwei; Ding, Ya-qiong; Ren, Jie; Sun, Yong; Li, Yunhui; Jiang, Haitao; Chen, Hong

2018-05-01

The Zak phase, which refers to Berry's phase picked up by a particle moving across the Brillouin zone, characterizes the topological properties of Bloch bands in a one-dimensional periodic system. Here the Zak phase in dimerized one-dimensional locally resonant metamaterials is investigated. It is found that there are some singular points in the bulk band across which the Bloch states contribute π to the Zak phase, whereas in the rest of the band the contribution is nearly zero. These singular points associated with zero reflection are caused by two different mechanisms: the dimerization-independent antiresonance of each branch and the dimerization-dependent destructive interference in multiple backscattering. The structure undergoes a topological phase-transition point in the band structure where the band inverts, and the Zak phase, which is determined by the numbers of singular points in the bulk band, changes following a shift in dimerization parameter. Finally, the interface state between two dimerized metamaterial structures with different topological properties in the first band gap is demonstrated experimentally. The quasi-one-dimensional configuration of the system allows one to explore topology-inspired new methods and applications on the subwavelength scale.

Lifecourse social position and D-dimer; findings from the 1958 British birth cohort.

Science.gov (United States)

Tabassum, Faiza; Kumari, Meena; Rumley, Ann; Power, Chris; Strachan, David P; Lowe, Gordon

2014-01-01

The aim is to examine the association of lifecourse socioeconomic position (SEP) on circulating levels of D-dimer. Data from the 1958 British birth cohort were used, social class was determined at three stages of respondents' life: at birth, at 23 and at 42 years. A cumulative indicator score of SEP (CIS) was calculated ranging from 0 (always in the highest social class) to 9 (always in the lowest social class). In men and women, associations were observed between CIS and D-dimer (P<0.05). Thus, the respondents in more disadvantaged social classes had elevated levels of D-dimer compared to respondents in less disadvantaged social class. In multivariate analyses, the association of disadvantaged social position with D-dimer was largely explained by fibrinogen, C-reactive protein and von Willebrand Factor in women, and additionally by smoking, alcohol consumption and physical activity in men. Socioeconomic circumstances across the lifecourse at various stages also contribute independently to raised levels of D-dimer in middle age in women only. Risk exposure related to SEP accumulates across life and contributes to raised levels of D-dimer. The association of haemostatic markers and social differences in health may be mediated by inflammatory and other markers.

Delay Bounded Multi-Source Multicast in Software-Defined Networking

Directory of Open Access Journals (Sweden)

Thabo Semong

2018-01-01

Full Text Available Software-Defined Networking (SDN is the next generation network architecture with exciting application prospects. The control function in SDN is decoupled from the data forwarding plane, hence it provides a new centralized architecture with flexible network resource management. Although SDN is attracting much attention from both industry and research, its advantage over the traditional networks has not been fully utilized. Multicast is designed to deliver content to multiple destinations. The current traffic engineering in SDN focuses mainly on unicast, however, multicast can effectively reduce network resource consumption by serving multiple clients. This paper studies a novel delay-bounded multi-source multicast SDN problem, in which among the set of potential sources, we select a source to build the multicast-tree, under the constraint that the transmission delay for every destination is bounded. This problem is more difficult than the traditional Steiner minimum tree (SMT problem, since it needs to find a source from the set of all potential sources. We model the problem as a mixed-integer linear programming (MILP and prove its NP-Hardness. To solve the problem, a delay bounded multi-source (DBMS scheme is proposed, which includes a DBMS algorithm to build a minimum delay cost DBMS-Forest. Through a MATLAB experiment, we demonstrate that DBMS is significantly more efficient and outperforms other existing algorithms in the literature.

Nicotinamidase/pyrazinamidase of Mycobacterium tuberculosis forms homo-dimers stabilized by disulfide bonds.

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Rueda, Daniel; Sheen, Patricia; Gilman, Robert H; Bueno, Carlos; Santos, Marco; Pando-Robles, Victoria; Batista, Cesar V; Zimic, Mirko

2014-12-01

Recombinant wild-pyrazinamidase from H37Rv Mycobacterium tuberculosis was analyzed by gel electrophoresis under differential reducing conditions to evaluate its quaternary structure. PZAse was fractionated by size exclusion chromatography under non-reducing conditions. PZAse activity was measured and mass spectrometry analysis was performed to determine the identity of proteins by de novo sequencing and to determine the presence of disulfide bonds. This study confirmed that M. tuberculosis wild type PZAse was able to form homo-dimers in vitro. Homo-dimers showed a slightly lower specific PZAse activity compared to monomeric PZAse. PZAse dimers were dissociated into monomers in response to reducing conditions. Mass spectrometry analysis confirmed the existence of disulfide bonds (C72-C138 and C138-C138) stabilizing the quaternary structure of the PZAse homo-dimer. Copyright © 2014 Elsevier Ltd. All rights reserved.

Dimer-flipping-assisted diffusion on a Si(001) surface

International Nuclear Information System (INIS)

Zi, J.; Min, B. J.; Lu, Y.; Wang, C. Z.; Ho, K. M.

2000-01-01

The binding sites and diffusion pathways of Si adatoms on a c(4x2) reconstructed Si(001) surface are investigated by a tight-binding method with an environment-dependent silicon potential in conjunction with ab initio calculations using the Car--Parrinello method. A new diffusion pathway along the trough edge driven by dimer flipping is found with a barrier of 0.74 eV, comparable to that of 0.68 eV along the top of the dimer rows

Solid-phase synthesis of 2{sup '}-O-methoxyethyl oligonucleotides using dimeric phosphoramidate blocks

Energy Technology Data Exchange (ETDEWEB)

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

2016-11-15

This research focused on the method of using dimeric phosphoramidite blocks to synthesize oligonucleotides for development as oligonucleotide drugs. A 16-mer oligonucleotide with the randomly selected sequence of C*C*T*C*G*C *T*C*T*C*G*C*C* C*G*C was synthesized using CC, GC, and TC dimers, a combination of monomers and dimers, or only monomers as building blocks. Using dimer blocks in this synthetic method provided a significant decrease in critical impurities that had similar properties to the main product, which was confirmed by LC-MS and HPLC analysis.

Analysis of the dimerized Sb/Si(001)-(2x1) surface by x-ray standing waves

International Nuclear Information System (INIS)

Lyman, P.F.; Qian, Y.; Bedzyk, M.J.

1994-12-01

X-ray standing wave measurements were undertaken to study the bonding position of Sb adatoms on the Sb-saturated Si(001)-(2x1) surface. Using the (004) and (022) Bragg reflections, the authors find that the Sb atoms form dimers, and that the center of the Sb ad-dimers lies 1.64 angstrom above the bulk-like Si(004) surface atomic plane. These in-plane results are compared to two structural models consisting of dimers whose bonds are parallel to the surface plane and whose centers are either shifted or unshifted (parallel to the dimer bond direction) relative to the underlying substrate planes. The authors thus find two special cases consistent with these data: one with symmetric (unshifted) dimers having a dimer bond length of 2.81 angstrom, and the other with midpoint-shifted dimers, having a bond length of 2.88 angstrom and a lateral shift of 0.21 angstrom

The intrinsically disordered RNR inhibitor Sml1 is a dynamic dimer

DEFF Research Database (Denmark)

Danielsson, Jens; Liljedahl, Leena; Ba´ra´ny-Wallje, Elsa

2008-01-01

. Sml1 belongs to the class of intrinsically disordered proteins with a high degree of dynamics and very little stable structure. Earlier suggestions for a dimeric structure of Sml1 were confirmed, and from translation diffusion NMR measurements, a dimerization dissociation constant of 0.1 mM at 4...... natively disordered proteins....

Dimerization effect of sucrose octasulfate on rat FGF1

International Nuclear Information System (INIS)

Kulahin, N.; Kiselyov, V.; Kochoyan, A.; Kristensen, O.; Kastrup, Jette S.; Berezin, V.; Bock, E.; Gajhede, M.

2008-01-01

The work describes the sucrose octasulfate-mediated dimerization of rat FGF1 by gel-filtration experiments and crystal structure determination. Fibroblast growth factors (FGFs) constitute a family of at least 23 structurally related heparin-binding proteins that are involved in regulation of cell growth, survival, differentiation and migration. Sucrose octasulfate (SOS), a chemical analogue of heparin, has been demonstrated to activate FGF signalling pathways. The structure of rat FGF1 crystallized in the presence of SOS has been determined at 2.2 Å 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, Lys118, Arg122 and Lys128. An arginine at position 116 is a consensus residue in mammalian FGF molecules; however, it is a serine in rat FGF1. This difference may be important for SOS-mediated FGF1 dimerization in rat

Role of distonic dimer radical cations in the radiation-induced polymerisation of vinyl ethers

International Nuclear Information System (INIS)

Naumov, Sergej; Janovsky, Igor; Knolle, Wolfgang; Mehnert, Reiner

2005-01-01

The experimental low-temperature EPR results and the quantum chemical calculations suggest that dimer radical cations of cyclic and aliphatic vinyl ethers (VE) plays a key role in starting of radiation-induced polymerisation. The main species observed at high 2,3-dihydrofuran (DHF), 2,3-dihydropyran (DHP) and VE concentration is the dimer radical cation. In the case of cyclic VE the dimer radical cation transforms through H-abstraction from neutral molecule into a carbocation and radical, which could start both cationic and free-radical polymerisation. However, in the case of aliphatic VE no further reactive species, which could start polymerisation, were observed. This is caused (in agreement with experiment and quantum chemical calculations) by the very high stability of dimer radical cation and calculated endothermity of H-abstraction reaction by dimer radical cation from monomer

An introduction to the dimer model

International Nuclear Information System (INIS)

Kenyon, R.

2004-01-01

A perfect matching of a graph is a subset of edges which covers every vertex exactly once, that is, for every vertex there is exactly one edge in the set with that vertex as endpoint. The dimer model is the study of the set of perfect matchings of a (possibly infinite) graph. The most well-known example is when the graph is Z 2 , for which perfect matchings are equivalent (via a simple duality) to domino tilings, that is, tilings of the plane with 2 x 1 and 1 x 2 rectangles. In the first three sections we study domino tilings of the plane and of finite polygonal regions, or equivalently, perfect matchings on Z 2 and subgraphs of Z 2 . In the last two sections we study the FK-percolation model and the dimer model on a more general family of planar graphs

Ultrafast dynamics of ligand and substrate interaction in endothelial nitric oxide synthase under Soret excitation.

Science.gov (United States)

Hung, Chih-Chang; Yabushita, Atsushi; Kobayashi, Takayoshi; Chen, Pei-Feng; Liang, Keng S

2016-01-01

Ultrafast transient absorption spectroscopy of endothelial NOS oxygenase domain (eNOS-oxy) was performed to study dynamics of ligand or substrate interaction under Soret band excitation. Photo-excitation dissociates imidazole ligand in 4ps. The eNOS-oxy without additive is partially bound with water molecule, thus its photoexcited dynamics also shows ligand dissociation in <800fs. Then it followed by vibrational cooling coupled with charge transfer in 4.8ps, and recombination of ligand to distal side of heme in 12ps. Copyright © 2016 Elsevier B.V. All rights reserved.

Neutral dipole-dipole dimers: A new field in science

Science.gov (United States)

Kosower, Edward M.; Borz, Galina

2018-03-01

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

Violet-green excitation for NIR luminescence of Yb3+ ions in Bi2O3-B2O3-SiO2-Ga2O3 glasses.

Science.gov (United States)

Li, Weiwei; Cheng, Jimeng; Zhao, Guoying; Chen, Wei; Hu, Lili; Guzik, Malgorzata; Boulon, Georges

2014-04-21

60Bi(2)O(3)-20B(2)O(3)-10SiO(2)-10Ga(2)O(3) glasses doped with 1-9 mol% Yb(2)O(3) were prepared and investigated mainly on their violet-green excitation for the typical NIR emission of Yb(3+), generally excited in the NIR. Two violet excitation bands at 365 nm and 405 nm are related to Yb(2+) and Bi(3+). 465 nm excitation band and 480 nm absorption band in the blue-green are assigned to Bi(0) metal nanoparticles/grains. Yb-content-dependence of the excitation and absorption means that Bi(0) is the reduced product of Bi(3+), but greatly competed by the redox reaction of Yb(2+) ↔ Yb(3+). It is proved that the violet-green excitations result in the NIR emission of Yb(3+). On the energy transfer, the virtual level of Yb(3+)-Yb(3+) as well as Bi(0) dimers probably plays an important role. An effective and controllable way is suggested to achieve nano-optical applications by Bi(0) metal nanoparticles/grains and Yb(3+).

Probing Intermolecular Electron Delocalization in Dimer Radical Anions by Vibrational Spectroscopy

International Nuclear Information System (INIS)

Mani, Tomoyasu; Brookhaven National Laboratory; Grills, David C.

2017-01-01

Delocalization of charges is one of the factors controlling charge transport in conjugated molecules. It is considered to play an important role in the performance of a wide range of molecular technologies, including organic solar cells and organic electronics. Dimerization reactions are well-suited as a model to investigate intermolecular spatial delocalization of charges. And while dimerization reactions of radical cations are well investigated, studies on radical anions are still scarce. Upon dimerization of radical anions with neutral counterparts, an electron is considered to delocalize over the two molecules. By using time-resolved infrared (TRIR) detection coupled with pulse radiolysis, we show that radical anions of 4-n-hexyl-4'-cyanobiphenyl (6CB) undergo such dimerization reactions, with an electron equally delocalized over the two molecules. We have recently demonstrated that nitrile ν(C≡N) vibrations respond to the degree of electron localization of nitrile-substituted anions: we can quantify the changes in the electronic charges from the neutral to the anion states in the nitriles by monitoring the ν(C≡N) IR shifts. In the first part of this article, we show that the sensitivity of the ν(C≡N) IR shifts does not depend on solvent polarity. In the second part, we describe how probing the shifts of the nitrile IR vibrational band unambiguously confirms the formation of dimer radical anions, with K dim = 3 × 10 4 M –1 . IR findings are corroborated by electronic absorption spectroscopy and electronic structure calculations. We find that the presence of a hexyl chain and the formation of π–π interactions are both crucial for dimerization of radical anions of 6CB with neutral 6CB. Our study provides clear evidence of spatial delocalization of electrons over two molecular fragments.

Presence of the propeptide on recombinant lysosomal dipeptidase controls both activation and dimerization.

Science.gov (United States)

Dolenc, Iztok; Pain, Roger; Turk, Vito

2007-01-01

Lysosomal dipeptidase catalyzes the hydrolysis of dipeptides with unsubstituted terminals. It is a homodimer and binds zinc. Dimerization is an important issue in understanding the enzyme's function. In this study, we investigated the influence of the propeptide on the folding and dimerization of recombinant lysosomal dipeptidase. For this purpose, we separately cloned and overexpressed the mature protein and the proenzyme. The overexpressed proteins were localized exclusively to insoluble inclusion bodies. Refolding of the urea-solubilized inclusion bodies showed that only dipeptidase lacking the propeptide was dimeric. The soluble renatured proenzyme was a monomer, although circular dichroism and fluorescence spectra of the proenzyme indicated the formation of secondary and tertiary structure. The propeptide thus controls dimerization, as well as activation, of lysosomal dipeptidase.

Fibrin d-dimer concentration, deep vein thrombosis symptom duration, and venous thrombus volume.

Science.gov (United States)

Kurklinsky, Andrew K; Kalsi, Henna; Wysokinski, Waldemar E; Mauck, Karen F; Bhagra, Anjali; Havyer, Rachel D; Thompson, Carrie A; Hayes, Sharonne N; McBane, Robert D

2011-04-01

To determine the relationship between fibrin D-dimer levels, symptom duration, and thrombus volume, consecutive patients with incident deep venous thrombosis (DVT) were evaluated. In a cross-sectional study design, patient symptom onset was determined by careful patient questioning. Venous thrombosis was confirmed by compression duplex ultrasonography. Thrombus volume was estimated based on patient's femur length using a forensic anthropology method. Fibrin D-dimer was measured by latex immunoassay. 72 consecutive patients with confirmed leg DVT agreed to participate. The median symptom duration at the time of diagnosis was 10 days. The median D-dimer concentration was 1050 ng/dL. The median thrombus volume was 12.92 cm(3). D-Dimer levels correlated with estimated thrombus volume (P venous thrombosis and correlates with thrombus volume.