Assignment of Pre-edge Features in the Ru K-edge X-ray Absorption Spectra of Organometallic Ruthenium Complexes

PubMed Central

Getty, Kendra; Delgado-Jaime, Mario Ulises

2010-01-01

The nature of the lowest energy bound-state transition in the Ru K-edge X-ray Absorption Spectra for a series of Grubbs-type ruthenium complexes was investigated. The pre-edge feature was unambiguously assigned as resulting from formally electric dipole forbidden Ru 4d←1s transitions. The intensities of these transitions are extremely sensitive to the ligand environment and the symmetry of the metal centre. In centrosymmetric complexes the pre-edge is very weak since it is limited by the weak electric quadrupole intensity mechanism. By contrast, upon breaking centrosymmetry, Ru 5p-4d mixing allows for introduction of electric dipole allowed character resulting in a dramatic increase in the pre-edge intensity. The information content of this approach is explored as it relates to complexes of importance in olefin metathesis and its relevance as a tool for the study of reactive intermediates. PMID:20151030

Infrared Laser Stark Spectroscopy and AB Initio Computations of the OH\\cdotsCO Complex

NASA Astrophysics Data System (ADS)

Liang, Tao; Raston, Paul; Douberly, Gary

2014-06-01

Following the sequential pick-up of OH and CO by helium nanodroplets, the infrared depletion spectrum is measured in the fundamental OH stretching region. Although several potentially accessible minima exist on the associated OH + CO reactive potential energy surface [e.g. J. Ma, J. Li, and H. Guo, J. Phys. Chem. Lett. 3 (2012) 2482], such as the weakly bound OH-OC dimer and the chemically bound HOCO molecule, we only observe the weakly bound OH-CO dimer. The rovibrational spectrum of this complex displays narrow (0.02 cm-1) Lorentzian shaped peaks with spacings that are characteristic of a linear complex with unquenched electronic angular momentum, similar to what was previously observed in the gas phase [M.I. Lester, B.V. Pond, D.T. Anderson, L.B. Harding, and A.F. Wagner, J. Chem. Phys. 113 (2000) 9889]. Analogous spectra involving OD were collected, for which we also only observe the OD-CO isomer. From the Stark spectra, the dipole moments for OH-CO are determined to be 1.85(3) and 1.89(3) D for v=0 and v=1, respectively, while the analogous dipole moments for OD-CO are determined to be 1.88(8) and 1.94(5) D. The computed equilibrium ground state dipole moment at the CCSD(T)/Def2-TZVPD level of theory is 2.185 D, in disagreement with experiment. The role of vibrational averaging is investigated via the solution of a three-dimensional vibrational Schrödinger equation, which is constructed in internal bond-angle coordinates. The computed expectation value of the ground state dipole moment is in excellent agreement with experiment, indicating a floppy molecular complex.

Camphor revisited: studies of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453.

PubMed Central

Taylor, D G; Trudgill, P W

1986-01-01

The oxygenating component of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453 was purified to homogeneity by a combination of ammonium sulfate fractionation and chromatography on DEAE-cellulose and polyanion SI-17 columns. It had an Mr of 78,000, bound one molecule of nonautooxidizable flavin mononucleotide (FMN), consisted of two subunits of equal molecular weight, and existed in two electrophoretically distinguishable active forms. The oxygenating complex was constructed from equimolecular amounts of an NADH oxidase, which could be purified separately (Mr, 36,000), and the oxygenating component. Most of the NADH oxidase dissociated from the oxygenating component during purification, although traces remained, to give the final preparation of the oxygenating component significant oxygenase activity. FMN did not dissociate significantly from the oxygenating component during purification, but it was not covalently bound and could be removed under a variety of conditions. Binding between the two proteins that made up the active complex was fairly weak and freely reversible. It probably occurred through the FMN which was strongly bound to the oxygenating component and for which the NADH had a weak binding site. Iron was not present at a significant level in the oxygenating component, and in common with other characterized Baeyer Villiger monooxygenases, 2,5-diketocamphane 1,2-monooxygenase was found to be a simple flavoprotein. Images PMID:3944058

Camphor revisited: studies of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453.

PubMed

Taylor, D G; Trudgill, P W

1986-02-01

The oxygenating component of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453 was purified to homogeneity by a combination of ammonium sulfate fractionation and chromatography on DEAE-cellulose and polyanion SI-17 columns. It had an Mr of 78,000, bound one molecule of nonautooxidizable flavin mononucleotide (FMN), consisted of two subunits of equal molecular weight, and existed in two electrophoretically distinguishable active forms. The oxygenating complex was constructed from equimolecular amounts of an NADH oxidase, which could be purified separately (Mr, 36,000), and the oxygenating component. Most of the NADH oxidase dissociated from the oxygenating component during purification, although traces remained, to give the final preparation of the oxygenating component significant oxygenase activity. FMN did not dissociate significantly from the oxygenating component during purification, but it was not covalently bound and could be removed under a variety of conditions. Binding between the two proteins that made up the active complex was fairly weak and freely reversible. It probably occurred through the FMN which was strongly bound to the oxygenating component and for which the NADH had a weak binding site. Iron was not present at a significant level in the oxygenating component, and in common with other characterized Baeyer Villiger monooxygenases, 2,5-diketocamphane 1,2-monooxygenase was found to be a simple flavoprotein.

Optical signatures of molecular particles via mass-selected cluster spectroscopy

NASA Technical Reports Server (NTRS)

Duncan, Michael A.

1990-01-01

A new molecular beam apparatus was developed to study optical absorption in cold (less than 100 K) atomic clusters and complexes produced by their condensation with simple molecular gases. In this instrument, ionized clusters produced in a laser vaporization nozzle source are mass selected and studied with photodissociation spectroscopy at visible and ultraviolet wavelengths. This new approach can be applied to synthesize and characterize numerous particulates and weakly bound complexes expected in planetary atmospheres and in comets.

Matrix metalloproteinase-10/TIMP-2 structure and analyses define conserved core interactions and diverse exosite interactions in MMP/TIMP complexes.

PubMed

Batra, Jyotica; Soares, Alexei S; Mehner, Christine; Radisky, Evette S

2013-01-01

Matrix metalloproteinases (MMPs) play central roles in vertebrate tissue development, remodeling, and repair. The endogenous tissue inhibitors of metalloproteinases (TIMPs) regulate proteolytic activity by binding tightly to the MMP active site. While each of the four TIMPs can inhibit most MMPs, binding data reveal tremendous heterogeneity in affinities of different TIMP/MMP pairs, and the structural features that differentiate stronger from weaker complexes are poorly understood. Here we report the crystal structure of the comparatively weakly bound human MMP-10/TIMP-2 complex at 2.1 Å resolution. Comparison with previously reported structures of MMP-3/TIMP-1, MT1-MMP/TIMP-2, MMP-13/TIMP-2, and MMP-10/TIMP-1 complexes offers insights into the structural basis of binding selectivity. Our analyses identify a group of highly conserved contacts at the heart of MMP/TIMP complexes that define the conserved mechanism of inhibition, as well as a second category of diverse adventitious contacts at the periphery of the interfaces. The AB loop of the TIMP N-terminal domain and the contact loops of the TIMP C-terminal domain form highly variable peripheral contacts that can be considered as separate exosite interactions. In some complexes these exosite contacts are extensive, while in other complexes the AB loop or C-terminal domain contacts are greatly reduced and appear to contribute little to complex stability. Our data suggest that exosite interactions can enhance MMP/TIMP binding, although in the relatively weakly bound MMP-10/TIMP-2 complex they are not well optimized to do so. Formation of highly variable exosite interactions may provide a general mechanism by which TIMPs are fine-tuned for distinct regulatory roles in biology.

Photodissociation Studies of Metal-Containing Clusters and Complexes

NASA Astrophysics Data System (ADS)

Pilgrim, Jeffrey Scott

1995-01-01

There have been two major areas of investigation for researchers working with laser ablation in molecular beams. The first area is the study of weakly-bound complexes. These complexes are bound by electrostatic interactions. In the present study the weakly bound interactions of the rare gases with the magnesium ion are investigated with electronic spectroscopy. The second major area is the study of metal and metal-containing clusters. Examples of previous investigations are the alkali metal clusters and the fullerenes. The present investigation is on metal -carbon clusters. The so-called metallo-carbohedrenes and metal-carbon nanocrystals are studied. Resonance enhanced photodissociation spectroscopy is used to obtain electronic excitation spectra of the Mg^+-rare gas species in the ultraviolet region. This investigation is facilitated by a reflectron time-of-flight mass spectrometer. The interaction of the rare gas with the metal ion is attributed to a "solvation" of the atomic ion transition. Simple bonding arguments predict that the excited state is more bound than the ground state for these complexes. This will result in a shift of the complex vibronic origin to lower energy from the atomic ion transition. This is exactly what is observed in the experiment with progressively larger shifts for the heavier rare gases. The electronic excitation spectra allow the vibrational frequencies and anharmonicities for these complexes to be obtained for the excited state. In turn, the excited state bond dissociation energies can be determined. Finally, conservation of energy allows calculation of the ground state bond dissociation energies. In the metal-carbon systems the stability of the metallo-carbohedrene, met-car, stoichiometry is shown to extend into the transition period at least to the iron group. Photodissociation with a 532 nm laser causes a loss of metal atoms for met-cars formed with first row transition metals and a loss of metal-carbon units for met-cars formed from second-row transition metal atoms. Larger metal-carbon clusters are found to be face-centered-cubic nanocrystals. Photodissociation of these nanocrystals causes fragmentation into smaller nanocrystals. In addition, nanocrystals also dissociatively rearrange into the met -car structure. Two of the metal-carbon nanocrystals ( rm Ti_{14}C_{13 }^+ and rm V_{14 }C_{13}^+) fragment into the met-car with a trapped carbon atom.

Thermodynamics of Computational Copying in Biochemical Systems

NASA Astrophysics Data System (ADS)

Ouldridge, Thomas E.; Govern, Christopher C.; ten Wolde, Pieter Rein

2017-04-01

Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that, as in computation, a canonical biochemical readout network generates correlations; extracting no work from these correlations sets a lower bound on dissipation. For general input, the biochemical network cannot reach this bound, even with arbitrarily slow reactions or weak thermodynamic driving. It faces an accuracy-dissipation trade-off that is qualitatively distinct from and worse than implied by the bound, and more complex steady-state copy processes cannot perform better. Nonetheless, the cost remains close to the thermodynamic bound unless accuracy is extremely high. Additionally, we show that biomolecular reactions could be used in thermodynamically optimal devices under exogenous manipulation of chemical fuels, suggesting an experimental system for testing computational thermodynamics.

Matrix Isolation and ab initio study of the noncovalent complexes between formamide and acetylene.

PubMed

Mardyukov, Artur; Sánchez-García, Elsa; Sander, Wolfram

2009-02-12

Matrix isolation spectroscopy in combination with ab initio calculations is a powerful technique for the identification of weakly bound intermolecular complexes. Here, weak complexes between formamide and acetylene are studied, and three 1:1 complexes with binding energies of -2.96, -2.46, and -1.79 kcal/mol have been found at the MP2 level of theory (MP2/cc-pVTZ + ZPE + BSSE). The two most stable dimers A and B are identified in argon and nitrogen matrices by comparison between the experimental and calculated infrared frequencies. Both complexes are stabilized by the formamide C=O...HC acetylene and H...pi interactions. Large shifts have been observed experimentally for the C-H stretching vibrations of the acetylene molecule, in very good agreement with the calculated values. Eight 1:2 FMA-acetylene trimers (T-A to T-H) with binding energies between -5.44 and -2.62 kcal/mol (MP2/aug-cc-pVDZ + ZPE + BSSE) were calculated. The two most stable trimers T-A and T-B are very close in energy and have similar infrared spectra. Several weak bands that are in agreement with the calculated frequencies of the trimers T-A and T-B are observed under matrix isolation conditions. However, the differences are too small for a definitive assignment.

Nilsson diagrams for light neutron-rich nuclei with weakly-bound neutrons

NASA Astrophysics Data System (ADS)

Hamamoto, Ikuko

2007-11-01

Using Woods-Saxon potentials and the eigenphase formalism for one-particle resonances, one-particle bound and resonant levels for neutrons as a function of quadrupole deformation are presented, which are supposed to be useful for the interpretation of spectroscopic properties of some light neutron-rich nuclei with weakly bound neutrons. Compared with Nilsson diagrams in textbooks that are constructed using modified oscillator potentials, we point out a systematic change of the shell structure in connection with both weakly bound and resonant one-particle levels related to small orbital angular momenta ℓ. Then, it is seen that weakly bound neutrons in nuclei such as C15-19 and Mg33-37 may prefer being deformed as a result of the Jahn-Teller effect, due to the near degeneracy of the 1d5/2-2s1/2 levels and the 1f7/2-2p3/2 levels in the spherical potential, respectively. Furthermore, the absence of some one-particle resonant levels compared with the Nilsson diagrams in textbooks is illustrated.

An ionic-chemical-mechanical model for muscle contraction.

PubMed

Manning, Gerald S

2016-12-01

The dynamic process underlying muscle contraction is the parallel sliding of thin actin filaments along an immobile thick myosin fiber powered by oar-like movements of protruding myosin cross bridges (myosin heads). The free energy for functioning of the myosin nanomotor comes from the hydrolysis of ATP bound to the myosin heads. The unit step of translational movement is based on a mechanical-chemical cycle involving ATP binding to myosin, hydrolysis of the bound ATP with ultimate release of the hydrolysis products, stress-generating conformational changes in the myosin cross bridge, and relief of built-up stress in the myosin power stroke. The cycle is regulated by a transition between weak and strong actin-myosin binding affinities. The dissociation of the weakly bound complex by addition of salt indicates the electrostatic basis for the weak affinity, while structural studies demonstrate that electrostatic interactions among negatively charged amino acid residues of actin and positively charged residues of myosin are involved in the strong binding interface. We therefore conjecture that intermediate states of increasing actin-myosin engagement during the weak-to-strong binding transition also involve electrostatic interactions. Methods of polymer solution physics have shown that the thin actin filament can be regarded in some of its aspects as a net negatively charged polyelectrolyte. Here we employ polyelectrolyte theory to suggest how actin-myosin electrostatic interactions might be of significance in the intermediate stages of binding, ensuring an engaged power stroke of the myosin motor that transmits force to the actin filament, and preventing the motor from getting stuck in a metastable pre-power stroke state. We provide electrostatic force estimates that are in the pN range known to operate in the cycle. © 2016 Wiley Periodicals, Inc.

Intercalation of Transition Metals into Stacked Benzene Rings: A Model Study of the Intercalation of Transition Metals into Bilayered Graphene.

PubMed

Youn, Il Seung; Kim, Dong Young; Singh, N Jiten; Park, Sung Woo; Youn, Jihee; Kim, Kwang S

2012-01-10

Structures of neutral metal-dibenzene complexes, M(C6H6)2 (M = Sc-Zn), are investigated by using Møller-Plesset second order perturbation theory (MP2). The benzene molecules change their conformation and shape upon complexation with the transition metals. We find two types of structures: (i) stacked forms for early transition metal complexes and (ii) distorted forms for late transition metal ones. The benzene molecules and the metal atom are bound together by δ bonds which originate from the interaction of π-MOs and d orbitals. The binding energy shows a maximum for Cr(C6H6)2, which obeys the 18-electron rule. It is noticeable that Mn(C6H6)2, a 19-electron complex, manages to have a stacked structure with an excess electron delocalized. For other late transition metal complexes having more than 19 electrons, the benzene molecules are bent or stray away from each other to reduce the electron density around a metal atom. For the early transition metals, the M(C6H6) complexes are found to be more weakly bound than M(C6H6)2. This is because the M(C6H6) complexes do not have enough electrons to satisfy the 18-electron rule, and so the M(C6H6)2 complexes generally tend to have tighter binding with a shorter benzene-metal length than the M(C6H6) complexes, which is quite unusual. The present results could provide a possible explanation of why on the Ni surface graphene tends to grow in a few layers, while on the Cu surface the weak interaction between the copper surface and graphene allows for the formation of a single layer of graphene, in agreement with chemical vapor deposition experiments.

Structure effects on reaction mechanisms in collisions induced by radioactive ion beams

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

Pietro, A. Di, E-mail: dipietro@lns.infn.it; Figuera, P.; Scuderi, V.

2006-08-15

The present paper concerns the study of reactions induced by radioactive beams of halo and weakly bound nuclei at energies around and above the Coulomb barrier. The results obtained for the reaction induced by the halo nucleus {sup 6}He on {sup 64}Zn have been compared with the results for the reaction induced by {sup 4}He on the same target. The results of the reaction induced by the weakly bound unstable {sup 13}N on the weakly bound {sup 9}Be have been compared with those for the reaction {sup 10}B + {sup 12}C.

Effect of temperature on residual force enhancement in single skeletal muscle fibers.

PubMed

Lee, Eun-Jeong; Herzog, Walter

2008-08-28

It is well accepted that the steady-state isometric force following active stretching of a muscle is greater than the steady-state isometric force obtained in a purely isometric contraction at the same length. This property of skeletal muscle has been called residual force enhancement (FE). Despite decades of research the mechanisms responsible for FE have remained largely unknown. Based on previous studies showing increases in FE in fibers in which cross-bridges were biased towards weakly bound states, we hypothesized that FE might be associated with a stretch-induced facilitation of transitioning from weakly to strongly bound cross-bridges. In order to test this hypothesis, single fibers (n=11) from the lumbrical muscles of frog (Rana pipiens) were used to determine FE at temperatures of 7 and 20 degrees C. At the cold temperature, cross-bridges are biased towards weakly bound states, therefore we expected FE to be greater at 7 degrees C compared to 20 degrees C. The average FE was significantly greater at 7 degrees C (11.5+/-1.1%) than at 20 degrees C (7.8+/-1.0%), as expected. The enhancement of force/stiffness was also significantly greater at the low (13.3+/-1.4%) compared to the high temperature (5.6+/-1.7%), indicating an increased conversion from weakly to strongly bound cross-bridges at the low temperature. We conclude from the results of this study that muscle preparations that are biased towards weakly bound cross-bridge states show increased FE for given stretch conditions, thereby supporting the idea that FE might be caused, in part, by a stretch-induced facilitation of the conversion of weakly to strongly bound cross-bridges.

Tunable far infrared laser spectrometers

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

Blake, G.A.; Laughlin, K.B.; Cohen, R.C.

The state of the art in far infrared (FIR) spectroscopy is reviewed. The development of tunable, coherent FIR radiation sources is discussed. Applications of tunable FIR laser spectrometers for measurement of rotational spectra and dipole moments of molecular ions and free radicals, vibration-rotation-tunneling (VRT) spectra of weakly bound complexes, and vibration-rotation spectra of linear carbon clusters are presented. A detailed description of the Berkeley tunable FIR laser spectrometers is presented in the following article.

Remarks on High Reynolds Numbers Hydrodynamics and the Inviscid Limit

NASA Astrophysics Data System (ADS)

Constantin, Peter; Vicol, Vlad

2018-04-01

We prove that any weak space-time L^2 vanishing viscosity limit of a sequence of strong solutions of Navier-Stokes equations in a bounded domain of R^2 satisfies the Euler equation if the solutions' local enstrophies are uniformly bounded. We also prove that t-a.e. weak L^2 inviscid limits of solutions of 3D Navier-Stokes equations in bounded domains are weak solutions of the Euler equation if they locally satisfy a scaling property of their second-order structure function. The conditions imposed are far away from boundaries, and wild solutions of Euler equations are not a priori excluded in the limit.

Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase.

PubMed Central

Gao, J; Wu, Q; Carbeck, J; Lei, Q P; Smith, R D; Whitesides, G M

1999-01-01

This paper describes the use of electrospray ionization-Fourier transform ion cyclotron mass spectrometry (ESI-FTICR-MS) to study the relative stabilities of noncovalent complexes of carbonic anhydrase II (CAII, EC 4.2.1.1) and benzenesulfonamide inhibitors in the gas phase. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) was used to determine the energetics of dissociation of these CAII-sulfonamide complexes in the gas phase. When two molecules of a benzenesulfonamide (1) were bound simultaneously to one molecule of CAII, one of them was found to exhibit significantly weaker binding (DeltaE50 = 0.4 V, where E50 is defined as the amplitude of sustained off-resonance irradiation when 50% of the protein-ligand complexes are dissociated). In solution, the benzenesulfonamide group coordinates as an anion to a Zn(II) ion bound at the active site of the enzyme. The gas phase stability of the complex with the weakly bound inhibitor was the same as that of the inhibitor complexed with apoCAII (i.e., CAII with the Zn(II) ion removed from the binding site). These results indicate that specific interactions between the sulfonamide group on the inhibitor and the Zn(II) ion on CAII were preserved in the gas phase. Experiments also showed a higher gas phase stability for the complex of para-NO2-benzenesulfonamide-CAII than that for ortho-NO2-benzenesulfonamide-CAII complex. This result further suggests that steric interactions of the inhibitors with the binding pocket of CAII parallel those in solution. Overall, these results are consistent with the hypothesis that CAII retains, at least partially, the structure of its binding pocket in the gas phase on the time scale (seconds to minutes) of the ESI-FTICR measurements. PMID:10354450

Theoretical study on complexation of the perchlorate, permanganate, pertechnate and perrhenate anions with dodecabenzylbambus[6]uril

NASA Astrophysics Data System (ADS)

Böhm, Stanislav; Makrlík, Emanuel; Vaňura, Petr

2017-07-01

By using quantum chemical calculations, the most probable structures of the anionic complex species dodecabenzylbambus[6]uril-ClO4-, dodecabenzylbambus[6]uril-MnO4-, dodecabenzylbambus[6]uril-TcO4- and dodecabenzylbambus[6]uril-ReO4- were derived. In these four complexes, each of the considered anions, included in the macrocyclic cavity, is bound by 12 weak hydrogen bonds between methine hydrogen atoms on the convex face of glycoluril units and the respective anion. Further, the corresponding interaction energies of the investigated four anionic complexes were calculated; the absolute values of these calculated energies increase in the series of ReO4- < TcO4- < MnO4- < ClO4-.

Complexity is simple!

NASA Astrophysics Data System (ADS)

Cottrell, William; Montero, Miguel

2018-02-01

In this note we investigate the role of Lloyd's computational bound in holographic complexity. Our goal is to translate the assumptions behind Lloyd's proof into the bulk language. In particular, we discuss the distinction between orthogonalizing and `simple' gates and argue that these notions are useful for diagnosing holographic complexity. We show that large black holes constructed from series circuits necessarily employ simple gates, and thus do not satisfy Lloyd's assumptions. We also estimate the degree of parallel processing required in this case for elementary gates to orthogonalize. Finally, we show that for small black holes at fixed chemical potential, the orthogonalization condition is satisfied near the phase transition, supporting a possible argument for the Weak Gravity Conjecture first advocated in [1].

Bounding the solutions of parametric weakly coupled second-order semilinear parabolic partial differential equations

DOE PAGES

Azunre, P.

2016-09-21

Here in this paper, two novel techniques for bounding the solutions of parametric weakly coupled second-order semilinear parabolic partial differential equations are developed. The first provides a theorem to construct interval bounds, while the second provides a theorem to construct lower bounds convex and upper bounds concave in the parameter. The convex/concave bounds can be significantly tighter than the interval bounds because of the wrapping effect suffered by interval analysis in dynamical systems. Both types of bounds are computationally cheap to construct, requiring solving auxiliary systems twice and four times larger than the original system, respectively. An illustrative numerical examplemore » of bound construction and use for deterministic global optimization within a simple serial branch-and-bound algorithm, implemented numerically using interval arithmetic and a generalization of McCormick's relaxation technique, is presented. Finally, problems within the important class of reaction-diffusion systems may be optimized with these tools.« less

Near infrared overtone (vOH = 2 ← 0) spectroscopy of Ne-H2O clusters

NASA Astrophysics Data System (ADS)

Ziemkiewicz, Michael P.; Pluetzer, Christian; Wojcik, Michael; Loreau, Jérôme; van der Avoird, Ad; Nesbitt, David J.

2017-03-01

Vibrationally state selective overtone spectroscopy and dynamics of weakly bound Ne-H2O complexes (D0(para) = 31.67 cm-1, D0(ortho) = 34.66 cm-1) are reported for the first time, based on near infrared excitation of van der Waals cluster bands correlating with vOH = 2 ← 0 overtone transitions (|02-⟩←|00+⟩ and |02+⟩ ←|00+⟩ ) out of the ortho (101) and para (000) internal rotor states of the H2O moiety. Quantum theoretical calculations for nuclear motion on a high level ab initio potential energy surface (CCSD(T)/VnZ-f12 (n = 3,4), corrected for basis set superposition error and extrapolated to the complete basis set limit) are employed for assignment of Σ ←Σ ,Π ←Σ , and Σ ←Π infrared bands in the overtone spectra, where Σ ( K = 0) and Π (K = 1) represent approximate projections (K) of the body angular momentum along the Ne-H2O internuclear axis. End-over-end tumbling of the ortho Ne-H2O cluster is evident via rotational band contours observed, with band origins and rotational progressions in excellent agreement with ab initio frequency and intensity predictions. A clear Q branch in the corresponding |02+⟩fΠ (111) ←eΣ (000) para Ne-H2O spectrum provides evidence for a novel e/f parity-dependent metastability in these weakly bound clusters, in agreement with ab initio bound state calculations and attributable to the symmetry blocking of an energetically allowed channel for internal rotor predissociation. Finally, Boltzmann analysis of the rotational spectra reveals anomalously low jet temperatures (Trot ≈ 4(1) K), which are attributed to "evaporative cooling" of weakly bound Ne-H2O clusters and provide support for similar cooling dynamics in rare gas-tagging studies.

Shape and color conjunction stimuli are represented as bound objects in visual working memory.

PubMed

Luria, Roy; Vogel, Edward K

2011-05-01

The integrated object view of visual working memory (WM) argues that objects (rather than features) are the building block of visual WM, so that adding an extra feature to an object does not result in any extra cost to WM capacity. Alternative views have shown that complex objects consume additional WM storage capacity so that it may not be represented as bound objects. Additionally, it was argued that two features from the same dimension (i.e., color-color) do not form an integrated object in visual WM. This led some to argue for a "weak" object view of visual WM. We used the contralateral delay activity (the CDA) as an electrophysiological marker of WM capacity, to test those alternative hypotheses to the integrated object account. In two experiments we presented complex stimuli and color-color conjunction stimuli, and compared performance in displays that had one object but varying degrees of feature complexity. The results supported the integrated object account by showing that the CDA amplitude corresponded to the number of objects regardless of the number of features within each object, even for complex objects or color-color conjunction stimuli. Copyright © 2010 Elsevier Ltd. All rights reserved.

An ultra-weak sector, the strong CP problem and the pseudo-Goldstone dilaton

DOE PAGES

Allison, Kyle; Hill, Christopher T.; Ross, Graham G.

2014-12-29

In the context of a Coleman–Weinberg mechanism for the Higgs boson mass, we address the strong CP problem. We show that a DFSZ-like invisible axion model with a gauge-singlet complex scalar field S, whose couplings to the Standard Model are naturally ultra-weak, can solve the strong CP problem and simultaneously generate acceptable electroweak symmetry breaking. The ultra-weak couplings of the singlet S are associated with underlying approximate shift symmetries that act as custodial symmetries and maintain technical naturalness. The model also contains a very light pseudo-Goldstone dilaton that is consistent with cosmological Polonyi bounds, and the axion can be themore » dark matter of the universe. As a result, we further outline how a SUSY version of this model, which may be required in the context of Grand Unification, can avoid introducing a hierarchy problem.« less

An ultra-weak sector, the strong CP problem and the pseudo-Goldstone dilaton

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

Allison, Kyle; Hill, Christopher T.; Ross, Graham G.

In the context of a Coleman–Weinberg mechanism for the Higgs boson mass, we address the strong CP problem. We show that a DFSZ-like invisible axion model with a gauge-singlet complex scalar field S, whose couplings to the Standard Model are naturally ultra-weak, can solve the strong CP problem and simultaneously generate acceptable electroweak symmetry breaking. The ultra-weak couplings of the singlet S are associated with underlying approximate shift symmetries that act as custodial symmetries and maintain technical naturalness. The model also contains a very light pseudo-Goldstone dilaton that is consistent with cosmological Polonyi bounds, and the axion can be themore » dark matter of the universe. As a result, we further outline how a SUSY version of this model, which may be required in the context of Grand Unification, can avoid introducing a hierarchy problem.« less

Molecular complexes in close and far away

PubMed Central

Klemperer, William; Vaida, Veronica

2006-01-01

In this review, gas-phase chemistry of interstellar media and some planetary atmospheres is extended to include molecular complexes. Although the composition, density, and temperature of the environments discussed are very different, molecular complexes have recently been considered as potential contributors to chemistry. The complexes reviewed include strongly bound aggregates of molecules with ions, intermediate-strength hydrogen bonded complexes (primarily hydrates), and weakly bonded van der Waals molecules. In low-density, low-temperature environments characteristic of giant molecular clouds, molecular synthesis, known to involve gas-phase ion-molecule reactions and chemistry at the surface of dust and ice grains is extended here to involve molecular ionic clusters. At the high density and high temperatures found on planetary atmospheres, molecular complexes contribute to both atmospheric chemistry and climate. Using the observational, laboratory, and theoretical database, the role of molecular complexes in close and far away is discussed. PMID:16740667

Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly.

PubMed

Cai, Kai; Frederick, Ronnie O; Tonelli, Marco; Markley, John L

2018-06-01

Frataxin (FXN) is involved in mitochondrial iron‑sulfur (Fe-S) cluster biogenesis and serves to accelerate Fe-S cluster formation. FXN deficiency is associated with Friedreich ataxia, a neurodegenerative disease. We have used a combination of isothermal titration calorimetry and multinuclear NMR spectroscopy to investigate interactions among the components of the biological machine that carries out the assembly of iron‑sulfur clusters in human mitochondria. Our results show that FXN tightly binds a single Fe 2+ but not Fe 3+ . While FXN (with or without bound Fe 2+ ) does not bind the scaffold protein ISCU directly, the two proteins interact mutually when each is bound to the cysteine desulfurase complex ([NFS1] 2 :[ISD11] 2 :[Acp] 2 ), abbreviated as (NIA) 2 , where "N" represents the cysteine desulfurase (NFS1), "I" represents the accessory protein (ISD11), and "A" represents acyl carrier protein (Acp). FXN binds (NIA) 2 weakly in the absence of ISCU but more strongly in its presence. Fe 2+ -FXN binds to the (NIA) 2 -ISCU 2 complex without release of iron. However, upon the addition of both l-cysteine and a reductant (either reduced FDX2 or DTT), Fe 2+ is released from FXN as consistent with Fe 2+ -FXN being the proximal source of iron for Fe-S cluster assembly. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Organic complexation and translocation of ferric iron in podzols of the Negro River watershed. Separation of secondary Fe species from Al species

NASA Astrophysics Data System (ADS)

Fritsch, E.; Allard, Th.; Benedetti, M. F.; Bardy, M.; do Nascimento, N. R.; Li, Y.; Calas, G.

2009-04-01

The development of podzols in lateritic landscapes of the upper Amazon basin contributes to the exportation of organic carbon and associated metals in the black waters of the Negro River watershed. We have investigated the distribution of Fe III in the clay-size fraction of eight organic-rich horizons of waterlogged plateau podzols, to unravel the weathering conditions and mechanisms that control its transfer to the rivers. The speciation and amount of Fe III stored in residual mineral phases of laterites, or bound to organic compounds of weakly and well-expressed podzols, were determined by electron paramagnetic resonance spectroscopy combined with chemical analyses. Reducing conditions restrict the production of organo-Fe complexes in the subsoil B-horizons of waterlogged podzols and most of the Fe 2+ released from the dissolution of Fe-oxides is exported to the rivers via the perched groundwater. However, significant amounts of diluted Fe III bound to organic ligands (Fe IIIOM) and nano Fe-oxides are produced at the margin of the depression in the topsoil A horizons of weakly expressed podzols due to shorter periods of anoxia. The downward translocation of organically bound metals from topsoil A to subsoil B-horizons of podzols occurs in shorter distances for Fe than it does for Al. This separation of secondary Fe species from Al species is attributed to the physical fractionation of their organic carriers in texture contrasted B-horizons of podzols, as well as to the effect of pH on metal speciation in soil solutions and metal binding onto soil organic ligands (mostly for Al). This leads us to consider the topsoil A horizons of weakly expressed podzols, as well as the subsoil Bh horizon of better-expressed ones, as the main sources for the transfer of Fe IIIOM to the rivers. The concentration of Fe IIIOM rises from soil sources to river colloids, suggesting drastic biogeochemical changes in more oxygenated black waters of the Negro River watershed. The contribution of soil organic matter to the transfer of Fe to rivers is likely at the origin of the peculiar Fe isotope pattern recently recognized in podzolic environments.

Constraining the generalized uncertainty principle with the atomic weak-equivalence-principle test

NASA Astrophysics Data System (ADS)

Gao, Dongfeng; Wang, Jin; Zhan, Mingsheng

2017-04-01

Various models of quantum gravity imply the Planck-scale modifications of Heisenberg's uncertainty principle into a so-called generalized uncertainty principle (GUP). The GUP effects on high-energy physics, cosmology, and astrophysics have been extensively studied. Here, we focus on the weak-equivalence-principle (WEP) violation induced by the GUP. Results from the WEP test with the 85Rb-87Rb dual-species atom interferometer are used to set upper bounds on parameters in two GUP proposals. A 1045-level bound on the Kempf-Mangano-Mann proposal and a 1027-level bound on Maggiore's proposal, which are consistent with bounds from other experiments, are obtained. All these bounds have huge room for improvement in the future.

Co-potentiation of antigen recognition: A mechanism to boost weak T cell responses and provide immunotherapy in vivo

PubMed Central

Hoffmann, Michele M.; Molina-Mendiola, Carlos; Nelson, Alfreda D.; Parks, Christopher A.; Reyes, Edwin E.; Hansen, Michael J.; Rajagopalan, Govindarajan; Pease, Larry R.; Schrum, Adam G.; Gil, Diana

2015-01-01

Adaptive immunity is mediated by antigen receptors that can induce weak or strong immune responses depending on the nature of the antigen that is bound. In T lymphocytes, antigen recognition triggers signal transduction by clustering T cell receptor (TCR)/CD3 multiprotein complexes. In addition, it hypothesized that biophysical changes induced in TCR/CD3 that accompany receptor engagement may contribute to signal intensity. Nonclustering monovalent TCR/CD3 engagement is functionally inert despite the fact that it may induce changes in conformational arrangement or in the flexibility of receptor subunits. We report that the intrinsically inert monovalent engagement of TCR/CD3 can specifically enhance physiologic T cell responses to weak antigens in vitro and in vivo without stimulating antigen-unengaged T cells and without interrupting T cell responses to strong antigens, an effect that we term as “co-potentiation.” We identified Mono-7D6-Fab, which biophysically altered TCR/CD3 when bound and functionally enhanced immune reactivity to several weak antigens in vitro, including a gp100-derived peptide associated with melanoma. In vivo, Mono-7D6-Fab induced T cell antigen–dependent therapeutic responses against melanoma lung metastases, an effect that synergized with other anti-melanoma immunotherapies to significantly improve outcome and survival. We conclude that Mono-7D6-Fab directly co-potentiated TCR/CD3 engagement by weak antigens and that such concept can be translated into an immunotherapeutic design. The co-potentiation principle may be applicable to other receptors that could be regulated by otherwise inert compounds whose latent potency is only invoked in concert with specific physiologic ligands. PMID:26601285

Bound and resonance states of the dipolar anion of hydrogen cyanide: Competition between threshold effects and rotation in an open quantum system

DOE PAGES

Fossez, K.; Michel, N.; Nazarewicz, W.; ...

2015-01-12

In this paper, bound and resonance states of the dipole-bound anion of hydrogen cyanide HCN – are studied using a nonadiabatic pseudopotential method and the Berggren expansion technique involving bound states, decaying resonant states, and nonresonant scattering continuum. We devise an algorithm to identify the resonant states in the complex energy plane. To characterize spatial distributions of electronic wave functions, we introduce the body-fixed density and use it to assign families of resonant states into collective rotational bands. We find that the nonadiabatic coupling of electronic motion to molecular rotation results in a transition from the strong-coupling to weak-coupling regime.more » In the strong-coupling limit, the electron moving in a subthreshold, spatially extended halo state follows the rotational motion of the molecule. Above the ionization threshold, the electron's motion in a resonance state becomes largely decoupled from molecular rotation. Finally, the widths of resonance-band members depend primarily on the electron orbital angular momentum.« less

Evidence for weakly bound electrons in non-irradiated alkane crystals: The electrons as a probe of structural differences in crystals.

PubMed

Pietrow, M; Gagoś, M; Misiak, L E; Kornarzyński, K; Szurkowski, J; Rochowski, P; Grzegorczyk, M

2015-02-14

It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents evidence for the presence of these electrons in non-irradiated samples of docosane. This can be due to the triboelectrification process. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. Electrons from the former ones are bound more weakly than electrons from the latter ones. The origin of Vis absorption for the samples is explained. These spectra can be used as a probe indicating differences in the solid structures of hydrocarbons.

Diffraction Theory and Almost Periodic Distributions

NASA Astrophysics Data System (ADS)

Strungaru, Nicolae; Terauds, Venta

2016-09-01

We introduce and study the notions of translation bounded tempered distributions, and autocorrelation for a tempered distribution. We further introduce the spaces of weakly, strongly and null weakly almost periodic tempered distributions and show that for weakly almost periodic tempered distributions the Eberlein decomposition holds. For translation bounded measures all these notions coincide with the classical ones. We show that tempered distributions with measure Fourier transform are weakly almost periodic and that for this class, the Eberlein decomposition is exactly the Fourier dual of the Lebesgue decomposition, with the Fourier-Bohr coefficients specifying the pure point part of the Fourier transform. We complete the project by looking at few interesting examples.

A Reduced Basis Method with Exact-Solution Certificates for Symmetric Coercive Equations

DTIC Science & Technology

2013-11-06

the energy associated with the infinite - dimensional weak solution of parametrized symmetric coercive partial differential equations with piecewise...builds bounds with respect to the infinite - dimensional weak solution, aims to entirely remove the issue of the “truth” within the certified reduced basis...framework. We in particular introduce a reduced basis method that provides rigorous upper and lower bounds

Evidence for weakly bound electrons in non-irradiated alkane crystals: The electrons as a probe of structural differences in crystals

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

Pietrow, M., E-mail: mrk@kft.umcs.lublin.pl; Misiak, L. E.; Gagoś, M.

2015-02-14

It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents evidence for the presence of these electrons in non-irradiated samples of docosane. This can be due to the triboelectrification process. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. Electrons from the former ones are bound more weakly than electrons from the latter ones. The origin of Vis absorption for the samples is explained. These spectra canmore » be used as a probe indicating differences in the solid structures of hydrocarbons.« less

Photochemistry and reactivity of the phenyl radical-water system: a matrix isolation and computational study.

PubMed

Mardyukov, Artur; Crespo-Otero, Rachel; Sanchez-Garcia, Elsa; Sander, Wolfram

2010-08-02

The reaction of the phenyl radical 1 with water has been investigated by using matrix isolation spectroscopy and quantum chemical calculations. The primary thermal product of the reaction between 1 and water is a weakly bound complex stabilized by an OH...pi interaction. This complex is photolabile, and visible-light irradiation (lambda>420 nm) results in hydrogen atom transfer from water to radical 1 and the formation of a highly labile complex between benzene and the OH radical. This complex is stable under the conditions of matrix isolation, however, continuous irradiation with lambda>420 nm light results in the complete destruction of the aromatic system and formation of an acylic unsaturated ketene. The mechanisms of all reaction steps are discussed in the light of ab initio and DFT calculations.

Energetics of dendrimer binding to HIV-1 gp120-CD4 complex and mechanismic aspects of its role as an entry-inhibitor

NASA Astrophysics Data System (ADS)

Saurabh, Suman; Sahoo, Anil Kumar; Maiti, Prabal K.

2016-10-01

Experiments and computational studies have established that de-protonated dendrimers (SPL7013 and PAMAM) act as entry-inhibitors of HIV. SPL7013 based Vivagel is currently under clinical development. The dendrimer binds to gp120 in the gp120-CD4 complex, destabilizes it by breaking key contacts between gp120 and CD4 and prevents viral entry into target cells. In this work, we provide molecular details and energetics of the formation of the SPL7013-gp120-CD4 ternary complex and decipher modes of action of the dendrimer in preventing viral entry. It is also known from experiments that the dendrimer binds weakly to gp120 that is not bound to CD4. It binds even more weakly to the CD4-binding region of gp120 and thus cannot directly block gp120-CD4 complexation. In this work, we examine the feasibility of dendrimer binding to the gp120-binding region of CD4 and directly blocking gp120-CD4 complex formation. We find that the process of the dendrimer binding to CD4 can compete with gp120-CD4 binding due to comparable free energy change for the two processes, thus creating a possibility for the dendrimer to directly block gp120-CD4 complexation by binding to the gp120-binding region of CD4.

Decay of Complex-Time Determinantal and Pfaffian Correlation Functionals in Lattices

NASA Astrophysics Data System (ADS)

Aza, N. J. B.; Bru, J.-B.; de Siqueira Pedra, W.

2018-04-01

We supplement the determinantal and Pfaffian bounds of Sims and Warzel (Commun Math Phys 347:903-931, 2016) for many-body localization of quasi-free fermions, by considering the high dimensional case and complex-time correlations. Our proof uses the analyticity of correlation functions via the Hadamard three-line theorem. We show that the dynamical localization for the one-particle system yields the dynamical localization for the many-point fermionic correlation functions, with respect to the Hausdorff distance in the determinantal case. In Sims and Warzel (2016), a stronger notion of decay for many-particle configurations was used but only at dimension one and for real times. Considering determinantal and Pfaffian correlation functionals for complex times is important in the study of weakly interacting fermions.

Decay of Complex-Time Determinantal and Pfaffian Correlation Functionals in Lattices

NASA Astrophysics Data System (ADS)

Aza, N. J. B.; Bru, J.-B.; de Siqueira Pedra, W.

2018-06-01

We supplement the determinantal and Pfaffian bounds of Sims and Warzel (Commun Math Phys 347:903-931, 2016) for many-body localization of quasi-free fermions, by considering the high dimensional case and complex-time correlations. Our proof uses the analyticity of correlation functions via the Hadamard three-line theorem. We show that the dynamical localization for the one-particle system yields the dynamical localization for the many-point fermionic correlation functions, with respect to the Hausdorff distance in the determinantal case. In Sims and Warzel (2016), a stronger notion of decay for many-particle configurations was used but only at dimension one and for real times. Considering determinantal and Pfaffian correlation functionals for complex times is important in the study of weakly interacting fermions.

Reaction Mechanisms in Collisions Induced by Halo and/or Weakly Bound Nuclei Around the Barrier: the 13N+9Be and 6He+64Zn Collisions

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

Figuera, P.; Cardella, G.; Di Pietro, A.

2006-08-14

The study of reaction mechanisms in collisions induced by halo and/or weakly bound nuclei around the barrier has recently been the subject of many theoretical and experimental papers. Here we discuss our recent results concerning the study of the systems 13N+9Be and 6He+64Zn.

Selenium fractions in organic matter from Se-rich soils and weathered stone coal in selenosis areas of China.

PubMed

Qin, Hai-bo; Zhu, Jian-ming; Su, Hui

2012-02-01

A high degree of association between Selenium (Se) and organic matter has been demonstrated in natural environments, but Se fractions and speciation in organic matter is unclear. In this study, a method for quantifying organic matter associated with Se (OM-Se) was developed to investigate Se fractions in organic matter in Se-rich soils and weathered stone coal from Enshi, China, where Se poisoning of humans and livestock has been documented. Initially, Se was extracted using water and a phosphate buffer. Subsequently, OM-Se was extracted using NaOH, and then speciated into Se associated with fulvic acids (FA-Se) and humic acids (HA-Se). Both FA-Se and HA-Se were further speciated into the weakly bound and strongly bound fractions using a customized hydride generation reactor. The results show that FA-Se (1.91-479 mg kg(-1)) is the predominant form of Se in all Se-rich soils and the weathered stone coal samples, accounting for more than 62% of OM-Se (3.07-484 mg kg(-1)). Weakly bound FA-Se (1.33-450 mg kg(-1)) was prevalent in the total FA-Se, while weakly bound HA-Se (0.62-26.2 mg kg(-1)) was variable in the total HA-Se (1.15-32.5 mg kg(-1)). These data indicate that OM-Se could play a significant source and sink role in the biogeochemical cycling of Se in the supergene environment. Weakly bound FA-Se seems to act as a potential source for bioavailable Se, whereas strongly bound HA-Se is a possible OM-Se sink which is not readily transformed into bioavailable Se. Copyright © 2011 Elsevier Ltd. All rights reserved.

Why three-body physics does not solve the proton-radius puzzle.

PubMed

Karr, Jean-Philippe; Hilico, Laurent

2012-09-07

The possible involvement of weakly bound three-body systems in the muonic hydrogen spectroscopy experiment, which could resolve the current discrepancy between determinations of the proton radius, is investigated. Using variational calculations with complex coordinate rotation, we show that in the pμe ion, which was recently proposed as a possible candidate, the pμ core fails to bind the outer electron tightly enough to explain the discrepancy. It is also shown that the ppμ molecular ion cannot play any role in the observed line.

The Influence of Fluorination on Structure of the Trifluoroacetonitrile Water Complex

NASA Astrophysics Data System (ADS)

Lin, Wei; Wu, Anan; Lu, Xin; Obenchain, Daniel A.; Novick, Stewart E.

2015-06-01

Acetonitrile, CH_3CN, and trifluoroacetonitrile, CF_3CN, are symmetric tops. In a recent study of the rotational spectrum of the acetonitrile and water complex, it was observed that the structure was also an effective symmetric top, with the external hydrogen freely rotating about the O-H bond aligned towards the nitrogen of the cyanide of CH_3CN. Unlike the CH_3CN-H_2O complex, the CH_3CN-Ar and CF_3CN-Ar complexes were observed to be asymmetric tops. Having a series of symmetric and asymmetric top complexes of acetonitrile and trifluoracetonitrile for comparison, we report the rotational spectrum of the weakly bound complex between trifluoroacetonitrile and water. Rotational constants and quadrupole coupling constants will be presented, and the structure of CF_3CN-H_2O will be revealed. Lovas, F.J.; Sobhanadri, J. Microwave rotational spectral study of CH_3CN-H_2O and Ar-CH_3CN. J. Mol. Spetrosc. 2015, 307, 59-64. SPOILER ALERT: It's an asymmetric top.

Weak hydrogen bonds in complexes pairing monohalomethanes with neutral formic acid

NASA Astrophysics Data System (ADS)

Solimannejad, Mohammad; Scheiner, Steve

2006-06-01

Ab initio calculations are used to analyze the interaction between formic acid and CH 3X, for X equal to each of F, Cl, and Br. All minima are cyclic in that they contain more than one H-bond. The most strongly bound contain a OH⋯X bond, along with CH⋯O, and the others contain CH⋯X and CH⋯O interactions. Alterations of the covalent bond lengths within each subunit, and vibrational frequency shifts, coupled with electronic charge shifts, reveal fundamental features of these complexes, and the nature of the interactions. The OH⋯X bond is the strongest of those examined here, followed by CH⋯X and CH⋯O.

Information-theoretic measures of hydrogen-like ions in weakly coupled Debye plasmas

NASA Astrophysics Data System (ADS)

Zan, Li Rong; Jiao, Li Guang; Ma, Jia; Ho, Yew Kam

2017-12-01

Recent development of information theory provides researchers an alternative and useful tool to quantitatively investigate the variation of the electronic structure when atoms interact with the external environment. In this work, we make systematic studies on the information-theoretic measures for hydrogen-like ions immersed in weakly coupled plasmas modeled by Debye-Hückel potential. Shannon entropy, Fisher information, and Fisher-Shannon complexity in both position and momentum spaces are quantified in high accuracy for the hydrogen atom in a large number of stationary states. The plasma screening effect on embedded atoms can significantly affect the electronic density distributions, in both conjugate spaces, and it is quantified by the variation of information quantities. It is shown that the composite quantities (the Shannon entropy sum and the Fisher information product in combined spaces and Fisher-Shannon complexity in individual space) give a more comprehensive description of the atomic structure information than single ones. The nodes of wave functions play a significant role in the changes of composite information quantities caused by plasmas. With the continuously increasing screening strength, all composite quantities in circular states increase monotonously, while in higher-lying excited states where nodal structures exist, they first decrease to a minimum and then increase rapidly before the bound state approaches the continuum limit. The minimum represents the most reduction of uncertainty properties of the atom in plasmas. The lower bounds for the uncertainty product of the system based on composite information quantities are discussed. Our research presents a comprehensive survey in the investigation of information-theoretic measures for simple atoms embedded in Debye model plasmas.

Effect of soil properties on pure and formulated mesotrione adsorption onto vertisol (Limagne plane, Puy-de-Dôme, France).

PubMed

Alekseeva, Tatiana; Kolyagin, Yury; Sancelme, Martine; Besse-Hoggan, Pascale

2014-09-01

The fate of ionisable pesticides in the environment is complex as it is importantly related to many soil properties: pH, mineralogy, organic matter content and other soil characteristics. The adsorption of a weak acid herbicide, mesotrione, was studied in detail on whole and peroxide-treated vertisol topsoil and also on its granulometric fractions (clay, silt, sand) to evaluate the role of mineralogy and different organic matter pools. The soil studied is alkaline silty loam with smectite as the main clay mineral. It contains 1.7% organic carbon, mostly stabilized as a complex with smectite. Humus is of fulvic type. Mesotrione adsorption occurs on both mineral and organic constituents. Adsorption is weak and mesotrione can be easily and totally desorbed. As shown with (13)C NMR experiments, adsorption best correlates with the alkyl and carboxylic carbon content, and occurs on both bound and free organic matter. No difference of mesotrione sorption was observed with the formulation Callisto®. Copyright © 2014 Elsevier Ltd. All rights reserved.

Exploring Photoinduced Excited State Evolution in Heterobimetallic Ru(II)-Co(III) Complexes.

PubMed

Kuhar, Korina; Fredin, Lisa A; Persson, Petter

2015-06-18

Quantum chemical calculations provide detailed theoretical information concerning key aspects of photoinduced electron and excitation transfer processes in supramolecular donor-acceptor systems, which are particularly relevant to fundamental charge separation in emerging molecular approaches for solar energy conversion. Here we use density functional theory (DFT) calculations to explore the excited state landscape of heterobimetallic Ru-Co systems with varying degrees of interaction between the two metal centers, unbound, weakly bound, and tightly bound systems. The interplay between structural and electronic factors involved in various excited state relaxation processes is examined through full optimizations of multiple charge/spin states of each of the investigated systems. Low-energy relaxed heterobimetallic states of energy transfer and excitation transfer character are characterized in terms of energy, structure, and electronic properties. These findings support the notion of efficient photoinduced charge separation from a Ru(II)-Co(III) ground state, via initial optical excitation of the Ru-center, to low-energy Ru(III)-Co(II) states. The strongly coupled system has significant involvement of the conjugated bridge, qualitatively distinguishing it from the other two weakly coupled systems. Finally, by constructing potential energy surfaces for the three systems where all charge/spin state combinations are projected onto relevant reaction coordinates, excited state decay pathways are explored.

Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion.

PubMed

Oyen, David; Fenwick, R Bryn; Aoto, Phillip C; Stanfield, Robyn L; Wilson, Ian A; Dyson, H Jane; Wright, Peter E

2017-08-16

The rate-determining step in the catalytic cycle of E. coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate as compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remain elusive. Here, we use side-chain proton NMR relaxation dispersion measurements, X-ray crystallography, and structure-based chemical shift predictions to explore the structural basis of allosteric product release. In the excited state of the E:THF:NADPH product release complex, the reduced nicotinamide ring of the cofactor transiently enters the active site where it displaces the pterin ring of the THF product. The p-aminobenzoyl-l-glutamate tail of THF remains weakly bound in a widened binding cleft. Thus, through transient entry of the nicotinamide ring into the active site, the NADPH cofactor remodels the enzyme structure and the conformation of the THF to form a weakly populated excited state that is poised for rapid product release.

Phonon coupling in optical transitions for singlet-triplet pairs of bound excitons in semiconductors

NASA Astrophysics Data System (ADS)

Pistol, M. E.; Monemar, B.

1986-05-01

A model is presented for the observed strong difference in selection rules for coupling of phonons in the one-phonon sideband of optical spectra related to bound excitons in semiconductors. The present treatment is specialized to the case of a closely spaced pair of singlet-triplet character as the lowest electronic states, as is common for bound excitons associated with neutral complexes in materials like GaP and Si. The optical transition for the singlet bound-exciton state is found to couple strongly only to symmetric A1 modes. The triplet state has a similar coupling strength to A1 modes, but in addition strong contributions are found for replicas corresponding to high-density-of-states phonons TAX, LAX, and TOX. This can be explained by a treatment of particle-phonon coupling beyond the ordinary adiabatic approximation. A weak mixing between the singlet and triplet states is mediated by the phonon coupling, as described in first-order perturbation theory. The model derived in this work, for such phonon-induced mixing of closely spaced electronic states, is shown to explain the observed phonon coupling for several bound-exciton systems of singlet-triplet character in GaP. In addition, the observed oscillator strength of the forbidden triplet state may be explained as partly derived from phonon-induced mixing with the singlet state, which has a much larger oscillator strength.

Study of breakup and transfer of weakly bound nucleus 6Li to explore the low energy reaction dynamics

NASA Astrophysics Data System (ADS)

Zhang, G. L.; Zhang, G. X.; Hu, S. P.; Zhang, H. Q.; Gomes, P. R. S.; Lubian, J.; Guo, C. L.; Wu, X. G.; Yang, J. C.; Zheng, Y.; Li, C. B.; He, C. Y.; Zhong, J.; Li, G. S.; Yao, Y. J.; Guo, M. F.; Sun, H. B.; Valiente-Dobòn, J. J.; Goasduff, A.; Siciliano, M.; Galtarosa, F.; Francesco, R.; Testov, D.; Mengoni, D.; Bazzacco, D.; John, P. R.; Qu, W. W.; Wang, F.; Zheng, L.; Yu, L.; Chen, Q. M.; Luo, P. W.; Li, H. W.; Wu, Y. H.; Zhou, W. K.; Zhu, B. J.; Li, E. T.; Hao, X.

2017-11-01

Investigation of the breakup and transfer effect of weakly bound nuclei on the fusion process has been an interesting research topic in the past several years. However, owing to the low intensities of the presently available radioactive ion beam (RIB), it is difficult to clearly explore the reaction mechanisms of nuclear systems with unstable nuclei. In comparison with RIB, the beam intensities of stable weakly bound nuclei such as 6,7Li and 9Be, which have significant breakup probability, are orders of magnitude higher. Precise fusion measurements have already been performed with those stable weakly bound nuclei, and the effect of breakup of those nuclei on the fusion process has been extensively studied. Those nuclei indicated large production cross sections for particles other than the α + x breakup. The particles are originated from non-capture breakup (NCBU), incomplete fusion (ICF) and transfer processes. However, the conclusion of reaction dynamics was not clear and has the contradiction. In our previous experiments we have performed 6Li+96Zr and 154Sm at HI-13 Tandem accelerator of China Institute of Atomic Energy (CIAE) by using HPGe array. It is shown that there is a small complete fusion (CF) suppression on medium-mass target nucleus 96Zr different from about 35% suppression on heavier target nucleus 154Sm at near-barrier energies. It seems that the CF suppression factor depends on the charge of target nuclei. We also observed one neutron transfer process. However, the experimental data are scarce for medium-mass target nuclei. In order to have a proper understanding of the influence of breakup and transfer of weakly bound projectiles on the fusion process, we performed the 6Li+89Y experiment with incident energies of 22 MeV and 34 MeV on Galileo array in cooperation with Si-ball EUCLIDES at Legnaro National Laboratory (LNL) in Italy. Using particle-particle and particle-γ coincidences, the different reaction mechanisms can be clearly explored.

Engineering On-Surface Spin Crossover: Spin-State Switching in a Self-Assembled Film of Vacuum-Sublimable Functional Molecule.

PubMed

Kumar, Kuppusamy Senthil; Studniarek, Michał; Heinrich, Benoît; Arabski, Jacek; Schmerber, Guy; Bowen, Martin; Boukari, Samy; Beaurepaire, Eric; Dreiser, Jan; Ruben, Mario

2018-03-01

The realization of spin-crossover (SCO)-based applications requires study of the spin-state switching characteristics of SCO complex molecules within nanostructured environments, especially on surfaces. Except for a very few cases, the SCO of a surface-bound thin molecular film is either quenched or heavily altered due to: (i) molecule-surface interactions and (ii) differing intermolecular interactions in films relative to the bulk. By fabricating SCO complexes on a weakly interacting surface, the interfacial quenching problem is tackled. However, engineering intermolecular interactions in thin SCO active films is rather difficult. Here, a molecular self-assembly strategy is proposed to fabricate thin spin-switchable surface-bound films with programmable intermolecular interactions. Molecular engineering of the parent complex system [Fe(H 2 B(pz) 2 ) 2 (bpy)] (pz = pyrazole, bpy = 2,2'-bipyridine) with a dodecyl (C 12 ) alkyl chain yields a classical amphiphile-like functional and vacuum-sublimable charge-neutral Fe II complex, [Fe(H 2 B(pz) 2 ) 2 (C 12 -bpy)] (C 12 -bpy = dodecyl[2,2'-bipyridine]-5-carboxylate). Both the bulk powder and 10 nm thin films sublimed onto either quartz glass or SiO x surfaces of the complex show comparable spin-state switching characteristics mediated by similar lamellar bilayer like self-assembly/molecular interactions. This unprecedented observation augurs well for the development of SCO-based applications, especially in molecular spintronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical predictions of vibration-rotation-tunneling dynamics of the weakly bound trimer (H 2O) 2HCl

NASA Astrophysics Data System (ADS)

Struniewicz, Cezary; Korona, Tatiana; Moszynski, Robert; Milet, Anne

2001-08-01

In this Letter we report a theoretical study of the vibration-rotation-tunneling (VRT) states of the (H 2O) 2HCl trimer. Five degrees of freedom are considered: two angles corresponding to the torsional (flipping) motions of the free, non-hydrogen-bonded, hydrogen atoms in the complex, and three angles describing the overall rotation of the trimer in the space. A two-dimensional potential energy surface is generated ab initio by symmetry-adapted perturbation theory (SAPT). Tunneling splittings, frequencies of the intermolecular vibrations, and vibrational line strengths of spectroscopic transitions are predicted.

Broadband Microwave Spectroscopy as a Tool to Study Intermolecular Interactions in the Diphenyl Ether - Water System

NASA Astrophysics Data System (ADS)

Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie

2017-06-01

Many biological processes, such as chemical recognition and protein folding, are mainly controlled by the interplay of hydrogen bonds and dispersive forces. This interplay also occurs between organic molecules and solvent water molecules. Broadband rotational spectroscopy studies of weakly bound complexes are able to accurately reveal the structures and internal dynamics of molecular clusters isolated in the gas phase. Amongst them, water clusters with organic molecules are of particular interest. In this work, we investigate the interplay between different types of weak intermolecular interactions and how it controls the preferred interaction sites of aromatic ethers, where dispersive interactions may play a significant role. We present our results on diphenyl ether (C_{12}H_{10}O, 1,1'-Oxydibenzene) complexed with up to three molecules of water. Diphenyl ether is a flexible molecule, and it offers two competing binding sites for water: the ether oxygen and the aromatic π system. In order to determine the structure of the diphenyl ether-water complexes, we targeted transitions in the 2-8 GHz range using broadband rotational spectroscopy. We identify two isomers with one water, one with two water, and one with three water molecules. Further analysis from isotopic substitution measurements provided accurate structural information. The preferred interactions, as well as the observed structural changes induced upon complexation, will be presented and discussed.

Supramolecular Structures with Blood Plasma Proteins, Sugars and Nanosilica

NASA Astrophysics Data System (ADS)

Turov, V. V.; Gun'ko, V. M.; Galagan, N. P.; Rugal, A. A.; Barvinchenko, V. M.; Gorbyk, P. P.

Supramolecular structures with blood plasma proteins (albumin, immunoglobulin and fibrinogen (HPF)), protein/water/silica and protein/water/ silica/sugar (glucose, fructose and saccharose) were studied by NMR, adsorption, IR and UV spectroscopy methods. Hydration parameters, amounts of weakly and strongly bound waters and interfacial energy (γ S) were determined over a wide range of component concentrations. The γ S(C protein,C silica) graphs were used to estimate the energy of protein-protein, protein-surface and particle-particle interactions. It was shown that interfacial energy of self-association (γ as) of protein molecules depends on a type of proteins. A large fraction of water bound to proteins can be displaced by sugars, and the effect of disaccharide (saccharose) was greater than that of monosugars. Changes in the structural parameters of cavities in HPF molecules and complexes with HPF/silica nanoparticles filled by bound water were analysed using NMR-cryoporometry showing that interaction of proteins with silica leads to a significant decrease in the amounts of water bound to both protein and silica surfaces. Bionanocomposites with BSA/nanosilica/sugar can be used to influence states of living cells and tissues after cryopreservation or other treatments. It was shown that interaction of proteins with silica leads to strong decrease in the volume of all types of internal cavities filled by water.

Dynamics at Lys-553 of the acto-myosin interface in the weakly and strongly bound states.

PubMed Central

MacLean, J J; Chrin, L R; Berger, C L

2000-01-01

Lys-553 of skeletal muscle myosin subfragment 1 (S1) was specifically labeled with the fluorescent probe FHS (6-[fluorescein-5(and 6)-carboxamido]hexanoic acid succinimidyl ester) and fluorescence quenching experiments were carried out to determine the accessibility of this probe at Lys-553 in both the strongly and weakly actin-bound states of the MgATPase cycle. Solvent quenchers of varying charge [nitromethane, (2,2,6, 6-tetramethyl-1-piperinyloxy) (TEMPO), iodide (I(-)), and thallium (Tl(+))] were used to assess both the steric and electrostatic accessibilities of the FHS probe at Lys-553. In the strongly bound rigor (nucleotide-free) and MgADP states, actin offered no protection from solvent quenching of FHS by nitromethane, TEMPO, or thallium, but did decrease the Stern-Volmer constant by almost a factor of two when iodide was used as the quencher. The protection from iodide quenching was almost fully reversed with the addition of 150 mM KCl, suggesting this effect is ionic in nature rather than steric. Conversely, actin offered no protection from iodide quenching at low ionic strength during steady-state ATP hydrolysis, even with a significant fraction of the myosin heads bound to actin. Thus, the lower 50 kD subdomain of myosin containing Lys-553 appears to interact differently with actin in the weakly and strongly bound states. PMID:10692329

Selection of different reaction channels in 6Li induced fusion reaction by a powerful combination of a charged particle array and a high-resolution gamma spectrometer

NASA Astrophysics Data System (ADS)

Zhang, G. X.; Hu, S. P.; Zhang, G. L.; Zhang, H. Q.; Yao, Y. J.; Huang, Z.; Wang, M. L.; Sun, H. B.; Valiente-Dobòn, J. J.; Testov, D.; Goasduff, A.; John, P. R.; Siciliano, M.; Galtarosa, F.; Francesco, R.; Mengoni, D.; Bazzacco, D.; Li, E. T.; Hao, X.

2018-05-01

Investigation of the breakup and transfer effect of weakly bound nuclei on the fusion process has been an interesting research topic in the past several years. In comparison with radioactive ion beam (RIB), the beam intensities of stable weakly bound nuclei such as 6,7Li and 9Be, which have significant breakup probability, are orders of magnitude higher. Precise fusion measurements induced by these nuclei have already been performed. However, the conclusion of reaction dynamics was not clear and has contradiction. In order to have a proper understanding of the influence of breakup and transfer of weakly bound projectiles on the fusion process, the 6Li+89Y experiment with incident energies of 22 MeV and 34 MeV was performed on Galileo array in combination with Si-ball EUCLIDES at Legnaro National Laboratory (LNL) in Italy. Using the coincidence by the charged particles and γ-rays, the different reaction channels can be clearly identified.

Vibration-rotation-tunneling spectroscopy of the van der Waals Bond: A new look at intermolecular forces

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

Cohen, R.C.; Saykally, R.J.

Measurements of the low-frequency van der Waals vibrations in weakly bound complexes by high-resolution laser spectroscopy provide a means to probe intermolecular forces at unprecedented levels of detail and precision. Several new methods are presently being used to record vibration/rotation-tunneling (VRT) transitions associated with the motions of the weak bonds in van der Waals clusters. The most direct measurements are those probing only the van der Waals modes themselves, which occur at far-infrared wavelengths. This article presents a review of the information on both intramolecular forces and intramolecular dynamics that has been obtained from far-infrared VRT spectra of 18 complexesmore » during the past several years. Some rotationally resolved measurements of van der Waals modes observed in combination with electronic or vibrational excitation are also discussed. 185 refs., 15 figs., 1 tab.« less

Conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules.

PubMed

Tocheva, Elitza I; Eltis, Lindsay D; Murphy, Michael E P

2008-04-15

The interaction of copper-containing dissimilatory nitrite reductase from Alcaligenes faecalis S-6 ( AfNiR) with each of five small molecules was studied using crystallography and steady-state kinetics. Structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of AfNiR. Three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. These three anions bound to the copper ion in the same asymmetric, bidentate manner as nitrite. Consistent with their weak inhibition of the enzyme ( K i >50 mM), the Cu-O distances in these AfNiR-inhibitor complexes were approximately 0.15 A longer than that observed in the AfNiR-nitrite complex. The binding mode of each inhibitor is determined in part by steric interactions with the side chain of active site residue Ile257. Moreover, the side chain of Asp98, a conserved residue that hydrogen bonds to type 2 copper-bound nitrite and nitric oxide, was either disordered or pointed away from the inhibitors. Acetate and formate inhibited AfNiR in a mixed fashion, consistent with the occurrence of second acetate binding site in the AfNiR-acetate complex that occludes access to the type 2 copper. A fourth small molecule, nitrous oxide, bound to the oxidized metal in a side-on fashion reminiscent of nitric oxide to the reduced copper. Nevertheless, nitrous oxide bound at a farther distance from the metal. The fifth small molecule, azide, inhibited the reduction of nitrite by AfNiR most strongly ( K ic = 2.0 +/- 0.1 mM). This ligand bound to the type 2 copper center end-on with a Cu-N c distance of approximately 2 A, and was the only inhibitor to form a hydrogen bond with Asp98. Overall, the data substantiate the roles of Asp98 and Ile257 in discriminating substrate from other small anions.

Transferred nuclear Overhauser enhancement experiments show that the monoclonal antibody strep 9 selects a local minimum conformation of a Streptococcus group A trisaccharide-hapten.

PubMed

Weimar, T; Harris, S L; Pitner, J B; Bock, K; Pinto, B M

1995-10-17

Transferred nuclear Overhauser enhancement (TRNOE) experiments have been performed to investigate the bound conformation of the trisaccharide repeating unit of the Streptococcus Group A cell-wall polysaccharide. Thus, the conformations of propyl 3-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-2-O-(alpha-L-rhamnopyran osyl)- alpha-L-rhamnopyranoside [C(A')B] (1) as a free ligand and when complexed to the monoclonal antibody Strep 9 were examined. Improved insights about the conformational preferences of the glycosidic linkages of the trisaccharide ligand showed that the free ligand populates various conformations in aqueous solution, thus displaying relatively flexible behavior. The NOE HNAc-H2A', which was not detected in previous work, accounts for a conformation at the beta-(1-->3) linkage with a phi angle of approximately 180 degrees. Observed TRNOEs for the complex are weak, and their analysis was further complicated by spin diffusion. With the use of transferred rotating-frame Overhauser enhancement (TRROE) experiments, the amount of spin diffusion was assessed experimentally, proving that all of the observed long-range TRNOEs arose through spin diffusion. Four interglycosidic distances, derived from the remaining TRNOEs and TRROEs, together with repulsive constraints, derived from the absence of TRROE effects, were used as input parameters in simulated annealing and molecular mechanics calculations to determine the bound conformation of the trisaccharide. Complexation by the antibody results in the selection of one defined conformation of the carbohydrate hapten. This bound conformation, which is a local energy minimum on the energy maps calculated for the trisaccharide ligand, shows only a change from a +gauche to a -gauche orientation at the psi angle of the alpha-(1-->2) linkage when compared to the global minimum conformation. The results infer that the bound conformation of the Streptococcus Group A cell-wall polysaccharide is different from its previously proposed solution structure (Kreis et al., 1995).

Broadband Microwave Spectroscopy as a Tool to Study the Structures of Odorant Molecules and Weakly Bound Complexes in the Gas Phase

NASA Astrophysics Data System (ADS)

Zinn, Sabrina; Betz, Thomas; Medcraft, Chris; Schnell, Melanie

2015-06-01

The rotational spectrum of trans-cinnamaldehyde ((2E)-3-phenylprop-2-enal) has been obtained with chirped-pulse microwave spectroscopy in the frequency range of 2 - 8.5 GHz. The odorant molecule is the essential component in cinnamon oil and causes the characteristic smell. In the measured high-resolution spectrum, we were able to assign the rotational spectra of two conformers of trans-cinnamaldehyde as well as all singly 13C-substituted species of the lowest-energy conformer in natural abundance. Two different methods were used to determine the structure from the rotational constants, which will be compared within this contribution. In addition, the current progress of studying ether-alcohol complexes, aiming at an improved understanding of the interplay between hydrogen bonding and dispersion interaction, will be reported. Here, a special focus is placed on the complexes of diphenylether with small aliphatic alcohols.

Near optimal pentamodes as a tool for guiding stress while minimizing compliance in 3d-printed materials: A complete solution to the weak G-closure problem for 3d-printed materials

NASA Astrophysics Data System (ADS)

Milton, Graeme W.; Camar-Eddine, Mohamed

2018-05-01

For a composite containing one isotropic elastic material, with positive Lame moduli, and void, with the elastic material occupying a prescribed volume fraction f, and with the composite being subject to an average stress, σ0 , Gibiansky, Cherkaev, and Allaire provided a sharp lower bound Wf(σ0) on the minimum compliance energy σ0 :ɛ0 , in which ɛ0 is the average strain. Here we show these bounds also provide sharp bounds on the possible (σ0 ,ɛ0) -pairs that can coexist in such composites, and thus solve the weak G-closure problem for 3d-printed materials. The materials we use to achieve the extremal (σ0 ,ɛ0) -pairs are denoted as near optimal pentamodes. We also consider two-phase composites containing this isotropic elasticity material and a rigid phase with the elastic material occupying a prescribed volume fraction f, and with the composite being subject to an average strain, ɛ0. For such composites, Allaire and Kohn provided a sharp lower bound W˜f(ɛ0) on the minimum elastic energy σ0 :ɛ0 . We show that these bounds also provide sharp bounds on the possible (σ0 ,ɛ0) -pairs that can coexist in such composites of the elastic and rigid phases, and thus solve the weak G-closure problem in this case too. The materials we use to achieve these extremal (σ0 ,ɛ0) -pairs are denoted as near optimal unimodes.

Study of weak solutions for parabolic variational inequalities with nonstandard growth conditions.

PubMed

Dong, Yan

2018-01-01

In this paper, we study the degenerate parabolic variational inequality problem in a bounded domain. First, the weak solutions of the variational inequality are defined. Second, the existence and uniqueness of the solutions in the weak sense are proved by using the penalty method and the reduction method.

Communication: THz absorption spectrum of the CO2-H2O complex: observation and assignment of intermolecular van der Waals vibrations.

PubMed

Andersen, J; Heimdal, J; Mahler, D W; Nelander, B; Larsen, R Wugt

2014-03-07

Terahertz absorption spectra have been recorded for the weakly bound CO2-H2O complex embedded in cryogenic neon matrices at 2.8 K. The three high-frequency van der Waals vibrational transitions associated with out-of-plane wagging, in-plane rocking, and torsional motion of the isotopic H2O subunit have been assigned and provide crucial observables for benchmark theoretical descriptions of this systems' flat intermolecular potential energy surface. A (semi)-empirical value for the zero-point energy of 273 ± 15 cm(-1) from the class of intermolecular van der Waals vibrations is proposed and the combination with high-level quantum chemical calculations provides a value of 726 ± 15 cm(-1) for the dissociation energy D0.

A simple elution strategy for biotinylated proteins bound to streptavidin conjugated beads using excess biotin and heat.

PubMed

Cheah, Joleen S; Yamada, Soichiro

2017-12-02

Protein-protein interactions are the molecular basis of cell signaling. Recently, proximity based biotin identification (BioID) has emerged as an alternative approach to traditional co-immunoprecipitation. In this protocol, a mutant biotin ligase promiscuously labels proximal binding partners with biotin, and resulting biotinylated proteins are purified using streptavidin conjugated beads. This approach does not require preservation of protein complexes in vitro, making it an ideal approach to identify transient or weak protein complexes. However, due to the high affinity bond between streptavidin and biotin, elution of biotinylated proteins from streptavidin conjugated beads requires harsh denaturing conditions, which are often incompatible with downstream processing. To effectively release biotinylated proteins bound to streptavidin conjugated beads, we designed a series of experiments to determine optimal binding and elution conditions. Interestingly, the concentrations of SDS and IGEPAL-CA630 during the incubation with streptavidin conjugated beads were the key to effective elution of biotinylated proteins using excess biotin and heating. This protocol provides an alternative method to isolate biotinylated proteins from streptavidin conjugated beads that is suitable for further downstream analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

The Cauchy Problem in Local Spaces for the Complex Ginzburg-Landau EquationII. Contraction Methods

NASA Astrophysics Data System (ADS)

Ginibre, J.; Velo, G.

We continue the study of the initial value problem for the complex Ginzburg-Landau equation (with a > 0, b > 0, g>= 0) in initiated in a previous paper [I]. We treat the case where the initial data and the solutions belong to local uniform spaces, more precisely to spaces of functions satisfying local regularity conditions and uniform bounds in local norms, but no decay conditions (or arbitrarily weak decay conditions) at infinity in . In [I] we used compactness methods and an extended version of recent local estimates [3] and proved in particular the existence of solutions globally defined in time with local regularity of the initial data corresponding to the spaces Lr for r>= 2 or H1. Here we treat the same problem by contraction methods. This allows us in particular to prove that the solutions obtained in [I] are unique under suitable subcriticality conditions, and to obtain for them additional regularity properties and uniform bounds. The method extends some of those previously applied to the nonlinear heat equation in global spaces to the framework of local uniform spaces.

Lewis acid-base interactions in weakly bound formaldehyde complexes with CO2, HCN, and FCN: considerations on the cooperative H-bonding effects.

PubMed

Rivelino, Roberto

2008-01-17

Ab initio quantum chemistry calculations reveal that HCN and mainly FCN can form Lewis acid-base complexes with formaldehyde associated with cooperative H bonds, as first noticed by Wallen et al. (Blatchford, M. A.; Raveendran, P.; Wallen, S. L. J. Am. Chem. Soc. 2002, 124, 14818-14819) for CO2-philic materials under supercritical conditions. The present results, obtained with MP2(Full)/aug-cc-pVDZ calculations, show that the degeneracy of the nu(2) mode in free HCN or FCN is removed upon complexation in the same fashion as that of CO2. The splitting of these bands along with the electron structure analysis provides substantial evidence of the interaction of electron lone pairs of the carbonyl oxygen with the electron-deficient carbon atom of the cyanides. Also, this work investigates the role of H bonds acting as additional stabilizing interactions in the complexes by performing the energetic and geometric characterization.

Spectroscopic study of the benchmark Mn+-H2 complex.

PubMed

Dryza, Viktoras; Poad, Berwyck L J; Bieske, Evan J

2009-05-28

We have recorded the rotationally resolved infrared spectrum of the weakly bound Mn+-H2 complex in the H-H stretch region (4022-4078 cm(-1)) by monitoring Mn+ photodissociation products. The band center of Mn+-H2, the H-H stretch transition, is shifted by -111.8 cm(-1) from the transition of the free H2 molecule. The spectroscopic data suggest that the Mn+-H2 complex consists of a slightly perturbed H2 molecule attached to the Mn+ ion in a T-shaped configuration with a vibrationally averaged intermolecular separation of 2.73 A. Together with the measured Mn+...H2 binding energy of 7.9 kJ/mol (Weis, P.; et al. J. Phys. Chem. A 1997, 101, 2809.), the spectroscopic parameters establish Mn+-H2 as the most thoroughly characterized transition-metal cation-dihydrogen complex and a benchmark for calibrating quantum chemical calculations on noncovalent systems involving open d-shell configurations. Such systems are of possible importance for hydrogen storage applications.

Global low-energy weak solution and large-time behavior for the compressible flow of liquid crystals

NASA Astrophysics Data System (ADS)

Wu, Guochun; Tan, Zhong

2018-06-01

In this paper, we consider the weak solution of the simplified Ericksen-Leslie system modeling compressible nematic liquid crystal flows in R3. When the initial data are of small energy and initial density is positive and essentially bounded, we prove the existence of a global weak solution in R3. The large-time behavior of a global weak solution is also established.

Existence of global weak solution for a reduced gravity two and a half layer model

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

Guo, Zhenhua, E-mail: zhenhua.guo.math@gmail.com; Li, Zilai, E-mail: lizilai0917@163.com; Yao, Lei, E-mail: yaolei1056@hotmail.com

2013-12-15

We investigate the existence of global weak solution to a reduced gravity two and a half layer model in one-dimensional bounded spatial domain or periodic domain. Also, we show that any possible vacuum state has to vanish within finite time, then the weak solution becomes a unique strong one.

A new div-curl result. Applications to the homogenization of elliptic systems and to the weak continuity of the Jacobian

NASA Astrophysics Data System (ADS)

Briane, M.; Casado Díaz, J.

2016-04-01

In this paper a new div-curl result is established in an open set Ω of RN, N ≥ 2, for the product σn ṡηn of two sequences of vector-valued functions σn, ηn such that σn is bounded in Lp(Ω)N, ηn is bounded in Lq(Ω)N, with 1 / p + 1 / q = 1 + 1 / (N - 1), and such that divσn, curlηn are compact in suitable spaces. The new assumption is that the product converges weakly in W - 1 , 1 (Ω). The approach is also new in the topic, and is based on a compactness result for bounded sequences in W 1 , q (Ω) through a suitable selection of annuli on which the gradients are not too high, in the spirit of [26,32] and using the imbedding of W 1 , q into Lp‧ for the unit sphere of RN. The div-curl result is applied to the homogenization of equi-coercive systems whose coefficients are equi-bounded in Lρ (Ω) for some ρ >N-1/2 if N > 2, or in L1 (Ω) if N = 2. It also allows us to prove a weak continuity result for the Jacobian for bounded sequences in W 1 , N - 1 (Ω) satisfying an alternative assumption to the L∞-strong estimate of [8]. Two examples show the sharpness of the results.

Selecting the spin crossover profile with controlled crystallization of mononuclear Fe(iii) polymorphs.

PubMed

Vicente, Ana I; Ferreira, Liliana P; Carvalho, Maria de Deus; Rodrigues, Vítor H N; Dîrtu, Marinela M; Garcia, Yann; Calhorda, Maria José; Martinho, Paulo N

2018-05-08

Two polymorphic species of the [Fe(5-Br-salEen)2]ClO4 compound were obtained, each of them being selectively recovered after evaporation of the solvent at a controlled rate. While polymorph 1a is formed during slow evaporation, fast evaporation favors polymorph 1b. The importance of the evaporation rate was recognized after detailed studies of the reaction temperature, solvent evaporation rate and crystallization temperature effects. The complex in the new polymorphic form 1a showed an abrupt spin crossover at 172 K with a small 1 K hysteresis window and over a narrow 10 K range. 57Fe Mössbauer spectroscopy and differential scanning calorimetry, complemented by X-ray studies for both the high-spin and low-spin forms, were used to further characterize the new polymorphic phase 1a. Both polymorphs are based on the same Fe(iii) complex cation hydrogen bonded to the perchlorate anion. These units are loosely bound in the crystals via weak interactions. In the new polymorph 1a, the hydrogen bonds are stronger, while the weak hydrogen and halogen bonds, as well as π-π stacking, create a cooperative network, not present in 1b, responsible for the spin transition profile.

Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution.

PubMed

Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P

2016-07-14

The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.

Alignment and Imaging of the CS2 Dimer Inside Helium Nanodroplets

NASA Astrophysics Data System (ADS)

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.

Theoretical studies of association and dissociation of Feshbach molecules in a microgravity environment

NASA Astrophysics Data System (ADS)

D'Incao, Jose; Williams, Jason

2017-04-01

NASA's Cold Atom Laboratory (CAL) is a multi-user facility scheduled for launch to the ISS in 2017. Our flight experiments with CAL will characterize and mitigate leading-order systematics in dual-atomic-species atom interferometers in microgravity relevant for future fundamental physics missions in space. As part of the initial state preparation for interferometry studies, here, we study the RF association and dissociation of weakly bound heteronuclear Feshbach molecules for expected parameters relevant for the microgravity environment of CAL. This includes temperatures on the pico-Kelvin range and atomic densities as low as 108/cm3. We show that under such conditions, thermal and loss effects can be greatly suppressed, resulting in high efficiency in both association and dissociation of extremely weakly bound Feshbach molecules and allowing for high accuracy determination coherent properties of such processes. In addition we study the possibility to implement delta-kick cooling techniques for weakly bound heteronuclear molecules and explore numerically other methods for molecular association and dissociation including the effects of three-body interactions. This research is supported by the National Aeronautics and Space Administration.

Weakly Bound Free Radicals in Combustion: "Prompt" Dissociation of Formyl Radicals and Its Effect on Laminar Flame Speeds

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

Labbe, Nicole J.; Sivaramakrishnan, Raghu; Goldsmith, C. Franklin

2016-01-07

Weakly bound free radicals have low-dissociation thresholds such that at high temperatures, timescales for dissociation and collisional relaxation become comparable, leading to significant dissociation during the vibrational-rotational relaxation process. Here we characterize this “prompt” dissociation of formyl (HCO), an important combustion radical, using direct dynamics calculations for OH + CH2O and H + CH2O (key HCO-forming reactions). For all other HCO-forming reactions, presumption of a thermal incipient HCO distribution was used to derive prompt dissociation fractions. Inclusion of these theoretically derived HCO prompt dissociation fractions into combustion kinetics models provides an additional source for H-atoms that feeds chain branching reactions.more » Simulations using these updated combustion models are therefore shown to enhance flame propagation in 1,3,5-trioxane and acetylene. The present results suggest that HCO prompt dissociation should be included when simulating flames of hydrocarbons and oxygenated molecules and that prompt dissociations of other weakly bound radicals may also impact combustion simulations« less

Communication complexity and information complexity

NASA Astrophysics Data System (ADS)

Pankratov, Denis

Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information complexity of two of the most studied functions in the communication complexity literature: Gap Hamming Distance (GHD) and Inner Product mod 2 (IP). In our first result we affirm the conjecture that the information complexity of GHD is linear even under the uniform distribution. This strengthens the O(n) bound shown by Kerenidis et al. (2012) and answers an open problem by Chakrabarti et al. (2012). We also prove that the information complexity of IP is arbitrarily close to the trivial upper bound n as the permitted error tends to zero, again strengthening the O(n) lower bound proved by Braverman and Weinstein (2011). More importantly, our proofs demonstrate that self-reducibility makes the connection between information complexity and communication complexity lower bounds a two-way connection. Whereas numerous results in the past used information complexity techniques to derive new communication complexity lower bounds, we explore a generic way, in which communication complexity lower bounds imply information complexity lower bounds in a black-box manner. In the third contribution we consider the roles that private and public randomness play in the definition of information complexity. In communication complexity, private randomness can be trivially simulated by public randomness. Moreover, the communication cost of simulating public randomness with private randomness is well understood due to Newman's theorem (1991). In information complexity, the roles of public and private randomness are reversed: public randomness can be trivially simulated by private randomness. However, the information cost of simulating private randomness with public randomness is not understood. We show that protocols that use only public randomness admit a rather strong compression. In particular, efficient simulation of private randomness by public randomness would imply a version of a direct sum theorem in the setting of communication complexity. This establishes a yet another connection between the two areas. (Abstract shortened by UMI.).

Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP

PubMed Central

Helgeson, Luke A; Nolen, Brad J

2013-01-01

Nucleation promoting factors (NPFs) initiate branched actin network assembly by activating Arp2/3 complex, a branched actin filament nucleator. Cellular actin networks contain multiple NPFs, but how they coordinately regulate Arp2/3 complex is unclear. Cortactin is an NPF that activates Arp2/3 complex weakly on its own, but with WASP/N-WASP, another class of NPFs, potently activates. We dissect the mechanism of synergy and propose a model in which cortactin displaces N-WASP from nascent branches as a prerequisite for nucleation. Single-molecule imaging revealed that unlike WASP/N-WASP, cortactin remains bound to junctions during nucleation, and specifically targets junctions with a ∼160-fold increased on rate over filament sides. N-WASP must be dimerized for potent synergy, and targeted mutations indicate release of dimeric N-WASP from nascent branches limits nucleation. Mathematical modeling shows cortactin-mediated displacement but not N-WASP recycling or filament recruitment models can explain synergy. Our results provide a molecular basis for coordinate Arp2/3 complex regulation. DOI: http://dx.doi.org/10.7554/eLife.00884.001 PMID:24015358

Low-energy fusion dynamics of weakly bound nuclei: A time dependent perspective

NASA Astrophysics Data System (ADS)

Diaz-Torres, A.; Boselli, M.

2016-05-01

Recent dynamical fusion models for weakly bound nuclei at low incident energies, based on a time-dependent perspective, are briefly presented. The main features of both the PLATYPUS model and a new quantum approach are highlighted. In contrast to existing timedependent quantum models, the present quantum approach separates the complete and incomplete fusion from the total fusion. Calculations performed within a toy model for 6Li + 209Bi at near-barrier energies show that converged excitation functions for total, complete and incomplete fusion can be determined with the time-dependent wavepacket dynamics.

Adaptive multi-resolution 3D Hartree-Fock-Bogoliubov solver for nuclear structure

NASA Astrophysics Data System (ADS)

Pei, J. C.; Fann, G. I.; Harrison, R. J.; Nazarewicz, W.; Shi, Yue; Thornton, S.

2014-08-01

Background: Complex many-body systems, such as triaxial and reflection-asymmetric nuclei, weakly bound halo states, cluster configurations, nuclear fragments produced in heavy-ion fusion reactions, cold Fermi gases, and pasta phases in neutron star crust, are all characterized by large sizes and complex topologies in which many geometrical symmetries characteristic of ground-state configurations are broken. A tool of choice to study such complex forms of matter is an adaptive multi-resolution wavelet analysis. This method has generated much excitement since it provides a common framework linking many diversified methodologies across different fields, including signal processing, data compression, harmonic analysis and operator theory, fractals, and quantum field theory. Purpose: To describe complex superfluid many-fermion systems, we introduce an adaptive pseudospectral method for solving self-consistent equations of nuclear density functional theory in three dimensions, without symmetry restrictions. Methods: The numerical method is based on the multi-resolution and computational harmonic analysis techniques with a multi-wavelet basis. The application of state-of-the-art parallel programming techniques include sophisticated object-oriented templates which parse the high-level code into distributed parallel tasks with a multi-thread task queue scheduler for each multi-core node. The internode communications are asynchronous. The algorithm is variational and is capable of solving coupled complex-geometric systems of equations adaptively, with functional and boundary constraints, in a finite spatial domain of very large size, limited by existing parallel computer memory. For smooth functions, user-defined finite precision is guaranteed. Results: The new adaptive multi-resolution Hartree-Fock-Bogoliubov (HFB) solver madness-hfb is benchmarked against a two-dimensional coordinate-space solver hfb-ax that is based on the B-spline technique and a three-dimensional solver hfodd that is based on the harmonic-oscillator basis expansion. Several examples are considered, including the self-consistent HFB problem for spin-polarized trapped cold fermions and the Skyrme-Hartree-Fock (+BCS) problem for triaxial deformed nuclei. Conclusions: The new madness-hfb framework has many attractive features when applied to nuclear and atomic problems involving many-particle superfluid systems. Of particular interest are weakly bound nuclear configurations close to particle drip lines, strongly elongated and dinuclear configurations such as those present in fission and heavy-ion fusion, and exotic pasta phases that appear in neutron star crust.

Synchronization of Coupled Dynamical Systems: Tolerance to Weak Connectivity and Arbitrarily Bounded Time-Varying Delays

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

Meng, Ziyang; Yang, Tao; Li, Guoqi

We study synchronization of coupled linear systems over networks with weak connectivity and time-varying delays. We focus on the case that the internal dynamics are time-varying but non-expansive. Both uniformly connected and infinitely connected communication topologies are considered. A new concept of P-synchronization is introduced and we first show that global asymptotic P-synchronization can be achieved over directed networks with uniform joint connectivity and arbitrarily bounded delays. We then study the case of the infinitely jointly connected communication topology. In particular, for the undirected communication topologies, it turns out that the existence of a uniform time interval for the communicationmore » topology is not necessary and P-synchronization can be achieved when the time varying delays are arbitrarily bounded. Simulations are given to validate the theoretical results.« less

Heat kernel for the elliptic system of linear elasticity with boundary conditions

NASA Astrophysics Data System (ADS)

Taylor, Justin; Kim, Seick; Brown, Russell

2014-10-01

We consider the elliptic system of linear elasticity with bounded measurable coefficients in a domain where the second Korn inequality holds. We construct heat kernel of the system subject to Dirichlet, Neumann, or mixed boundary condition under the assumption that weak solutions of the elliptic system are Hölder continuous in the interior. Moreover, we show that if weak solutions of the mixed problem are Hölder continuous up to the boundary, then the corresponding heat kernel has a Gaussian bound. In particular, if the domain is a two dimensional Lipschitz domain satisfying a corkscrew or non-tangential accessibility condition on the set where we specify Dirichlet boundary condition, then we show that the heat kernel has a Gaussian bound. As an application, we construct Green's function for elliptic mixed problem in such a domain.

Complexity Bounds for Quantum Computation

DTIC Science & Technology

2007-06-22

Programs Trustees of Boston University Boston, MA 02215 - Complexity Bounds for Quantum Computation REPORT DOCUMENTATION PAGE 18. SECURITY CLASSIFICATION...Complexity Bounds for Quantum Comp[utation Report Title ABSTRACT This project focused on upper and lower bounds for quantum computability using constant...classical computation models, particularly emphasizing new examples of where quantum circuits are more powerful than their classical counterparts. A second

Renorming c0 and closed, bounded, convex sets with fixed point property for affine nonexpansive mappings

NASA Astrophysics Data System (ADS)

Nezir, Veysel; Mustafa, Nizami

2017-04-01

In 2008, P.K. Lin provided the first example of a nonreflexive space that can be renormed to have fixed point property for nonexpansive mappings. This space was the Banach space of absolutely summable sequences l1 and researchers aim to generalize this to c0, Banach space of null sequences. Before P.K. Lin's intriguing result, in 1979, Goebel and Kuczumow showed that there is a large class of non-weak* compact closed, bounded, convex subsets of l1 with fixed point property for nonexpansive mappings. Then, P.K. Lin inspired by Goebel and Kuczumow's ideas to give his result. Similarly to P.K. Lin's study, Hernández-Linares worked on L1 and in his Ph.D. thesis, supervisored under Maria Japón, showed that L1 can be renormed to have fixed point property for affine nonexpansive mappings. Then, related questions for c0 have been considered by researchers. Recently, Nezir constructed several equivalent norms on c0 and showed that there are non-weakly compact closed, bounded, convex subsets of c0 with fixed point property for affine nonexpansive mappings. In this study, we construct a family of equivalent norms containing those developed by Nezir as well and show that there exists a large class of non-weakly compact closed, bounded, convex subsets of c0 with fixed point property for affine nonexpansive mappings.

On the Conservation and Convergence to Weak Solutions of Global Schemes

NASA Technical Reports Server (NTRS)

Carpenter, Mark H.; Gottlieb, David; Shu, Chi-Wang

2001-01-01

In this paper we discuss the issue of conservation and convergence to weak solutions of several global schemes, including the commonly used compact schemes and spectral collocation schemes, for solving hyperbolic conservation laws. It is shown that such schemes, if convergent boundedly almost everywhere, will converge to weak solutions. The results are extensions of the classical Lax-Wendroff theorem concerning conservative schemes.

Cooperativity of self-organized Brownian motors pulling on soft cargoes.

PubMed

Orlandi, Javier G; Blanch-Mercader, Carles; Brugués, Jan; Casademunt, Jaume

2010-12-01

We study the cooperative dynamics of Brownian motors moving along a one-dimensional track when an external load is applied to the leading motor, mimicking molecular motors pulling on membrane-bound cargoes in intracellular traffic. Due to the asymmetric loading, self-organized motor clusters form spontaneously. We model the motors with a two-state noise-driven ratchet formulation and study analytically and numerically the collective velocity-force and efficiency-force curves resulting from mutual interactions, mostly hard-core repulsion and weak (nonbinding) attraction. We analyze different parameter regimes including the limits of weak noise, mean-field behavior, rigid coupling, and large numbers of motors, for the different interactions. We present a general framework to classify and quantify cooperativity. We show that asymmetric loading leads generically to enhanced cooperativity beyond the simple superposition of the effects of individual motors. For weakly attracting interactions, the cooperativity is mostly enhanced, including highly coordinated motion of motors and complex nonmonotonic velocity-force curves, leading to self-regulated clusters. The dynamical scenario is enriched by resonances associated to commensurability of different length scales. Large clusters exhibit synchronized dynamics and bidirectional motion. Biological implications are discussed.

Cooperativity of self-organized Brownian motors pulling on soft cargoes

NASA Astrophysics Data System (ADS)

Orlandi, Javier G.; Blanch-Mercader, Carles; Brugués, Jan; Casademunt, Jaume

2010-12-01

We study the cooperative dynamics of Brownian motors moving along a one-dimensional track when an external load is applied to the leading motor, mimicking molecular motors pulling on membrane-bound cargoes in intracellular traffic. Due to the asymmetric loading, self-organized motor clusters form spontaneously. We model the motors with a two-state noise-driven ratchet formulation and study analytically and numerically the collective velocity-force and efficiency-force curves resulting from mutual interactions, mostly hard-core repulsion and weak (nonbinding) attraction. We analyze different parameter regimes including the limits of weak noise, mean-field behavior, rigid coupling, and large numbers of motors, for the different interactions. We present a general framework to classify and quantify cooperativity. We show that asymmetric loading leads generically to enhanced cooperativity beyond the simple superposition of the effects of individual motors. For weakly attracting interactions, the cooperativity is mostly enhanced, including highly coordinated motion of motors and complex nonmonotonic velocity-force curves, leading to self-regulated clusters. The dynamical scenario is enriched by resonances associated to commensurability of different length scales. Large clusters exhibit synchronized dynamics and bidirectional motion. Biological implications are discussed.

Sound Velocity Bound and Neutron Stars

DOE PAGES

Bedaque, Paulo; Steiner, Andrew W.

2015-01-21

A conjecture that the velocity of sound in any medium is smaller than the velocity of light in vacuum divided by sqrt(3). Simple arguments support this bound in nonrelativistic and/or weakly coupled theories. Moreover, the bound has been demonstrated in several classes of strongly coupled theories with gravity duals and is saturated only in conformal theories. Here, we point out that the existence of neutron stars with masses around two solar masses combined with the knowledge of the equation of state of hadronic matter at low densities is in strong tension with this bound.

Structural and Computational Studies of Cp(CO)2(PCy3)MoFBF3, a Complex with a Bound BF4- Ligand

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

Cheng, Tan-Yun; Szalda, David J.; Franz, James A.

2010-02-15

Hydride transfer from Cp(CO)2(PCy3)MoH to Ph3C+BF4 gives Cp(CO)2(PCy3)MoFBF3, and the crystal structure of this complex was determined. In the weakly bound FBF3 ligand, the B-F(bridging) bond length is 1.475(8) Å, which is 0.15 Å longer than the average length of the three B-F(terminal) bonds. The PCy3 and FBF3 ligands are cis to each other in the four-legged piano stool structure. Electronic structure (DFT) calculations predict the trans isomer of Cp(CO)2(PCy3)MoFBF3 to be 9.5 kcal/mol (in ΔGog,298)) less stable than the cis isomer that was crystallographically characterized. Hydride transfer from Cp(CO)2(PCy3)MoH to Ph3C+BAr'4 [Ar' = 3,5-bis(trifluoromethyl)phenyl] in CH2Cl2 solvent produces [Cp(CO)2(PCy3)Mo(ClCH2Cl)]+[BAr'4]more » , in which CH2Cl2 is coordinated to the metal. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

Fungal mediator tail subunits contain classical transcriptional activation domains.

PubMed

Liu, Zhongle; Myers, Lawrence C

2015-04-01

Classical activation domains within DNA-bound eukaryotic transcription factors make weak interactions with coactivator complexes, such as Mediator, to stimulate transcription. How these interactions stimulate transcription, however, is unknown. The activation of reporter genes by artificial fusion of Mediator subunits to DNA binding domains that bind to their promoters has been cited as evidence that the primary role of activators is simply to recruit Mediator. We have identified potent classical transcriptional activation domains in the C termini of several tail module subunits of Saccharomyces cerevisiae, Candida albicans, and Candida dubliniensis Mediator, while their N-terminal domains are necessary and sufficient for their incorporation into Mediator but do not possess the ability to activate transcription when fused to a DNA binding domain. This suggests that Mediator fusion proteins actually are functioning in a manner similar to that of a classical DNA-bound activator rather than just recruiting Mediator. Our finding that deletion of the activation domains of S. cerevisiae Med2 and Med3, as well as C. dubliniensis Tlo1 (a Med2 ortholog), impairs the induction of certain genes shows these domains function at native promoters. Activation domains within coactivators are likely an important feature of these complexes and one that may have been uniquely leveraged by a common fungal pathogen. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Structure and decays of nuclear three-body systems: The Gamow coupled-channel method in Jacobi coordinates

NASA Astrophysics Data System (ADS)

Wang, S. M.; Michel, N.; Nazarewicz, W.; Xu, F. R.

2017-10-01

Background: Weakly bound and unbound nuclear states appearing around particle thresholds are prototypical open quantum systems. Theories of such states must take into account configuration mixing effects in the presence of strong coupling to the particle continuum space. Purpose: To describe structure and decays of three-body systems, we developed a Gamow coupled-channel (GCC) approach in Jacobi coordinates by employing the complex-momentum formalism. We benchmarked the complex-energy Gamow shell model (GSM) against the new framework. Methods: The GCC formalism is expressed in Jacobi coordinates, so that the center-of-mass motion is automatically eliminated. To solve the coupled-channel equations, we use hyperspherical harmonics to describe the angular wave functions while the radial wave functions are expanded in the Berggren ensemble, which includes bound, scattering, and Gamow states. Results: We show that the GCC method is both accurate and robust. Its results for energies, decay widths, and nucleon-nucleon angular correlations are in good agreement with the GSM results. Conclusions: We have demonstrated that a three-body GSM formalism explicitly constructed in the cluster-orbital shell model coordinates provides results similar to those with a GCC framework expressed in Jacobi coordinates, provided that a large configuration space is employed. Our calculations for A =6 systems and 26O show that nucleon-nucleon angular correlations are sensitive to the valence-neutron interaction. The new GCC technique has many attractive features when applied to bound and unbound states of three-body systems: it is precise, is efficient, and can be extended by introducing a microscopic model of the core.

Experimental phase synchronization detection in non-phase coherent chaotic systems by using the discrete complex wavelet approach

NASA Astrophysics Data System (ADS)

Ferreira, Maria Teodora; Follmann, Rosangela; Domingues, Margarete O.; Macau, Elbert E. N.; Kiss, István Z.

2017-08-01

Phase synchronization may emerge from mutually interacting non-linear oscillators, even under weak coupling, when phase differences are bounded, while amplitudes remain uncorrelated. However, the detection of this phenomenon can be a challenging problem to tackle. In this work, we apply the Discrete Complex Wavelet Approach (DCWA) for phase assignment, considering signals from coupled chaotic systems and experimental data. The DCWA is based on the Dual-Tree Complex Wavelet Transform (DT-CWT), which is a discrete transformation. Due to its multi-scale properties in the context of phase characterization, it is possible to obtain very good results from scalar time series, even with non-phase-coherent chaotic systems without state space reconstruction or pre-processing. The method correctly predicts the phase synchronization for a chemical experiment with three locally coupled, non-phase-coherent chaotic processes. The impact of different time-scales is demonstrated on the synchronization process that outlines the advantages of DCWA for analysis of experimental data.

Existence and uniqueness of weak solutions of the compressible spherically symmetric Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Huang, Xiangdi

2017-02-01

One of the most influential fundamental tools in harmonic analysis is the Riesz transforms. It maps Lp functions to Lp functions for any p ∈ (1 , ∞) which plays an important role in singular operators. As an application in fluid dynamics, the norm equivalence between ‖∇u‖Lp and ‖ div u ‖ Lp +‖ curl u ‖ Lp is well established for p ∈ (1 , ∞). However, since Riesz operators sent bounded functions only to BMO functions, there is no hope to bound ‖∇u‖L∞ in terms of ‖ div u ‖ L∞ +‖ curl u ‖ L∞. As pointed out by Hoff (2006) [11], this is the main obstacle to obtain uniqueness of weak solutions for isentropic compressible flows. Fortunately, based on new observations, see Lemma 2.2, we derive an exact estimate for ‖∇u‖L∞ ≤ (2 + 1 / N)‖ div u ‖ L∞ for any N-dimensional radially symmetric vector functions u. As a direct application, we give an affirmative answer to the open problem of uniqueness of some weak solutions to the compressible spherically symmetric flows in a bounded ball.

Chemotaxis with logistic source

NASA Astrophysics Data System (ADS)

Winkler, Michael

2008-12-01

We consider the chemotaxis system in a smooth bounded domain , where [chi]>0 and g generalizes the logistic function g(u)=Au-bu[alpha] with [alpha]>1, A[greater-or-equal, slanted]0 and b>0. A concept of very weak solutions is introduced, and global existence of such solutions for any nonnegative initial data u0[set membership, variant]L1([Omega]) is proved under the assumption that . Moreover, boundedness properties of the constructed solutions are studied. Inter alia, it is shown that if b is sufficiently large and u0[set membership, variant]L[infinity]([Omega]) has small norm in L[gamma]([Omega]) for some then the solution is globally bounded. Finally, in the case that additionally holds, a bounded set in L[infinity]([Omega]) can be found which eventually attracts very weak solutions emanating from arbitrary L1 initial data. The paper closes with numerical experiments that illustrate some of the theoretically established results.

Synchronization of Coupled Dynamical Systems: Tolerance to Weak Connectivity and Arbitrarily Bounded Time-Varying Delays

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

Meng, Ziyang; Yang, Tao; Li, Guoqi

Here, we study synchronization of coupled linear systems over networks with weak connectivity and nonuniform time-varying delays. We focus on the case where the internal dynamics are time-varying but non-expansive (stable dynamics with a quadratic Lyapunov function). Both uniformly jointly connected and infinitely jointly connected communication topologies are considered. A new concept of quadratic synchronization is introduced. We first show that global asymptotic quadratic synchronization can be achieved over directed networks with uniform joint connectivity and arbitrarily bounded delays. We then study the case of infinitely jointly connected communication topology. In particular, for the undirected communication topologies, it turns outmore » that the existence of a uniform time interval for the jointly connected communication topology is not necessary and quadratic synchronization can be achieved when the time-varying nonuniform delays are arbitrarily bounded. Finally, simulation results are provided to validate the theoretical results.« less

Synchronization of Coupled Dynamical Systems: Tolerance to Weak Connectivity and Arbitrarily Bounded Time-Varying Delays

DOE PAGES

Meng, Ziyang; Yang, Tao; Li, Guoqi; ...

2017-09-18

Here, we study synchronization of coupled linear systems over networks with weak connectivity and nonuniform time-varying delays. We focus on the case where the internal dynamics are time-varying but non-expansive (stable dynamics with a quadratic Lyapunov function). Both uniformly jointly connected and infinitely jointly connected communication topologies are considered. A new concept of quadratic synchronization is introduced. We first show that global asymptotic quadratic synchronization can be achieved over directed networks with uniform joint connectivity and arbitrarily bounded delays. We then study the case of infinitely jointly connected communication topology. In particular, for the undirected communication topologies, it turns outmore » that the existence of a uniform time interval for the jointly connected communication topology is not necessary and quadratic synchronization can be achieved when the time-varying nonuniform delays are arbitrarily bounded. Finally, simulation results are provided to validate the theoretical results.« less

Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution

PubMed Central

Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J.; Golovanov, Alexander P.

2016-01-01

The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (SosCat) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of SosCat, while SosCat also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos. PMID:27412770

Vortex-soliton complexes in coupled nonlinear Schrödinger equations with unequal dispersion coefficients.

PubMed

Charalampidis, E G; Kevrekidis, P G; Frantzeskakis, D J; Malomed, B A

2016-08-01

We consider a two-component, two-dimensional nonlinear Schrödinger system with unequal dispersion coefficients and self-defocusing nonlinearities, chiefly with equal strengths of the self- and cross-interactions. In this setting, a natural waveform with a nonvanishing background in one component is a vortex, which induces an effective potential well in the second component, via the nonlinear coupling of the two components. We show that the potential well may support not only the fundamental bound state, but also multiring excited radial state complexes for suitable ranges of values of the dispersion coefficient of the second component. We systematically explore the existence, stability, and nonlinear dynamics of these states. The complexes involving the excited radial states are weakly unstable, with a growth rate depending on the dispersion of the second component. Their evolution leads to transformation of the multiring complexes into stable vortex-bright solitons ones with the fundamental state in the second component. The excited states may be stabilized by a harmonic-oscillator trapping potential, as well as by unequal strengths of the self- and cross-repulsive nonlinearities.

Gateways, Not Gatekeepers

ERIC Educational Resources Information Center

Murray, Linda

2012-01-01

In its analysis of more than 15,000 high school transcripts, the Education Trust-West found that non-college-bound students tend to take a weak academic load and disconnected electives. As a result, far too many students--most often low-income students and students of color--are bound for low-level jobs, prepared for neither college nor career.…

Methods for quantifying T cell receptor binding affinities and thermodynamics

PubMed Central

Piepenbrink, Kurt H.; Gloor, Brian E.; Armstrong, Kathryn M.; Baker, Brian M.

2013-01-01

αβ T cell receptors (TCRs) recognize peptide antigens bound and presented by class I or class II major histocompatibility complex (MHC) proteins. Recognition of a peptide/MHC complex is required for initiation and propagation of a cellular immune response, as well as the development and maintenance of the T cell repertoire. Here we discuss methods to quantify the affinities and thermodynamics of interactions between soluble ectodomains of TCRs and their peptide/MHC ligands, focusing on titration calorimetry, surface plasmon resonance, and fluorescence anisotropy. As TCRs typically bind ligand with weak-to-moderate affinities, we focus the discussion on means to enhance the accuracy and precision of low affinity measurements. In addition to further elucidating the biology of the T cell mediated immune response, more reliable low affinity measurements will aid with more probing studies with mutants or altered peptides that can help illuminate the physical underpinnings of how TCRs achieve their remarkable recognition properties. PMID:21609868

Ab initio study of the CO-N2 complex: a new highly accurate intermolecular potential energy surface and rovibrational spectrum.

PubMed

Cybulski, Hubert; Henriksen, Christian; Dawes, Richard; Wang, Xiao-Gang; Bora, Neha; Avila, Gustavo; Carrington, Tucker; Fernández, Berta

2018-05-09

A new, highly accurate ab initio ground-state intermolecular potential-energy surface (IPES) for the CO-N2 complex is presented. Thousands of interaction energies calculated with the CCSD(T) method and Dunning's aug-cc-pVQZ basis set extended with midbond functions were fitted to an analytical function. The global minimum of the potential is characterized by an almost T-shaped structure and has an energy of -118.2 cm-1. The symmetry-adapted Lanczos algorithm was used to compute rovibrational energies (up to J = 20) on the new IPES. The RMSE with respect to experiment was found to be on the order of 0.038 cm-1 which confirms the very high accuracy of the potential. This level of agreement is among the best reported in the literature for weakly bound systems and considerably improves on those of previously published potentials.

Ellipsoidal analysis of coordination polyhedra

PubMed Central

Cumby, James; Attfield, J. Paul

2017-01-01

The idea of the coordination polyhedron is essential to understanding chemical structure. Simple polyhedra in crystalline compounds are often deformed due to structural complexity or electronic instabilities so distortion analysis methods are useful. Here we demonstrate that analysis of the minimum bounding ellipsoid of a coordination polyhedron provides a general method for studying distortion, yielding parameters that are sensitive to various orders in metal oxide examples. Ellipsoidal analysis leads to discovery of a general switching of polyhedral distortions at symmetry-disallowed transitions in perovskites that may evidence underlying coordination bistability, and reveals a weak off-centre ‘d5 effect' for Fe3+ ions that could be exploited in multiferroics. Separating electronic distortions from intrinsic deformations within the low temperature superstructure of magnetite provides new insights into the charge and trimeron orders. Ellipsoidal analysis can be useful for exploring local structure in many materials such as coordination complexes and frameworks, organometallics and organic molecules. PMID:28146146

Elastic Green’s Function in Anisotropic Bimaterials Considering Interfacial Elasticity

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

Juan, Pierre -Alexandre; Dingreville, Remi

Here, the two-dimensional elastic Green’s function is calculated for a general anisotropic elastic bimaterial containing a line dislocation and a concentrated force while accounting for the interfacial structure by means of a generalized interfacial elasticity paradigm. The introduction of the interface elasticity model gives rise to boundary conditions that are effectively equivalent to those of a weakly bounded interface. The equations of elastic equilibrium are solved by complex variable techniques and the method of analytical continuation. The solution is decomposed into the sum of the Green’s function corresponding to the perfectly bonded interface and a perturbation term corresponding to themore » complex coupling nature between the interface structure and a line dislocation/concentrated force. Such construct can be implemented into the boundary integral equations and the boundary element method for analysis of nano-layered structures and epitaxial systems where the interface structure plays an important role.« less

Elastic Green’s Function in Anisotropic Bimaterials Considering Interfacial Elasticity

DOE PAGES

Juan, Pierre -Alexandre; Dingreville, Remi

2017-09-13

Here, the two-dimensional elastic Green’s function is calculated for a general anisotropic elastic bimaterial containing a line dislocation and a concentrated force while accounting for the interfacial structure by means of a generalized interfacial elasticity paradigm. The introduction of the interface elasticity model gives rise to boundary conditions that are effectively equivalent to those of a weakly bounded interface. The equations of elastic equilibrium are solved by complex variable techniques and the method of analytical continuation. The solution is decomposed into the sum of the Green’s function corresponding to the perfectly bonded interface and a perturbation term corresponding to themore » complex coupling nature between the interface structure and a line dislocation/concentrated force. Such construct can be implemented into the boundary integral equations and the boundary element method for analysis of nano-layered structures and epitaxial systems where the interface structure plays an important role.« less

Unraveling the benzocaine-receptor interaction at molecular level using mass-resolved spectroscopy.

PubMed

Aguado, Edurne; León, Iker; Millán, Judith; Cocinero, Emilio J; Jaeqx, Sander; Rijs, Anouk M; Lesarri, Alberto; Fernández, José A

2013-10-31

The benzocaine-toluene cluster has been used as a model system to mimic the interaction between the local anesthetic benzocaine and the phenylalanine residue in Na(+) channels. The cluster was generated in a supersonic expansion of benzocaine and toluene in helium. Using a combination of mass-resolved laser-based experimental techniques and computational methods, the complex was fully characterized, finding four conformational isomers in which the molecules are bound through N-H···π and π···π weak hydrogen bonds. The structures of the detected isomers closely resemble those predicted for benzocaine in the inner pore of the ion channels, giving experimental support to previously reported molecular chemistry models.

On Critical Spaces for the Navier-Stokes Equations

NASA Astrophysics Data System (ADS)

Prüss, Jan; Wilke, Mathias

2017-10-01

The abstract theory of critical spaces developed in Prüss and Wilke (J Evol Equ, 2017. doi: 10.1007/s00028-017-0382-6), Prüss et al. (Critical spaces for quasilinear parabolic evolution equations and applications, 2017) is applied to the Navier-Stokes equations in bounded domains with Navier boundary conditions as well as no-slip conditions. Our approach unifies, simplifies and extends existing work in the L_p -L_q setting, considerably. As an essential step, it is shown that the strong and weak Stokes operators with Navier conditions admit an H^∞-calculus with H^∞-angle 0, and the real and complex interpolation spaces of these operators are identified.

On the role of Fe ions on magnetic properties of doped TiO2 nanoparticles

NASA Astrophysics Data System (ADS)

Tolea, F.; Grecu, M. N.; Kuncser, V.; Constantinescu, S. Gr.; Ghica, D.

2015-04-01

The role of iron doping on magnetic properties of hydrothermal anatase TiO2:57Fe (0-1 at. %) nanoparticles is investigated by combining superconducting quantum interference device magnetometry with Mössbauer and electron paramagnetic resonance techniques. The results on both as-prepared and thermally treated samples in reduced air atmosphere reveal complexity of magnetic interactions, in connection to certain iron ion electron configurations and defects (oxygen vacancies, F-center, and Ti3+ ions). The distribution of iron ions is predominantly at nanoparticle surface layers. Formation of weak ferromagnetic domains up to 380 K is mainly related to defects, supporting the bound magnetic polaron model.

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

Azunre, P.

Here in this paper, two novel techniques for bounding the solutions of parametric weakly coupled second-order semilinear parabolic partial differential equations are developed. The first provides a theorem to construct interval bounds, while the second provides a theorem to construct lower bounds convex and upper bounds concave in the parameter. The convex/concave bounds can be significantly tighter than the interval bounds because of the wrapping effect suffered by interval analysis in dynamical systems. Both types of bounds are computationally cheap to construct, requiring solving auxiliary systems twice and four times larger than the original system, respectively. An illustrative numerical examplemore » of bound construction and use for deterministic global optimization within a simple serial branch-and-bound algorithm, implemented numerically using interval arithmetic and a generalization of McCormick's relaxation technique, is presented. Finally, problems within the important class of reaction-diffusion systems may be optimized with these tools.« less

Co-Binding of Pharmaceutical Compounds at Mineral Surfaces: Molecular Investigations of Dimer Formation at Goethite/Water Interfaces.

PubMed

Xu, Jing; Marsac, Rémi; Costa, Dominique; Cheng, Wei; Wu, Feng; Boily, Jean-François; Hanna, Khalil

2017-08-01

The emergence of antibiotic and anti-inflammatory agents in aquatic and terrestrial systems is becoming a serious threat to human and animal health worldwide. Because pharmaceutical compounds rarely exist individually in nature, interactions between various compounds can have unforeseen effects on their binding to mineral surfaces. This work demonstrates this important possibility for the case of two typical antibiotic and anti-inflammatory agents (nalidixic acid (NA) and niflumic acid (NFA)) bound at goethite (α-FeOOH) used as a model mineral surface. Our multidisciplinary study, which makes use of batch sorption experiments, vibration spectroscopy and periodic density functional theory calculations, reveals enhanced binding of the otherwise weakly bound NFA caused by unforeseen intermolecular interactions with mineral-bound NA. This enhancement is ascribed to the formation of a NFA-NA dimer whose energetically favored formation (-0.5 eV compared to free molecules) is predominantly driven by van der Waals interactions. A parallel set of efforts also showed that no cobinding occurred with sulfamethoxazole (SMX) because of the lack of molecular interactions with coexisting contaminants. As such, this article raises the importance of recognizing drug cobinding, and lack of cobinding, for predicting and developing policies on the fate of complex mixtures of antibiotics and anti-inflammatory agents in nature.

High-throughput Screening Identification of Poliovirus RNA-dependent RNA Polymerase Inhibitors

PubMed Central

Campagnola, Grace; Gong, Peng; Peersen, Olve B.

2011-01-01

Viral RNA-dependent RNA polymerase (RdRP) enzymes are essential for the replication of positive-strand RNA viruses and established targets for the development of selective antiviral therapeutics. In this work we have carried out a high-throughput screen of 154,267 compounds to identify poliovirus polymerase inhibitors using a fluorescence based RNA elongation assay. Screening and subsequent validation experiments using kinetic methods and RNA product analysis resulted in the identification of seven inhibitors that affect the RNA binding, initiation, or elongation activity of the polymerase. X-ray crystallography data show clear density for five of the compounds in the active site of the poliovirus polymerase elongation complex. The inhibitors occupy the NTP binding site by stacking on the priming nucleotide and interacting with the templating base, yet competition studies show fairly weak IC50 values in the low μM range. A comparison with nucleotide bound structures suggests that weak binding is likely due to the lack of a triphosphate group on the inhibitors. Consequently, the inhibitors are primarily effective at blocking polymerase initiation and do not effectively compete with NTP binding during processive elongation. These findings are discussed in the context of the polymerase elongation complex structure and allosteric control of the viral RdRP catalytic cycle. PMID:21722674

Azole affinity of sterol 14α-demethylase (CYP51) enzymes from Candida albicans and Homo sapiens.

PubMed

Warrilow, Andrew G; Parker, Josie E; Kelly, Diane E; Kelly, Steven L

2013-03-01

Candida albicans CYP51 (CaCYP51) (Erg11), full-length Homo sapiens CYP51 (HsCYP51), and truncated Δ60HsCYP51 were expressed in Escherichia coli and purified to homogeneity. CaCYP51 and both HsCYP51 enzymes bound lanosterol (K(s), 14 to 18 μM) and catalyzed the 14α-demethylation of lanosterol using Homo sapiens cytochrome P450 reductase and NADPH as redox partners. Both HsCYP51 enzymes bound clotrimazole, itraconazole, and ketoconazole tightly (dissociation constants [K(d)s], 42 to 131 nM) but bound fluconazole (K(d), ~30,500 nM) and voriconazole (K(d), ~2,300 nM) weakly, whereas CaCYP51 bound all five medical azole drugs tightly (K(d)s, 10 to 56 nM). Selectivity for CaCYP51 over HsCYP51 ranged from 2-fold (clotrimazole) to 540-fold (fluconazole) among the medical azoles. In contrast, selectivity for CaCYP51 over Δ60HsCYP51 with agricultural azoles ranged from 3-fold (tebuconazole) to 9-fold (propiconazole). Prothioconazole bound extremely weakly to CaCYP51 and Δ60HsCYP51, producing atypical type I UV-visible difference spectra (K(d)s, 6,100 and 910 nM, respectively), indicating that binding was not accomplished through direct coordination with the heme ferric ion. Prothioconazole-desthio (the intracellular derivative of prothioconazole) bound tightly to both CaCYP51 and Δ60HsCYP51 (K(d), ~40 nM). These differences in binding affinities were reflected in the observed 50% inhibitory concentration (IC(50)) values, which were 9- to 2,000-fold higher for Δ60HsCYP51 than for CaCYP51, with the exception of tebuconazole, which strongly inhibited both CYP51 enzymes. In contrast, prothioconazole weakly inhibited CaCYP51 (IC(50), ~150 μM) and did not significantly inhibit Δ60HsCYP51.

Broadband Microwave Spectroscopy as a Tool to Study Dispersion Interactions in Camphor-Alcohol Systems

NASA Astrophysics Data System (ADS)

Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie

2016-06-01

Many biological processes such as chemical recognition and protein folding are mainly controlled by the interplay between hydrogen bonds and dispersive forces. Broadband rotational spectroscopy studies of weakly bound complexes are able to accurately reveal the structures and internal dynamics of molecular clusters isolated in the gas phase. To investigate the influence of the interplay between different types of weak intermolecular interactions and how it controls the preferred active sites of an amphiphilic molecule, we are using camphor (C10H16O, 1,7,7-trimethylbicyclo[2.2.1]hepta-2-one) with different aliphatic alcohol systems. Camphor is a conformationally rigid bicyclic molecule endowed with considerable steric hindrance and has a single polar group (-C=O). The rotational spectrum of camphor and its structure has been previously reported [1] as well as multiple clusters with water [2]. In order to determine the structure of the camphor-alcohol complexes, we targeted low energy rotational transitions in the 2-8 GHz range under the isolated conditions of a molecular jet in the gas phase. The data obtained suggests that camphor forms one complex with methanol and two with ethanol, with differences in the intermolecular interaction in both complexes. With these results, we aim to study the shift in intermolecular interaction from hydrogen bonding to dispersion with the increase in the size of the aliphatic alcohol. [1] Z. Kisiel, et al., Phys. Chem. Chem. Phys., 5 (2003), 820-826. [2] C. Pérez, et al, J. Phys. Chem. Lett., 7 (2016), 154-160.

Quantifying Protein-Ligand Binding Constants using Electrospray Ionization Mass Spectrometry: A Systematic Binding Affinity Study of a Series of Hydrophobically Modified Trypsin Inhibitors

NASA Astrophysics Data System (ADS)

Cubrilovic, Dragana; Biela, Adam; Sielaff, Frank; Steinmetzer, Torsten; Klebe, Gerhard; Zenobi, Renato

2012-10-01

NanoESI-MS is used for determining binding strengths of trypsin in complex with two different series of five congeneric inhibitors, whose binding affinity in solution depends on the size of the P3 substituent. The ligands of the first series contain a 4-amidinobenzylamide as P1 residue, and form a tight complex with trypsin. The inhibitors of the second series have a 2-aminomethyl-5-chloro-benzylamide as P1 group, and represent a model system for weak binders. The five different inhibitors of each group are based on the same scaffold and differ only in the length of the hydrophobic side chain of their P3 residue, which modulates the interactions in the S3/4 binding pocket of trypsin. The dissociation constants (KD) for high affinity ligands investigated by nanoESI-MS ranges from 15 nM to 450 nM and decreases with larger hydrophobic P3 side chains. Collision-induced dissociation (CID) experiments of five trypsin and benzamidine-based complexes show a correlation between trends in KD and gas-phase stability. For the second inhibitor series we could show that the effect of imidazole, a small stabilizing additive, can avoid the dissociation of the complex ions and as a result increases the relative abundance of weakly bound complexes. Here the KD values ranging from 2.9 to 17.6 μM, some 1-2 orders of magnitude lower than the first series. For both ligand series, the dissociation constants (KD) measured via nanoESI-MS were compared with kinetic inhibition constants (Ki) in solution.

Silver(I) complexes of the weakly coordinating solvents SO(2) and CH(2)Cl(2): crystal structures, bonding, and energetics of [Ag(OSO)][Al{OC(CF(3))(3)}(4)], [Ag(OSO)(2/2)][SbF(6)], and [Ag(CH(2)Cl(2))(2)][SbF(6)].

PubMed

Decken, Andreas; Knapp, Carsten; Nikiforov, Grigori B; Passmore, Jack; Rautiainen, J Mikko; Wang, Xinping; Zeng, Xiaoqing

2009-06-22

Pushing the limits of coordination chemistry: The most weakly coordinated silver complexes of the very weakly coordinating solvents dichloromethane and liquid sulfur dioxide were prepared. Special techniques at low temperatures and the use of weakly coordinating anions allowed structural characterization of [Ag(OSO)][Al{OC(CF(3))(3)}(4)], [Ag(OSO)(2/2)][SbF(6)], and [Ag(Cl(2)CH(2))(2)][SbF(6)] (see figure). An investigation of the bonding shows that these complexes are mainly stabilized by electrostatic monopole-dipole interactions.The synthetically useful solvent-free silver(I) salt Ag[Al(pftb)(4)] (pftb=--OC(CF(3))(3)) was prepared by metathesis reaction of Li[Al(pftb)(4)] with Ag[SbF(6)] in liquid SO(2). The solvated complexes [Ag(OSO)][Al(pftb)(4)], [Ag(OSO)(2/2)][SbF(6)], and [Ag(CH(2)Cl(2))(2)][SbF(6)] were prepared and isolated by special techniques at low temperatures and structurally characterized by single-crystal X-ray diffraction. The SO(2) complexes provide the first examples of coordination of the very weak Lewis base SO(2) to silver(I). The SO(2) molecule in [Ag(OSO)][Al(pftb)(4)] is eta(1)-O coordinated to Ag(+), while the SO(2) ligands in [Ag(OSO)(2/2)][SbF(6)] bridge two Ag(+) ions in an eta(2)-O,O' (trans,trans) manner. [Ag(CH(2)Cl(2))(2)][SbF(6)] contains [Ag(CH(2)Cl(2))(2)](+) ions linked through [SbF(6)](-) ions to give a polymeric structure. The solid-state silver(I) ion affinities (SIA) of SO(2) and CH(2)Cl(2), based on bond lengths and corresponding valence units in the corresponding complexes and tensimetric titrations of Ag[Al(pftb)(4)] and Ag[SbF(6)] with SO(2) vapor, show that SO(2) is a weaker ligand to Ag(+) than the commonly used weakly coordinating solvent CH(2)Cl(2) and indicated that binding strength of SO(2) to silver(I) in the silver(I) salts increases with increasing size of the corresponding counteranion ([Al(pftb)(4)](-)>[SbF(6)](-)). The experimental findings are in good agreement with theoretical gas-phase ligand-binding energies of [Ag(L)(n)](+) (L=SO(2), CH(2)Cl(2); n=1, 2) and solid-state enthalpies obtained from Born-Fajans-Haber cycles by using the volume-based thermodynamics (VBT) approach. Bonding analysis (VB, NBO, MO) of [Ag(L)(n)](+) suggests that these complexes are almost completely stabilized by electrostatic interaction, that is, monopole-dipole interaction, with almost no covalent contribution by electron donation from the ligand orbitals into the vacant 5s orbital of Ag(+). All experimental findings and theoretical considerations demonstrate that SO(2) is less covalently bound to Ag(+) than CH(2)Cl(2) and support the thesis that SO(2) is a polar but non-coordinating solvent towards Ag(+).

Homoleptic nickel(II) complexes of redox-tunable pincer-type ligands.

PubMed

Hewage, Jeewantha S; Wanniarachchi, Sarath; Morin, Tyler J; Liddle, Brendan J; Banaszynski, Megan; Lindeman, Sergey V; Bennett, Brian; Gardinier, James R

2014-10-06

Different synthetic methods have been developed to prepare eight new redox-active pincer-type ligands, H(X,Y), that have pyrazol-1-yl flanking donors attached to an ortho-position of each ring of a diarylamine anchor and that have different groups, X and Y, at the para-aryl positions. Together with four previously known H(X,Y) ligands, a series of 12 Ni(X,Y)2 complexes were prepared in high yields by a simple one-pot reaction. Six of the 12 derivatives were characterized by single-crystal X-ray diffraction, which showed tetragonally distorted hexacoordinate nickel(II) centers. The nickel(II) complexes exhibit two quasi-reversible one-electron oxidation waves in their cyclic voltammograms, with half-wave potentials that varied over a remarkable 700 mV range with the average of the Hammett σ(p) parameters of the para-aryl X, Y groups. The one- and two-electron oxidized derivatives [Ni(Me,Me)2](BF4)n (n = 1, 2) were prepared synthetically, were characterized by X-band EPR, electronic spectroscopy, and single-crystal X-ray diffraction (for n = 2), and were studied computationally by DFT methods. The dioxidized complex, [Ni(Me,Me)2](BF4)2, is an S = 2 species, with nickel(II) bound to two ligand radicals. The mono-oxidized complex [Ni(Me,Me)2](BF4), prepared by comproportionation, is best described as nickel(II) with one ligand centered radical. Neither the mono- nor the dioxidized derivative shows any substantial electronic coupling between the metal and their bound ligand radicals because of the orthogonal nature of their magnetic orbitals. On the other hand, weak electronic communication occurs between ligands in the mono-oxidized complex as evident from the intervalence charge transfer (IVCT) transition found in the near-IR absorption spectrum. Band shape analysis of the IVCT transition allowed comparisons of the strength of the electronic interaction with that in the related, previously known, Robin-Day class II mixed valence complex, [Ga(Me,Me)2](2+).

Bounds on complex polarizabilities and a new perspective on scattering by a lossy inclusion

NASA Astrophysics Data System (ADS)

Milton, Graeme W.

2017-09-01

Here, we obtain explicit formulas for bounds on the complex electrical polarizability at a given frequency of an inclusion with known volume that follow directly from the quasistatic bounds of Bergman and Milton on the effective complex dielectric constant of a two-phase medium. We also describe how analogous bounds on the orientationally averaged bulk and shear polarizabilities at a given frequency can be obtained from bounds on the effective complex bulk and shear moduli of a two-phase medium obtained by Milton, Gibiansky, and Berryman, using the quasistatic variational principles of Cherkaev and Gibiansky. We also show how the polarizability problem and the acoustic scattering problem can both be reformulated in an abstract setting as "Y problems." In the acoustic scattering context, to avoid explicit introduction of the Sommerfeld radiation condition, we introduce auxiliary fields at infinity and an appropriate "constitutive law" there, which forces the Sommerfeld radiation condition to hold. As a consequence, we obtain minimization variational principles for acoustic scattering that can be used to obtain bounds on the complex backwards scattering amplitude. Some explicit elementary bounds are given.

Weak gravity conjecture as a razor criterium for exotic D-brane instantons

NASA Astrophysics Data System (ADS)

Addazi, Andrea

2017-01-01

We discuss implications of weak gravity conjecture (WGC) for exotic D-brane instantons. In particular, WGC leads to indirect stringent bounds on non-perturbative superpotentials generated by exotic instantons with many implications for phenomenology: R-parity violating processes, neutrino mass, μ-problem, neutron-antineutron transitions and collider physics.

Effect of carbonaceous soil amendments on potential mobility of weak acid herbicides in soil

USDA-ARS?s Scientific Manuscript database

Use of carbonaceous amendments in soil has been proposed to decrease potential offsite transport of weak acid herbicides and metabolites by increasing their sorption to soil. The effects of organic olive mill waste, biochars from different feed stocks, and humic acid bound to clay on sorption of MCP...

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis.

PubMed

Yamagami, Ryota; Bingaman, Jamie L; Frankel, Erica A; Bevilacqua, Philip C

2018-06-01

Most RNA folding studies have been performed under non-physiological conditions of high concentrations (≥10 mM) of Mg 2+ free , while actual cellular concentrations of Mg 2+ free are only ~1 mM in a background of greater than 50 mM Mg 2+ total . To uncover cellular behavior of RNA, we devised cytoplasm mimic systems that include biological concentrations of amino acids, which weakly chelate Mg 2+ . Amino acid-chelated Mg 2+ (aaCM) of ~15 mM dramatically increases RNA folding and prevents RNA degradation. Furthermore, aaCM enhance self-cleavage of several different ribozymes, up to 100,000-fold at Mg 2+ free of just 0.5 mM, indirectly through RNA compaction. Other metabolites that weakly chelate magnesium offer similar beneficial effects, which implies chelated magnesium may enhance RNA function in the cell in the same way. Overall, these results indicate that the states of Mg 2+ should not be limited to free and bound only, as weakly bound Mg 2+ strongly promotes RNA function under cellular conditions.

Bounds for the Z-spectral radius of nonnegative tensors.

PubMed

He, Jun; Liu, Yan-Min; Ke, Hua; Tian, Jun-Kang; Li, Xiang

2016-01-01

In this paper, we have proposed some new upper bounds for the largest Z-eigenvalue of an irreducible weakly symmetric and nonnegative tensor, which improve the known upper bounds obtained in Chang et al. (Linear Algebra Appl 438:4166-4182, 2013), Song and Qi (SIAM J Matrix Anal Appl 34:1581-1595, 2013), He and Huang (Appl Math Lett 38:110-114, 2014), Li et al. (J Comput Anal Appl 483:182-199, 2015), He (J Comput Anal Appl 20:1290-1301, 2016).

Determining modes for the 3D Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Cheskidov, Alexey; Dai, Mimi; Kavlie, Landon

2018-07-01

We introduce a determining wavenumber for the forced 3D Navier-Stokes equations (NSE) defined for each individual solution. Even though this wavenumber blows up if the solution blows up, its time average is uniformly bounded for all solutions on the weak global attractor. The bound is compared to Kolmogorov's dissipation wavenumber and the Grashof constant.

Nitrate-to-nitrite-to-nitric oxide conversion modulated by nitrate-containing {Fe(NO)2}9 dinitrosyl iron complex (DNIC).

PubMed

Tsai, Fu-Te; Lee, Yu-Ching; Chiang, Ming-Hsi; Liaw, Wen-Feng

2013-01-07

Nitrosylation of high-spin [Fe(κ(2)-O(2)NO)(4)](2-) (1) yields {Fe(NO)}(7) mononitrosyl iron complex (MNIC) [(κ(2)-O(2)NO)(κ(1)-ONO(2))(3)Fe(NO)](2-) (2) displaying an S = 3/2 axial electron paramagnetic resonance (EPR) spectrum (g(⊥) = 3.988 and g(∥) = 2.000). The thermally unstable nitrate-containing {Fe(NO)(2)}(9) dinitrosyl iron complex (DNIC) [(κ(1)-ONO(2))(2)Fe(NO)(2)](-) (3) was exclusively obtained from reaction of HNO(3) and [(OAc)(2)Fe(NO)(2)](-) and was characterized by IR, UV-vis, EPR, superconducting quantum interference device (SQUID), X-ray absorption spectroscopy (XAS), and single-crystal X-ray diffraction (XRD). In contrast to {Fe(NO)(2)}(9) DNIC [(ONO)(2)Fe(NO)(2)](-) constructed by two monodentate O-bound nitrito ligands, the weak interaction between Fe(1) and the distal oxygens O(5)/O(7) of nitrato-coordinated ligands (Fe(1)···O(5) and Fe(1)···O(7) distances of 2.582(2) and 2.583(2) Å, respectively) may play important roles in stabilizing DNIC 3. Transformation of nitrate-containing DNIC 3 into N-bound nitro {Fe(NO)}(6) [(NO)(κ(1)-NO(2))Fe(S(2)CNEt(2))(2)] (7) triggered by bis(diethylthiocarbamoyl) disulfide ((S(2)CNEt(2))(2)) implicates that nitrate-to-nitrite conversion may occur via the intramolecular association of the coordinated nitrate and the adjacent polarized NO-coordinate ligand (nitrosonium) of the proposed {Fe(NO)(2)}(7) intermediate [(NO)(2)(κ(1)-ONO(2))Fe(S(2)CNEt(2))(2)] (A) yielding {Fe(NO)}(7) [(NO)Fe(S(2)CNEt(2))(2)] (6) along with the release of N(2)O(4) (·NO(2)) and the subsequent binding of ·NO(2) to complex 6. The N-bound nitro {Fe(NO)}(6) complex 7 undergoes Me(2)S-promoted O-atom transfer facilitated by imidazole to give {Fe(NO)}(7) complex 6 accompanied by release of nitric oxide. This result demonstrates that nitrate-containing DNIC 3 acts as an active center to modulate nitrate-to-nitrite-to-nitric oxide conversion.

Infrared Spectrum of CO-O2, a 'new' Weakly-Bound Complex

NASA Astrophysics Data System (ADS)

McKellar, Bob; Barclay, A. J.; Michaelian, K. H.; Moazzen-Ahmadi, Nasser

2016-06-01

Only a few weakly-bound complexes containing the O2 molecule have been characterized by high-resolution spectroscopy, notably N2O-O2 [1] and HF-O2 [2]. This neglect is no doubt due in part to the complications added by the oxygen unpaired electron spin. Here we report an extensive infrared spectrum of CO-O2, as observed in the CO fundamental band region (˜2150 wn) using a tunable quantum cascade laser to probe a pulsed supersonic jet expansion. The derived energy level pattern consists of 'stacks' characterized by K, the projection of the total angular momentum on the intermolecular axis. Five such stacks are observed in the ground vibrational state, and ten in the excited state, v(CO) = 1. They are divided into two groups, with no observed transitions between groups, and we believe these groups correlate with the two lowest rotational states of O2, namely (N, J) = (1, 0) and (1, 2). In many ways, the spectrum and energy levels are similar to those of CO-N2 [3], and we use the same approach for analysis, simply fitting each stack with its own origin, B-value, and distortion constants. The rotational constant of the lowest stack in the ground state (with K = 0) implies an effective intermolecular separation of 3.82 Å, but this should be interpreted with caution since it ignores possible effects of electron spin. [1] H.-B. Qian, D. Seccombe, and B.J. Howard, J. Chem. Phys. 107, 7658 (1997). [2] W.M. Fawzy, C.M. Lovejoy, D.J. Nesbitt, and J.T. Hougen, J. Chem. Phys. 117, 693 (2002); S. Wu, G. Sedo, E.M. Grumstrup, and K.R. Leopold, J. Chem. Phys. 127, 204315 (2007). [3] M. Rezaei, K.H. Michaelian, N. Moazzen-Ahmadi, and A.R.W. McKellar, J. Phys. Chem. A 117, 13752 (2013), and references therein.

Influence of a weak gravitational wave on a bound system of two point-masses. [of binary stars

NASA Technical Reports Server (NTRS)

Turner, M. S.

1979-01-01

The problem of a weak gravitational wave impinging upon a nonrelativistic bound system of two point masses is considered. The geodesic equation for each mass is expanded in terms of two small parameters, v/c and dimensionless wave amplitude, in a manner similar to the post-Newtonian expansion; the geodesic equations are resolved into orbital and center-of-mass equations of motion. The effect of the wave on the orbit is determined by using Lagrange's planetary equations to calculate the time evolution of the orbital elements. The gauge properties of the solutions and, in particular, the gauge invariance of the secular effects are discussed.

Uniqueness of solutions for a mathematical model for magneto-viscoelastic flows

NASA Astrophysics Data System (ADS)

Schlömerkemper, A.; Žabenský, J.

2018-06-01

We investigate uniqueness of weak solutions for a system of partial differential equations capturing behavior of magnetoelastic materials. This system couples the Navier–Stokes equations with evolutionary equations for the deformation gradient and for the magnetization obtained from a special case of the micromagnetic energy. It turns out that the conditions on uniqueness coincide with those for the well-known Navier–Stokes equations in bounded domains: weak solutions are unique in two spatial dimensions, and weak solutions satisfying the Prodi–Serrin conditions are unique among all weak solutions in three dimensions. That is, we obtain the so-called weak-strong uniqueness result in three spatial dimensions.

High precision optical spectroscopy and quantum state selected photodissociation of ultracold 88Sr2 molecules in an optical lattice

NASA Astrophysics Data System (ADS)

McDonald, Mickey Patrick

Over the past several decades, rapid progress has been made toward the accurate characterization and control of atoms, made possible largely by the development of narrow-linewidth lasers and techniques for trapping and cooling at ultracold temperatures. Extending this progress to molecules will have exciting implications for chemistry, condensed matter physics, and precision tests of physics beyond the Standard Model. These possibilities are all consequences of the richness of molecular structure, which is governed by physics substantially different from that characterizing atomic structure. This same richness of structure, however, increases the complexity of any molecular experiment manyfold over its atomic counterpart, magnifying the difficulty of everything from trapping and cooling to the comparison of theory with experiment. This thesis describes work performed over the past six years to establish the state of the art in manipulation and quantum control of ultracold molecules. Our molecules are produced via photoassociation of ultracold strontium atoms followed by spontaneous decay to a stable ground state. We describe a thorough set of measurements characterizing the rovibrational structure of very weakly bound (and therefore very large) 88Sr2 molecules from several different perspectives, including determinations of binding energies; linear, quadratic, and higher order Zeeman shifts; transition strengths between bound states; and lifetimes of narrow subradiant states. The physical intuition gained in these experiments applies generally to weakly bound diatomic molecules, and suggests extensive applications in precision measurement and metrology. In addition, we present a detailed analysis of the thermally broadened spectroscopic lineshape of molecules in a non-magic optical lattice trap, showing how such lineshapes can be used to directly determine the temperature of atoms or molecules in situ, addressing a long-standing problem in ultracold physics. Finally, we discuss the measurement of photofragment angular distributions produced by photodissociation, leading to an exploration of quantum-state-resolved ultracold chemistry.

Block Slides on Extremely Weak Tectonic Clay Seams in Openly Folded Tertiary Mud-Rocks at Auckland and the Rangitikei Valley, North Island, New Zealand

NASA Astrophysics Data System (ADS)

Prebble, Warwick M.; Williams, Ann L.

2016-06-01

Block slides have developed on extremely weak, thin clay seams of tectonic origin, parallel to bedding in gently dipping sandstones and mudstones of Tertiary age. Two areas of noted instability are investigated at Auckland and the Rangitikei valley. Dimensions range from 100 m across × 100 m long for short displacement block slides up to 4 km across × 3 km long for large landslide complexes in which block slides are a major component. Displacements of blocks range from incipient (cm) through short (30 m) to 2 or 3 km for large slides. Many of the Auckland slides are dormant but likely to move in a 2000 year return period earthquake or 100 year high intensity rain storm. At Rangitikei there are many active, younger slides. Sliding rates for active failures vary from a few cm/year to 50 m in 30 min. Host rocks are weak to very weak clayey sandstones and sandy mudstones. The seams are rich in smectite. They have polished and crushed walls, may have slickensides and some contain rounded rock fragments. Laboratory shear strength of the seams is 13 kPa cohesion and 13° friction, with a lower bound of 8° at zero cohesion. Strength is increased at the field scale by waviness, steps and splays. Continuity can be demonstrated over distances of hundreds of metres. Key investigation methods were mapping, shafts and trenches. Tectonic uplift, folding and faulting of the weak Tertiary strata and river down-cutting are perpetuating block slide development.

Faithful Squashed Entanglement

NASA Astrophysics Data System (ADS)

Brandão, Fernando G. S. L.; Christandl, Matthias; Yard, Jon

2011-09-01

Squashed entanglement is a measure for the entanglement of bipartite quantum states. In this paper we present a lower bound for squashed entanglement in terms of a distance to the set of separable states. This implies that squashed entanglement is faithful, that is, it is strictly positive if and only if the state is entangled. We derive the lower bound on squashed entanglement from a lower bound on the quantum conditional mutual information which is used to define squashed entanglement. The quantum conditional mutual information corresponds to the amount by which strong subadditivity of von Neumann entropy fails to be saturated. Our result therefore sheds light on the structure of states that almost satisfy strong subadditivity with equality. The proof is based on two recent results from quantum information theory: the operational interpretation of the quantum mutual information as the optimal rate for state redistribution and the interpretation of the regularised relative entropy of entanglement as an error exponent in hypothesis testing. The distance to the set of separable states is measured in terms of the LOCC norm, an operationally motivated norm giving the optimal probability of distinguishing two bipartite quantum states, each shared by two parties, using any protocol formed by local quantum operations and classical communication (LOCC) between the parties. A similar result for the Frobenius or Euclidean norm follows as an immediate consequence. The result has two applications in complexity theory. The first application is a quasipolynomial-time algorithm solving the weak membership problem for the set of separable states in LOCC or Euclidean norm. The second application concerns quantum Merlin-Arthur games. Here we show that multiple provers are not more powerful than a single prover when the verifier is restricted to LOCC operations thereby providing a new characterisation of the complexity class QMA.

Role of protons in the pump cycle of KdpFABC investigated by time-resolved kinetic experiments.

PubMed

Damnjanovic, Bojana; Apell, Hans-Jürgen

2014-05-20

The time-resolved kinetics of the KdpFABC complex solubilized in Aminoxide WS-35 was investigated by ATP concentration jump experiments. ATP was photoreleased from its inactive precursor, caged ATP, and charge movements in the membrane domain of the KdpFABC were detected by the electrochromic dye RH421. At low ATP concentrations, the ATP binding step became rate-limiting with an apparent, pH-independent ATP binding affinity of ~70 μM. At saturating ATP concentrations, the rate-limiting step is the conformational transition (E1-P → P-E2) with a rate constant of ~1.7 s(-1) at 20 °C that was independent of K(+) concentration. This observation together with the detected fluorescence decrease indicates that K(+) (or another positive ion) is bound in the membrane domain after enzyme phosphorylation and the conformational transition to the P-E2 state. pH dependence experiments revealed different roles of H(+) in the transport mechanism. Two different functions of protons for the ion pump must be distinguished. On one hand, there are electrogenically bound "functional" protons, which are not transported but prerequisite for the performance of the ATP-driven half-cycle. On the other hand, protons bind to the transport sites, acting as weak congeners of K(+). There possibly are noncompetitively bound protons, affecting the enzyme activity and/or coupling between KdpA and KdpB subunits. Finally, the recently proposed Post-Albers model for the KdpFABC complex was supplemented with stoichiometry factors of 2 for K(+) and 3 for H(+), and additional inhibitory side reactions controlled by H(+) were introduced, which are relevant at pH <6.5 and/or in the absence of K(+).

A simple method for determining polymeric IgA-containing immune complexes.

PubMed

Sancho, J; Egido, J; González, E

1983-06-10

A simplified assay to measure polymeric IgA-immune complexes in biological fluids is described. The assay is based upon the specific binding of a secretory component for polymeric IgA. In the first step, multimeric IgA (monomeric and polymeric) immune complexes are determined by the standard Raji cell assay. Secondly, labeled secretory component added to the assay is bound to polymeric IgA-immune complexes previously fixed to Raji cells, but not to monomeric IgA immune complexes. To avoid false positives due to possible complement-fixing IgM immune complexes, prior IgM immunoadsorption is performed. Using anti-IgM antiserum coupled to CNBr-activated Sepharose 4B this step is not time-consuming. Polymeric IgA has a low affinity constant and binds weakly to Raji cells, as Scatchard analysis of the data shows. Thus, polymeric IgA immune complexes do not bind to Raji cells directly through Fc receptors, but through complement breakdown products, as with IgG-immune complexes. Using this method, we have been successful in detecting specific polymeric-IgA immune complexes in patients with IgA nephropathy (Berger's disease) and alcoholic liver disease, as well as in normal subjects after meals of high protein content. This new, simple, rapid and reproducible assay might help to study the physiopathological role of polymeric IgA immune complexes in humans and animals.

Aspartate aminotransferase is potently inhibited by copper complexes: Exploring copper complex-binding proteome.

PubMed

Jia, Yuqi; Lu, Liping; Yuan, Caixia; Feng, Sisi; Zhu, Miaoli

2017-05-01

Recent researches indicated that a copper complex-binding proteome that potently interacted with copper complexes and then influenced cellular metabolism might exist in organism. In order to explore the copper complex-binding proteome, a copper chelating ion-immobilized affinity chromatography (Cu-IMAC) column and mass spectrometry were used to separate and identify putative Cu-binding proteins in primary rat hepatocytes. A total of 97 putative Cu-binding proteins were isolated and identified. Five higher abundance proteins, aspartate aminotransferase (AST), malate dehydrogenase (MDH), catalase (CAT), calreticulin (CRT) and albumin (Alb) were further purified using a SP-, and (or) Q-Sepharose Fast Flow column. The interaction between the purified proteins and selected 11 copper complexes and CuCl 2 was investigated. The enzymes inhibition tests demonstrated that AST was potently inhibited by copper complexes while MDH and CAT were weakly inhibited. Schiff-based copper complexes 6 and 7 potently inhibited AST with the IC 50 value of 3.6 and 7.2μM, respectively and exhibited better selectivity over MDH and CAT. Fluorescence titration results showed the two complexes tightly bound to AST with binding constant of 3.89×10 6 and 3.73×10 6 M -1 , respectively and a stoichiometry ratio of 1:1. Copper complex 6 was able to enter into HepG2 cells and further inhibit intracellular AST activity. Copyright © 2017 Elsevier Inc. All rights reserved.

A Carrier Estimation Method Based on MLE and KF for Weak GNSS Signals.

PubMed

Zhang, Hongyang; Xu, Luping; Yan, Bo; Zhang, Hua; Luo, Liyan

2017-06-22

Maximum likelihood estimation (MLE) has been researched for some acquisition and tracking applications of global navigation satellite system (GNSS) receivers and shows high performance. However, all current methods are derived and operated based on the sampling data, which results in a large computation burden. This paper proposes a low-complexity MLE carrier tracking loop for weak GNSS signals which processes the coherent integration results instead of the sampling data. First, the cost function of the MLE of signal parameters such as signal amplitude, carrier phase, and Doppler frequency are used to derive a MLE discriminator function. The optimal value of the cost function is searched by an efficient Levenberg-Marquardt (LM) method iteratively. Its performance including Cramér-Rao bound (CRB), dynamic characteristics and computation burden are analyzed by numerical techniques. Second, an adaptive Kalman filter is designed for the MLE discriminator to obtain smooth estimates of carrier phase and frequency. The performance of the proposed loop, in terms of sensitivity, accuracy and bit error rate, is compared with conventional methods by Monte Carlo (MC) simulations both in pedestrian-level and vehicle-level dynamic circumstances. Finally, an optimal loop which combines the proposed method and conventional method is designed to achieve the optimal performance both in weak and strong signal circumstances.

Autapse-induced multiple stochastic resonances in a modular neuronal network

NASA Astrophysics Data System (ADS)

Yang, XiaoLi; Yu, YanHu; Sun, ZhongKui

2017-08-01

This study investigates the nontrivial effects of autapse on stochastic resonance in a modular neuronal network subjected to bounded noise. The resonance effect of autapse is detected by imposing a self-feedback loop with autaptic strength and autaptic time delay to each constituent neuron. Numerical simulations have demonstrated that bounded noise with the proper level of amplitude can induce stochastic resonance; moreover, the noise induced resonance dynamics can be significantly shaped by the autapse. In detail, for a specific range of autaptic strength, multiple stochastic resonances can be induced when the autaptic time delays are appropriately adjusted. These appropriately adjusted delays are detected to nearly approach integer multiples of the period of the external weak signal when the autaptic strength is very near zero; otherwise, they do not match the period of the external weak signal when the autaptic strength is slightly greater than zero. Surprisingly, in both cases, the differences between arbitrary two adjacent adjusted autaptic delays are always approximately equal to the period of the weak signal. The phenomenon of autaptic delay induced multiple stochastic resonances is further confirmed to be robust against the period of the external weak signal and the intramodule probability of subnetwork. These findings could have important implications for weak signal detection and information propagation in realistic neural systems.

Benchmark calculations of excess electrons in water cluster cavities: balancing the addition of atom-centered diffuse functions versus floating diffuse functions.

PubMed

Zhang, Changzhe; Bu, Yuxiang

2016-09-14

Diffuse functions have been proved to be especially crucial for the accurate characterization of excess electrons which are usually bound weakly in intermolecular zones far away from the nuclei. To examine the effects of diffuse functions on the nature of the cavity-shaped excess electrons in water cluster surroundings, both the HOMO and LUMO distributions, vertical detachment energies (VDEs) and visible absorption spectra of two selected (H2O)24(-) isomers are investigated in the present work. Two main types of diffuse functions are considered in calculations including the Pople-style atom-centered diffuse functions and the ghost-atom-based floating diffuse functions. It is found that augmentation of atom-centered diffuse functions contributes to a better description of the HOMO (corresponding to the VDE convergence), in agreement with previous studies, but also leads to unreasonable diffuse characters of the LUMO with significant red-shifts in the visible spectra, which is against the conventional point of view that the more the diffuse functions, the better the results. The issue of designing extra floating functions for excess electrons has also been systematically discussed, which indicates that the floating diffuse functions are necessary not only for reducing the computational cost but also for improving both the HOMO and LUMO accuracy. Thus, the basis sets with a combination of partial atom-centered diffuse functions and floating diffuse functions are recommended for a reliable description of the weakly bound electrons. This work presents an efficient way for characterizing the electronic properties of weakly bound electrons accurately by balancing the addition of atom-centered diffuse functions and floating diffuse functions and also by balancing the computational cost and accuracy of the calculated results, and thus is very useful in the relevant calculations of various solvated electron systems and weakly bound anionic systems.

Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics.

PubMed

Koziol, Lucas; Essiz, Sebnem G; Wong, Sergio E; Lau, Edmond Y; Valdez, Carlos A; Satcher, Joe H; Aines, Roger D; Lightstone, Felice C

2013-03-12

Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supramolecular tris(imidazolyl) calix[6]arene Zn(2+) aqua complex, as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate, H2O + CO2 → H(+) + HCO3(-). On the basis of potential-of-mean-force (PMF) calculations, stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (ΔG = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile, proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (ΔΔG = 1.4 kcal/mol), suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast, the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity, due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme, providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis, both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.

The random coding bound is tight for the average code.

NASA Technical Reports Server (NTRS)

Gallager, R. G.

1973-01-01

The random coding bound of information theory provides a well-known upper bound to the probability of decoding error for the best code of a given rate and block length. The bound is constructed by upperbounding the average error probability over an ensemble of codes. The bound is known to give the correct exponential dependence of error probability on block length for transmission rates above the critical rate, but it gives an incorrect exponential dependence at rates below a second lower critical rate. Here we derive an asymptotic expression for the average error probability over the ensemble of codes used in the random coding bound. The result shows that the weakness of the random coding bound at rates below the second critical rate is due not to upperbounding the ensemble average, but rather to the fact that the best codes are much better than the average at low rates.

Optical Feshbach resonances and ground-state-molecule production in the RbHg system

NASA Astrophysics Data System (ADS)

Borkowski, Mateusz; Muñoz Rodriguez, Rodolfo; Kosicki, Maciej B.; Ciuryło, Roman; Żuchowski, Piotr S.

2017-12-01

We present the prospects for photoassociation, optical control of interspecies scattering lengths, and, finally, the production of ultracold absolute ground-state molecules in the Rb+Hg system. We use the state-of-the-art ab initio methods for the calculations of ground- [CCSD(T)] and excited-state (EOM-CCSD) potential curves. The RbHg system, thanks to the wide range of stable Hg bosonic isotopes, offers possibilities for mass tuning of ground-state interactions. The optical lengths describing the strengths of optical Feshbach resonances near the Rb transitions are favorable even at large laser detunings. Ground-state RbHg molecules can be produced with efficiencies ranging from about 20% for deeply bound to at least 50% for weakly bound states close to the dissociation limit. Finally, electronic transitions with favorable Franck-Condon factors can be found for the purposes of a STIRAP transfer of the weakly bound RbHg molecules to the absolute ground state using commercially available lasers.

Rotational spectrum of 14N 2 · H 35Cl and 14N 2 · H 37Cl: electric field gradients at the nitrogen nuclei

NASA Astrophysics Data System (ADS)

Kisiel, Z.; Pszczólkowski, L.; Fowler, P. W.; Legon, A. C.

1997-09-01

Rotational spectra of the most abundant isotopic species of the weakly bound dimer formed between dinitrogen and hydrogen chloride were investigated. Spectroscopic constants for 14N 2 · H 37Cl were determined for the first time and those for 14N 2 · H 35Cl improved. Analysis of observed nuclear quadrupole spliting patterns within the framework of coupling of three nonequivalent nuclear spins allowed determination of splitting constants for both nuclei in the complexed dinitrogen molecule. Electric field gradient calculations at the SCF supermolecule level for the dimer are presented and account for the observed values of the nitrogen splitting constants.

Tight Bell Inequalities and Nonlocality in Weak Measurement

NASA Astrophysics Data System (ADS)

Waegell, Mordecai

A general class of Bell inequalities is derived based on strict adherence to probabilistic entanglement correlations observed in nature. This derivation gives significantly tighter bounds on local hidden variable theories for the well-known Clauser-Horne-Shimony-Holt (CHSH) inequality, and also leads to new proofs of the Greenberger-Horne-Zeilinger (GHZ) theorem. This method is applied to weak measurements and reveals nonlocal correlations between the weak value and the post-selection, which rules out various classical models of weak measurement. Implications of these results are discussed. Fetzer-Franklin Fund of the John E. Fetzer Memorial Trust.

A strategy for co-translational folding studies of ribosome-bound nascent chain complexes using NMR spectroscopy.

PubMed

Cassaignau, Anaïs M E; Launay, Hélène M M; Karyadi, Maria-Evangelia; Wang, Xiaolin; Waudby, Christopher A; Deckert, Annika; Robertson, Amy L; Christodoulou, John; Cabrita, Lisa D

2016-08-01

During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dynamic nature of emerging nascent chains, which precluded most structural techniques. NMR spectroscopy is able to provide atomic-resolution information for ribosome-nascent chain complexes (RNCs), but it requires large quantities (≥10 mg) of homogeneous, isotopically labeled RNCs. Further challenges include limited sample working concentration and stability of the RNC sample (which contribute to weak NMR signals) and resonance broadening caused by attachment to the large (2.4-MDa) ribosomal complex. Here, we present a strategy to generate isotopically labeled RNCs in Escherichia coli that are suitable for NMR studies. Uniform translational arrest of the nascent chains is achieved using a stalling motif, and isotopically labeled RNCs are produced at high yield using high-cell-density E. coli growth conditions. Homogeneous RNCs are isolated by combining metal affinity chromatography (to isolate ribosome-bound species) with sucrose density centrifugation (to recover intact 70S monosomes). Sensitivity-optimized NMR spectroscopy is then applied to the RNCs, combined with a suite of parallel NMR and biochemical analyses to cross-validate their integrity, including RNC-optimized NMR diffusion measurements to report on ribosome attachment in situ. Comparative NMR studies of RNCs with the analogous isolated proteins permit a high-resolution description of the structure and dynamics of a nascent chain during its progressive biosynthesis on the ribosome.

Re-derived overclosure bound for the inert doublet model

NASA Astrophysics Data System (ADS)

Biondini, S.; Laine, M.

2017-08-01

We apply a formalism accounting for thermal effects (such as modified Sommerfeld effect; Salpeter correction; decohering scatterings; dissociation of bound states), to one of the simplest WIMP-like dark matter models, associated with an "inert" Higgs doublet. A broad temperature range T ˜ M/20 . . . M/104 is considered, stressing the importance and less-understood nature of late annihilation stages. Even though only weak interactions play a role, we find that resummed real and virtual corrections increase the tree-level overclosure bound by 1 . . . 18%, depending on quartic couplings and mass splittings.

Chiral self-recognition: direct spectroscopic detection of the homochiral and heterochiral dimers of propylene oxide in the gas phase.

PubMed

Su, Zheng; Borho, Nicole; Xu, Yunjie

2006-12-27

In this report, we describe rotational spectroscopic and high-level ab initio studies of the 1:1 chiral molecular adduct of propylene oxide dimer. The complexes are bound by weak secondary hydrogen bonds, that is, the O(epoxy)...H-C noncovalent interactions. Six homochiral and six heterochiral conformers were predicted to be the most stable configurations where each monomer acts as a proton acceptor and a donor simultaneously, forming two six- or five-membered intermolecular hydrogen-bonded rings. Rotational spectra of six, that is, three homochiral and heterochiral conformer pairs, out of the eight conformers that were predicted to have sufficiently large permanent electric dipole moments were measured and analyzed. The relative conformational stability order and the signs of the chiral recognition energies of the six conformers were determined experimentally and were compared to the ab initio computational results. The experimental observations and the ab initio calculations suggest that the concerted effort of these weak secondary hydrogen bonds can successfully lock the subunits in a particular orientation and that the overall binding strength is comparable to a classic hydrogen bond.

Lifshitz phase: the microscopic structure of aqueous and ethanol mixtures of 1,n-diols.

PubMed

Požar, Martina; Perera, Aurélien

2017-06-14

We study binary mixtures of ethylene glycol and 1,3-propandiol with water or ethanol using computer simulations. Despite strong hydrogen bonding tendencies between all these molecules, we find that these mixtures are surprisingly homogeneous, in contrast to the strong micro-heterogeneity found in aqueous ethanol mixtures. The aqueous diol mixtures are found to be close to ideal mixtures, with near-ideal Kirkwood-Buff integrals. Ethanol-diol mixtures show weak non-ideality. The origin of this unexpected randomness is due to the fact that the two hydrogen bonding hydroxyl groups of the 1,n-diol are bound by the neutral alkyl bond, which prevents the micro-segregation of the different types of hydroxyl groups. These findings suggest that random disorder can arise in the presence of strong interactions - in contrast to the usual picture of random disorder due to weak interactions between the components. They point to the important role of molecular topology in tuning concentration fluctuations in complex liquids. We propose and justify herein the name of Lifshitz phases to designate such types of disordered systems.

Some peculiarities of interactions of weakly bound lithium nuclei at near-barrier energies

NASA Astrophysics Data System (ADS)

Kabyshev, A. M.; Kuterbekov, K. A.; Sobolev, Yu G.; Penionzhkevich, Yu E.; Kubenova, M. M.; Azhibekov, A. K.; Mukhambetzhan, A. M.; Lukyanov, S. M.; Maslov, V. A.; Kabdrakhimova, G. D.

2018-02-01

This paper presents new experimental data on the total cross sections of 9Li + 28Si reactions at low energies as well as the analysis of previously obtained data for 6,7Li. Based on a large collection of data (authors’ and literature data) we carried out a comparative analysis of the two main experimental interaction cross sections (angular distributions of the differential cross sections and total reaction cross sections) for weakly bound lithium (6-9Li, 11Li) nuclei in the framework of Kox parameterization and the macroscopic optical model. We identified specific features of these interactions and predicted the experimental trend in the total reaction cross sections for Li isotopes at energies close to the Coulomb barrier.

Quantum dice rolling: a multi-outcome generalization of quantum coin flipping

NASA Astrophysics Data System (ADS)

Aharon, N.; Silman, J.

2010-03-01

The problem of quantum dice rolling (DR)—a generalization of the problem of quantum coin flipping (CF) to more than two outcomes and parties—is studied in both its weak and strong variants. We prove by construction that quantum mechanics allows for (i) weak N-sided DR admitting arbitrarily small bias for any N and (ii) two-party strong N-sided DR saturating Kitaev's bound for any N. To derive (ii) we also prove by construction that quantum mechanics allows for (iii) strong imbalanced CF saturating Kitaev's bound for any degree of imbalance. Furthermore, as a corollary of (ii) we introduce a family of optimal 2m-party strong nm-sided DR protocols for any pair m and n.

Density Large Deviations for Multidimensional Stochastic Hyperbolic Conservation Laws

NASA Astrophysics Data System (ADS)

Barré, J.; Bernardin, C.; Chetrite, R.

2018-02-01

We investigate the density large deviation function for a multidimensional conservation law in the vanishing viscosity limit, when the probability concentrates on weak solutions of a hyperbolic conservation law. When the mobility and diffusivity matrices are proportional, i.e. an Einstein-like relation is satisfied, the problem has been solved in Bellettini and Mariani (Bull Greek Math Soc 57:31-45, 2010). When this proportionality does not hold, we compute explicitly the large deviation function for a step-like density profile, and we show that the associated optimal current has a non trivial structure. We also derive a lower bound for the large deviation function, valid for a more general weak solution, and leave the general large deviation function upper bound as a conjecture.

Weak Compactness and Control Measures in the Space of Unbounded Measures

PubMed Central

Brooks, James K.; Dinculeanu, Nicolae

1972-01-01

We present a synthesis theorem for a family of locally equivalent measures defined on a ring of sets. This theorem is then used to exhibit a control measure for weakly compact sets of unbounded measures. In addition, the existence of a local control measure for locally strongly bounded vector measures is proved by means of the synthesis theorem. PMID:16591980

Interactions of NO and CO with Pd and Pt atoms

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

Smith, G.W.; Carter, E.A.

1991-03-21

The authors report ab initio generalized valence bond and correlation-consistent configuration interaction studies of CO and NO interacting with Pd and Pt atoms. They find dramatically different bonding mechanisms for the two ligands, which are easily understood in terms of changes in the electronic structure of the metal and the ligand. CO bonds to both Pd and pt by a {sigma} donor/{pi} back-bonding mechanism, yielding linear geometries. Their calculations predict that the ground ({sup 1}{Sigma}{sup +}) state of PdCO is bound by 27 kcal/mol, while the ground ({sup 1}{Sigma}{sup +}) state of PtCO is bound by only 18.5 kcal/mol. Bymore » contrast, PdNO and PtNO are both bent, with the dominant bonding involving a covalent {sigma} bond between a singly occupied metal d{sigma} orbital and the singly occupied NO 2{pi}* orbital. While the ground ({sup 2}A{prime}) state of PtNO is strongly bound (D{sub e}(Pt-NO) {approximately} 20 kcal/mol), NO binds very weakly to Pd (D{sub e}(Pd-NO) {le} 4 kcal/mol). Linear excited states ({sup 2}{Sigma} and {sup 2}{Pi}) of PtNO and PdNO are predicted to be only weakly bound or unbound. However, corresponding linear cationic states ({sup 1}{Sigma}{sup +} and {sup 3}{Pi}) are strongly bound, but the cationic bent ({sup 1}A{prime}) states are still the ground states of PtNO{sup +} and PdNO{sup +}. These stark contrasts, in which NO binds strongly to Pt but weakly to Pd while CO binds much more strongly to Pd, are due to the preference for closed-shell species to bind strongly to other closed-shell species (e.g., CO to Pd) and for radicals to bind strongly to other radicals (e.g., NO to Pt).« less

STUDIES ON MAMMALIAN AND HUMAN PYRUVATE AND ALPHA-KETOGLUTARATE DEHYDROGENATION COMPLEXES

DTIC Science & Technology

bound lipoic acid and 17 moles of bound FAD. Alpha -ketoglutarate dehydrogenase complex contains approximately 10 moles of protein-bound lipoic acid , 9...typical metal activators of oxidative decarboxylation reaction of alpha -keto acid . These activating effects were in good agreement with the results of...A coenzyme A- and NAD-linked pyruvate and alpha -ketoglutarate dehydrogenase complexes have been isolated from pig heart muscle as multienzyme units

Evolution of complexity following a global quench

NASA Astrophysics Data System (ADS)

Moosa, Mudassir

2018-03-01

The rate of complexification of a quantum state is conjectured to be bounded from above by the average energy of the state. A different conjecture relates the complexity of a holographic CFT state to the on-shell gravitational action of a certain bulk region. We use `complexity equals action' conjecture to study the time evolution of the complexity of the CFT state after a global quench. We find that the rate of growth of complexity is not only consistent with the conjectured bound, but it also saturates the bound soon after the system has achieved local equilibrium.

Scalable service architecture for providing strong service guarantees

NASA Astrophysics Data System (ADS)

Christin, Nicolas; Liebeherr, Joerg

2002-07-01

For the past decade, a lot of Internet research has been devoted to providing different levels of service to applications. Initial proposals for service differentiation provided strong service guarantees, with strict bounds on delays, loss rates, and throughput, but required high overhead in terms of computational complexity and memory, both of which raise scalability concerns. Recently, the interest has shifted to service architectures with low overhead. However, these newer service architectures only provide weak service guarantees, which do not always address the needs of applications. In this paper, we describe a service architecture that supports strong service guarantees, can be implemented with low computational complexity, and only requires to maintain little state information. A key mechanism of the proposed service architecture is that it addresses scheduling and buffer management in a single algorithm. The presented architecture offers no solution for controlling the amount of traffic that enters the network. Instead, we plan on exploiting feedback mechanisms of TCP congestion control algorithms for the purpose of regulating the traffic entering the network.

Minor groove binding of a bis-quaternary ammonium compound: the crystal structure of SN 7167 bound to d(CGCGAATTCGCG)2.

PubMed Central

Squire, C J; Clark, G R; Denny, W A

1997-01-01

The X-ray crystal structure of the complex between the synthetic antitumour and antiviral DNA binding ligand SN 7167 and the DNA oligonucleotide d(CGCGAATTCGCG)2 has been determined to an R factor of 18.3% at 2.6 A resolution. The ligand is located within the minor groove and covers almost 6 bp with the 1-methylpyridinium ring extending as far as the C9-G16 base pair and the 1-methylquinolinium ring lying between the G4-C21 and A5-T20 base pairs. The ligand interacts only weakly with the DNA, as evidenced by long range contacts and shallow penetration into the groove. This structure is compared with that of the complex between the parent compound SN 6999 and the alkylated DNA sequence d(CGC[e6G]AATTCGCG)2. There are significant differences between the two structures in the extent of DNA bending, ligand conformation and groove binding. PMID:9321660

Data-collection strategy for challenging native SAD phasing.

PubMed

Olieric, Vincent; Weinert, Tobias; Finke, Aaron D; Anders, Carolin; Li, Dianfan; Olieric, Natacha; Borca, Camelia N; Steinmetz, Michel O; Caffrey, Martin; Jinek, Martin; Wang, Meitian

2016-03-01

Recent improvements in data-collection strategies have pushed the limits of native SAD (single-wavelength anomalous diffraction) phasing, a method that uses the weak anomalous signal of light elements naturally present in macromolecules. These involve the merging of multiple data sets from either multiple crystals or from a single crystal collected in multiple orientations at a low X-ray dose. Both approaches yield data of high multiplicity while minimizing radiation damage and systematic error, thus ensuring accurate measurements of the anomalous differences. Here, the combined use of these two strategies is described to solve cases of native SAD phasing that were particular challenges: the integral membrane diacylglycerol kinase (DgkA) with a low Bijvoet ratio of 1% and the large 200 kDa complex of the CRISPR-associated endonuclease (Cas9) bound to guide RNA and target DNA crystallized in the low-symmetry space group C2. The optimal native SAD data-collection strategy based on systematic measurements performed on the 266 kDa multiprotein/multiligand tubulin complex is discussed.

Dissociation and purification of the endogenous membrane-bound Vo complex from Pichia pastoris.

PubMed

Li, Sumei; Hong, Tao; Wang, Kun; Lu, Yinghong; Zhou, Min

2017-10-01

Most proteins occur and function in complexes rather than as isolated entities in membranes. In most cases macromolecules with multiple subunits are purified from endogenous sources. In this study, an endogenous membrane-protein complex was obtained from Pichia pastoris, which can be grown at high densities to significantly improve the membrane protein yield. We successfully isolated the membrane-bound Vo complex of V-ATPase from P. pastoris using a fusion FLAG tag attached to the C-terminus of subunit a to generate the vph-tag strain, which was used for dissociation and purification. After FLAG affinity and size exclusion chromatography purification, the production quantity and purity of the membrane-bound Vo complex was 20 μg l -1 and >98%, respectively. The subunits of the endogenous membrane-bound Vo complex observed in P. pastoris were similar to those obtained from S. cerevisiae, as demonstrated by liquid chromatography-tandem mass spectrometry (LC-MS-MS). Therefore, successful dissociation and purification of the membrane-bound Vo complex at a high purity and sufficient quantity was achieved via a rapid and simple procedure that can be used to obtain the endogenous membrane-protein complexes from P. pastoris. Copyright © 2017 Elsevier Inc. All rights reserved.

Upper bounds on quantum uncertainty products and complexity measures

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

Guerrero, Angel; Sanchez-Moreno, Pablo; Dehesa, Jesus S.

The position-momentum Shannon and Renyi uncertainty products of general quantum systems are shown to be bounded not only from below (through the known uncertainty relations), but also from above in terms of the Heisenberg-Kennard product . Moreover, the Cramer-Rao, Fisher-Shannon, and Lopez-Ruiz, Mancini, and Calbet shape measures of complexity (whose lower bounds have been recently found) are also bounded from above. The improvement of these bounds for systems subject to spherically symmetric potentials is also explicitly given. Finally, applications to hydrogenic and oscillator-like systems are done.

On absence of bound states for weakly attractive δ'-interactions supported on non-closed curves in ℝ2

NASA Astrophysics Data System (ADS)

Jex, Michal; Lotoreichik, Vladimir

2016-02-01

Let Λ ⊂ ℝ2 be a non-closed piecewise-C1 curve, which is either bounded with two free endpoints or unbounded with one free endpoint. Let u±|Λ ∈ L2(Λ) be the traces of a function u in the Sobolev space H1(ℝ2∖Λ) onto two faces of Λ. We prove that for a wide class of shapes of Λ the Schrödinger operator Hω Λ with δ'-interaction supported on Λ of strength ω ∈ L∞(Λ; ℝ) associated with the quadratic form H 1 ( R 2 ∖ Λ ) ∋ u ↦ ∫ R 2 |" separators=" ∇ u | 2 d x - ∫ Λ ω |" separators=" u + | Λ - u - | Λ | 2 d s has no negative spectrum provided that ω is pointwise majorized by a strictly positive function explicitly expressed in terms of Λ. If, additionally, the domain ℝ2∖Λ is quasi-conical, we show that σ ( Hω Λ ) = [ 0 , + ∞ ) . For a bounded curve Λ in our class and non-varying interaction strength ω ∈ ℝ, we derive existence of a constant ω∗ > 0 such that σ ( Hω Λ ) = [ 0 , + ∞ ) for all ω ∈ (-∞, ω∗]; informally speaking, bound states are absent in the weak coupling regime.

Low capping group surface density on zinc oxide nanocrystals.

PubMed

Valdez, Carolyn N; Schimpf, Alina M; Gamelin, Daniel R; Mayer, James M

2014-09-23

The ligand shell of colloidal nanocrystals can dramatically affect their stability and reaction chemistry. We present a methodology to quantify the dodecylamine (DDA) capping shell of colloidal zinc oxide nanocrystals in a nonpolar solvent. Using NMR spectroscopy, three different binding regimes are observed: strongly bound, weakly associated, and free in solution. The surface density of bound DDA is constant over a range of nanocrystal sizes, and is low compared to both predictions of the number of surface cations and maximum coverages of self-assembled monolayers. The density of strongly bound DDA ligands on the as-prepared ZnO NCs is 25% of the most conservative estimate of the maximum surface DDA density. Thus, these NCs do not resemble the common picture of a densely capped surface ligand layer. Annealing the ZnO NCs in molten DDA for 12 h at 160 °C, which is thought to remove surface hydroxide groups, resulted in a decrease of the weakly associated DDA and an increase in the density of strongly bound DDA, to ca. 80% of the estimated density of a self-assembled monolayer on a flat ZnO surface. These findings suggest that as-prepared nanocrystal surfaces contain hydroxide groups (protons on the ZnO surfaces) that inhibit strong binding of DDA.

Self-assembly of acetate adsorbates drives atomic rearrangement on the Au(110) surface

DOE PAGES

Hiebel, Fanny; Shong, Bonggeun; Chen, Wei; ...

2016-10-12

Weak inter-adsorbate interactions are shown to play a crucial role in determining surface structure, with major implications for its catalytic reactivity. This is exemplified here in the case of acetate bound to Au(110), where the small extra energy of the van der Waals interactions among the surface-bound groups drives massive restructuring of the underlying Au. Acetate is a key intermediate in electro-oxidation of CO 2 and a poison in partial oxidation reactions. Metal atom migration originates at surface defects and is likely facilitated by weakened Au–Au interactions due to bonding with the acetate. Even though the acetate is a relativelymore » small molecule, weak intermolecular interaction provides the energy required for molecular self-assembly and reorganization of the metal surface.« less

Investigation of large α production in reactions involving weakly bound 7Li

NASA Astrophysics Data System (ADS)

Pandit, S. K.; Shrivastava, A.; Mahata, K.; Parkar, V. V.; Palit, R.; Keeley, N.; Rout, P. C.; Kumar, A.; Ramachandran, K.; Bhattacharyya, S.; Nanal, V.; Palshetkar, C. S.; Nag, T. N.; Gupta, Shilpi; Biswas, S.; Saha, S.; Sethi, J.; Singh, P.; Chatterjee, A.; Kailas, S.

2017-10-01

The origin of the large α -particle production cross sections in systems involving weakly bound 7Li projectiles has been investigated by measuring the cross sections of all possible fragment-capture as well as complete fusion using the particle-γ coincidence, in-beam, and off-beam γ -ray counting techniques for the 7Li+93Nb system at near Coulomb barrier energies. Almost all of the inclusive α -particle yield has been accounted for. While the t -capture mechanism is found to be dominant (˜70 % ), compound nuclear evaporation and breakup processes contribute ˜15 % each to the inclusive α -particle production in the measured energy range. Systematic behavior of the t capture and inclusive α cross sections for reactions involving 7Li over a wide mass range is also reported.

Self-assembly of acetate adsorbates drives atomic rearrangement on the Au(110) surface

PubMed Central

Hiebel, Fanny; Shong, Bonggeun; Chen, Wei; Madix, Robert J.; Kaxiras, Efthimios; Friend, Cynthia M.

2016-01-01

Weak inter-adsorbate interactions are shown to play a crucial role in determining surface structure, with major implications for its catalytic reactivity. This is exemplified here in the case of acetate bound to Au(110), where the small extra energy of the van der Waals interactions among the surface-bound groups drives massive restructuring of the underlying Au. Acetate is a key intermediate in electro-oxidation of CO2 and a poison in partial oxidation reactions. Metal atom migration originates at surface defects and is likely facilitated by weakened Au–Au interactions due to bonding with the acetate. Even though the acetate is a relatively small molecule, weak intermolecular interaction provides the energy required for molecular self-assembly and reorganization of the metal surface. PMID:27731407

Second law of thermodynamics and quantum feedback control: Maxwell's demon with weak measurements

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

Jacobs, Kurt

2009-07-15

Recently Sagawa and Ueda [Phys. Rev. Lett. 100, 080403 (2008)] derived a bound on the work that can be extracted from a quantum system with the use of feedback control. For many quantum measurements their bound was not tight. We show that a tight version of this bound follows straightforwardly from recent work on Maxwell's demon by Alicki et al. [Open Syst. Inf. Dyn. 11, 205 (2004)], for both discrete and continuous feedback control. Our analysis also shows that bare, efficient measurements always do non-negative work on a system in equilibrium, but do not add heat.

A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase.

PubMed

Edwards, Marcus J; Flatman, Ruth H; Mitchenall, Lesley A; Stevenson, Clare E M; Le, Tung B K; Clarke, Thomas A; McKay, Adam R; Fiedler, Hans-Peter; Buttner, Mark J; Lawson, David M; Maxwell, Anthony

2009-12-04

Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.

N-acetylglyoxylic amide bearing a nitrophenyl group as anion receptors: NMR and X-ray investigations on anion binding and selectivity

NASA Astrophysics Data System (ADS)

Suryanti, Venty; Bhadbhade, Mohan; Black, David StC; Kumar, Naresh

2017-10-01

N-Nitrophenylglyoxylic amides 1 and 2 in presence of tetrabutylammonium cation (TBA) act as receptors for anions HSO4-, Cl-, Br- and NO3- as investigated by NMR studies. The receptors formed 1:1 host-guest complexes in solution. X-ray structure of 1 along with TBA that bind a chloride anion is reported. Molecule 1 showed the highest selectivity for HSO4- anion over others measured. X-ray structure of the bound Cl- revealed a pocket containing the anion making strong (Nsbnd H⋯Cl) and weak hydrogen bonds (Csbnd H⋯Cl) that contribute to the recognition of the chloride anion. Nsbnd H and Csbnd H hydrogen bonds resulted in a relatively strong binding for chloride ions.

Oxidative Formation and Removal of Complexed Mn(III) by Pseudomonas Species

PubMed Central

Wright, Mitchell H.; Geszvain, Kati; Oldham, Véronique E.; Luther, George W.; Tebo, Bradley M.

2018-01-01

The observation of significant concentrations of soluble Mn(III) complexes in oxic, suboxic, and some anoxic waters has triggered a re-evaluation of the previous Mn paradigm which focused on the cycling between soluble Mn(II) and insoluble Mn(III,IV) species as operationally defined by filtration. Though Mn(II) oxidation in aquatic environments is primarily bacterially-mediated, little is known about the effect of Mn(III)-binding ligands on Mn(II) oxidation nor on the formation and removal of Mn(III). Pseudomonas putida GB-1 is one of the most extensively investigated of all Mn(II) oxidizing bacteria, encoding genes for three Mn oxidases (McoA, MnxG, and MopA). P. putida GB-1 and associated Mn oxidase mutants were tested alongside environmental isolates Pseudomonas hunanensis GSL-007 and Pseudomonas sp. GSL-010 for their ability to both directly oxidize weakly and strongly bound Mn(III), and to form these complexes through the oxidation of Mn(II). Using Mn(III)-citrate (weak complex) and Mn(III)-DFOB (strong complex), it was observed that P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 and mutants expressing only MnxG and McoA were able to directly oxidize both species at varying levels; however, no oxidation was detected in cultures of a P. putida mutant expressing only MopA. During cultivation in the presence of Mn(II) and citrate or DFOB, P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 formed Mn(III) complexes transiently as an intermediate before forming Mn(III/IV) oxides with the overall rates and extents of Mn(III,IV) oxide formation being greater for Mn(III)-citrate than for Mn(III)-DFOB. These data highlight the role of bacteria in the oxidative portion of the Mn cycle and suggest that the oxidation of strong Mn(III) complexes can occur through enzymatic mechanisms involving multicopper oxidases. The results support the observations from field studies and further emphasize the complexity of the geochemical cycling of manganese. PMID:29706936

Oxidative Formation and Removal of Complexed Mn(III) by Pseudomonas Species.

PubMed

Wright, Mitchell H; Geszvain, Kati; Oldham, Véronique E; Luther, George W; Tebo, Bradley M

2018-01-01

The observation of significant concentrations of soluble Mn(III) complexes in oxic, suboxic, and some anoxic waters has triggered a re-evaluation of the previous Mn paradigm which focused on the cycling between soluble Mn(II) and insoluble Mn(III,IV) species as operationally defined by filtration. Though Mn(II) oxidation in aquatic environments is primarily bacterially-mediated, little is known about the effect of Mn(III)-binding ligands on Mn(II) oxidation nor on the formation and removal of Mn(III). Pseudomonas putida GB-1 is one of the most extensively investigated of all Mn(II) oxidizing bacteria, encoding genes for three Mn oxidases (McoA, MnxG, and MopA). P. putida GB-1 and associated Mn oxidase mutants were tested alongside environmental isolates Pseudomonas hunanensis GSL-007 and Pseudomonas sp. GSL-010 for their ability to both directly oxidize weakly and strongly bound Mn(III), and to form these complexes through the oxidation of Mn(II). Using Mn(III)-citrate (weak complex) and Mn(III)-DFOB (strong complex), it was observed that P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 and mutants expressing only MnxG and McoA were able to directly oxidize both species at varying levels; however, no oxidation was detected in cultures of a P. putida mutant expressing only MopA. During cultivation in the presence of Mn(II) and citrate or DFOB, P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 formed Mn(III) complexes transiently as an intermediate before forming Mn(III/IV) oxides with the overall rates and extents of Mn(III,IV) oxide formation being greater for Mn(III)-citrate than for Mn(III)-DFOB. These data highlight the role of bacteria in the oxidative portion of the Mn cycle and suggest that the oxidation of strong Mn(III) complexes can occur through enzymatic mechanisms involving multicopper oxidases. The results support the observations from field studies and further emphasize the complexity of the geochemical cycling of manganese.

Bound states of water in gelatin discriminated by near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Otsuka, Yukiko; Shirakashi, Ryo; Hirakawa, Kazuhiko

2017-11-01

By near-infrared spectroscopy, we classified water molecules in hydrated gelatin membranes in a drying process. Absorbance spectra in the frequency range of 4500-5500 cm-1 were resolved into three peaks, S0, S1, and S2, that correspond to water molecules with different hydrogen bond states. From the areas of the absorbance peaks as a function of the water content of gelatin, together with the information on the freezing properties of water measured by differential scanning calorimetry, we found that, when the water content is less than 20%, free water disappears and only weakly and strongly bound waters remain. We also found that the weakly bound water consists of S0, S1, and S2 water molecules with a simple composition of \\text{S}0:\\text{S}1:\\text{S}2 ≈ 1:2:0. Using this information, most of the freezable water was determined to be free water. Our classification provides a simple method of estimating the retention and freezing properties of processed foods or drugs by infrared spectroscopy.

Biosynthesis of edeine: II. Localization of edeine synthetase within Bacillus brevis Vm4.

PubMed

Kurylo-Borowska, Z

1975-07-14

Edeine-synthesizing polyenzymes, associated with a complex of sytoplasmic membrane and DNA, were obtained from gently lysed cells of Bacillus brevis Vm4. The polyenzymes-membrane-DNA complex, isolated from dells intensively synthesizing edeines (18--20 h culture) contained edeine B. Edeine B was found to be bound covalently t o the edeine synthetase. The amount of edeine bound to polyenzymes was 0.1--0.3 mumol/mg protein, depending on the age of cells. Detachment of deeine synthetase with a covalently bound edeine B from the membrane-DNA complex was accomplished by a treatment with (NH4)2-SO4 at 45--55% saturation or by DEAE-cellulose column fractionation. In contrast to other components of the complex, the edeine-polyenzymes fragment was not adsorbed to the DEAE-cellulose. Sephadex G-200 column chromatography separated the edeine-polyenzymes complex into 3 fractions. Edeine-polyenzymes complex, obtained from lysozyme-Brij-58-DNAase treated cells, contained edeine B bound to two protein fractions of mol. wt 210 000 and 160 000. Edeine-polyenzymes complex detached from the complex with the membrane and DNA contained edeine B, bound only to protein fraction of mol. wt 210 000. Edeine A was not found in the edeine-polyenzymes complex. No accumulation of free antibiotics within 16--22 h old cells of B. brevis Vm4 was detected. The edeine-polyenzymes complex associated with the DNA-membrane complex has shown no antimicrobial activity. By treating of above with alkali, edeine B of specific activity: 80 units/mjmol was released. The complex of DNA-membrane associated with edeine-polyenzymes complex was able to synthesize DNA, under the conditions described for synthesis, directed by a DNA-membrane complex. Edeine when associated with this complex did not effect the DNA-synthesizing activity.

Phosphorus-31 and carbon-13 nuclear magnetic resonance studies of divalent cation binding to phosphatidylserine membranes. Use of cobalt as a paramagnetic probe

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

McLaughlin, A.C.

1982-01-01

The paramagnetic divalent cation cobalt has large and well-understood effects on NMR signals from ligands bound in the first coordination sphere, i.e., inner-sphere ligands, and the authors have used these effects to identify divalent cation binding sites at the surface of phosphatidylserine membranes. /sup 31/P NMR results show that 13% of the bound cobalt ions are involved in inner-sphere complexes with the phosphodiester group, while /sup 13/C NMR results show that 54% of the bound cobalt ions are involved in unidentate inner sphere complexes with the carboxyl group. No evidence is found for cobalt binding to the carbonyl groups, butmore » proton release studies suggest that 32% of the bound cobalt ions are involved in chelate complexes that contain both the carboxyl and the amine groups. All of the bound cobalt ions can thus be accounted for in terms of inner sphere complexes with the phosphodiester group or the carboxyl group. They suggest that the unidentate inner-sphere complex between cobalt and the carboxyl group of phosphatidylserine and the inner-sphere complex between cobalt and the phosphodiester group of phosphatidylserine provide reasonable models for complexes between alkaline earth cations and phosphatidylserine membranes.« less

Phosphorus-31 and carbon-13 nuclear magnetic resonance studies of divalent cation binding to phosphatidylserine membranes: use of cobalt as a paramagnetic probe

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

McLaughlin, A.C.

1982-09-28

The paramagnetic divalent cation cobalt has large and well-understood effects on NMR signals from ligands bound in the first coordination sphere, i.e., inner-sphere ligands, and we have used these effects to identify divalent cation binding sites at the surface of phosphatidylserine membranes. /sup 31/P NMR results show that 13% of the bound cobalt ions are involved in inner-sphere complexes with the phosphodiester group, while /sup 13/C NMR results show that 54% of the bound cobalt ions are involved in unidentate inner sphere complexes with the carboxyl group. No evidence is found for cobalt binding to the carbonyl groups, but protonmore » release studies suggest that 32% of the bound cobalt ions are involved in chelate complexes that contain both the carboxyl and the amine groups. All (i.e., 13% + 54% + 32% = 99%) of the bound cobalt ions can thus be accounted for in terms of inner sphere complexes with the phosphodiester group or the carboxyl group. We suggest that the unidentate inner-sphere complex between cobalt and the carboxyl group of phosphatidylserine and the inner-sphere complex between cobalt and the phosphodiester group of phosphatidylserine provide reasonable models for complexes between alkaline earth cations and phosphatidylserine membranes.« less

Infrared Spectroscopy of Metal Ion Complexes: Models for Metal Ligand Interactions and Solvation

NASA Astrophysics Data System (ADS)

Duncan, Michael

2006-03-01

Weakly bound complexes of the form M^+-Lx (M=Fe, Ni, Co, etc.; L=CO2, C2H2, H2O, benzene, N2) are prepared in supersonic molecular beams by laser vaporization in a pulsed-nozzle cluster source. These species are mass analyzed and size-selected in a reflectron time-of-flight mass spectrometer. Clusters are photodissociated at infrared wavelengths with a Nd:YAG pumped infrared optical parametric oscillator/amplifier (OPO/OPA) laser or with a tunable infrared free-electron laser. M^+-(CO2)x complexes absorb near the free CO2 asymmetric stretch near 2349 cm-1 but with an interesting size dependent variation in the resonances. Small clusters have blue-shifted resonances, while larger complexes have additional bands due to surface CO2 molecules not attached to the metal. M^+(C2H2)n complexes absorb near the C-H stretches in acetylene, but resonances in metal complexes are red-shifted with repect to the isolated molecule. Ni^+ and Co^+ complexes with acetylene undergo intracluster cyclization reactions to form cyclobutadiene. Transition metal water complexes are studied in the O-H stretch region, and partial rotational structure can be measured. M^+(benzene) and M^+(benzene)2 ions (M=V, Ti, Al) represent half-sandwich and sandwich species, whose spectra are measured near the free benzene modes. These new IR spectra and their assignments will be discussed as well as other new IR spectra for similar complexes.

New insights into silica-based NMR “chromatography”

NASA Astrophysics Data System (ADS)

Pemberton, Chava; Hoffman, Roy; Aserin, Abraham; Garti, Nissim

2011-02-01

Silica is used as an important component for NMR “chromatography”. In this study the effect of the binding strength to silica of a variety of compounds on their diffusion rate is measured for the first time. Over two orders of magnitude of diffusion difference enhancement was obtained in the presence of silica for some compounds. An explanation of the enhancement is given that also allows one to predict the “chromatographic” behavior of new compounds or mixtures. The binding strength is divided into categories of weakly bound, singly bound and multiply bound. Carboxylates, sulfonates, and diols are found to be particularly strongly bound and to diffuse up to 2½ orders of magnitude more slowly in the presence of silica.

Pressure-induced structural transition of mature HIV-1 protease from a combined NMR/MD simulation approach.

PubMed

Roche, Julien; Louis, John M; Bax, Ad; Best, Robert B

2015-12-01

We investigate the pressure-induced structural changes in the mature human immunodeficiency virus type 1 protease dimer, using residual dipolar coupling (RDC) measurements in a weakly oriented solution. (1)DNH RDCs were measured under high-pressure conditions for an inhibitor-free PR and an inhibitor-bound complex, as well as for an inhibitor-free multidrug resistant protease bearing 20 mutations (PR20). While PR20 and the inhibitor-bound PR were little affected by pressure, inhibitor-free PR showed significant differences in the RDCs measured at 600 bar compared with 1 bar. The structural basis of such changes was investigated by MD simulations using the experimental RDC restraints, revealing substantial conformational perturbations, specifically a partial opening of the flaps and the penetration of water molecules into the hydrophobic core of the subunits at high pressure. This study highlights the exquisite sensitivity of RDCs to pressure-induced conformational changes and illustrates how RDCs combined with MD simulations can be used to determine the structural properties of metastable intermediate states on the folding energy landscape. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Interaction of pseudolaric acid B with the colchicine site of tubulin.

PubMed

Sarkar, Taradas; Nguyen, Tam Luong; Su, Zhi-Wei; Hao, Jun; Bai, Ruoli; Gussio, Rick; Qiu, Samuel X; Hamel, Ernest

2012-08-15

We purified pseudolaric acid B (PAB) from the root and stem bark of Pseudolarix kaempferi (Lindl.) Gorden. Confirming previous findings, we found that the compound had high nanomolar IC₅₀ antiproliferative effects in several cultured cell lines, causing mitotic arrest and the disappearance of intracellular microtubules. PAB strongly inhibited tubulin assembly (IC₅₀, 1.1 μM) but weakly inhibited the binding of colchicine to tubulin, as demonstrated by fluorescence and with [³H]colchicine. Kinetic analysis demonstrated that the mechanism of inhibition was competitive, with an apparent K(i) of 12-15 μM. Indirect studies demonstrated that PAB bound rapidly to tubulin and dissociated more rapidly from tubulin than the colchicine analog 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone, whose complex with tubulin is known to have a half-life of 17s at 37 °C. We modeled PAB into the colchicine site of tubulin, using the crystal structure 1SA0 that contains two αβ-tubulin heterodimers, both bound to a colchicinoid and to a stathmin fragment. The binding model of PAB revealed common pharmacophoric features between PAB and colchicinoids, not readily apparent from their chemical structures. Published by Elsevier Inc.

Constraints on the dark matter and dark energy interactions from weak lensing bispectrum tomography

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

An, Rui; Feng, Chang; Wang, Bin, E-mail: an_rui@sjtu.edu.cn, E-mail: chang.feng@uci.edu, E-mail: wang_b@sjtu.edu.cn

We estimate uncertainties of cosmological parameters for phenomenological interacting dark energy models using weak lensing convergence power spectrum and bispectrum. We focus on the bispectrum tomography and examine how well the weak lensing bispectrum with tomography can constrain the interactions between dark sectors, as well as other cosmological parameters. Employing the Fisher matrix analysis, we forecast parameter uncertainties derived from weak lensing bispectra with a two-bin tomography and place upper bounds on strength of the interactions between the dark sectors. The cosmic shear will be measured from upcoming weak lensing surveys with high sensitivity, thus it enables us to usemore » the higher order correlation functions of weak lensing to constrain the interaction between dark sectors and will potentially provide more stringent results with other observations combined.« less

Local Rademacher Complexity: sharper risk bounds with and without unlabeled samples.

PubMed

Oneto, Luca; Ghio, Alessandro; Ridella, Sandro; Anguita, Davide

2015-05-01

We derive in this paper a new Local Rademacher Complexity risk bound on the generalization ability of a model, which is able to take advantage of the availability of unlabeled samples. Moreover, this new bound improves state-of-the-art results even when no unlabeled samples are available. Copyright © 2015 Elsevier Ltd. All rights reserved.

Pair-Wise and Many-Body Dispersive Interactions Coupled to an Optimally Tuned Range-Separated Hybrid Functional.

PubMed

Agrawal, Piyush; Tkatchenko, Alexandre; Kronik, Leeor

2013-08-13

We propose a nonempirical, pair-wise or many-body dispersion-corrected, optimally tuned range-separated hybrid functional. This functional retains the advantages of the optimal-tuning approach in the prediction of the electronic structure. At the same time, it gains accuracy in the prediction of binding energies for dispersively bound systems, as demonstrated on the S22 and S66 benchmark sets of weakly bound dimers.

Reactivity of tris(acetylacetonato) iron(III) with tridentate [ONO] donor Schiff base as an access to newer mixed-ligand iron(III) complexes

NASA Astrophysics Data System (ADS)

Bhattacharjee, Chira R.; Goswami, Pankaj; Pramanik, Harun A. R.; Paul, Pradip C.; Mondal, Paritosh

2011-05-01

Two new mixed-ligand iron(III) complexes, [Fe(L n)(acac)(C 2H 5OH)] incorporating coordinated ethanol from the reaction solvent were accessed from the reaction of [Fe(acac) 3] with [ONO] donor dibasic tridentate unsymmetrical Schiff base ligands derived from condensation of 2-hydroxy-1-napthaldehyde with 2-aminophenol (H 2L 1) or 2-aminobenzoic acid (H 2L 2). The thermal study (TGA-DTA) provided evidence for weakly bound ethanol which is readily substituted by neutral N-donor molecule imidazole, benzimidazole or pyridine to produce an array of newer complexes, [Fe(L n)(acac)X] ( n = 1, 2; X = Im, Bim, Py). The compounds were characterized by elemental analyses, FT-IR, UV-vis, solution electrical conductivity, FAB mass, 1H and 13C NMR spectroscopy. Room temperature magnetic susceptibility measurements ( μeff ˜ 5.8 B.M.) are consistent with spin-free octahedral iron(III) complexes. Cyclic voltammetry of ethanol complexes revealed a quasi-reversible one electron redox response (Δ Ep > 100 mV) for the Fe(III)/Fe(II) couple. Low half wave redox potential ( E1/2) values suggested easy redox susceptibility. The ground state geometries of the ethanol and imidazole complexes have been ascertained to be distorted octahedral by density functional theory using DMol3 program at BLYP/DNP level.

The charge conserving Poisson-Boltzmann equations: Existence, uniqueness, and maximum principle

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

Lee, Chiun-Chang, E-mail: chlee@mail.nhcue.edu.tw

2014-05-15

The present article is concerned with the charge conserving Poisson-Boltzmann (CCPB) equation in high-dimensional bounded smooth domains. The CCPB equation is a Poisson-Boltzmann type of equation with nonlocal coefficients. First, under the Robin boundary condition, we get the existence of weak solutions to this equation. The main approach is variational, based on minimization of a logarithm-type energy functional. To deal with the regularity of weak solutions, we establish a maximum modulus estimate for the standard Poisson-Boltzmann (PB) equation to show that weak solutions of the CCPB equation are essentially bounded. Then the classical solutions follow from the elliptic regularity theorem.more » Second, a maximum principle for the CCPB equation is established. In particular, we show that in the case of global electroneutrality, the solution achieves both its maximum and minimum values at the boundary. However, in the case of global non-electroneutrality, the solution may attain its maximum value at an interior point. In addition, under certain conditions on the boundary, we show that the global non-electroneutrality implies pointwise non-electroneutrality.« less

Identification of RNA species in the RNA-toxin complex and structure of the complex in Clostridium botulinum type E.

PubMed

Kitamura, Masaru

2002-02-15

Clostridium botulinum type E toxin was isolated in the form of a complex with RNA(s) from bacterial cells. Characterization of the complexed RNA remains to be elucidated. The RNA is identified here as ribosomal RNA (rRNA) having 23S and 16S components. The RNA-toxin complexes were found to be made up of three types with different molecular sizes. The three types of RNA-toxin complex are toxin bound to both the 23S and 16S rRNA, toxin bound to the 16S rRNA and a small amount of 23S rRNA, and toxin bound only to the 16S rRNA. ©2002 Elsevier Science (USA).

Maternal drug use: evaluation of risks to breast-fed infants.

PubMed

Kirksey, A; Groziak, S M

1984-01-01

This paper, based on a review of the literature, evaluates the risks to infants of maternal drug use during lactation. The potential harm of a particular drug to the breastfed infant is related both to the complex mechanism of milk synthesis and secretion and the mode of passage of the drug from plasma into milk. The 1st part of the paper discusses mammary cell and milk synthesis, milk secretion and composition, the mode of passage of drugs into milk, and factors influencing drug concentrations in milk. Drug concentrations in milk are dependent on 6 major factors: drug dosage, proportion bound in plasma, molecular weight, lipid solubility, degree of ionization, and pH difference between plasma and milk. Drugs that are weak acids are ionized to a greater extent and are more protein-bound than weak alkaline drugs. The 2nd part of the paper evaluates the risks to breastfed infants of selected pharmacons. Some categories of drugs that contain pharmacons that should be limited or avoided by nursing mothers are alkylating agents, analgesics and anti-inflammatory agents, anticoagulants, anticonvulsants, anti-infective agents, central nervous system stimulants, hormones, laxatives, minerals, provitamins, psychotherapeutic agents, thyroid affecting agents, and vitamins. The following precautions are suggested to minimize the risks of potentially harmful pharmacons: 1) all unnecessary medications should be avoided by nrusing mothers; 2) if medication is necessary during lactation, drug dosage should be controlled and the infant should be monitored for adverse symptoms; 3) drugs should be administered shortly after breastfeeding and the interval prolonged before the next feeding; and 4) if the infant must be fed soon after a potentially harmful drug has been taken by the mother, bottle feeding is recommended.

A code for analysis of the fine structure in near-rigid weakly-bonded open-shell complexes that consist of a diatomic radical in a Σ3 state and a closed-shell molecule

NASA Astrophysics Data System (ADS)

Fawzy, Wafaa M.

2010-10-01

A FORTRAN code is developed for simulation and fitting the fine structure of a planar weakly-bonded open-shell complex that consists of a diatomic radical in a Σ3 electronic state and a diatomic or a polyatomic closed-shell molecule. The program sets up the proper total Hamiltonian matrix for a given J value and takes account of electron-spin-electron-spin, electron-spin rotation interactions, and the quartic and sextic centrifugal distortion terms within the complex. Also, R-dependence of electron-spin-electron-spin and electron-spin rotation couplings are considered. The code does not take account of effects of large-amplitude internal rotation of the diatomic radical within the complex. It is assumed that the complex has a well defined equilibrium geometry so that effects of large amplitude motion are negligible. Therefore, the computer code is suitable for a near-rigid rotor. Numerical diagonalization of the matrix provides the eigenvalues and the eigenfunctions that are necessary for calculating energy levels, frequencies, relative intensities of infrared or microwave transitions, and expectation values of the quantum numbers within the complex. Goodness of all the quantum numbers, with exception of J and parity, depends on relative sizes of the product of the rotational constants and quantum numbers (i.e. BJ, CJ, and AK), electron-spin-electron-spin, and electron-spin rotation couplings, as well as the geometry of the complex. Therefore, expectation values of the quantum numbers are calculated in the eigenfunctions basis of the complex. The computational time for the least squares fits has been significantly reduced by using the Hellman-Feynman theory for calculating the derivatives. The computer code is useful for analysis of high resolution infrared and microwave spectra of a planar near-rigid weakly-bonded open-shell complex that contains a diatomic fragment in a Σ3 electronic state and a closed-shell molecule. The computer program was successfully applied to analysis and fitting the observed high resolution infrared spectra of the O 2sbnd HF/O 2sbnd DF and O 2sbnd N 2O complexes. Test input file for simulation and fitting the high resolution infrared spectrum of the O 2sbnd DF complex is provided. Program summaryProgram title: TSIG_COMP Catalogue identifier: AEGM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 10 030 No. of bytes in distributed program, including test data, etc.: 51 663 Distribution format: tar.gz Programming language: Fortran 90, free format Computer: SGI Origin 3400, workstations and PCs Operating system: Linux, UNIX and Windows (see Restrictions below) RAM: Case dependent Classification: 16.2 Nature of problem: TSIG_COMP calculates frequencies, relative intensities, and expectation values of the various quantum numbers and parities of bound states involved in allowed ro-vibrational transitions in semi-rigid planar weakly-bonded open-shell complexes. The complexes of interest contain a free radical in a Σ3 state and a closed-shell partner, where the electron-spin-electron-spin interaction, electron-spin rotation interaction, and centrifugal forces significantly modify the spectral patterns. To date, ab initio methods are incapable of taking these effects into account to provide accurate predictions for the ro-vibrational energy levels of the complexes of interest. In the TSIG_COMP program, the problem is solved by using the proper effective Hamiltonian and molecular basis set. Solution method: The program uses a Hamiltonian operator that takes into account vibration, end-over-end rotation, electron-spin-electron-spin and electron-spin rotation interactions as well as the various centrifugal distortion terms. The Hamiltonian operator and the molecular basis set are used to set up the Hamiltonian matrix in the inertial axis system of the complex of interest. Diagonalization of the Hamiltonian matrix provides the eigenvalues and the eigenfunctions for the bound ro-vibrational states. These eigenvalues and eigenfunctions are used to calculate frequencies and relative intensities of the allowed infrared or microwave transitions as well as expectation values of all the quantum numbers and parities of states involved in the transitions. The program employs the method of least squares fits to fit the observed frequencies to the calculated frequencies to provide the molecular parameters that determine the geometry of the complex of interest. Restrictions: The number of transitions and parameters included in the fits is limited to 80 parameters and 200 transitions. However, these numbers can be increased by adjusting dimensions of the arrays (not recommended). Running the program under MS windows is recommended for simulations of any number of transitions and for fitting a relatively small number of parameters and transitions (maximum 15 parameters and 82 transitions), for fitting larger number of parameters run time error may occur. Because spectra of weakly bonded complexes are recorded at low temperatures, in most of cases fittings can be performed under MS windows. Running time: Problem-dependent. The provided test input for Linux fits 82 transitions and 21 parameters, the actual run time is 62 minutes. The provided test input file for MS windows fits 82 transitions and 15 parameters; the actual runtime is 5 minutes.

Polystyrene bound oxidovanadium(IV) and dioxidovanadium(V) complexes of histamine derived ligand for the oxidation of methyl phenyl sulfide, diphenyl sulfide and benzoin.

PubMed

Maurya, Mannar R; Arya, Aarti; Kumar, Amit; Pessoa, João Costa

2009-03-28

Ligand Hsal-his (I) derived from salicylaldehyde and histamine has been covalently bound to chloromethylated polystyrene cross-linked with 5% divinylbenzene. Upon treatment with [VO(acac)(2)] in DMF, the polystyrene-bound ligand (abbreviated as PS-Hsal-his, II) gave the stable polystyrene-bound oxidovanadium(iv) complex PS-[V(IV)O(sal-his)(acac)] , which upon oxidation yielded the dioxidovanadium(v) PS-[V(V)O(2)(sal-his)] complex. The corresponding non polymer-bound complexes [V(IV)O(sal-his)(acac)] and [V(V)O(2)(sal-his)] have also been obtained. These complexes have been characterised by IR, electronic, (51)V NMR and EPR spectral studies, and thermal as well as scanning electron micrograph studies. Complexes and have been used as a catalyst for the oxidation of methyl phenyl sulfide, diphenyl sulfide and benzoin with 30% H(2)O(2) as oxidant. Under the optimised reaction conditions, a maximum of 93.8% conversion of methyl phenyl sulfide with 63.7% selectivity towards methyl phenyl sulfoxide and 36.3% towards methyl phenyl sulfone has been achieved in 2 h with 2 . Under similar conditions, diphenyl sulfide gave 83.4% conversion where selectivity of reaction products varied in the order: diphenyl sulfoxide (71.8%) > diphenyl sulfone (28.2%). A maximum of 91.2% conversion of benzoin has been achieved within 6 h, and the selectivities of reaction products are: methylbenzoate (37.0%) > benzil (30.5%) > benzaldehyde-dimethylacetal (22.5%) > benzoic acid (8.1%). The PS-bound complex, 1 exhibits very comparable catalytic potential. These polymer-anchored heterogeneous catalysts do not leach during catalytic action, are recyclable and show higher catalytic activity and turnover frequency than the corresponding non polymer-bound complexes. EPR and (51)V NMR spectroscopy was used to characterise methanolic solutions of 3 and 4 and to identify species formed upon addition of H(2)O(2) and/or acid and/or methyl phenyl sulfide.

The Charm and Beauty of Strong Interactions

NASA Astrophysics Data System (ADS)

El-Bennich, Bruno

2018-01-01

We briefly review common features and overlapping issues in hadron and flavor physics focussing on continuum QCD approaches to heavy bound states, their mass spectrum and weak decay constants in different strong interaction models.

Population of Nuclei Via 7Li-Induced Binary Reactions

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

Clark, Rodney M.; Phair, Larry W.; Descovich, M.

2005-08-08

The authors have investigated the population of nuclei formed in binary reactions involving {sup 7}Li beams on targets of {sup 160}Gd and {sup 184}W. The {sup 7}Li + {sup 184}W data were taken in the first experiment using the LIBERACE Ge-array in combination with the STARS Si {Delta}E-E telescope system at the 88-Inch Cyclotron of the Lawrence Berkeley National Laboratory. By using the Wilczynski binary transfer model, in combination with a standard evaporation model, they are able to reproduce the experimental results. This is a useful method for predicting the population of neutron-rich heavy nuclei formed in binary reactions involvingmore » beams of weakly bound nuclei formed in binary reactions involving beams of weakly bound nuclei and will be of use in future spectroscopic studies.« less

CO Depletion: A Microscopic Perspective

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

Cazaux, S.; Martín-Doménech, R.; Caro, G. M. Muñoz

In regions where stars form, variations in density and temperature can cause gas to freeze out onto dust grains forming ice mantles, which influences the chemical composition of a cloud. The aim of this paper is to understand in detail the depletion (and desorption) of CO on (from) interstellar dust grains. Experimental simulations were performed under two different (astrophysically relevant) conditions. In parallel, Kinetic Monte Carlo simulations were used to mimic the experimental conditions. In our experiments, CO molecules accrete onto water ice at temperatures below 27 K, with a deposition rate that does not depend on the substrate temperature.more » During the warm-up phase, the desorption processes do exhibit subtle differences, indicating the presence of weakly bound CO molecules, therefore highlighting a low diffusion efficiency. IR measurements following the ice thickness during the TPD confirm that diffusion occurs at temperatures close to the desorption. Applied to astrophysical conditions, in a pre-stellar core, the binding energies of CO molecules, ranging between 300 and 850 K, depend on the conditions at which CO has been deposited. Because of this wide range of binding energies, the depletion of CO as a function of A{sub V} is much less important than initially thought. The weakly bound molecules, easily released into the gas phase through evaporation, change the balance between accretion and desorption, which result in a larger abundance of CO at high extinctions. In addition, weakly bound CO molecules are also more mobile, and this could increase the reactivity within interstellar ices.« less

Selenophene transition metal complexes

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

White, Carter James

1994-07-27

This research shows that selenophene transition metal complexes have a chemistry that is similar to their thiophene analogs. Selenophene coordination has been demonstrated and confirmed by molecular structure in both the η 5- and the η 1(Se)-coordination modes. The reaction chemistry of selenophene complexes closely resembles that of the analogous thiophene complexes. One major difference, however, is that selenophene is a better donor ligand than thiophene making the selenophene complexes more stable than the corresponding thiophene complexes. The 77Se NMR chemical shift values for selenophene complexes fall within distinct regions primarily depending on the coordination mode of the selenophene ligand.more » In the final paper, the C-H bond activation of η 1(S)-bound thiophenes, η 1(S)-benzothiophene and η 1(Se)-bound selenophenes has been demonstrated. The deprotonation and rearrangement of the η 1(E)-bound ligand to the carbon bound L-yl complex readily occurs in the presence of base. Reprotonation with a strong acid gives a carbene complex that is unreactive towards nucleophilic attack at the carbene carbon and is stable towards exposure to air. The molecular structure of [Cp(NO)(PPh 3)Re(2-benzothioenylcarbene)]O 3SCF 3 was determined and contains a Re-C bond with substantial double bond character. Methyl substitution for the thienylcarbene or selenylcarbene gives a carbene that rearranges thermally to give back the η 1(E)-bound complex. Based on these model reactions, a new mechanism for the H/D exchange of thiophene over the hydrodesulfurization catalyst has been proposed.« less

Long-distance measurement-device-independent quantum key distribution with coherent-state superpositions.

PubMed

Yin, H-L; Cao, W-F; Fu, Y; Tang, Y-L; Liu, Y; Chen, T-Y; Chen, Z-B

2014-09-15

Measurement-device-independent quantum key distribution (MDI-QKD) with decoy-state method is believed to be securely applied to defeat various hacking attacks in practical quantum key distribution systems. Recently, the coherent-state superpositions (CSS) have emerged as an alternative to single-photon qubits for quantum information processing and metrology. Here, in this Letter, CSS are exploited as the source in MDI-QKD. We present an analytical method that gives two tight formulas to estimate the lower bound of yield and the upper bound of bit error rate. We exploit the standard statistical analysis and Chernoff bound to perform the parameter estimation. Chernoff bound can provide good bounds in the long-distance MDI-QKD. Our results show that with CSS, both the security transmission distance and secure key rate are significantly improved compared with those of the weak coherent states in the finite-data case.

Upper Bound on Diffusivity

NASA Astrophysics Data System (ADS)

Hartman, Thomas; Hartnoll, Sean A.; Mahajan, Raghu

2017-10-01

The linear growth of operators in local quantum systems leads to an effective light cone even if the system is nonrelativistic. We show that the consistency of diffusive transport with this light cone places an upper bound on the diffusivity: D ≲v2τeq. The operator growth velocity v defines the light cone, and τeq is the local equilibration time scale, beyond which the dynamics of conserved densities is diffusive. We verify that the bound is obeyed in various weakly and strongly interacting theories. In holographic models, this bound establishes a relation between the hydrodynamic and leading nonhydrodynamic quasinormal modes of planar black holes. Our bound relates transport data—including the electrical resistivity and the shear viscosity—to the local equilibration time, even in the absence of a quasiparticle description. In this way, the bound sheds light on the observed T -linear resistivity of many unconventional metals, the shear viscosity of the quark-gluon plasma, and the spin transport of unitary fermions.

Complexes of monocationic Group 13 elements with pentaphospha- and pentaarsaferrocene.

PubMed

Fleischmann, Martin; Welsch, Stefan; Krauss, Hannes; Schmidt, Monika; Bodensteiner, Michael; Peresypkina, Eugenia V; Sierka, Marek; Gröger, Christian; Scheer, Manfred

2014-03-24

Reactions of the sandwich complexes [Cp*Fe(η(5)-E5)] (Cp*=η(5)-C5Me5; E=P (1), As (2)) with the monovalent Group 13 metals Tl(+), In(+), and Ga(+) containing the weakly coordinating anion [TEF] ([TEF]=[Al{OC(CF3)3}4](-)) are described. Here, the one-dimensional coordination polymers [M(μ,η(5):η(1 -E5 FeCp*)3]n [TEF]n (E=P, M=Tl (3 a), In (3 b), Ga (3 c); E=As, M=Tl (4 a), In (4 b)) are obtained as sole products in good yields. All products were analyzed by single-crystal X-ray diffraction, revealing a similar assembly of the products with η(5)-bound E5 ligands and very weak σ-interactions between one P or As atom of the ring to the neighbored Group 13 metal cation. By exchanging the [TEF] anion of 4 a for the larger [FAl] anion ([FAl]=[FAl{OC6F10(C6F5)}3](-)), the coordination compound [Tl{(η(5)-As5)FeCp*}3][FAl] (5) without any σ-interactions of the As5-ring is obtained. All products are readily soluble in CH2 Cl2 and exhibit a dynamic coordination behavior in solution, which is supported by NMR spectroscopy and ESI-MS spectrometry as well as by osmometric molecular-weight determination. For a better understanding of the proceeding equilibrium DFT calculations of the cationic complexes were performed for the gas phase and in solution. Furthermore, the (31)P{(1)H} magic-angle spinning (MAS) NMR spectra of 3 a-c are presented and the first crystal structure of the starting material 2 was determined. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio study of weakly bound halogen complexes: RX⋯PH3.

PubMed

Georg, Herbert C; Fileti, Eudes E; Malaspina, Thaciana

2013-01-01

Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%).

Biomimetics of [NiFe]-Hydrogenase: Nickel- or Iron-Centered Proton Reduction Catalysis?

PubMed

Tang, Hao; Hall, Michael B

2017-12-13

The [NiFe] hydrogenase (H2ase) has been characterized in the Ni-R state with a hydride bridging between Fe and Ni but displaced toward the Ni. In nearly all of the synthetic Ni-R models reported so far, the hydride ligand is either displaced toward Fe, or terminally bound to Fe. Recently, a structural and functional [NiFe]-H2ase mimic ( Nat. Chem. 2016 , 8 , 1054 - 1060 ) was reported to produce H 2 catalytically via EECC mechanism through a Ni-centered hydride intermediate like the enzyme. Here, a comprehensive DFT study shows a much lower energy route via an E[ECEC] mechanism through an Fe-centered hydride intermediate. Although catalytic H 2 production occurs at the potential corresponding to the complex's second reduction, a third electron is needed to induce the second proton addition from the weak acid. The first two-electron reductions and a proton addition produce a semibridging hydride with a short Fe-H bond like other structured [NiFe]-biomimetics, but this species is not basic enough to add another proton from the weak acid without the third electron. The calculated mechanism provides insight into the origin of this structure in the enzyme.

Total enantioselectivity in the DNA binding of the dinuclear ruthenium(II) complex [[Ru(Me2bpy)2]2(mu-bpm)]4+ [bpm = 2,2'-bipyrimidine; Me2bpy = 4,4'-dimethyl-2,2'-bipyridine].

PubMed

Smith, Jayden A; Collins, J Grant; Patterson, Bradley T; Keene, F Richard

2004-05-07

The binding of the three stereoisomers (DeltaDelta-, LambdaLambda- and DeltaLambda-) of the dinuclear ruthenium(II) complex [[Ru(Me2bpy)2]2(mu-bpm)]4+ [Me2bpy = 4,4'-dimethyl-2,2'-bipyridine; bpm = 2,2'-bipyrimidine] to a tridecanucleotide containing a single adenine bulge has been studied by 1H NMR spectroscopy. The addition of the DeltaDelta-isomer to d(CCGAGAATTCCGG)2 induced significant chemical shift changes for the base and sugar resonances of the residues at the bulge site (G3A4G5/C11C10), whereas small shifts were observed upon addition of the enantiomeric LambdaLambda-form. NOESY spectra of the tridecanucleotide bound with the DeltaDelta-isomer revealed intermolecular NOE's between the metal complex and the nucleotide residues at the bulge site, while only weak NOE's were observed to terminal residues to the LambdaLambda-form. Competitive binding studies were performed where both enantiomers were simultaneously added to the tridecanucleotide, and for all ratios of the two stereoisomers the DeltaDelta-isomer remained selectively bound at the bulge site with the LambdaLambda-enantiomer localised at the terminal regions of the tridecanucleotide. The meso-diastereoisomer (DeltaLambda) was found to bind to the tridecanucleotide with characteristics intermediate between the DeltaDelta- and LambdaLambda-enantiomers of the rac form. Two distinct sets of metal complex resonances were observed, with one set having essentially the same shift as the free metal complex, whilst the other set of resonances exhibited significant shifts. The NOE data indicated that the meso-diastereoisomer does not bind as selectively as the DeltaDelta-isomer, with NOE's observed to a greater number of nucleotide residues compared to the DeltaDelta-form. This study provides a rare example of total enantioselectivity in the binding of an inert transition metal complex to DNA, produced by the shape recognition of both ruthenium(II) centres.

Weak Convergence of Bounded Influence Regression Estimates with Applications.

DTIC Science & Technology

1980-04-01

for bounded influence regression M-estimates and apply the results to sequential clinical trials , withI special reference to repeated significance...AUTHOR(s) S. CONTRACT O&GRANT NUIMBER(s) ,’ Raymond J. Carrol avv David/uppert v .. AFOSR-80-0 9. PERFORMING ORGANIZATION NAME AND ADDRESS PRO AM I...THIS PAGE (*%ten [)at& Eke 7") 2 1. Introduction. Our primary concern is the comparison of two treatments in a clinical setting, although our results

Midfield wireless powering of subwavelength autonomous devices.

PubMed

Kim, Sanghoek; Ho, John S; Poon, Ada S Y

2013-05-17

We obtain an analytical bound on the efficiency of wireless power transfer to a weakly coupled device. The optimal source is solved for a multilayer geometry in terms of a representation based on the field equivalence principle. The theory reveals that optimal power transfer exploits the properties of the midfield to achieve efficiencies far greater than conventional coil-based designs. As a physical realization of the source, we present a slot array structure whose performance closely approaches the theoretical bound.

Emergence of a confined state in a weakly bent wire

NASA Astrophysics Data System (ADS)

Granot, Er'El

2002-06-01

In this paper we use a simple straightforward technique to investigate the emergence of a bound state in a weakly bent wire. We show that the bend behaves like an infinitely shallow potential well, and in the limit of small bending angle (φ<<1) and low energy the bend can be presented by a simple one-dimensional δ-function potential, V(x)=-(2(cb)φ2)δ(x) where cb≅2.1.

Reconstitution of R-spondin:LGR4:ZNRF3 adult stem cell growth factor signaling complexes with recombinant proteins produced in Escherichia coli.

PubMed

Moad, Heather E; Pioszak, Augen A

2013-10-15

R-Spondins are secreted glycoproteins (RSPO1-RSPO4) that have proliferative effects on adult stem cells by potentiating Wnt signaling. RSPO actions are mediated by the leucine-rich repeat (LRR)-containing seven-transmembrane receptors LGR4-LGR6 and the transmembrane E3 ubiquitin ligases ZNRF3 and RNF43. Here, we present a methodology for the bacterial expression and purification of the signaling competent, cysteine-rich Fu1-Fu2 domains of the four human RSPOs, a fragment of the human LGR4 extracellular domain (ECD) containing LRR1-14, and the human ZNRF3 ECD. In a cell-based signaling assay, the nonglycosylated RSPOs enhanced low-dose Wnt3a signaling with potencies comparable to those of mammalian cell-produced RSPOs and RSPO2 and -3 were more potent than RSPO1 and -4. LGR4 LRR1-14 and ZNRF3 ECD inhibited RSPO2-enhanced Wnt3a signaling. The RSPOs bound LGR4 LRR1-14 with nanomolar affinities that decreased in the following order in a time-resolved fluorescence resonance energy transfer (TR-FRET) assay: RSPO4 > RSPO2 > RSPO3 > RSPO1. RSPO-receptor interactions were further characterized with a native gel electrophoretic mobility shift assay, which corroborated the RSPO-LGR4 TR-FRET results and indicated that RSPOs weakly bound ZNRF3 with affinities that decreased in the following order: RSPO2 > RSPO3 > RSPO1. RSPO4:ZNRF3 complexes were not detected. Lastly, ternary RSPO:LGR4:ZNRF3 complexes were detected for RSPO2 and -3. Our results indicate that RSPO and LGR4 N-glycans are dispensable for function, demonstrate RSPO-mediated ternary complex formation, and suggest that the stronger signaling potencies of RSPO2 and -3 result from their strong binding of both receptors. Our unique protein production methodology may provide a cost-effective source of recombinant RSPOs for regenerative medicine applications.

Mirror energy difference and the structure of loosely bound proton-rich nuclei around A =20

NASA Astrophysics Data System (ADS)

Yuan, Cenxi; Qi, Chong; Xu, Furong; Suzuki, Toshio; Otsuka, Takaharu

2014-04-01

The properties of loosely bound proton-rich nuclei around A =20 are investigated within the framework of the nuclear shell model. In these nuclei, the strength of the effective interactions involving the loosely bound proton s1/2 orbit is significantly reduced in comparison with that of those in their mirror nuclei. We evaluate the reduction of the effective interaction by calculating the monopole-based-universal interaction (VMU) in the Woods-Saxon basis. The shell-model Hamiltonian in the sd shell, such as USD, can thus be modified to reproduce the binding energies and energy levels of the weakly bound proton-rich nuclei around A =20. The effect of the reduction of the effective interaction on the structure and decay properties of these nuclei is also discussed.

Observation of three-photon bound states in a quantum nonlinear medium

NASA Astrophysics Data System (ADS)

Liang, Qi-Yu; Venkatramani, Aditya V.; Cantu, Sergio H.; Nicholson, Travis L.; Gullans, Michael J.; Gorshkov, Alexey V.; Thompson, Jeff D.; Chin, Cheng; Lukin, Mikhail D.; Vuletić, Vladan

2018-02-01

Bound states of massive particles, such as nuclei, atoms, or molecules, constitute the bulk of the visible world around us. By contrast, photons typically only interact weakly. We report the observation of traveling three-photon bound states in a quantum nonlinear medium where the interactions between photons are mediated by atomic Rydberg states. Photon correlation and conditional phase measurements reveal the distinct bunching and phase features associated with three-photon and two-photon bound states. Such photonic trimers and dimers possess shape-preserving wave functions that depend on the constituent photon number. The observed bunching and strongly nonlinear optical phase are described by an effective field theory of Rydberg-induced photon-photon interactions. These observations demonstrate the ability to realize and control strongly interacting quantum many-body states of light.

Entropic bounds on currents in Langevin systems

NASA Astrophysics Data System (ADS)

Dechant, Andreas; Sasa, Shin-ichi

2018-06-01

We derive a bound on generalized currents for Langevin systems in terms of the total entropy production in the system and its environment. For overdamped dynamics, any generalized current is bounded by the total rate of entropy production. We show that this entropic bound on the magnitude of generalized currents imposes power-efficiency tradeoff relations for ratchets in contact with a heat bath: Maximum efficiency—Carnot efficiency for a Smoluchowski-Feynman ratchet and unity for a flashing or rocking ratchet—can only be reached at vanishing power output. For underdamped dynamics, while there may be reversible currents that are not bounded by the entropy production rate, we show that the output power and heat absorption rate are irreversible currents and thus obey the same bound. As a consequence, a power-efficiency tradeoff relation holds not only for underdamped ratchets but also for periodically driven heat engines. For weak driving, the bound results in additional constraints on the Onsager matrix beyond those imposed by the second law. Finally, we discuss the connection between heat and entropy in a nonthermal situation where the friction and noise intensity are state dependent.

Probing gravitational parity violation with gravitational waves from stellar-mass black hole binaries

NASA Astrophysics Data System (ADS)

Yagi, Kent; Yang, Huan

2018-05-01

The recent discovery of gravitational-wave events has offered us unique test beds of gravity in the strong and dynamical field regime. One possible modification to General Relativity is the gravitational parity violation that arises naturally from quantum gravity. Such parity violation gives rise to the so-called amplitude birefringence in gravitational waves, in which one of the circularly polarized modes is amplified while the other one is suppressed during their propagation. In this paper, we study how well one can measure gravitational parity violation via the amplitude birefringence effect of gravitational waves sourced by stellar-mass black hole binaries. We choose Chern-Simons gravity as an example and work within an effective field theory formalism to ensure that the approximate theory is well posed. We consider gravitational waves from both individual sources and stochastic gravitational-wave backgrounds. Regarding bounds from individual sources, we estimate such bounds using a Fisher analysis and carry out Monte Carlo simulations by randomly distributing sources over their sky location and binary orientation. We find that the bounds on the scalar field evolution in Chern-Simons gravity from the recently discovered gravitational-wave events are too weak to satisfy the weak Chern-Simons approximation, while aLIGO with its design sensitivity can place meaningful bounds. Regarding bounds from stochastic gravitational-wave backgrounds, we set the threshold signal-to-noise ratio for detection of the parity-violation mode as 5 and estimate projected bounds with future detectors assuming that signals are consistent with no parity violation. In an ideal situation in which all the source parameters and binary black hole merger-rate history are known a priori, we find that a network of two third-generation detectors is able to place bounds that are comparable to or slightly stronger than binary pulsar bounds. In a more realistic situation in which one does not have such information beforehand, approximate bounds can be derived if the regular parity-insensitive mode is detected and the peak redshift of the merger-rate history is known theoretically. Since gravitational-wave observations probe either the difference in parity violation between the source and the detector (with individual sources) or the line-of-sight cosmological integration of the scalar field (with gravitational-wave backgrounds), such bounds are complementary to local measurements from solar system experiments and binary pulsar observations.

Quantitative and qualitative approaches in educational research — problems and examples of controlled understanding through interpretive methods

NASA Astrophysics Data System (ADS)

Neumann, Karl

1987-06-01

In the methodological discussion of recent years it has become apparent that many research problems, including problems relating to the theory of educational science, cannot be solved by using quantitative methods. The multifaceted aspects of human behaviour and all its environment-bound subtle nuances, especially the process of education or the development of identity, cannot fully be taken into account within a rigid neopositivist approach. In employing the paradigm of symbolic interactionism as a suitable model for the analysis of processes of education and formation, the research has generally to start out from complex reciprocal social interactions instead of unambigious connections of causes. In analysing several particular methodological problems, the article demonstrates some weaknesses of quantitative approaches and then shows the advantages in and the necessity for using qualitative research tools.

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

Scott, F.; Stec, B; Pop, C

The death inducing signalling complex (DISC) formed by Fas receptor, FADD (Fas-associated death domain protein) and caspase 8 is a pivotal trigger of apoptosis1, 2, 3. The Fas-FADD DISC represents a receptor platform, which once assembled initiates the induction of programmed cell death. A highly oligomeric network of homotypic protein interactions comprised of the death domains of Fas and FADD is at the centre of DISC formation4, 5. Thus, characterizing the mechanistic basis for the Fas-FADD interaction is crucial for understanding DISC signalling but has remained unclear largely because of a lack of structural data. We have successfully formed andmore » isolated the human Fas-FADD death domain complex and report the 2.7 A crystal structure. The complex shows a tetrameric arrangement of four FADD death domains bound to four Fas death domains. We show that an opening of the Fas death domain exposes the FADD binding site and simultaneously generates a Fas-Fas bridge. The result is a regulatory Fas-FADD complex bridge governed by weak protein-protein interactions revealing a model where the complex itself functions as a mechanistic switch. This switch prevents accidental DISC assembly, yet allows for highly processive DISC formation and clustering upon a sufficient stimulus. In addition to depicting a previously unknown mode of death domain interactions, these results further uncover a mechanism for receptor signalling solely by oligomerization and clustering events.« less

Hyperquarks and bosonic preon bound states

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

Schmid, Michael L.; Buchmann, Alfons J.

2009-11-01

In a model in which leptons, quarks, and the recently introduced hyperquarks are built up from two fundamental spin-(1/2) preons, the standard model weak gauge bosons emerge as preon bound states. In addition, the model predicts a host of new composite gauge bosons, in particular, those responsible for hyperquark and proton decay. Their presence entails a left-right symmetric extension of the standard model weak interactions and a scheme for a partial and grand unification of nongravitational interactions based on, respectively, the effective gauge groups SU(6){sub P} and SU(9){sub G}. This leads to a prediction of the Weinberg angle at lowmore » energies in good agreement with experiment. Furthermore, using evolution equations for the effective coupling strengths, we calculate the partial and grand unification scales, the hyperquark mass scale, as well as the mass and decay rate of the lightest hyperhadron.« less

An Onsager Singularity Theorem for Turbulent Solutions of Compressible Euler Equations

NASA Astrophysics Data System (ADS)

Drivas, Theodore D.; Eyink, Gregory L.

2017-12-01

We prove that bounded weak solutions of the compressible Euler equations will conserve thermodynamic entropy unless the solution fields have sufficiently low space-time Besov regularity. A quantity measuring kinetic energy cascade will also vanish for such Euler solutions, unless the same singularity conditions are satisfied. It is shown furthermore that strong limits of solutions of compressible Navier-Stokes equations that are bounded and exhibit anomalous dissipation are weak Euler solutions. These inviscid limit solutions have non-negative anomalous entropy production and kinetic energy dissipation, with both vanishing when solutions are above the critical degree of Besov regularity. Stationary, planar shocks in Euclidean space with an ideal-gas equation of state provide simple examples that satisfy the conditions of our theorems and which demonstrate sharpness of our L 3-based conditions. These conditions involve space-time Besov regularity, but we show that they are satisfied by Euler solutions that possess similar space regularity uniformly in time.

On the Singular Incompressible Limit of Inviscid Compressible Fluids

NASA Astrophysics Data System (ADS)

Secchi, P.

We consider the Euler equations of barotropic inviscid compressible fluids in a bounded domain. It is well known that, as the Mach number goes to zero, the compressible flows approximate the solution of the equations of motion of inviscid, incompressible fluids. In this paper we discuss, for the boundary case, the different kinds of convergence under various assumptions on the data, in particular the weak convergence in the case of uniformly bounded initial data and the strong convergence in the norm of the data space.

Interface with weakly singular points always scatter

NASA Astrophysics Data System (ADS)

Li, Long; Hu, Guanghui; Yang, Jiansheng

2018-07-01

Assume that a bounded scatterer is embedded into an infinite homogeneous isotropic background medium in two dimensions. The refractive index function is supposed to be piecewise constant. If the scattering interface contains a weakly singular point, we prove that the scattered field cannot vanish identically. This implies the absence of non-scattering energies for piecewise analytic interfaces with one singular point. Local uniqueness is obtained for shape identification problems in inverse medium scattering with a single far-field pattern.

Intermolecular dissociation energies of dispersively bound complexes of aromatics with noble gases and nitrogen

NASA Astrophysics Data System (ADS)

Knochenmuss, Richard; Sinha, Rajeev K.; Leutwyler, Samuel

2018-04-01

We measured accurate intermolecular dissociation energies D0 of the supersonic jet-cooled complexes of 1-naphthol (1NpOH) with the noble gases Ne, Ar, Kr, and Xe and with N2, using the stimulated-emission pumping resonant two-photon ionization method. The ground-state values D0(S0) for the 1NpOHṡS complexes with S= Ar, Kr, Xe, and N2 were bracketed to be within ±3.5%; they are 5.67 ± 0.05 kJ/mol for S = Ar, 7.34 ± 0.07 kJ/mol for S = Kr, 10.8 ± 0.28 kJ/mol for S = Xe, 6.67 ± 0.08 kJ/mol for isomer 1 of the 1NpOHṡN2 complex, and 6.62 ± 0.22 kJ/mol for the corresponding isomer 2. For S = Ne, the upper limit is D0 < 3.36 kJ/mol. The dissociation energies increase by 1%-5% upon S0 → S1 excitation of the complexes. Three dispersion-corrected density functional theory (DFT-D) methods (B97-D3, B3LYP-D3, and ωB97X-D) predict that the most stable form of these complexes involves dispersive binding to the naphthalene "face." A more weakly bound edge isomer is predicted in which the S moiety is H-bonded to the OH group of 1NpOH; however, no edge isomers were observed experimentally. The B97-D3 calculated dissociation energies D0(S0) of the face complexes with Ar, Kr, and N2 agree with the experimental values within <5%, but the D0(S0) for Xe is 12% too low. The B3LYP-D3 and ωB97X-D calculated D0(S0) values exhibit larger deviations to both larger and smaller dissociation energies. For comparison to 1-naphthol, we calculated the D0(S0) of the carbazole complexes with S = Ne, Ar, Kr, Xe, and N2 using the same DFT-D methods. The respective experimental values have been previously determined to be within <2%. Again, the B97-D3 results are in the best overall agreement with experiment.

Hypotensive Effect and Accumulation of Dinitrosyl Iron Complexes in Blood and Tissues after Intravenous and Subcutaneous Injection.

PubMed

Timoshin, A A; Lakomkin, V L; Abramov, A A; Ruuge, E K; Vanin, A F

2016-12-01

Subcutaneous injection of Oxacom with glutathione-bound dinitrosyl iron complex as the active principle produced a slower drop of mean BP and longer accumulation of protein-bound dinitrosyl iron complexes in whole blood and tissues than intravenous injection of this drug, while durations of hypotensive effect in both cases were practically identical. In contrast to intravenous injection of the drug, its subcutaneous administration was not characterized by a high concentration of protein-bound dinitrosyl iron complexes in the blood at the onset of experiment; in addition, accumulation of these NO forms in the lungs was more pronounced after subcutaneous injection than after intravenous one.

In-vitro evaluation of ion-exchange microspheres for the sustained release of liposomal-adenoviral conjugates.

PubMed

Steel, Jason C; Cavanagh, Heather M A; Burton, Mark A; Dingwall, Daniel; Kalle, Wouter H J

2004-03-24

This study looks at the development of a novel combination vector consisting of adenovirus conjugated to liposomes (AL complexes) bound to cation-exchanging microspheres (MAL complexes). With adenovirus having a net negative charge and the liposomes a net positive charge it was possible to modify the net charge of the AL complexes by varying the concentrations of adenovirus to liposomes. The modification of the net charge resulted in altered binding and release characteristics. Of the complexes tested, the 5:1 and 2:1 ratio AL complexes were able to be efficiently bound by the microspheres and exhibited sustained release over 24 h. The 1:1 and 1:2 AL complexes, however, bound poorly to the microspheres and were rapidly released. In addition the MAL complexes also were able to reduce the toxicity of the AL complexes, which was seen with the 10:1 ratio. The AL complexes showed considerably more toxicity alone than in combination with microspheres, highlighting a potential benefit of this vector.

Lanthanide chelates of (bis)-hydroxymethyl-substituted DTTA with potential application as contrast agents in magnetic resonance imaging.

PubMed

Silvério, Sara; Torres, Susana; Martins, André F; Martins, José A; André, João P; Helm, Lothar; Prata, M Isabel M; Santos, Ana C; Geraldes, Carlos F G C

2009-06-28

A novel bis-hydroxymethyl-substituted DTTA chelator N'-Bz-C(4,4')-(CH(2)OH)(2)-DTTA () and its DTPA analogue C(4,4')-(CH(2)OH)(2)-DTPA () were synthesized and characterized. A variable-temperature (1)H NMR spectroscopy study of the solution dynamics of their diamagnetic (La) and paramagnetic (Sm, Eu) Ln(3+) complexes showed them to be rigid when compared with analogous Ln(3+)-DTTA and Ln(3+)-DTPA complexes, as a result of their C(4,4')-(CH(2)OH)(2) ligand backbone substitution. The parameters that govern the water (1)H relaxivity of the [Gd()(H(2)O)(2)](-) and [Gd()(H(2)O)](2-) complexes were obtained by (17)O and (1)H NMR relaxometry. While the relaxometric behaviour of the [Gd()(H(2)O)](2-) complex is very similar to the parent [Gd(DTPA)(H(2)O)](2-) system, the [Gd()(H(2)O)(2)](-) complex displays higher relaxivity, due to the presence of two inner sphere water molecules and an accelerated, near optimal water exchange rate. The [Gd()(H(2)O)(2)](-) complex interacts weakly with human serum albumin (HSA), and its fully bound relaxivity is limited by slow water exchange, as monitored by (1)H NMR relaxometry. This complex interacts weakly with phosphate, but does not form ternary complexes with bidentate bicarbonate and l-lactate anions, indicating that the two inner-sphere water molecules of the [Gd()(H(2)O)(2)](-) complex are not located in adjacent positions in the coordination sphere of the Gd(3+) ion. The transmetallation reaction rate of [Gd()(H(2)O)(2)](-) with Zn(2+) in phosphate buffer solution (pH 7.0) was measured to be similar to that of the backbone unsubstituted [Gd(DTTA-Me)(H(2)O)(2)](-), but twice faster than for [Gd(DTPA-BMA)(H(2)O)]. The in vivo biodistribution studies of the (153)Sm(3+)-labelled ligand () in Wistar rats reveal slow blood elimination and short term fixation in various organs, indicating some dissociation. The bis-hydroxymethyl-substituted DTTA skeleton can be seen as a new lead for the synthesis of high relaxivity contrast agents, although its low thermodynamic and kinetic stability will limit its use to in vitro and animal studies.

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9.

PubMed

Singh, Digvijay; Sternberg, Samuel H; Fei, Jingyi; Doudna, Jennifer A; Ha, Taekjip

2016-09-14

Binding specificity of Cas9-guide RNA complexes to DNA is important for genome-engineering applications; however, how mismatches influence target recognition/rejection kinetics is not well understood. Here we used single-molecule FRET to probe real-time interactions between Cas9-RNA and DNA targets. The bimolecular association rate is only weakly dependent on sequence; however, the dissociation rate greatly increases from <0.006 s(-1) to >2 s(-1) upon introduction of mismatches proximal to protospacer-adjacent motif (PAM), demonstrating that mismatches encountered early during heteroduplex formation induce rapid rejection of off-target DNA. In contrast, PAM-distal mismatches up to 11 base pairs in length, which prevent DNA cleavage, still allow formation of a stable complex (dissociation rate <0.006 s(-1)), suggesting that extremely slow rejection could sequester Cas9-RNA, increasing the Cas9 expression level necessary for genome-editing, thereby aggravating off-target effects. We also observed at least two different bound FRET states that may represent distinct steps in target search and proofreading.

Modification and uptake of a cisplatin carbonato complex by Jurkat cells.

PubMed

Centerwall, Corey R; Tacka, Kirk A; Kerwood, Deborah J; Goodisman, Jerry; Toms, Bonnie B; Dubowy, Ronald L; Dabrowiak, James C

2006-07-01

The interactions of Jurkat cells with cisplatin, cis-[Pt(15NH3)2Cl2]1, are studied using 1H-15N heteronuclear single quantum coherence (HSQC) NMR and inductively coupled plasma mass spectrometry. We show that Jurkat cells in culture rapidly modify the monocarbonato complex cis-[Pt(15NH3)2(CO3)Cl]- (4), a cisplatin species that forms in culture media and probably also in blood. Analysis of the HSQC NMR peak intensity for 4 in the presence of different numbers of Jurkat cells reveals that each cell is capable of modifying 0.0028 pmol of 4 within approximately 0.6 h. The amounts of platinum taken up by the cell, weakly bound to the cell surface, remaining in the culture medium, and bound to genomic DNA were measured as functions of time of exposure to different concentrations of drug. The results show that most of the 4 that has been modified by the cells remains in the culture medium as a substance of molecular mass <3 kDa, which is HSQC NMR silent, and is not taken up by the cell. These results are consistent with a hitherto undocumented extracellular detoxification mechanism in which the cells rapidly modify 4, which is present in the culture medium, so it cannot bind to the cell. Because there is only a slow decrease in the amount of unmodified 4 remaining in the culture medium after 1 h, -1.1 +/- 0.4 microM h(-1), the cells subsequently lose their ability to modify 4. These observations have important implications for the mechanism of action of cisplatin.

Probes for dark matter physics

NASA Astrophysics Data System (ADS)

Khlopov, Maxim Yu.

The existence of cosmological dark matter is in the bedrock of the modern cosmology. The dark matter is assumed to be nonbaryonic and consists of new stable particles. Weakly Interacting Massive Particle (WIMP) miracle appeals to search for neutral stable weakly interacting particles in underground experiments by their nuclear recoil and at colliders by missing energy and momentum, which they carry out. However, the lack of WIMP effects in their direct underground searches and at colliders can appeal to other forms of dark matter candidates. These candidates may be weakly interacting slim particles, superweakly interacting particles, or composite dark matter, in which new particles are bound. Their existence should lead to cosmological effects that can find probes in the astrophysical data. However, if composite dark matter contains stable electrically charged leptons and quarks bound by ordinary Coulomb interaction in elusive dark atoms, these charged constituents of dark atoms can be the subject of direct experimental test at the colliders. The models, predicting stable particles with charge ‑ 2 without stable particles with charges + 1 and ‑ 1 can avoid severe constraints on anomalous isotopes of light elements and provide solution for the puzzles of dark matter searches. In such models, the excessive ‑ 2 charged particles are bound with primordial helium in O-helium atoms, maintaining specific nuclear-interacting form of the dark matter. The successful development of composite dark matter scenarios appeals for experimental search for doubly charged constituents of dark atoms, making experimental search for exotic stable double charged particles experimentum crucis for dark atoms of composite dark matter.

The generalized truncated exponential distribution as a model for earthquake magnitudes

NASA Astrophysics Data System (ADS)

Raschke, Mathias

2015-04-01

The random distribution of small, medium and large earthquake magnitudes follows an exponential distribution (ED) according to the Gutenberg-Richter relation. But a magnitude distribution is truncated in the range of very large magnitudes because the earthquake energy is finite and the upper tail of the exponential distribution does not fit well observations. Hence the truncated exponential distribution (TED) is frequently applied for the modelling of the magnitude distributions in the seismic hazard and risk analysis. The TED has a weak point: when two TEDs with equal parameters, except the upper bound magnitude, are mixed, then the resulting distribution is not a TED. Inversely, it is also not possible to split a TED of a seismic region into TEDs of subregions with equal parameters, except the upper bound magnitude. This weakness is a principal problem as seismic regions are constructed scientific objects and not natural units. It also applies to alternative distribution models. The presented generalized truncated exponential distribution (GTED) overcomes this weakness. The ED and the TED are special cases of the GTED. Different issues of the statistical inference are also discussed and an example of empirical data is presented in the current contribution.

Electron accommodation dynamics in the DNA base thymine

NASA Astrophysics Data System (ADS)

King, Sarah B.; Stephansen, Anne B.; Yokoi, Yuki; Yandell, Margaret A.; Kunin, Alice; Takayanagi, Toshiyuki; Neumark, Daniel M.

2015-07-01

The dynamics of electron attachment to the DNA base thymine are investigated using femtosecond time-resolved photoelectron imaging of the gas phase iodide-thymine (I-T) complex. An ultraviolet pump pulse ejects an electron from the iodide and prepares an iodine-thymine temporary negative ion that is photodetached with a near-IR probe pulse. The resulting photoelectrons are analyzed with velocity-map imaging. At excitation energies ranging from -120 meV to +90 meV with respect to the vertical detachment energy (VDE) of 4.05 eV for I-T, both the dipole-bound and valence-bound negative ions of thymine are observed. A slightly longer rise time for the valence-bound state than the dipole-bound state suggests that some of the dipole-bound anions convert to valence-bound species. No evidence is seen for a dipole-bound anion of thymine at higher excitation energies, in the range of 0.6 eV above the I-T VDE, which suggests that if the dipole-bound anion acts as a "doorway" to the valence-bound anion, it only does so at excitation energies near the VDE of the complex.

Electron accommodation dynamics in the DNA base thymine.

PubMed

King, Sarah B; Stephansen, Anne B; Yokoi, Yuki; Yandell, Margaret A; Kunin, Alice; Takayanagi, Toshiyuki; Neumark, Daniel M

2015-07-14

The dynamics of electron attachment to the DNA base thymine are investigated using femtosecond time-resolved photoelectron imaging of the gas phase iodide-thymine (I(-)T) complex. An ultraviolet pump pulse ejects an electron from the iodide and prepares an iodine-thymine temporary negative ion that is photodetached with a near-IR probe pulse. The resulting photoelectrons are analyzed with velocity-map imaging. At excitation energies ranging from -120 meV to +90 meV with respect to the vertical detachment energy (VDE) of 4.05 eV for I(-)T, both the dipole-bound and valence-bound negative ions of thymine are observed. A slightly longer rise time for the valence-bound state than the dipole-bound state suggests that some of the dipole-bound anions convert to valence-bound species. No evidence is seen for a dipole-bound anion of thymine at higher excitation energies, in the range of 0.6 eV above the I(-)T VDE, which suggests that if the dipole-bound anion acts as a "doorway" to the valence-bound anion, it only does so at excitation energies near the VDE of the complex.

PLATYPUS: A code for reaction dynamics of weakly-bound nuclei at near-barrier energies within a classical dynamical model

NASA Astrophysics Data System (ADS)

Diaz-Torres, Alexis

2011-04-01

A self-contained Fortran-90 program based on a three-dimensional classical dynamical reaction model with stochastic breakup is presented, which is a useful tool for quantifying complete and incomplete fusion, and breakup in reactions induced by weakly-bound two-body projectiles near the Coulomb barrier. The code calculates (i) integrated complete and incomplete fusion cross sections and their angular momentum distribution, (ii) the excitation energy distribution of the primary incomplete-fusion products, (iii) the asymptotic angular distribution of the incomplete-fusion products and the surviving breakup fragments, and (iv) breakup observables, such as angle, kinetic energy and relative energy distributions. Program summaryProgram title: PLATYPUS Catalogue identifier: AEIG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 332 342 No. of bytes in distributed program, including test data, etc.: 344 124 Distribution format: tar.gz Programming language: Fortran-90 Computer: Any Unix/Linux workstation or PC with a Fortran-90 compiler Operating system: Linux or Unix RAM: 10 MB Classification: 16.9, 17.7, 17.8, 17.11 Nature of problem: The program calculates a wide range of observables in reactions induced by weakly-bound two-body nuclei near the Coulomb barrier. These include integrated complete and incomplete fusion cross sections and their spin distribution, as well as breakup observables (e.g. the angle, kinetic energy, and relative energy distributions of the fragments). Solution method: All the observables are calculated using a three-dimensional classical dynamical model combined with the Monte Carlo sampling of probability-density distributions. See Refs. [1,2] for further details. Restrictions: The program is suited for a weakly-bound two-body projectile colliding with a stable target. The initial orientation of the segment joining the two breakup fragments is considered to be isotropic. Additional comments: Several source routines from Numerical Recipies, and the Mersenne Twister random number generator package are included to enable independent compilation. Running time: About 75 minutes for input provided, using a PC with 1.5 GHz processor.

Reactivity of tris(acetylacetonato) iron(III) with tridentate [ONO] donor Schiff base as an access to newer mixed-ligand iron(III) complexes.

PubMed

Bhattacharjee, Chira R; Goswami, Pankaj; Pramanik, Harun A R; Paul, Pradip C; Mondal, Paritosh

2011-05-01

Two new mixed-ligand iron(III) complexes, [Fe(L(n))(acac)(C(2)H(5)OH)] incorporating coordinated ethanol from the reaction solvent were accessed from the reaction of [Fe(acac)(3)] with [ONO] donor dibasic tridentate unsymmetrical Schiff base ligands derived from condensation of 2-hydroxy-1-napthaldehyde with 2-aminophenol (H(2)L(1)) or 2-aminobenzoic acid (H(2)L(2)). The thermal study (TGA-DTA) provided evidence for weakly bound ethanol which is readily substituted by neutral N-donor molecule imidazole, benzimidazole or pyridine to produce an array of newer complexes, [Fe(L(n))(acac)X] (n=1, 2; X=Im, Bim, Py). The compounds were characterized by elemental analyses, FT-IR, UV-vis, solution electrical conductivity, FAB mass, (1)H and (13)C NMR spectroscopy. Room temperature magnetic susceptibility measurements (μ(eff)∼5.8 B.M.) are consistent with spin-free octahedral iron(III) complexes. Cyclic voltammetry of ethanol complexes revealed a quasi-reversible one electron redox response (ΔE(p)>100 mV) for the Fe(III)/Fe(II) couple. Low half wave redox potential (E(1/2)) values suggested easy redox susceptibility. The ground state geometries of the ethanol and imidazole complexes have been ascertained to be distorted octahedral by density functional theory using DMol3 program at BLYP/DNP level. Copyright © 2011 Elsevier B.V. All rights reserved.

Effects of cytotoxic cis- and trans-diammine monochlorido platinum(II) complexes on selenium-dependent redox enzymes and DNA.

PubMed

Lemmerhirt, Heidi; Behnisch, Steven; Bodtke, Anja; Lillig, Christopher H; Pazderova, Lucia; Kasparkova, Jana; Brabec, Viktor; Bednarski, Patrick J

2018-01-01

Here we present the preparation of 14 pairs of cis- and trans-diammine monochlorido platinum(II) complexes, coordinated to heterocycles (i.e., imidazole, 2-methylimidazole and pyrazole) and linked to various acylhydrazones, which were designed as potential inhibitors of the selenium-dependent enzymes glutathione peroxidase 1 (GPx-1) and thioredoxin reductase 1 (TrxR-1). However, no inhibition of bovine GPx-1 and only weak inhibition of murine TrxR-1 was observed in in vitro assays. Nonetheless, the cis configured diammine monochlorido Pt(II) complexes exhibited cytotoxic and apoptotic properties on various human cancer cell lines, whereas the trans configured complexes generally showed weaker potency with a few exceptions. On the other hand, the trans complexes were generally more likely to lack cross-resistance to cisplatin than the cis analogues. Platinum was found bound to the nuclear DNA of cancer cells treated with representative Pt complexes, suggesting that DNA might be a possible target. Thus, detailed in vitro binding experiments with DNA were conducted. Interactions of the compounds with calf thymus DNA were investigated, including Pt binding kinetics, circular dichroism (CD) spectral changes, changes in DNA melting temperatures, unwinding of supercoiled plasmids and ethidium bromide displacement in DNA. The CD results indicate that the most active cis configured pyrazole-derived complex causes unique structural changes in the DNA compared to the other complexes as well as to those caused by cisplatin, suggesting a denaturation of the DNA structure. This may be important for the antiproliferative activity of this compound in the cancer cells. Copyright © 2017. Published by Elsevier Inc.

Selenolate Complexes of CYP101 and the Heme-bound hHO-1/H25A Proximal Cavity Mutant

PubMed Central

Jiang, Yongying; Ortiz de Montellano, Paul R.

2009-01-01

Thiolate and selenolate complexes of CYP101 (P450cam) and the H25A proximal cavity mutant of heme-bound human heme oxygenase-1 (hHO-1) have been examined by UV-visible spectroscopy. Both thiolate and selenolate ligands bound to the heme distal side in CYP101 and gave rise to characteristic hyperporphyrin spectra. Thiolate ligands also bound to the proximal side of the heme in the cavity created by the H25A mutation in hHO-1, giving a Soret absorption similar to that of the H25C hHO-1 mutant. Selenolate ligands also bound to this cavity mutant under anaerobic conditions, but reduced the heme iron to the ferrous state as shown by formation of a ferrous-CO complex. Under aerobic conditions, the selenolate but not thiolate ligand was rapidly oxidized. These results indicate that selenocysteine-coordinated heme proteins will not be stable species in the absence of a redox potential stabilizing effect. PMID:18376820

Selenolate complexes of CYP101 and the heme-bound hHO-1/H25A proximal cavity mutant.

PubMed

Jiang, Yongying; Ortiz de Montellano, Paul R

2008-05-05

Thiolate and selenolate complexes of CYP101 (P450cam) and the H25A proximal cavity mutant of heme-bound human heme oxygenase-1 (hHO-1) have been examined by UV-vis spectroscopy. Both thiolate and selenolate ligands bound to the heme distal side in CYP101 and gave rise to characteristic hyperporphyrin spectra. Thiolate ligands also bound to the proximal side of the heme in the cavity created by the H25A mutation in hHO-1, giving a Soret absorption similar to that of the H25C hHO-1 mutant. Selenolate ligands also bound to this cavity mutant under anaerobic conditions but reduced the heme iron to the ferrous state, as shown by the formation of a ferrous CO complex. Under aerobic conditions, the selenolate ligand but not the thiolate ligand was rapidly oxidized. These results indicate that selenocysteine-coordinated heme proteins will not be stable species in the absence of a redox potential stabilizing effect.

Age differences in change-of-direction performance and its subelements in female football players.

PubMed

Hirose, Norikazu; Nakahori, Chikako

2015-05-01

To describe cross-sectional age differences in change-of-direction performance (CODp) in female football players and investigate the relationship between CODp and linear-sprint speed, muscle power, and body size. A sample of 135 well-trained female football players was divided into 8 age groups. Anthropometry (height, body mass, and lean body mass) and athletic performance (10-m sprint speed, 10-m×5-CODp, and 5-step bounding distance) were compared to determine interage differences using ANOVA. Then, the participants were divided into 3 age groups: 12- to 14-y-olds, 15- to 17-y-olds, and ≥18 y-olds. Simple- and multiple-regression analyses were conducted to determine the correlation between CODp and the other measurement variables in each age group. Age-related differences were found for CODp (F=10.41, P<.01), sprint speed (F=3.27, P<.01), and bounding distance (F=4.20, P<.01). Post hoc analysis revealed that the CODp of 17-y-old players was faster than that of 16-y-old players (P<.01), with no interage differences in sprint speed and bounding distance. Sprint speed and bounding distance were weakly correlated with CODp in 15- to ≥18-y-old players, but only sprint speed was correlated with CODp in 12- to 14-y-old players. CODp improves from 16 to 17 y of age in female players. Linear-sprint speed, muscle power, and body size were weakly correlated with the age differences in CODp.

Persistence of noncompact normally hyperbolic invariant manifolds in bounded geometry

NASA Astrophysics Data System (ADS)

Edwards, Monroe

Traveling wave tubes must operate in a metal and ceramic vacuum for efficient electron amplification. Weak metallize bonds lead to vacuum leaks and a higher cost of poor quality. The management of TWT Manufacturing (pseudonym) has used a team of metallize workers to attack the problem through brainstorming and subsequent design of experiments (DOE). The purpose of the DOE, which is the focus of this project, is to determine if certain parameters can be changed to increase the strength enough to eliminate failures to weak metallize bonds. The experimental results show the strength can be increased enough and have been recorded in the process instructions. The implementation of the DOE results has saved over nine percent in the budgeted cost of weak metallize bond scrap. This study concludes that raising the metallize tensile strength practically eliminates weak metallize bonds and the cost of poor quality due to this weakness.

Constraining stochastic gravitational wave background from weak lensing of CMB B-modes

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

Shaikh, Shabbir; Mukherjee, Suvodip; Souradeep, Tarun

2016-09-01

A stochastic gravitational wave background (SGWB) will affect the CMB anisotropies via weak lensing. Unlike weak lensing due to large scale structure which only deflects photon trajectories, a SGWB has an additional effect of rotating the polarization vector along the trajectory. We study the relative importance of these two effects, deflection and rotation, specifically in the context of E-mode to B-mode power transfer caused by weak lensing due to SGWB. Using weak lensing distortion of the CMB as a probe, we derive constraints on the spectral energy density (Ω{sub GW}) of the SGWB, sourced at different redshifts, without assuming anymore » particular model for its origin. We present these bounds on Ω{sub GW} for different power-law models characterizing the SGWB, indicating the threshold above which observable imprints of SGWB must be present in CMB.« less

Testing the Standard Model by precision measurement of the weak charges of quarks

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

Ross Young; Roger Carlini; Anthony Thomas

In a global analysis of the latest parity-violating electron scattering measurements on nuclear targets, we demonstrate a significant improvement in the experimental knowledge of the weak neutral-current lepton-quark interactions at low-energy. The precision of this new result, combined with earlier atomic parity-violation measurements, limits the magnitude of possible contributions from physics beyond the Standard Model - setting a model-independent, lower-bound on the scale of new physics at ~1 TeV.

Testing the standard model by precision measurement of the weak charges of quarks.

PubMed

Young, R D; Carlini, R D; Thomas, A W; Roche, J

2007-09-21

In a global analysis of the latest parity-violating electron scattering measurements on nuclear targets, we demonstrate a significant improvement in the experimental knowledge of the weak neutral-current lepton-quark interactions at low energy. The precision of this new result, combined with earlier atomic parity-violation measurements, places tight constraints on the size of possible contributions from physics beyond the standard model. Consequently, this result improves the lower-bound on the scale of relevant new physics to approximately 1 TeV.

Mitochondrial rhodanese: membrane-bound and complexed activity.

PubMed

Ogata, K; Volini, M

1990-05-15

We have proposed that phosphorylated and dephosphorylated forms of the mitochondrial sulfurtransferase, rhodanese, function as converter enzymes that interact with membrane-bound iron-sulfur centers of the electron transport chain to modulate the rate of mitochondrial respiration (Ogata, K., Dai, X., and Volini, M. (1989) J. Biol. Chem. 204, 2718-2725). In the present studies, we have explored some structural aspects of the mitochondrial rhodanese system. By sequential extraction of lysed mitochondria with phosphate buffer and phosphate buffer containing 20 mM cholate, we have shown that 30% of the rhodanese activity of bovine liver is membrane-bound. Resolution of cholate extracts on Sephadex G-100 indicates that part of the bound rhodanese is complexed with other mitochondrial proteins. Tests with the complex show that it forms iron-sulfur centers when incubated with the rhodanese sulfur-donor substrate thiosulfate, iron ions, and a reducing agent. Experiments on the rhodanese activity of rat liver mitochondria give similar results. Taken together, the findings indicate that liver rhodanese is in part bound to the mitochondrial membrane as a component of a multiprotein complex that forms iron-sulfur centers. The findings are consistent with the role we propose for rhodanese in the modulation of mitochondrial respiratory activity.

Cooperation between bound waters and hydroxyls in controlling isotope-exchange rates

NASA Astrophysics Data System (ADS)

Panasci, Adele F.; McAlpin, J. Gregory; Ohlin, C. André; Christensen, Shauna; Fettinger, James C.; Britt, R. David; Rustad, James R.; Casey, William H.

2012-02-01

Mineral oxides differ from aqueous ions in that the bound water molecules are usually attached to different metal centers, or vicinal, and thus separated from one another. In contrast, for most monomeric ions used to establish kinetic reactivity trends, such as octahedral aquo ions (e.g., Al(H 2O) 63+), the bound waters are closely packed, or geminal. Because of this structural difference, the existing literature about ligand substitution in monomer ions may be a poor guide to the reactions of geochemical interest. To understand how coordination of the reactive functional groups might affect the rates of simple water-exchange reactions, we synthesized two structurally similar Rh(III) complexes, [Rh(phen) 2(H 2O) 2] 3+ [ 1] and [Rh(phen) 2(H 2O)Cl] 2+ [ 2] where (phen) = 1,10-phenanthroline. Complex [ 1] has two adjacent, geminal, bound waters in the inner-coordination sphere and [ 2] has a single bound water adjacent to a bound chloride ion. We employed Rh(III) as a trivalent metal rather than a more geochemically relevant metal like Fe(III) or Al(III) to slow the rate of reaction, which makes possible measurement of the rates of isotopic substitution by simple mass spectrometry. We prepared isotopically pure versions of the molecules, dissolved them into isotopically dissimilar water, and measured the rates of exchange from the extents of 18O and 16O exchange at the bound waters. The pH dependency of rates differ enormously between the two complexes. Pseudo-first-order rate coefficients at 298 K for water exchanges from the fully protonated molecules are close: k0298 = 5 × 10 -8(±0.5 × 10 -8) s -1 for [ 1] and k0298 = 2.5 × 10 -9(±1 × 10 -9) for [ 2]. Enthalpy and entropy activation parameters (Δ H‡ and Δ S‡) were measured to be 119(±3) kJ mol -1, and 14(±1) J mol -1 K -1, respectively for [ 1]. The corresponding parameters for the mono-aquo complex, [ 2], are 132(±3) kJ mol -1 and 41.5(±2) J mol -1 K -1. Rates increase by many orders of magnitude upon deprotonation of one of the bound waters in complex [ 1] because of the close proximity of a transferable proton that can convert the bound hydroxyl to a bound water. This interconversion allows the oxygen to exchange as a bound water, rather than as a bound hydroxyl, which is slow at near-neutral pH conditions.

Carbon dioxide is tightly bound in the [Co(Pyridine)(CO2)]- anionic complex

NASA Astrophysics Data System (ADS)

Graham, Jacob D.; Buytendyk, Allyson M.; Zhang, Xinxing; Kim, Seong K.; Bowen, Kit H.

2015-11-01

The [Co(Pyridine)(CO2)]- anionic complex was studied through the combination of photoelectron spectroscopy and density functional theory calculations. This complex was envisioned as a primitive model system for studying CO2 binding to negatively charged sites in metal organic frameworks. The vertical detachment energy (VDE) measured via the photoelectron spectrum is 2.7 eV. Our calculations imply a structure for [Co(Pyridine)(CO2)]- in which a central cobalt atom is bound to pyridine and CO2 moieties on either sides. This structure was validated by acceptable agreement between the calculated and measured VDE values. Based on our calculations, we found CO2 to be bound within the anionic complex by 1.4 eV.

Carbon dioxide is tightly bound in the [Co(Pyridine)(CO2)](-) anionic complex.

PubMed

Graham, Jacob D; Buytendyk, Allyson M; Zhang, Xinxing; Kim, Seong K; Bowen, Kit H

2015-11-14

The [Co(Pyridine)(CO2)](-) anionic complex was studied through the combination of photoelectron spectroscopy and density functional theory calculations. This complex was envisioned as a primitive model system for studying CO2 binding to negatively charged sites in metal organic frameworks. The vertical detachment energy (VDE) measured via the photoelectron spectrum is 2.7 eV. Our calculations imply a structure for [Co(Pyridine)(CO2)](-) in which a central cobalt atom is bound to pyridine and CO2 moieties on either sides. This structure was validated by acceptable agreement between the calculated and measured VDE values. Based on our calculations, we found CO2 to be bound within the anionic complex by 1.4 eV.

Bounds on Block Error Probability for Multilevel Concatenated Codes

NASA Technical Reports Server (NTRS)

Lin, Shu; Moorthy, Hari T.; Stojanovic, Diana

1996-01-01

Maximum likelihood decoding of long block codes is not feasable due to large complexity. Some classes of codes are shown to be decomposable into multilevel concatenated codes (MLCC). For these codes, multistage decoding provides good trade-off between performance and complexity. In this paper, we derive an upper bound on the probability of block error for MLCC. We use this bound to evaluate difference in performance for different decompositions of some codes. Examples given show that a significant reduction in complexity can be achieved when increasing number of stages of decoding. Resulting performance degradation varies for different decompositions. A guideline is given for finding good m-level decompositions.

Structures of the Substrate-free and Product-bound Forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae

PubMed Central

Unno, Masaki; Ardèvol, Albert; Rovira, Carme; Ikeda-Saito, Masao

2013-01-01

Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe3+-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe3+-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe3+-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe3+-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit. PMID:24106279

Crystal structures of RIalpha subunit of cyclic adenosine 5'-monophosphate (cAMP)-dependent protein kinase complexed with (Rp)-adenosine 3',5'-cyclic monophosphothioate and (Sp)-adenosine 3',5'-cyclic monophosphothioate, the phosphothioate analogues of cAMP.

PubMed

Wu, Jian; Jones, John M; Nguyen-Huu, Xuong; Ten Eyck, Lynn F; Taylor, Susan S

2004-06-01

Cyclic adenosine 5'-monophosphate (cAMP) is an ancient signaling molecule, and in vertebrates, a primary target for cAMP is cAMP-dependent protein kinase (PKA). (R(p))-adenosine 3',5'-cyclic monophosphothioate ((R(p))-cAMPS) and its analogues are the only known competitive inhibitors and antagonists for cAMP activation of PKA, while (S(p))-adenosine 3',5'-cyclic monophosphothioate ((S(p))-cAMPS) functions as an agonist. The crystal structures of a Delta(1-91) deletion mutant of the RIalpha regulatory subunit of PKA bound to (R(p))-cAMPS and (S(p))-cAMPS were determined at 2.4 and 2.3 A resolution, respectively. While the structures are similar to each other and to the crystal structure of RIalpha bound to cAMP, differences in the dynamical properties of the protein when (R(p))-cAMPS is bound are apparent. The structures highlight the critical importance of the exocyclic oxygen's interaction with the invariant arginine in the phosphate binding cassette (PBC) and the importance of this interaction for the dynamical properties of the interactions that radiate out from the PBC. The conformations of the phosphate binding cassettes containing two invariant arginine residues (Arg209 on domain A, and Arg333 on domain B) are somewhat different due to the sulfur interacting with this arginine. Furthermore, the B-site ligand together with the entire domain B show significant differences in their overall dynamic properties in the crystal structure of Delta(1-91) RIalpha complexed with (R(p))-cAMPS phosphothioate analogue ((R(p))-RIalpha) compared to the cAMP- and (S(p))-cAMPS-bound type I and II regulatory subunits, based on the temperature factors. In all structures, two structural solvent molecules exist within the A-site ligand binding pocket; both mediate water-bridged interactions between the ligand and the protein. No structured waters are in the B-site pocket. Owing to the higher resolution data, the N-terminal segment (109-117) of the RIalpha subunit can also be traced. This strand forms an intermolecular antiparallel beta-sheet with the same strand in an adjacent molecule and implies that the RIalpha subunit can form a weak homodimer even in the absence of its dimerization domain.

Regulation of the protein-conducting channel by a bound ribosome

PubMed Central

Gumbart, James; Trabuco, Leonardo G.; Schreiner, Eduard; Villa, Elizabeth; Schulten, Klaus

2009-01-01

Summary During protein synthesis, it is often necessary for the ribosome to form a complex with a membrane-bound channel, the SecY/Sec61 complex, in order to translocate nascent proteins across a cellular membrane. Structural data on the ribosome-channel complex are currently limited to low-resolution cryo-electron microscopy maps, including one showing a bacterial ribosome bound to a monomeric SecY complex. Using that map along with available atomic-level models of the ribosome and SecY, we have determined, through molecular dynamics flexible fitting (MDFF), an atomic-resolution model of the ribosome-channel complex. We characterized computationally the sites of ribosome-SecY interaction within the complex and determined the effect of ribosome binding on the SecY channel. We also constructed a model of a ribosome in complex with a SecY dimer by adding a second copy of SecY to the MDFF-derived model. The study involved 2.7-million-atom simulations over altogether nearly 50 ns. PMID:19913480

Structures of glycans bound to receptors from saturation transfer difference (STD) NMR spectroscopy: quantitative analysis by using CORCEMA-ST.

PubMed

Enríquez-Navas, Pedro M; Guzzi, Cinzia; Muñoz-García, Juan C; Nieto, Pedro M; Angulo, Jesús

2015-01-01

Glycan-receptor interactions are of fundamental relevance for a large number of biological processes, and their kinetics properties (medium/weak binding affinities) make them appropriated to be studied by ligand observed NMR techniques, among which saturation transfer difference (STD) NMR spectroscopy has been shown to be a very robust and powerful approach. The quantitative analysis of the results from a STD NMR study of a glycan-receptor interaction is essential to be able to translate the resulting spectral intensities into a 3D molecular model of the complex. This chapter describes how to carry out such a quantitative analysis by means of the Complete Relaxation and Conformational Exchange Matrix Approach for STD NMR (CORCEMA-ST), in general terms, and an example of a previous work on an antibody-glycan interaction is also shown.

Interaction of alkanes with an amorphous methanol film at 15-180 K

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

Souda, Ryutaro

2005-09-15

The hydrogen-bond imperfections and glass-liquid transition of the amorphous methanol film have been investigated on the basis of the film dewetting and the incorporation/desorption of alkane molecules adsorbed on the surface. The butane is incorporated completely in the bulk of the porous methanol film up to 70 K. At least two distinct states exist for the incorporated butane; one is assignable to solvated molecules in the bulk and the other is weakly bound species at the surface or in the subsurface site. For the nonporous methanol film, the uptake of butane in the bulk is quenched but butane forms amore » surface complex with methanol above 80 K. The butane incorporated in the bulk of the glassy methanol film is released at 120 K, where dewetting of the methanol film occurs simultaneously due to evolution of the supercooled liquid phase.« less

Mechanics of finite cracks in dissimilar anisotropic elastic media considering interfacial elasticity

DOE PAGES

Juan, Pierre -Alexandre; Dingreville, Remi

2016-10-31

Interfacial crack fields and singularities in bimaterial interfaces (i.e., grain boundaries or dissimilar materials interfaces) are considered through a general formulation for two-dimensional (2-D) anisotropic elasticity while accounting for the interfacial structure by means of an interfacial elasticity paradigm. The interfacial elasticity formulation introduces boundary conditions that are effectively equivalent to those for a weakly bounded interface. This formalism considers the 2-D crack-tip elastic fields using complex variable techniques. While the consideration of the interfacial elasticity does not affect the order of the singularity, it modifies the oscillatory effects associated with problems involving interface cracks. Constructive or destructive “interferences” aremore » directly affected by the interface structure and its elastic response. Furthermore, this general formulation provides an insight on the physical significance and the obvious coupling between the interface structure and the associated mechanical fields in the vicinity of the crack tip.« less

Mechanics of finite cracks in dissimilar anisotropic elastic media considering interfacial elasticity

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

Juan, Pierre -Alexandre; Dingreville, Remi

Interfacial crack fields and singularities in bimaterial interfaces (i.e., grain boundaries or dissimilar materials interfaces) are considered through a general formulation for two-dimensional (2-D) anisotropic elasticity while accounting for the interfacial structure by means of an interfacial elasticity paradigm. The interfacial elasticity formulation introduces boundary conditions that are effectively equivalent to those for a weakly bounded interface. This formalism considers the 2-D crack-tip elastic fields using complex variable techniques. While the consideration of the interfacial elasticity does not affect the order of the singularity, it modifies the oscillatory effects associated with problems involving interface cracks. Constructive or destructive “interferences” aremore » directly affected by the interface structure and its elastic response. Furthermore, this general formulation provides an insight on the physical significance and the obvious coupling between the interface structure and the associated mechanical fields in the vicinity of the crack tip.« less

Biased migration of confined neutrophil-like cells in asymmetric hydraulic environments.

PubMed

Prentice-Mott, Harrison V; Chang, Chi-Han; Mahadevan, L; Mitchison, Timothy J; Irimia, Daniel; Shah, Jagesh V

2013-12-24

Cells integrate multiple measurement modalities to navigate their environment. Soluble and substrate-bound chemical gradients and physical cues have all been shown to influence cell orientation and migration. Here we investigate the role of asymmetric hydraulic pressure in directional sensing. Cells confined in microchannels identified and chose a path of lower hydraulic resistance in the absence of chemical cues. In a bifurcating channel with asymmetric hydraulic resistances, this choice was preceded by the elaboration of two leading edges with a faster extension rate along the lower resistance channel. Retraction of the "losing" edge appeared to precipitate a final choice of direction. The pressure differences altering leading edge protrusion rates were small, suggesting weak force generation by leading edges. The response to the physical asymmetry was able to override a dynamically generated chemical cue. Motile cells may use this bias as a result of hydraulic resistance, or "barotaxis," in concert with chemotaxis to navigate complex environments.

Communication: Charge-population based dispersion interactions for molecules and materials

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

Stöhr, Martin; Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching; Michelitsch, Georg S.

2016-04-21

We introduce a system-independent method to derive effective atomic C{sub 6} coefficients and polarizabilities in molecules and materials purely from charge population analysis. This enables the use of dispersion-correction schemes in electronic structure calculations without recourse to electron-density partitioning schemes and expands their applicability to semi-empirical methods and tight-binding Hamiltonians. We show that the accuracy of our method is en par with established electron-density partitioning based approaches in describing intermolecular C{sub 6} coefficients as well as dispersion energies of weakly bound molecular dimers, organic crystals, and supramolecular complexes. We showcase the utility of our approach by incorporation of the recentlymore » developed many-body dispersion method [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012)] into the semi-empirical density functional tight-binding method and propose the latter as a viable technique to study hybrid organic-inorganic interfaces.« less

Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems

PubMed Central

Huang, Xuhui; Hagen, Morten; Kim, Byungchan; Friesner, Richard A.; Zhou, Ruhong; Berne, B. J.

2009-01-01

We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an α-helix, a β-hairpin, and a TrpCage, with these peptides defined as the “central group”. We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities. REST, however, is expected to remain useful for a large class of systems for which the energy gap between the two states is not large, such as weakly bound protein–ligand complexes. Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper. PMID:17439169

Random-Phase Approximation Methods

NASA Astrophysics Data System (ADS)

Chen, Guo P.; Voora, Vamsee K.; Agee, Matthew M.; Balasubramani, Sree Ganesh; Furche, Filipp

2017-05-01

Random-phase approximation (RPA) methods are rapidly emerging as cost-effective validation tools for semilocal density functional computations. We present the theoretical background of RPA in an intuitive rather than formal fashion, focusing on the physical picture of screening and simple diagrammatic analysis. A new decomposition of the RPA correlation energy into plasmonic modes leads to an appealing visualization of electron correlation in terms of charge density fluctuations. Recent developments in the areas of beyond-RPA methods, RPA correlation potentials, and efficient algorithms for RPA energy and property calculations are reviewed. The ability of RPA to approximately capture static correlation in molecules is quantified by an analysis of RPA natural occupation numbers. We illustrate the use of RPA methods in applications to small-gap systems such as open-shell d- and f-element compounds, radicals, and weakly bound complexes, where semilocal density functional results exhibit strong functional dependence.

Search for weakly decaying Λn ‾ and ΛΛ exotic bound states in central Pb-Pb collisions at √{sNN} = 2.76 TeV

NASA Astrophysics Data System (ADS)

Adam, J.; Adamová, D.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahmed, I.; Ahn, S. U.; Aimo, I.; Aiola, S.; Ajaz, M.; Akindinov, A.; Alam, S. N.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Anielski, J.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Armesto, N.; Arnaldi, R.; Aronsson, T.; Arsene, I. C.; Arslandok, M.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Bach, M.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Baldisseri, A.; Ball, M.; Baltasar Dos Santos Pedrosa, F.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Basu, S.; Bathen, B.; Batigne, G.; Batista Camejo, A.; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Belyaev, V.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biswas, S.; Bjelogrlic, S.; Blanco, F.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Bøggild, H.; Boldizsár, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossú, F.; Botje, M.; Botta, E.; Böttger, S.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Buxton, J. T.; Caffarri, D.; Cai, X.; Caines, H.; Calero Diaz, L.; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Cavicchioli, C.; Ceballos Sanchez, C.; Cepila, J.; Cerello, P.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Chung, S. U.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Conesa Balbastre, G.; Conesa del Valle, Z.; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danu, A.; Das, D.; Das, I.; Das, S.; Dash, A.; Dash, S.; De, S.; De Caro, A.; de Cataldo, G.; de Cuveland, J.; De Falco, A.; De Gruttola, D.; De Marco, N.; De Pasquale, S.; Deisting, A.; Deloff, A.; Dénes, E.; D'Erasmo, G.; Di Bari, D.; Di Mauro, A.; Di Nezza, P.; Diaz Corchero, M. A.; Dietel, T.; Dillenseger, P.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Dobrowolski, T.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Engel, H.; Erazmus, B.; Erhardt, F.; Eschweiler, D.; Espagnon, B.; Estienne, M.; Esumi, S.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Felea, D.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernández Téllez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Gargiulo, C.; Gasik, P.; Germain, M.; Gheata, A.; Gheata, M.; Ghosh, P.; Ghosh, S. K.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glässel, P.; Gomez Ramirez, A.; González-Zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Graczykowski, L. K.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Grosse-Oetringhaus, J. F.; Grossiord, J.-Y.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gulkanyan, H.; Gunji, T.; Gupta, A.; Gupta, R.; Haake, R.; Haaland, Ø.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hanratty, L. D.; Hansen, A.; Harris, J. W.; Hartmann, H.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Heide, M.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hilden, T. E.; Hillemanns, H.; Hippolyte, B.; Hristov, P.; Huang, M.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Ilkiv, I.; Inaba, M.; Ionita, C.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jachołkowski, A.; Jacobs, P. M.; Jahnke, C.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Jimenez Bustamante, R. T.; Jones, P. G.; Jung, H.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kang, J. H.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Khan, K. H.; Khan, M. M.; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, B.; Kim, D. W.; Kim, D. J.; Kim, H.; Kim, J. S.; Kim, M.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein, J.; Klein-Bösing, C.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobayashi, T.; Kobdaj, C.; Kofarago, M.; Köhler, M. K.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kouzinopoulos, C.; Kovalenko, V.; Kowalski, M.; Kox, S.; Koyithatta Meethaleveedu, G.; Kral, J.; Králik, I.; Kravčáková, A.; Krelina, M.; Kretz, M.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kučera, V.; Kucheriaev, Y.; Kugathasan, T.; Kuhn, C.; Kuijer, P. G.; Kulakov, I.; Kumar, J.; Kumar, L.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kushpil, S.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Legrand, I.; Lehnert, J.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; León Monzón, I.; Leoncino, M.; Lévai, P.; Li, S.; Li, X.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loggins, V. R.; Loginov, V.; Loizides, C.; Lopez, X.; López Torres, E.; Lowe, A.; Lu, X.-G.; Luettig, P.; Lunardon, M.; Luparello, G.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manceau, L.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martashvili, I.; Martin, N. A.; Martin Blanco, J.; Martinengo, P.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Martynov, Y.; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Massacrier, L.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; Mcdonald, D.; Meddi, F.; Menchaca-Rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Minervini, L. M.; Mischke, A.; Mishra, A. N.; Miśkowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Montes, E.; Morando, M.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Muhuri, S.; Mukherjee, M.; Müller, H.; Mulligan, J. D.; Munhoz, M. G.; Murray, S.; Musa, L.; Musinsky, J.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Nattrass, C.; Nayak, K.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira Da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, P.; Paić, G.; Pajares, C.; Pal, S. K.; Pan, J.; Pandey, A. K.; Pant, D.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Paul, B.; Pawlak, T.; Peitzmann, T.; Pereira Da Costa, H.; Pereira De Oliveira Filho, E.; Peresunko, D.; Pérez Lara, C. E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Płoskoń, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Porteboeuf-Houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Rascanu, B. T.; Rathee, D.; Razazi, V.; Read, K. F.; Real, J. S.; Redlich, K.; Reed, R. J.; Rehman, A.; Reichelt, P.; Reicher, M.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Rettig, F.; Revol, J.-P.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rivetti, A.; Rocco, E.; Rodríguez Cahuantzi, M.; Rodriguez Manso, A.; Røed, K.; Rogochaya, E.; Rohr, D.; Röhrich, D.; Romita, R.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Rubio Montero, A. J.; Rui, R.; Russo, R.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Sadovsky, S.; Šafařík, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salgado, C. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Sanchez Castro, X.; Šándor, L.; Sandoval, A.; Sano, M.; Santagati, G.; Sarkar, D.; Scapparone, E.; Scarlassara, F.; Scharenberg, R. P.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schuchmann, S.; Schukraft, J.; Schulc, M.; Schuster, T.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Seeder, K. S.; Seger, J. E.; Sekiguchi, Y.; Selyuzhenkov, I.; Senosi, K.; Seo, J.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shangaraev, A.; Sharma, A.; Sharma, N.; Shigaki, K.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Søgaard, C.; Soltz, R.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Srivastava, B. K.; Stachel, J.; Stan, I.; Stefanek, G.; Steinpreis, M.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Sultanov, R.; Šumbera, M.; Symons, T. J. M.; Szabo, A.; Szanto de Toledo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Takahashi, J.; Tanaka, N.; Tangaro, M. A.; Tapia Takaki, J. D.; Tarantola Peloni, A.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Muñoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thäder, J.; Thomas, D.; Tieulent, R.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vajzer, M.; Vala, M.; Valencia Palomo, L.; Vallero, S.; Van Der Maarel, J.; Van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vande Vyvre, P.; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vechernin, V.; Veen, A. M.; Veldhoen, M.; Velure, A.; Venaruzzo, M.; Vercellin, E.; Vergara Limón, S.; Vernet, R.; Verweij, M.; Vickovic, L.; Viesti, G.; Viinikainen, J.; Vilakazi, Z.; Villalobos Baillie, O.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Völkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; von Haller, B.; Vorobyev, I.; Vranic, D.; Vrláková, J.; Vulpescu, B.; Vyushin, A.; Wagner, B.; Wagner, J.; Wang, H.; Wang, M.; Wang, Y.; Watanabe, D.; Weber, M.; Weber, S. G.; Wessels, J. P.; Westerhoff, U.; Wiechula, J.; Wikne, J.; Wilde, M.; Wilk, G.; Wilkinson, J.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yaldo, C. G.; Yamaguchi, Y.; Yang, H.; Yang, P.; Yano, S.; Yasnopolskiy, S.; Yin, Z.; Yokoyama, H.; Yoo, I.-K.; Yurchenko, V.; Yushmanov, I.; Zaborowska, A.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zhu, X.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.

2016-01-01

We present results of a search for two hypothetical strange dibaryon states, i.e. the H-dibaryon and the possible Λn ‾ bound state. The search is performed with the ALICE detector in central (0-10%) Pb-Pb collisions at √{sNN} = 2.76 TeV, by invariant mass analysis in the decay modes Λn ‾ → d ‾π+ and H-dibaryon → Λpπ-. No evidence for these bound states is observed. Upper limits are determined at 99% confidence level for a wide range of lifetimes and for the full range of branching ratios. The results are compared to thermal, coalescence and hybrid UrQMD model expectations, which describe correctly the production of other loosely bound states, like the deuteron and the hypertriton.

Search for weakly decaying Λ n - and ΛΛ exotic bound states in central Pb–Pb collisions at s NN = 2.76  TeV

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

Adam, J.; Adamová, D.; Aggarwal, M. M.

Here, we present results of a search for two hypothetical strange dibaryon states, i.e. the H-dibaryon and the possiblemore » $$\\overline{Λn}$$ bound state. The search is performed with the ALICE detector in central (0-10%) Pb-Pb collisions at $$\\sqrt{s}$$$_ {NN}$$ = 2.76 TeV, by invariant mass analysis in the decay modes $$\\overline{Λn}$$ → $$\\bar{d}$$π + and H-dibaryon →Λpπ -. No evidence for these bound states is observed. Upper limits are determined at 99% confidence level for a wide range of lifetimes and for the full range of branching ratios. The results are compared to thermal, coalescence and hybrid UrQMD model expectations, which describe correctly the production of other loosely bound states, like the deuteron and the hypertriton.« less

Search for weakly decaying Λ n - and ΛΛ exotic bound states in central Pb–Pb collisions at s NN = 2.76  TeV

DOE PAGES

Adam, J.; Adamová, D.; Aggarwal, M. M.; ...

2016-11-28

Here, we present results of a search for two hypothetical strange dibaryon states, i.e. the H-dibaryon and the possiblemore » $$\\overline{Λn}$$ bound state. The search is performed with the ALICE detector in central (0-10%) Pb-Pb collisions at $$\\sqrt{s}$$$_ {NN}$$ = 2.76 TeV, by invariant mass analysis in the decay modes $$\\overline{Λn}$$ → $$\\bar{d}$$π + and H-dibaryon →Λpπ -. No evidence for these bound states is observed. Upper limits are determined at 99% confidence level for a wide range of lifetimes and for the full range of branching ratios. The results are compared to thermal, coalescence and hybrid UrQMD model expectations, which describe correctly the production of other loosely bound states, like the deuteron and the hypertriton.« less

Tumor necrosis factor interaction with gold nanoparticles

NASA Astrophysics Data System (ADS)

Tsai, De-Hao; Elzey, Sherrie; Delrio, Frank W.; Keene, Athena M.; Tyner, Katherine M.; Clogston, Jeffrey D.; Maccuspie, Robert I.; Guha, Suvajyoti; Zachariah, Michael R.; Hackley, Vincent A.

2012-05-01

We report on a systematic investigation of molecular conjugation of tumor necrosis factor-α (TNF) protein onto gold nanoparticles (AuNPs) and the subsequent binding behavior to its antibody (anti-TNF). We employ a combination of physical and spectroscopic characterization methods, including electrospray-differential mobility analysis, dynamic light scattering, polyacrylamide gel electrophoresis, attenuated total reflectance-Fourier transform infrared spectroscopy, fluorescence assay, and enzyme-linked immunosorbent assay. The native TNF used in this study exists in the active homotrimer configuration prior to conjugation. After binding to AuNPs, the maximum surface density of TNF is (0.09 +/- 0.02) nm-2 with a binding constant of 3 × 106 (mol L-1)-1. Dodecyl sulfate ions induce desorption of monomeric TNF from the AuNP surface, indicating a relatively weak intermolecular binding within the AuNP-bound TNF trimers. Anti-TNF binds to both TNF-conjugated and citrate-stabilized AuNPs, showing that non-specific binding is significant. Based on the number of anti-TNF molecules adsorbed, a substantially higher binding affinity was observed for the TNF-conjugated surface. The inclusion of thiolated polyethylene glycol (SH-PEG) on the AuNPs inhibits the binding of anti-TNF, and the amount of inhibition is related to the number ratio of surface bound SH-PEG to TNF and the way in which the ligands are introduced. This study highlights the challenges in quantitatively characterizing complex hybrid nanoscale conjugates, and provides insight on TNF-AuNP formation and activity.We report on a systematic investigation of molecular conjugation of tumor necrosis factor-α (TNF) protein onto gold nanoparticles (AuNPs) and the subsequent binding behavior to its antibody (anti-TNF). We employ a combination of physical and spectroscopic characterization methods, including electrospray-differential mobility analysis, dynamic light scattering, polyacrylamide gel electrophoresis, attenuated total reflectance-Fourier transform infrared spectroscopy, fluorescence assay, and enzyme-linked immunosorbent assay. The native TNF used in this study exists in the active homotrimer configuration prior to conjugation. After binding to AuNPs, the maximum surface density of TNF is (0.09 +/- 0.02) nm-2 with a binding constant of 3 × 106 (mol L-1)-1. Dodecyl sulfate ions induce desorption of monomeric TNF from the AuNP surface, indicating a relatively weak intermolecular binding within the AuNP-bound TNF trimers. Anti-TNF binds to both TNF-conjugated and citrate-stabilized AuNPs, showing that non-specific binding is significant. Based on the number of anti-TNF molecules adsorbed, a substantially higher binding affinity was observed for the TNF-conjugated surface. The inclusion of thiolated polyethylene glycol (SH-PEG) on the AuNPs inhibits the binding of anti-TNF, and the amount of inhibition is related to the number ratio of surface bound SH-PEG to TNF and the way in which the ligands are introduced. This study highlights the challenges in quantitatively characterizing complex hybrid nanoscale conjugates, and provides insight on TNF-AuNP formation and activity. Electronic supplementary information (ESI) available: Experimental procedures, instrumentation, materials and calculations. See DOI: 10.1039/c2nr30415e

Theory and Normal Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding

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

Mortisugu, Kei; Njunda, Brigitte; Smith, Jeremy C

2009-12-01

The change of protein vibrations on ligand binding is of functional and thermodynamic importance. Here, this process is characterized using a simple analytical 'ball-and-spring' model and all-atom normal-mode analysis (NMA) of the binding of the cancer drug, methotrexate (MTX) to its target, dihydrofolate reductase (DHFR). The analytical model predicts that the coupling between protein vibrations and ligand external motion generates entropy-rich, low-frequency vibrations in the complex. This is consistent with the atomistic NMA which reveals vibrational softening in forming the DHFR-MTX complex, a result also in qualitative agreement with neutron-scattering experiments. Energy minimization of the atomistic bound-state (B) structure whilemore » gradually decreasing the ligand interaction to zero allows the generation of a hypothetical 'intermediate' (I) state, without the ligand force field but with a structure similar to that of B. In going from I to B, it is found that the vibrational entropies of both the protein and MTX decrease while the complex structure becomes enthalpically stabilized. However, the relatively weak DHFR:MTX interaction energy results in the net entropy gain arising from coupling between the protein and MTX external motion being larger than the loss of vibrational entropy on complex formation. This, together with the I structure being more flexible than the unbound structure, results in the observed vibrational softening on ligand binding.« less

Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations.

PubMed

Chen, Ying; Bylaska, Eric J; Weare, John H

2017-03-31

Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick). The lowest energy goethite (100) surface termination model was determined to have an exposed surface Fe 3+ that was loosely capped by a water molecule and a shared hydroxide with a neighboring surface Fe 3+ . The water molecules capping surface Fe 3+ ions were found to be loosely bound at all DFT levels with and without Grimme corrections, indicative that each surface Fe 3+ was coordinated with only five neighbors. These long bonds were supported by bond valence theory calculations, which showed that the bond valence of the surface Fe 3+ was saturated and surface has a neutral charge. The polarization of the water layer adjacent to the surface was found to be small and affected only the nearest water. Analysis by density difference plots and localized Boys orbitals identified three types of water molecules: those loosely bound to the surface Fe 3+ , those hydrogen bonded to the surface hydroxyl, and bulk water with tetrahedral coordination. Boys orbital analysis showed that the spin down lone pair orbital of the weakly absorbed water interact more strongly with the spin up Fe 3+ ion. These weakly bound surface water molecules were found to rapidly exchange with the second water layer (~0.025 exchanges/ps) using a dissociative mechanism. Water molecules adjacent to the surface were found to only weakly interact with the surface and as a result were readily able to exchange with the bulk water. To account for the large surface Fe-OH 2 distances in the DFT calculations it was proposed that the surface Fe 3+ atoms, which already have their bond valence fully satisfied with only five neighbors, are under-coordinated with respect to the bulk coordination. Graphical abstract All first principle calculations, at all practically achievable levels, for the goethite 100 aqueous interface support a long bond and weak interaction between the exposed surface Fe 3+ and water molecules capping the surface. This result is supported by bond valence theory calculations and is indicative that each surface Fe 3+ is coordinated with only 5 neighbors.

Bound and continuum energy distributions of nuclear fragments resulting from tunneling ionization of molecules

NASA Astrophysics Data System (ADS)

Svensmark, Jens; Tolstikhin, Oleg I.; Madsen, Lars Bojer

2018-03-01

We present the theory of tunneling ionization of molecules with both electronic and nuclear motion treated quantum mechanically. The theory provides partial rates for ionization into the different final states of the molecular ion, including both bound vibrational and dissociative channels. The exact results obtained for a one-dimensional model of H2 and D2 are compared with two approximate approaches, the weak-field asymptotic theory and the Born-Oppenheimer approximation. The validity ranges and compatibility of the approaches are identified formally and illustrated by the calculations. The results quantify that at typical field strengths considered in strong-field physics, it is several orders of magnitude more likely to ionize into bound vibrational ionic channels than into the dissociative channel.

Monitoring bound HA1(H1N1) and HA1(H5N1) on freely suspended graphene over plasmonic platforms with infrared spectroscopy

NASA Astrophysics Data System (ADS)

Banerjee, Amrita; Chakraborty, Sumit; Altan-Bonnet, Nihal; Grebel, Haim

2013-09-01

Infrared (IR) spectroscopy provides fingerprinting of the energy and orientation of molecular bonds. The IR signals are generally weak and require amplification. Here we present a new plasmonic platform, made of freely suspended graphene, which was coating periodic metal structures. Only monolayer thick films were needed for a fast signal recording. We demonstrated unique IR absorption signals of bound proteins: these were the hemagglutinin area (HA1) of swine influenza (H1N1) and the avian influenza (H5N1) viruses bound to their respective tri-saccharides ligand receptors. The simplicity and sensitivity of such approach may find applications in fast monitoring of binding events.

Beating the photon-number-splitting attack in practical quantum cryptography.

PubMed

Wang, Xiang-Bin

2005-06-17

We propose an efficient method to verify the upper bound of the fraction of counts caused by multiphoton pulses in practical quantum key distribution using weak coherent light, given whatever type of Eve's action. The protocol simply uses two coherent states for the signal pulses and vacuum for the decoy pulse. Our verified upper bound is sufficiently tight for quantum key distribution with a very lossy channel, in both the asymptotic and nonasymptotic case. So far our protocol is the only decoy-state protocol that works efficiently for currently existing setups.

Astrophysics and cosmology confront the 17 keV neutrino

NASA Technical Reports Server (NTRS)

Kolb, Edward W.; Turner, Michael S.

1991-01-01

A host of astrophysical and cosmological arguments severely constrain the properties of a 17 keV Dirac neutrino. Such a neutrino must have interactions beyond those of the standard electroweak theory to reduce its cosmic abundance (through decay or annihilation) by a factor of two hundred. A predicament arises because the additional helicity states of the neutrino necessary to construct a Dirac mass must have interactions strong enough to evade the astrophysical bound from SN 1987A, but weak enough to avoid violating the bound from primordial nucleosynthesis.

Astrophysics and cosmology confront the 17-keV neutrino

NASA Technical Reports Server (NTRS)

Kolb, Edward W.; Turner, Michael S.

1991-01-01

A host of astrophysical and cosmological arguments severely constrain the properties of a 17 keV Dirac neutrino. Such a neutrino must have interactions beyond those of the standard electroweak theory to reduce its cosmic abundance (through decay or annihilation) by a factor of two hundred. A predicament arises because the additional helicity states of the neutrino necessary to construct a Dirac mass must have interactions strong enough to evade the astrophysical bound from SN 1987A, but weak enough to avoid violating the bound from primordial nucleosynthesis.

Structural Characterization of the Binding of Myosin*ADP*Pi to Actin in Permeabilized Rabbit Psoas Muscle

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

Xu,S.; Gu, J.; Belknap, B.

2006-01-01

When myosin is attached to actin in a muscle cell, various structures in the filaments are formed. The two strongly bound states (A{center_dot}M{center_dot}ADP and A{center_dot}M) and the weakly bound A{center_dot}M{center_dot}ATP states are reasonably well understood. The orientation of the strongly bound myosin heads is uniform ('stereospecific' attachment), and the attached heads exhibit little spatial fluctuation. In the prehydrolysis weakly bound A{center_dot}M{center_dot}ATP state, the orientations of the attached myosin heads assume a wide range of azimuthal and axial angles, indicating considerable flexibility in the myosin head. The structure of the other weakly bound state, A{center_dot}M{center_dot}ADP{center_dot}P{sub i}, however, is poorly understood. Thismore » state is thought to be the critical pre-power-stroke state, poised to make the transition to the strongly binding, force-generating states, and hence it is of particular interest for understanding the mechanism of contraction. However, because of the low affinity between myosin and actin in the A{center_dot}M{center_dot}ADP{center_dot}P{sub i} state, the structure of this state has eluded determination both in isolated form and in muscle cells. With the knowledge recently gained in the structures of the weakly binding M{center_dot}ATP, M{center_dot}ADP{center_dot}P{sub i} states and the weakly attached A{center_dot}M{center_dot}ATP state in muscle fibers, it is now feasible to delineate the in vivo structure of the attached state of A{center_dot}M{center_dot}ADP{center_dot}P{sub i}. The series of experiments presented in this article were carried out under relaxing conditions at 25{sup o}C, where {approx}95% of the myosin heads in the skinned rabbit psoas muscle contain the hydrolysis products. The affinity for actin is enhanced by adding polyethylene glycol (PEG) or by lowering the ionic strength in the bathing solution. Solution kinetics and binding constants were determined in the presence and in the absence of PEG. When the binding between actin and myosin was increased, both the myosin layer lines and the actin layer lines increased in intensity, but the intensity profiles did not change. The configuration (mode) of attachment in the A{center_dot}M{center_dot}ADP{center_dot}P{sub i} state is thus unique among the intermediate attached states of the cross-bridge ATP hydrolysis cycle. One of the simplest explanations is that both myosin filaments and actin filaments are stabilized (e.g., undergo reduced spatial fluctuations) by the attachment. The alignment of the myosin heads in the thick filaments and the alignment of the actin monomers in the thin filaments are improved as a result. The compact atomic structure of M{center_dot}ADP{center_dot}P{sub i} with strongly coupled domains may contribute to the unique attachment configuration: the 'primed' myosin heads may function as 'transient struts' when attached to the thin filaments.« less

Lithology-dependent minimum horizontal stress and in-situ stress estimate

NASA Astrophysics Data System (ADS)

Zhang, Yushuai; Zhang, Jincai

2017-04-01

Based on the generalized Hooke's law with coupling stresses and pore pressure, the minimum horizontal stress is solved with assumption that the vertical, minimum and maximum horizontal stresses are in equilibrium in the subsurface formations. From this derivation, we find that the uniaxial strain method is the minimum value or lower bound of the minimum stress. Using Anderson's faulting theory and this lower bound of the minimum horizontal stress, the coefficient of friction of the fault is derived. It shows that the coefficient of friction may have a much smaller value than what it is commonly assumed (e.g., μf = 0.6-0.7) for in-situ stress estimate. Using the derived coefficient of friction, an improved stress polygon is drawn, which can reduce the uncertainty of in-situ stress calculation by narrowing the area of the conventional stress polygon. It also shows that the coefficient of friction of the fault is dependent on lithology. For example, if the formation in the fault is composed of weak shales, then the coefficient of friction of the fault may be small (as low as μf = 0.2). This implies that this fault is weaker and more likely to have shear failures than the fault composed of sandstones. To avoid the weak fault from shear sliding, it needs to have a higher minimum stress and a lower shear stress. That is, the critically stressed weak fault maintains a higher minimum stress, which explains why a low shear stress appears in the frictionally weak fault.

Distinctive Spectral Features of Exciton and Excimer States in the Ultrafast Electronic Deactivation of the Adenine Dinucleotide

NASA Astrophysics Data System (ADS)

Stuhldreier, Mayra C.; Röttger, Katharina; Temps, Friedrich

We report the observation by transient absorption spectroscopy of distinctive spectro-temporal signatures of delocalized exciton versus relaxed, weakly bound excimer states in the ultrafast electronic deactivation after UV photoexcitation of the adenine dinucleotide.

The kinetics and mechanism of the organo-iridium catalysed racemisation of amines.

PubMed

Stirling, Matthew J; Mwansa, Joseph M; Sweeney, Gemma; Blacker, A John; Page, Michael I

2016-08-07

The dimeric iodo-iridium complex [IrCp*I2]2 (Cp* = pentamethylcyclopentadiene) is an efficient catalyst for the racemisation of secondary and tertiary amines at ambient and higher temperatures with a low catalyst loading. The racemisation occurs with pseudo-first-order kinetics and the corresponding four rate constants were obtained by monitoring the time dependence of the concentrations of the (R) and (S) enantiomers starting with either pure (R) or (S) and show a first-order dependence on catalyst concentration. Low temperature (1)H NMR data is consistent with the formation of a 1 : 1 complex with the amine coordinated to the iridium and with both iodide anions still bound to the metal-ion, but at the higher temperatures used for kinetic studies binding is weak and so no saturation zero-order kinetics are observed. A cross-over experiment with isotopically labelled amines demonstrates the intermediate formation of an imine which can dissociate from the iridium complex. Replacing the iodides in the catalyst by other ligands or having an amide substituent in Cp* results in a much less effective catalysts for the racemisation of amines. The rate constants for a deuterated amine yield a significant primary kinetic isotope effect kH/kD = 3.24 indicating that hydride transfer is involved in the rate-limiting step.

On the asymmetric autocatalysis of aldol reactions: The case of 4-nitrobenzaldehyde and acetone. A critical appraisal with a focus on theory.

PubMed

Romero-Fernández, M Pilar; Babiano, Reyes; Cintas, Pedro

2018-04-01

Under neutral conditions, spontaneous mirror symmetry breaking has been occasionally reported for aldol reactions starting from achiral reagents and conditions. Chiral induction might be interpreted in terms of autocatalysis exerted by chiral mono-aldol or bis-aldol products as source of initial enantiomeric excesses, which may account for such experimental observations. We describe here a thorough Density Functional Theory (DFT) study on this complex and otherwise difficult problem, which provides some insights into this phenomenon. The picture adds further rationale to an in-depth analysis by Moyano et al, who showed the isolation and characterization of bis-aldol adducts and their participation in a complex network of reversible steps. However, the lack of enantiodiscrimination (ees vanish rapidly in solution) suggests, according to the present results, a weak association in complexes formed by the catalysts and substrates. The latter would also be consistent with almost flat transition states having similar heights for competitive catalyst-bound transition structures (actually, we were unable to locate them at the level explored). Overall, neither autocatalysis as once conjectured nor mutual inhibition of enantiomers appears to be operating mechanisms. Asymmetric amplification in early stages harnessing unavoidable enantiomeric imbalances in reaction mixtures of chiral products represents a plausible interpretation. © 2018 Wiley Periodicals, Inc.

Absolute Configuration of 3-METHYLCYCLOHEXANONE by Chiral Tag Rotational Spectroscopy and Vibrational Circular Dichroism

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Holdren, Martin S.; Mayer, Kevin J.; Smart, Taylor; West, Channing; Pate, Brooks

2017-06-01

The absolute configuration of 3-methylcyclohexanone was established by chiral tag rotational spectroscopy measurements using 3-butyn-2-ol as the tag partner. This molecule was chosen because it is a benchmark measurement for vibrational circular dichroism (VCD). A comparison of the analysis approaches of chiral tag rotational spectroscopy and VCD will be presented. One important issue in chiral analysis by both methods is the conformational flexibility of the molecule being analyzed. The analysis of conformational composition of samples will be illustrated. In this case, the high spectral resolution of molecular rotational spectroscopy and potential for spectral simplification by conformational cooling in the pulsed jet expansion are advantages for chiral tag spectroscopy. The computational chemistry requirements for the two methods will also be discussed. In this case, the need to perform conformer searches for weakly bound complexes and to perform reasonably high level quantum chemistry geometry optimizations on these complexes makes the computational time requirements less favorable for chiral tag rotational spectroscopy. Finally, the issue of reliability of the determination of the absolute configuration will be considered. In this case, rotational spectroscopy offers a "gold standard" analysis method through the determination of the ^{13}C-subsitution structure of the complex between 3-methylcyclohexanone and an enantiopure sample of the 3-butyn-2-ol tag.

A method for deriving lower bounds for the complexity of monotone arithmetic circuits computing real polynomials

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

Gashkov, Sergey B; Sergeev, Igor' S

2012-10-31

This work suggests a method for deriving lower bounds for the complexity of polynomials with positive real coefficients implemented by circuits of functional elements over the monotone arithmetic basis {l_brace}x+y, x {center_dot} y{r_brace} Union {l_brace}a {center_dot} x | a Element-Of R{sub +}{r_brace}. Using this method, several new results are obtained. In particular, we construct examples of polynomials of degree m-1 in each of the n variables with coefficients 0 and 1 having additive monotone complexity m{sup (1-o(1))n} and multiplicative monotone complexity m{sup (1/2-o(1))n} as m{sup n}{yields}{infinity}. In this form, the lower bounds derived here are sharp. Bibliography: 72 titles.

Harmonic force spectroscopy reveals a force-velocity curve from a single human beta cardiac myosin motor

NASA Astrophysics Data System (ADS)

Sung, Jongmin; Nag, Suman; Vestergaard, Christian; Mortensen, Kim; Flyvbjerg, Henrik; Spudich, James

2014-03-01

A muscle contracts rapidly under low load, but slowly under high load. Its molecular mechanisms remain to be elucidated, however. During contraction, myosins in thick filaments interact with actin in thin filaments in the sarcomere, cycling between a strongly bound (force producing) state and a weakly bound (relaxed) state. Huxley et al. have previously proposed that the transition from the strong to the weak interaction can be modulated by a load. We use a new method we call ``harmonic force spectroscopy'' to extract a load-velocity curve from a single human beta cardiac myosin II motor. With a dual-beam optical trap, we hold an actin dumbbell over a myosin molecule anchored to the microscope stage that oscillates sinusoidally. Upon binding, the motor experiences an oscillatory load with a mean that is directed forward or backward, depending on binding location We find that the bound time at saturating [ATP] is exponentially correlated with the mean load, which is explained by Arrhenius transition theory. With a stroke size measurement, we obtained a load-velocity curve from a single myosin. We compare the curves for wild-type motors with mutants that cause hypertrophic cardiomyopathies, to understand the effects on the contractile cycle

Hydrogen-bonding interactions and protic equilibria in room-temperature ionic liquids containing crown ethers.

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

Marin, T.; Shkrob, I.; Dietz, M.

2011-04-14

Nuclear magnetic resonance (NMR) spectroscopy has been used to study hydrogen-bonding interactions between water, associated and dissociated acids (i.e., nitric and methanesulfonic acids), and the constituent ions of several water-immiscible room-temperature ionic liquids (ILs). In chloroform solutions also containing a crown ether (CE), water molecules strongly associate with the IL ions, and there is rapid proton exchange between these bound water molecules and hydronium associated with the CE. In neat ILs, the acids form clusters differing in their degree of association and ionization, and their interactions with the CEs are weak. The CE can either promote proton exchange between differentmore » clusters in IL solution when their association is weak or inhibit such exchange when the association is strong. Even strongly hydrophobic ILs are shown to readily extract nitric acid from aqueous solution, typically via the formation of a 1:1:1 {l_brace}H{sub 3}O{sup +} {center_dot} CE{r_brace}NO{sub 3}{sup -} complex. In contrast, the extraction of methanesulfonic acid is less extensive and proceeds mainly by IL cation-hydronium ion exchange. The relationship of these protic equilibria to the practical application of hydrophobic ILs (e.g., in spent nuclear fuel reprocessing) is discussed.« less

Evaluating the Energetic Driving Force for Cocrystal Formation

PubMed Central

2017-01-01

We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol–1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems—hydrogen-bonded, halogen-bonded, and weakly bound cocrystals—finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition—more densely packed cocrystals with stronger hydrogen bonding tend to be more stable—but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems. PMID:29445316

Evaluating the Energetic Driving Force for Cocrystal Formation.

PubMed

Taylor, Christopher R; Day, Graeme M

2018-02-07

We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol -1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems-hydrogen-bonded, halogen-bonded, and weakly bound cocrystals-finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition-more densely packed cocrystals with stronger hydrogen bonding tend to be more stable-but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems.

Ligand Binding Phenomena that Pertain to the Metabolic Function of Renalase

PubMed Central

Beaupre, Brett A.; Roman, Joseph V.; Hoag, Matthew R.; Meneely, Kathleen M.; Silvaggi, Nicholas R.; Lamb, Audrey L.; Moran, Graham R.

2017-01-01

Renalase catalyzes the oxidation of isomers of β-NAD(P)H that carry the hydride in the 2 or 6 positions of the nicotinamide base to form β-NAD(P)+. This activity is thought to alleviate inhibition of multiple β-NAD(P)-dependent enzymes of primary and secondary metabolism by these isomers. Here we present evidence for a variety of ligand binding phenomena relevant to the function of renalase. We offer evidence of the potential for primary metabolism inhibition with structures of malate dehydrogenase and lactate dehydrogenase bound to the 6-dihydroNAD isomer. The previously observed preference of renalase from Pseudomonas for NAD-derived substrates over those derived from NADP is accounted for by the structure of the enzyme in complex with NADPH. We also show that nicotinamide nucleosides and mononucloetides reduced in the 2- and 6-positions are renalase substrates, but bind weakly. A seven-fold enhancement of acquisition (kred/Kd) for 6-dihydronicotinamide riboside was observed for human renalase in the presence of ADP. However, generally the addition of complement ligands, ADP for mononucloetide or AMP for nucleoside substrates, did not enhance the reductive half-reaction. Non-substrate nicotinamide nucleosides or nucleotides bind weakly suggesting that only β-NADH and β-NADPH compete with dinucleotide substrates for access to the active site. PMID:27769837

Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

Physicochemical characterization of mineral (iron/zinc) bound caseinate and their mineral uptake in Caco-2 cells.

PubMed

Shilpashree, B G; Arora, Sumit; Kapila, Suman; Sharma, Vivek

2018-08-15

Milk proteins (especially caseins) are widely accepted as good vehicle for the delivery of various bioactive compounds including minerals. Succinylation is one of the most acceptable chemical modification techniques to enhance the mineral binding ability of caseins. Addition of minerals to succinylated proteins may alter their physicochemical and biochemical properties. Physicochemical characteristics of succinylated sodium caseinate (S.NaCN)-mineral (iron/zinc) complexes were elucidated. Chromatographic behaviour and fluorescence intensity confirmed the structural modification of S.NaCN upon binding with minerals. The bound mineral from protein complexes showed significantly higher (P < 0.05) in vitro bioavailability (mineral uptake) than mineral salts in Caco-2 cells. Also, iron bound S.NaCN showed higher cellular ferritin formation than iron in its free form. These mineral bound protein complexes with improved bioavailability could safely replace inorganic fortificants in various functional food formulations. Copyright © 2018 Elsevier Ltd. All rights reserved.

Reaction dynamics studies for the system 7Be+58Ni

NASA Astrophysics Data System (ADS)

Torresi, D.; Mazzocco, M.; Acosta, L.; Boiano, A.; Boiano, C.; Diaz-Torres, A.; Fierro, N.; Glodariu, T.; Grilj, L.; Guglielmetti, A.; Keeley, N.; La Commara, M.; Martel, I.; Mazzocchi, C.; Molini, P.; Pakou, A.; Parascandolo, C.; Parkar, V. V.; Patronis, N.; Pierroutsakou, D.; Romoli, M.; Rusek, K.; Sanchez-Benitez, A. M.; Sandoli, M.; Signorini, C.; Silvestri, R.; Soramel, F.; Stiliaris, E.; Strano, E.; Stroe, L.; Zerva, K.

2015-04-01

The study of reactions induced by exotic weakly bound nuclei at energies around the Coulomb barrier had attracted a large interest in the last decade, since the features of these nuclei can deeply affect the reaction dynamics. The discrimination between different reaction mechanisms is, in general, a rather difficult task. It can be achieved by using detector arrays covering high solid angle and with high granularity that allow to measure the reaction products and, possibly, coincidences between them, as, for example, recently done for stable weakly bound nuclei [1, 2]. We investigated the collision of the weakly bound nucleus 7Be on a 58Ni target at the beam energy of 1.1 times the Coulomb barrier, measuring the elastic scattering angular distribution and the energy and angular distributions of 3He and 4He. The 7Be radioactive ion beam was produced by the facility EXOTIC at INFN-LNL with an energy of 22 MeV and an intensity of ~3×105 pps. Results showed that the 4He yeld is about 4 times larger than 3He yield, suggesting that reaction mechanisms other than the break-up mostly produce the He isotopes. Theoretical calculations for transfer channels and compound nucleus reactions suggest that complete fusion accounts for (41±5%) of the total reaction cross section extracted from optical model analysis of the elastic scattering data, and that 3He and 4He stripping are the most populated reaction channels among direct processes. Eventually estimation of incomplete fusion contributions to the 3,4He production cross sections was performed through semi-classical calculations with the code PLATYPUS [3].

Evidence for the Existence of One Antenna-Associated, Lipid-Dissolved and Two Protein-Bound Pools of Diadinoxanthin Cycle Pigments in Diatoms[C][W

PubMed Central

Lepetit, Bernard; Volke, Daniela; Gilbert, Matthias; Wilhelm, Christian; Goss, Reimund

2010-01-01

We studied the localization of diadinoxanthin cycle pigments in the diatoms Cyclotella meneghiniana and Phaeodactylum tricornutum. Isolation of pigment protein complexes revealed that the majority of high-light-synthesized diadinoxanthin and diatoxanthin is associated with the fucoxanthin chlorophyll protein (FCP) complexes. The characterization of intact cells, thylakoid membranes, and pigment protein complexes by absorption and low-temperature fluorescence spectroscopy showed that the FCPs contain certain amounts of protein-bound diadinoxanthin cycle pigments, which are not significantly different in high-light and low-light cultures. The largest part of high-light-formed diadinoxanthin cycle pigments, however, is not bound to antenna apoproteins but located in a lipid shield around the FCPs, which is copurified with the complexes. This lipid shield is primarily composed of the thylakoid membrane lipid monogalactosyldiacylglycerol. We also show that the photosystem I (PSI) fraction contains a tightly connected FCP complex that is enriched in protein-bound diadinoxanthin cycle pigments. The peripheral FCP and the FCP associated with PSI are composed of different apoproteins. Tandem mass spectrometry analysis revealed that the peripheral FCP is composed mainly of the light-harvesting complex protein Lhcf and also significant amounts of Lhcr. The PSI fraction, on the other hand, shows an enrichment of Lhcr proteins, which are thus responsible for the diadinoxanthin cycle pigment binding. The existence of lipid-dissolved and protein-bound diadinoxanthin cycle pigments in the peripheral antenna and in PSI is discussed with respect to different specific functions of the xanthophylls. PMID:20935178

Vibrational Stark effect spectroscopy at the interface of Ras and Rap1A bound to the Ras binding domain of RalGDS reveals an electrostatic mechanism for protein-protein interaction.

PubMed

Stafford, Amy J; Ensign, Daniel L; Webb, Lauren J

2010-11-25

Electrostatic fields at the interface of the Ras binding domain of the protein Ral guanine nucleotide dissociation stimulator (RalGDS) with the structurally analogous GTPases Ras and Rap1A were measured with vibrational Stark effect (VSE) spectroscopy. Eleven residues on the surface of RalGDS that participate in this protein-protein interaction were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe in the form of the thiocyanate (SCN) functional group. The measured SCN absorption energy on the monomeric protein was compared with solvent-accessible surface area (SASA) calculations and solutions to the Poisson-Boltzmann equation using Boltzmann-weighted structural snapshots from molecular dynamics simulations. We found a weak negative correlation between SASA and measured absorption energy, indicating that water exposure of protein surface amino acids can be estimated from experimental measurement of the magnitude of the thiocyanate absorption energy. We found no correlation between calculated field and measured absorption energy. These results highlight the complex structural and electrostatic nature of the protein-water interface. The SCN-labeled RalGDS was incubated with either wild-type Ras or wild-type Rap1A, and the formation of the docked complex was confirmed by measurement of the dissociation constant of the interaction. The change in absorption energy of the thiocyanate functional group due to complex formation was related to the change in electrostatic field experienced by the nitrile functional group when the protein-protein interface forms. At some locations, the nitrile experiences the same shift in field when bound to Ras and Rap1A, but at others, the change in field is dramatically different. These differences identify residues on the surface of RalGDS that direct the specificity of RalGDS binding to its in vivo binding partner, Rap1A, through an electrostatic mechanism.

Grid-based lattice summation of electrostatic potentials by assembled rank-structured tensor approximation

NASA Astrophysics Data System (ADS)

Khoromskaia, Venera; Khoromskij, Boris N.

2014-12-01

Our recent method for low-rank tensor representation of sums of the arbitrarily positioned electrostatic potentials discretized on a 3D Cartesian grid reduces the 3D tensor summation to operations involving only 1D vectors however retaining the linear complexity scaling in the number of potentials. Here, we introduce and study a novel tensor approach for fast and accurate assembled summation of a large number of lattice-allocated potentials represented on 3D N × N × N grid with the computational requirements only weakly dependent on the number of summed potentials. It is based on the assembled low-rank canonical tensor representations of the collected potentials using pointwise sums of shifted canonical vectors representing the single generating function, say the Newton kernel. For a sum of electrostatic potentials over L × L × L lattice embedded in a box the required storage scales linearly in the 1D grid-size, O(N) , while the numerical cost is estimated by O(NL) . For periodic boundary conditions, the storage demand remains proportional to the 1D grid-size of a unit cell, n = N / L, while the numerical cost reduces to O(N) , that outperforms the FFT-based Ewald-type summation algorithms of complexity O(N3 log N) . The complexity in the grid parameter N can be reduced even to the logarithmic scale O(log N) by using data-sparse representation of canonical N-vectors via the quantics tensor approximation. For justification, we prove an upper bound on the quantics ranks for the canonical vectors in the overall lattice sum. The presented approach is beneficial in applications which require further functional calculus with the lattice potential, say, scalar product with a function, integration or differentiation, which can be performed easily in tensor arithmetics on large 3D grids with 1D cost. Numerical tests illustrate the performance of the tensor summation method and confirm the estimated bounds on the tensor ranks.

Three-color single molecule imaging shows WASP detachment from Arp2/3 complex triggers actin filament branch formation.

PubMed

Smith, Benjamin A; Padrick, Shae B; Doolittle, Lynda K; Daugherty-Clarke, Karen; Corrêa, Ivan R; Xu, Ming-Qun; Goode, Bruce L; Rosen, Michael K; Gelles, Jeff

2013-09-03

During cell locomotion and endocytosis, membrane-tethered WASP proteins stimulate actin filament nucleation by the Arp2/3 complex. This process generates highly branched arrays of filaments that grow toward the membrane to which they are tethered, a conflict that seemingly would restrict filament growth. Using three-color single-molecule imaging in vitro we revealed how the dynamic associations of Arp2/3 complex with mother filament and WASP are temporally coordinated with initiation of daughter filament growth. We found that WASP proteins dissociated from filament-bound Arp2/3 complex prior to new filament growth. Further, mutations that accelerated release of WASP from filament-bound Arp2/3 complex proportionally accelerated branch formation. These data suggest that while WASP promotes formation of pre-nucleation complexes, filament growth cannot occur until it is triggered by WASP release. This provides a mechanism by which membrane-bound WASP proteins can stimulate network growth without restraining it. DOI:http://dx.doi.org/10.7554/eLife.01008.001.

Photoswitching a Molecular Catalyst to Regulate CO 2 Hydrogenation

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

Priyadarshani, Nilusha; Ginovska-Pangovska, Bojana; Bays, J. Timothy

2015-07-24

Inspired by nature’s ability to regulate catalysis using physiological stimuli, azobenzene was incorporated into Rh(bis)diphosphine CO 2 hydrogenation catalysts to photoinitiate structural changes to modulate the resulting catalytic activity. The rhodium bound diphosphine ligands (P(Ph 2)-CH 2-N(R) CH 2-P(Ph2)) contain the terminal amine of a non-natural amino acid, either β-alanine (β-Ala) or γ-aminobutyric acid (GABA). For both β-ala and GABA containing complexes, the carboxylic acids of the amino acids were coupled to the amines of diaminoazobenzene, creating a rhodium bound trans-spanning tetraphosphine complex. The photo-induced cis-trans isomerization of the azobenzene-containing complexes imposes structural changes on these complexes, as evidenced bymore » 1H NMR. We found that the CO 2 hydrogenation activity for the β-ala bound Rh complex is 40% faster with azobenzene in the cis configuration (16 s -1) than in the trans conformation (11 s -1), while the γ-aminobutyric acid containing Rh complex has the same rate (~17 s -1) in either the cis or the trans configuration at 27 °C. The corresponding complexes without the attached azobenzene were also prepared, characterized, and catalytically tested for comparison, and have rates of 30 s -1. Computational studies were undertaken to evaluate the difference in rate between the cis and trans isomers for the β-Ala bound Rh complex, and revealed major structural changes between all cis and trans structures, but only minor structural changes that would be unique to the β-Ala bound Rh complex. We postulate that the slower rate of the azobenzene-containing β-Ala bound Rh complex is due to subtle changes in the bite angle arising from steric strain due to the trans-spanning azobenzene, altering hydricity and consequently rate. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for the DOE by Battelle. A portion of this research was performed using EMSL, 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.« less

Salmon theology: Return to traditional reasoning

Treesearch

Joseph Clair

2007-01-01

When beauty and utility are divorced in the loss of wonder, beauty begins to perish. Salmon go extinct. The fragility of beauty is the fragility of wilderness. It does not perish due to weakness but from the generosity and vulnerability that are bound up with its usefulness.

Phase behaviour and structure of stable complexes of oppositely charged polyelectrolytes

NASA Astrophysics Data System (ADS)

Mengarelli, V.; Auvray, L.; Zeghal, M.

2009-03-01

We study the formation and structure of stable electrostatic complexes between oppositely charged polyelectrolytes, a long polymethacrylic acid and a shorter polyethylenimine, at low pH, where the polyacid is weakly charged. We explore the phase diagram as a function of the charge and concentration ratio of the constituents. In agreement with theory, turbidity and ζ potential measurements show two distinct regimes of weak and strong complexation, which appear successively as the pH is increased and are separated by a well-defined limit. Weak complexes observed by neutron scattering and contrast matching have an open, non-compact structure, while strong complexes are condensed.

Multi-site binding of epigallocatechin gallate to human serum albumin measured by NMR and isothermal titration calorimetry

PubMed Central

Eaton, Joshua D.

2017-01-01

The affinity of epigallocatechin gallate (EGCG) for human serum albumin (HSA) was measured in physiological conditions using NMR and isothermal titration calorimetry (ITC). NMR estimated the Ka (self-dissociation constant) of EGCG as 50 mM. NMR showed two binding events: strong (n1=1.8 ± 0.2; Kd1 =19 ± 12 μM) and weak (n2∼20; Kd2 =40 ± 20 mM). ITC also showed two binding events: strong (n1=2.5 ± 0.03; Kd1 =21.6 ± 4.0 μM) and weak (n2=9 ± 1; Kd2 =22 ± 4 mM). The two techniques are consistent, with an unexpectedly high number of bound EGCG. The strong binding is consistent with binding in the two Sudlow pockets. These results imply that almost all EGCG is transported in the blood bound to albumin and explains the wide tissue distribution and chemical stability of EGCG in vivo. PMID:28424370

8B + 208Pb Elastic Scattering at Coulomb Barrier Energies

NASA Astrophysics Data System (ADS)

La Commara, M.; Mazzocco, M.; Boiano, A.; Boiano, C.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Signorini, C.; Strano, E.; Torresi, D.; Yamaguchi, H.; Kahl, D.; Di Meo, P.; Grebosz, J.; Imai, N.; Hirayama, Y.; Ishiyama, H.; Iwasa, N.; Jeong, S. C.; Jia, H. M.; Kim, Y. H.; Kimura, S.; Kubono, S.; Lin, C. J.; Miyatake, H.; Mukai, M.; Nakao, T.; Nicoletto, M.; Sakaguchi, Y.; Sánchez-Benítez, A. M.; Soramel, F.; Teranishi, T.; Wakabayashi, Y.; Watanabe, Y. X.; Yang, L.; Yang, Y. Y.

2018-02-01

The scattering process of weakly-bound nuclei at Coulomb barrier energies provides deep insights on the reaction dynamics induced by exotic nuclei. Within this framework, we measured for the first time the scattering process of the short-lived Radioactive Ion Beam (RIB) 8B (Sp = 0.1375 MeV) from a 208Pb target at 50 MeV beam energy. The 8B RIB was produced by means of the in-flight facility CRIB (RIKEN, Japan) with an average intensity on target of 10 kHz and a purity about 25%. Elastically scattering ions were detected in the angular range θc.m. = 10°-160° by means of the detector array EXPADES. A preliminary optical model analysis indicates a total reaction cross section of about 1 b, a value, once reduced, 2-3 times larger than those obtained for the reactions induced by the stable weakly-bound projectiles 6,7Li on a 208Pb target in the energy range around the Coulomb barrier.

8B + 208Pb Elastic Scattering at Coulomb Barrier Energies

NASA Astrophysics Data System (ADS)

La Commara, M.; Mazzocco, M.; Boiano, A.; Boiano, C.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Signorini, C.; Strano, E.; Torresi, D.; Yamaguchi, H.; Kahl, D.; Di Meo, P.; Grebosz, J.; Imai, N.; Hirayama, Y.; Ishiyama, H.; Iwasa, N.; Jeong, S. C.; Jia, H. M.; Kim, Y. H.; Kimura, S.; Kubono, S.; Lin, C. J.; Miyatake, H.; Mukai, M.; Nakao, T.; Nicoletto, M.; Sakaguchi, Y.; Sánchez-Benítez, A. M.; Soramel, F.; Teranishi, T.; Wakabayashi, Y.; Watanabe, Y. X.; Yang, L.; Yang, Y. Y.

2017-11-01

The scattering process of weakly-bound nuclei at Coulomb barrier energies provides deep insights on the reaction dynamics induced by exotic nuclei. Within this framework, we measured for the first time the scattering process of the short-lived Radioactive Ion Beam (RIB) 8B (S p = 0.1375 MeV) from a 208Pb target at 50 MeV beam energy. The 8B RIB was produced by means of the in-flight facility CRIB (RIKEN, Japan) with an average intensity on target of 10 kHz and a purity about 25%. Elastically scattering ions were detected in the angular range θc.m. = 10°-160° by means of the detector array EXPADES. A preliminary optical model analysis indicates a total reaction cross section of about 1 b, a value, once reduced, 2-3 times larger than those obtained for the reactions induced by the stable weakly-bound projectiles 6,7Li on a 208Pb target in the energy range around the Coulomb barrier.

Mechanistic Insight into Nanoparticle Surface Adsorption by Solution NMR Spectroscopy in an Aqueous Gel

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

Egner, Timothy K.; Naik, Pranjali; Nelson, Nicholas C.

Engineering nanoparticle (NP) functions at the molecular level requires a detailed understanding of the dynamic processes occurring at the NP surface. Herein we show that a combination of dark-state exchange saturation transfer (DEST) and relaxation dispersion (RD) NMR experiments on gel-stabilized NP samples enables the accurate determination of the kinetics and thermodynamics of adsorption. We used the former approach to describe the interaction of cholic acid (CA) and phenol (PhOH) with ceria NPs with a diameter of approximately 200 nm. Whereas CA formed weak interactions with the NPs, PhOH was tightly bound to the NP surface. Interestingly, we found thatmore » the adsorption of PhOH proceeds via an intermediate, weakly bound state in which the small molecule has residual degrees of rotational diffusion. Here we believe the use of aqueous gels for stabilizing NP samples will increase the applicability of solution NMR methods to the characterization of nanomaterials.« less

Mechanistic Insight into Nanoparticle Surface Adsorption by Solution NMR Spectroscopy in an Aqueous Gel

DOE PAGES

Egner, Timothy K.; Naik, Pranjali; Nelson, Nicholas C.; ...

2017-06-22

Engineering nanoparticle (NP) functions at the molecular level requires a detailed understanding of the dynamic processes occurring at the NP surface. Herein we show that a combination of dark-state exchange saturation transfer (DEST) and relaxation dispersion (RD) NMR experiments on gel-stabilized NP samples enables the accurate determination of the kinetics and thermodynamics of adsorption. We used the former approach to describe the interaction of cholic acid (CA) and phenol (PhOH) with ceria NPs with a diameter of approximately 200 nm. Whereas CA formed weak interactions with the NPs, PhOH was tightly bound to the NP surface. Interestingly, we found thatmore » the adsorption of PhOH proceeds via an intermediate, weakly bound state in which the small molecule has residual degrees of rotational diffusion. Here we believe the use of aqueous gels for stabilizing NP samples will increase the applicability of solution NMR methods to the characterization of nanomaterials.« less

Energy transfer studies in krypton-xenon mixtures excited in a cooled DC discharge

NASA Astrophysics Data System (ADS)

Krylov, B.; Gerasimov, G.; Morozov, A.; Arnesen, A.; Hallin, R.; Heijkenskjold, F.

2000-01-01

The VUV spectrum of gaseous mixtures of krypton with a small amount of xenon added was investigated in the range 115-200 nm. The mixtures were excited in a capillary DC discharge where the capillary could be cooled by using liquid nitrogen. The mixed molecule band around the Xe I resonance line at λ = 147 nm and the mixed molecule continuum to the long wavelength side from the line were analysed. The band around λ = 147 nm was identified as transitions between a weakly bound excited state and the weakly bound ground state of XeKr molecules. When cooling the capillary wall, the appearance of the Xe2 continuum was observed. The effect is ascribed to energy transfer between molecular states as a consequence of radiation trapping in the band around λ = 147 nm. The role of the mixed molecule in the formation of the VUV spectrum of the gas mixture is discussed and underlined.

The Energy Measure for the Euler and Navier-Stokes Equations

NASA Astrophysics Data System (ADS)

Leslie, Trevor M.; Shvydkoy, Roman

2018-04-01

The potential failure of energy equality for a solution u of the Euler or Navier-Stokes equations can be quantified using a so-called `energy measure': the weak-* limit of the measures {|u(t)|^2dx} as t approaches the first possible blowup time. We show that membership of u in certain (weak or strong) {L^q L^p} classes gives a uniform lower bound on the lower local dimension of E ; more precisely, it implies uniform boundedness of a certain upper s-density of E . We also define and give lower bounds on the `concentration dimension' associated to E , which is the Hausdorff dimension of the smallest set on which energy can concentrate. Both the lower local dimension and the concentration dimension of E measure the departure from energy equality. As an application of our estimates, we prove that any solution to the 3-dimensional Navier-Stokes Equations which is Type-I in time must satisfy the energy equality at the first blowup time.

Cyclotron transitions of bound ions

NASA Astrophysics Data System (ADS)

Bezchastnov, Victor G.; Pavlov, George G.

2017-06-01

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

Transfer of energy in Camassa-Holm and related models by use of nonunique characteristics

NASA Astrophysics Data System (ADS)

Jamróz, Grzegorz

2017-02-01

We study the propagation of energy density in finite-energy weak solutions of the Camassa-Holm and related equations. Developing the methods based on generalized nonunique characteristics, we show that the parts of energy related to positive and negative slopes are one-sided weakly continuous and of bounded variation, which allows us to define certain measures of dissipation of both parts of energy. The result is a step towards the open problem of uniqueness of dissipative solutions of the Camassa-Holm equation.

Synergistic capture of Clostridium botulinum Type A neurotoxin by scFv antibodies to novel epitopes

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

Gray, Sean A.; Barr, John R.; Kalb, Suzanne R.

2011-10-01

A non-immune library of human single chain fragment variable (scFv) antibodies displayed on Saccharomyces cerevisiae was screened for binding to the Clostridium botulinum neurotoxin serotype A binding domain [BoNT/A (Hc)] with the goal of identifying scFv to novel epitopes. To do this, an antibody-mediated labeling strategy was used in which antigen-binding yeast clones were selected after labeling with previously characterized monoclonal antibodies (MAbs) specific to the Hc. Twenty unique scFv clones were isolated that bound Hc. Of these, three also bound to full-length BoNT/A toxin complex with affinities ranging from 5 nM to 170 nM. Epitope binning showed that themore » three unique clones recognized at least two epitopes that were distinct from one another and from the detection MAbs. After production in E. coli, the scFv were coupled to magnetic particles and tested for their ability to capture BoNT/A holotoxin using an Endopep-MS assay. In this assay, toxin captured by scFv coated magnetic particles was detected by incubation of the complex with a peptide containing a BoNT/A-specific cleavage sequence. Mass spectrometry was used to detect the ratio of intact peptide to cleavage products as evidence for toxin capture. When tested individually, each of the scFv showed a weak positive Endopep-MS result. However, when the particles were coated with all three scFv simultaneously, they exhibited significantly higher Endopep-MS activity, consistent with synergistic binding. These results demonstrate novel approaches toward the isolation and characterization of scFv antibodies specific to unlabeled antigen. They also provide evidence that distinct scFv antibodies can work synergistically to increase the efficiency of antigen capture onto a solid support.« less

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

Rebowski, Grzegorz; Namgoong, Suk; Boczkowska, Malgorzata

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

Ab initio based study of the ArO- photoelectron spectra: Selectivity of spin-orbit transitions

NASA Astrophysics Data System (ADS)

Buchachenko, A. A.; Jakowski, Jacek; Chałasiński, Grzegorz; Szczȩśniak, M. M.; Cybulski, S. M.

2000-04-01

A combined ab initio atoms-in-molecule approach was implemented to model the photoelectron spectra of the ArO- anion. The lowest adiabatic states of Σ and Π symmetry of ArO and ArO- were investigated using the fourth-order Møller-Plessett perturbation theory including bond functions. The total energies were dissected into electrostatic, exchange, induction, and dispersion components. The complex of Ar with atomic oxygen is only weakly bound, primarily by dispersion interaction. The Π state possesses a deeper minimum (Re=3.4Å,De=380μEh) than the Σ state (Re=3.8Å,De=220μEh). In contrast, the anion complex is fairly strongly bound, primarily by ion-induced dipole induction forces, and the Σ state possesses a deeper minimum at shorter interatomic distances (Re=3.02Å,De=3600μEh) than the Π state (Re=3.35Å,De=2400μEh). The Σ-Π splittings in both systems are mainly due to differences in the exchange repulsion terms. Atoms-in-molecule models were used to account for the spin-orbit interaction, and to generate adiabatic relativistic potentials and wave functions. Collisional properties, diffusion, and mobility coefficients of O and O- in Ar, and absolute total Ar+O scattering cross sections, were calculated and found to agree well with the available experimental data. The photoelectron spectra were simulated within vibronic model, and were found in excellent agreement with the experimental measurements. The bimodal electron kinetic energy distribution was shown to stem from the strong selectivity of spin-orbit transitions, which split into two dense groups, depending on the initial electronic state of the anion. The latter feature cannot be described without explicit consideration of electronic intensity factor.

Subunit mass fingerprinting of mitochondrial complex I.

PubMed

Morgner, Nina; Zickermann, Volker; Kerscher, Stefan; Wittig, Ilka; Abdrakhmanova, Albina; Barth, Hans-Dieter; Brutschy, Bernhard; Brandt, Ulrich

2008-10-01

We have employed laser induced liquid bead ion desorption (LILBID) mass spectrometry to determine the total mass and to study the subunit composition of respiratory chain complex I from Yarrowia lipolytica. Using 5-10 pmol of purified complex I, we could assign all 40 known subunits of this membrane bound multiprotein complex to peaks in LILBID subunit fingerprint spectra by comparing predicted protein masses to observed ion masses. Notably, even the highly hydrophobic subunits encoded by the mitochondrial genome were easily detectable. Moreover, the LILBID approach allowed us to spot and correct several errors in the genome-derived protein sequences of complex I subunits. Typically, the masses of the individual subunits as determined by LILBID mass spectrometry were within 100 Da of the predicted values. For the first time, we demonstrate that LILBID spectrometry can be successfully applied to a complex I band eluted from a blue-native polyacrylamide gel, making small amounts of large multiprotein complexes accessible for subunit mass fingerprint analysis even if they are membrane bound. Thus, the LILBID subunit mass fingerprint method will be of great value for efficient proteomic analysis of complex I and its assembly intermediates, as well as of other water soluble and membrane bound multiprotein complexes.

A series of Ln-p-chlorobenzoic acid–terpyridine complexes: lanthanide contraction effects, supramolecular interactions and luminescent behavior

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

Carter, Korey P.; Pope, Simon J. A.; Cahill, Christopher L.

Fifteen new lanthanide p-chlorobenzoic acid complexes, [PrL3(terpy)(H2O)]2 (1), [LnL3(terpy)(H2O)]2 (Ln = Nd (2), Sm (3), and Eu (4)), and [LnL3(terpy)(H2O)] (Ln = Sm (3'), Eu (4'), Gd (5), Tb (6), Dy (7), Ho (8), Er (9), Tm (10), Yb (11), Lu (12), and Y (13); HL: p-chlorobenzoic acid; terpy: 2,2':6',2''-terpyridine), have been synthesized hydrothermally at varying temperatures and structurally characterized by single crystal and powder X-ray diffraction. The series is comprised of binuclear molecular units (Pr–Eu) that give way to mononuclear molecular complexes (Sm–Y) as the lanthanide contraction takes effect. All fifteen complexes feature a tridentate terpyridine ligand, p-chlorobenzoic acidmore » ligands exhibiting multiple binding modes, bidentate, bridging bidentate, and monodentate, and a bound water molecule. Binuclear complexes 1–4 are stitched together via intermolecular interactions: aromatic–aromatic interactions for 1, halogen•••halogen interactions for 2–4, to form 1D chains. Mononuclear complexes 3', 4', and 5–13 utilize supramolecular hydrogen and halogen bonding to form 2D sheets. Visible and near-IR solid state luminescence studies were performed on complexes 2, 3, 3', 4, 4', 6, 7 and 11 and the characteristic visible luminescence of Sm(III), Eu(III), Tb(III), and Dy(III) was exhibited. The near-IR spectra of the Nd(III) and Yb(III) complexes exhibit weak characteristic luminescence, showing that terpy can act as a sensitizing chromophore in these systems.« less

From "Weak" to "Strong" Multifunctionality: Conceptualising Farm-Level Multifunctional Transitional Pathways

ERIC Educational Resources Information Center

Wilson, Geoff A.

2008-01-01

Building on normative conceptualisations of multifunctionality as a decision-making spectrum bounded by productivist and non-productivist action and thought, this paper analyses farm-level multifunctional agricultural transitions. First, the paper suggests that it may be possible to categorise different farm types along the…

Partial stabilisation of non-homogeneous bilinear systems

NASA Astrophysics Data System (ADS)

Hamidi, Z.; Ouzahra, M.

2018-06-01

In this work, we study in a Hilbert state space, the partial stabilisation of non-homogeneous bilinear systems using a bounded control. Necessary and sufficient conditions for weak and strong stabilisation are formulated in term of approximate observability like assumptions. Applications to parabolic and hyperbolic equations are presented.

Synthesis, crystal structure and DFT studies of a Zinc(II) complex of 1,3-diaminopropane (Dap), [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]n. The additional stabilizing role of S⋯π chalcogen bond

NASA Astrophysics Data System (ADS)

Alotaibi, Mshari A.; Alharthi, Abdulrahman I.; Zierkiewicz, Wiktor; Akhtar, Muhammad; Tahir, Muhammad Nawaz; Mazhar, Muhammad; Isab, Anvarhusein A.; Ahmad, Saeed

2017-04-01

A zinc(II) complex of 1,3-diaminopropane (Dap), [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]n (1) has been prepared and characterized by elemental analysis, IR, 1H &13C NMR spectroscopy, and its crystal structure was determined by X-ray crystallography. The crystal structure of 1 consists of two types of molecules, a discrete monomer and a polymeric one. In the monomeric unit, the zinc atom is bound to one terminal Dap molecule and to two N-bound thiocyanate ions, while in the polymeric unit, Dap acts as a bridging ligand forming a linear chain. The Zn(II) ions in both assume a slightly distorted tetrahedral geometry. The structures of two systems: the [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]3 complex as a model of 1 and [Zn(Dap)(NCS)2]4 as a simple polymeric structure were optimized with the B3LYP-D3 method. The DFT results support that the experimentally determined structure (1) is more stable in comparison to a simple polymeric structure, [Zn(Dap)(NCS)2]n (2). The interaction energies (ΔE) for NCS anions obtained by B3LYP-D3 method are about -145 kcal mol-1, while the calculated ΔE values for neutral organic ligands are about twice smaller. The X-ray structure of 1 shows that the complex is stabilized mainly by hydrogen bonds. We also found that weak chalcogen bonds play an additional role in stabilization of compound 1. Some of the intermolecular S⋯N distances are smaller than the sum of the van der Waals radii of the corresponding atoms. To the best of our knowledge, this is the first study that shows the structure where the trivalent sulfur is involved in formation of a S⋯π chalcogen bond. The NBO and NCI analyses confirm the existence of this kind of interactions.

Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface.

PubMed

Buryak, Ilya; Vigasin, Andrey A

2015-12-21

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

Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

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

Buryak, Ilya; Vigasin, Andrey A., E-mail: vigasin@ifaran.ru

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

Potential estimates for the p-Laplace system with data in divergence form

NASA Astrophysics Data System (ADS)

Cianchi, A.; Schwarzacher, S.

2018-07-01

A pointwise bound for local weak solutions to the p-Laplace system is established in terms of data on the right-hand side in divergence form. The relevant bound involves a Havin-Maz'ya-Wolff potential of the datum, and is a counterpart for data in divergence form of a classical result of [25], recently extended to systems in [28]. A local bound for oscillations is also provided. These results allow for a unified approach to regularity estimates for broad classes of norms, including Banach function norms (e.g. Lebesgue, Lorentz and Orlicz norms), and norms depending on the oscillation of functions (e.g. Hölder, BMO and, more generally, Campanato type norms). In particular, new regularity properties are exhibited, and well-known results are easily recovered.

Wigner's quantum phase-space current in weakly-anharmonic weakly-excited two-state systems

NASA Astrophysics Data System (ADS)

Kakofengitis, Dimitris; Steuernagel, Ole

2017-09-01

There are no phase-space trajectories for anharmonic quantum systems, but Wigner's phase-space representation of quantum mechanics features Wigner current J . This current reveals fine details of quantum dynamics —finer than is ordinarily thought accessible according to quantum folklore invoking Heisenberg's uncertainty principle. Here, we focus on the simplest, most intuitive, and analytically accessible aspects of J. We investigate features of J for bound states of time-reversible, weakly-anharmonic one-dimensional quantum-mechanical systems which are weakly-excited. We establish that weakly-anharmonic potentials can be grouped into three distinct classes: hard, soft, and odd potentials. We stress connections between each other and the harmonic case. We show that their Wigner current fieldline patterns can be characterised by J's discrete stagnation points, how these arise and how a quantum system's dynamics is constrained by the stagnation points' topological charge conservation. We additionally show that quantum dynamics in phase space, in the case of vanishing Planck constant ℏ or vanishing anharmonicity, does not pointwise converge to classical dynamics.

Regularity gradient estimates for weak solutions of singular quasi-linear parabolic equations

NASA Astrophysics Data System (ADS)

Phan, Tuoc

2017-12-01

This paper studies the Sobolev regularity for weak solutions of a class of singular quasi-linear parabolic problems of the form ut -div [ A (x , t , u , ∇u) ] =div [ F ] with homogeneous Dirichlet boundary conditions over bounded spatial domains. Our main focus is on the case that the vector coefficients A are discontinuous and singular in (x , t)-variables, and dependent on the solution u. Global and interior weighted W 1 , p (ΩT , ω)-regularity estimates are established for weak solutions of these equations, where ω is a weight function in some Muckenhoupt class of weights. The results obtained are even new for linear equations, and for ω = 1, because of the singularity of the coefficients in (x , t)-variables.

Global, finite energy, weak solutions for the NLS with rough, time-dependent magnetic potentials

NASA Astrophysics Data System (ADS)

Antonelli, Paolo; Michelangeli, Alessandro; Scandone, Raffaele

2018-04-01

We prove the existence of weak solutions in the space of energy for a class of nonlinear Schrödinger equations in the presence of a external, rough, time-dependent magnetic potential. Under our assumptions, it is not possible to study the problem by means of usual arguments like resolvent techniques or Fourier integral operators, for example. We use a parabolic regularisation, and we solve the approximating Cauchy problem. This is achieved by obtaining suitable smoothing estimates for the dissipative evolution. The total mass and energy bounds allow to extend the solution globally in time. We then infer sufficient compactness properties in order to produce a global-in-time finite energy weak solution to our original problem.

Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

EPA Science Inventory

Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

A feasibility study of the use of bounded beams resembling the shape of evanescent and inhomogeneous waves.

PubMed

Declercq, Nico F; Leroy, Oswald

2011-08-01

Plane waves are solutions of the visco-elastic wave equation. Their wave vector can be real for homogeneous plane waves or complex for inhomogeneous and evanescent plane waves. Although interesting from a theoretical point of view, complex wave vectors normally only emerge naturally when propagation or scattering is studied of sound under the appearance of damping effects. Because of the particular behavior of inhomogeneous and evanescent waves and their estimated efficiency for surface wave generation, bounded beams, experimentally mimicking their infinite counterparts similar to (wide) Gaussian beams imitating infinite harmonic plane waves, are of special interest in this report. The study describes the behavior of bounded inhomogeneous and bounded evanescent waves in terms of amplitude and phase distribution as well as energy flow direction. The outcome is of importance to the applicability of bounded inhomogeneous ultrasonic waves for nondestructive testing. Copyright © 2011. Published by Elsevier B.V.

A Ligand-observed Mass Spectrometry Approach Integrated into the Fragment Based Lead Discovery Pipeline

PubMed Central

Chen, Xin; Qin, Shanshan; Chen, Shuai; Li, Jinlong; Li, Lixin; Wang, Zhongling; Wang, Quan; Lin, Jianping; Yang, Cheng; Shui, Wenqing

2015-01-01

In fragment-based lead discovery (FBLD), a cascade combining multiple orthogonal technologies is required for reliable detection and characterization of fragment binding to the target. Given the limitations of the mainstream screening techniques, we presented a ligand-observed mass spectrometry approach to expand the toolkits and increase the flexibility of building a FBLD pipeline especially for tough targets. In this study, this approach was integrated into a FBLD program targeting the HCV RNA polymerase NS5B. Our ligand-observed mass spectrometry analysis resulted in the discovery of 10 hits from a 384-member fragment library through two independent screens of complex cocktails and a follow-up validation assay. Moreover, this MS-based approach enabled quantitative measurement of weak binding affinities of fragments which was in general consistent with SPR analysis. Five out of the ten hits were then successfully translated to X-ray structures of fragment-bound complexes to lay a foundation for structure-based inhibitor design. With distinctive strengths in terms of high capacity and speed, minimal method development, easy sample preparation, low material consumption and quantitative capability, this MS-based assay is anticipated to be a valuable addition to the repertoire of current fragment screening techniques. PMID:25666181

H2O-CH4 and H2S-CH4 complexes: a direct comparison through molecular beam experiments and ab initio calculations.

PubMed

Cappelletti, David; Bartocci, Alessio; Frati, Federica; Roncaratti, Luiz F; Belpassi, Leonardo; Tarantelli, Francesco; Lakshmi, Prabha Aiswarya; Arunan, Elangannan; Pirani, Fernando

2015-11-11

New molecular beam scattering experiments have been performed to measure the total (elastic plus inelastic) cross sections as a function of the velocity in collisions between water and hydrogen sulfide projectile molecules and the methane target. Measured data have been exploited to characterize the range and strength of the intermolecular interaction in such systems, which are of relevance as they drive the gas phase molecular dynamics and the clathrate formation. Complementary information has been obtained by rotational spectra, recorded for the hydrogen sulfide-methane complex, with a pulsed nozzle Fourier transform microwave spectrometer. Extensive ab initio calculations have been performed to rationalize all the experimental findings. The combination of experimental and theoretical information has established the ground for the understanding of the nature of the interaction and allows for its basic components to be modelled, including charge transfer, in these weakly bound systems. The intermolecular potential for H2S-CH4 is significantly less anisotropic than for H2O-CH4, although both of them have potential minima that can be characterized as 'hydrogen bonded'.

Reevaluating αE-catenin monomer and homodimer functions by characterizing E-cadherin/αE-catenin chimeras

PubMed Central

Bianchini, Julie M.; Kitt, Khameeka N.; Gloerich, Martijn; Pokutta, Sabine; Weis, William I.

2015-01-01

As part of the E-cadherin–β-catenin–αE-catenin complex (CCC), mammalian αE-catenin binds F-actin weakly in the absence of force, whereas cytosolic αE-catenin forms a homodimer that interacts more strongly with F-actin. It has been concluded that cytosolic αE-catenin homodimer is not important for intercellular adhesion because E-cadherin/αE-catenin chimeras thought to mimic the CCC are sufficient to induce cell–cell adhesion. We show that, unlike αE-catenin in the CCC, these chimeras homodimerize, bind F-actin strongly, and inhibit the Arp2/3 complex, all of which are properties of the αE-catenin homodimer. To more accurately mimic the junctional CCC, we designed a constitutively monomeric chimera, and show that E-cadherin–dependent cell adhesion is weaker in cells expressing this chimera compared with cells in which αE-catenin homodimers are present. Our results demonstrate that E-cadherin/αE-catenin chimeras used previously do not mimic αE-catenin in the native CCC, and imply that both CCC-bound monomer and cytosolic homodimer αE-catenin are required for strong cell–cell adhesion. PMID:26416960

Stark absorption spectroscopy on the carotenoids bound to B800-820 and B800-850 type LH2 complexes from a purple photosynthetic bacterium, Phaeospirillum molischianum strain DSM120.

PubMed

Horibe, Tomoko; Qian, Pu; Hunter, C Neil; Hashimoto, Hideki

2015-04-15

Stark absorption spectroscopy was applied to clarify the structural differences between carotenoids bound to the B800-820 and B800-850 LH2 complexes from a purple photosynthetic bacterium Phaeospirillum (Phs.) molischianum DSM120. The former complex is produced when the bacteria are grown under stressed conditions of low temperature and dim light. These two LH2 complexes bind carotenoids with similar composition, 10% lycopene and 80% rhodopin, each with the same number of conjugated CC double bonds (n=11). Quantitative classical and semi-quantum chemical analyses of Stark absorption spectra recorded in the carotenoid absorption region reveal that the absolute values of the difference dipole moments |Δμ| have substantial differences (2 [D/f]) for carotenoids bound to either B800-820 or B800-850 complexes. The origin of this striking difference in the |Δμ| values was analyzed using the X-ray crystal structure of the B800-850 LH2 complex from Phs. molischianum DSM119. Semi-empirical molecular orbital calculations predict structural deformations of the major carotenoid, rhodopin, bound within the B800-820 complex. We propose that simultaneous rotations around neighboring CC and CC bonds account for the differences in the 2 [D/f] of the |Δμ| value. The plausible position of the rotation is postulated to be located around C21-C24 bonds of rhodopin. Copyright © 2014 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Hod, Shahar

2017-11-01

We study analytically the radial Schrödinger equation with long-range attractive potentials whose asymptotic behaviors are dominated by inverse power-law tails of the form V(r)=-β _n r^{-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^{ {max}}_l=E^{ {max}}_l(n,β _n,R), which characterizes the most weakly bound-state resonance (the most excited energy level) of the quantum system.

Response to “Comment on ‘Propagation of surface waves on a semi-bounded quantum magnetized collisional plasma’” [Phys. Plasmas 23, 044701 (2016)

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

Niknam, A. R., E-mail: a-niknam@sbu.ac.ir; Taheri Boroujeni, S.; Khorashadizadeh, S. M., E-mail: smkhorashadi@birjand.ac.ir

2016-04-15

We reply to the Comment of Moradi [Phys. Plasmas 23, 044701 (2016)] on our paper [Phys. Plasmas 20, 122106 (2013)]. It is shown that TM surface waves can propagate on the surface of a semi-bounded quantum magnetized collisional plasma in the Faraday configuration in the electrostatic limit. In addition, in the Faraday configuration, one can neglect the coupling of TM and TE modes in the two limiting cases of weak magnetic field (low cyclotron frequency) and strong magnetic field (high cyclotron frequency).

Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

NASA Astrophysics Data System (ADS)

Kates-Harbeck, Julian; Tilloy, Antoine; Prentiss, Mara

2013-07-01

Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites.

Kinetic theory of weakly ionized dilute gas of hydrogen-like atoms of the first principles of quantum statistics and dispersion laws of eigenwaves

NASA Astrophysics Data System (ADS)

Slyusarenko, Yurii V.; Sliusarenko, Oleksii Yu.

2017-11-01

We develop a microscopic approach to the construction of the kinetic theory of dilute weakly ionized gas of hydrogen-like atoms. The approach is based on the statements of the second quantization method in the presence of bound states of particles. The basis of the derivation of kinetic equations is the method of reduced description of relaxation processes. Within the framework of the proposed approach, a system of common kinetic equations for the Wigner distribution functions of free oppositely charged fermions of two kinds (electrons and cores) and their bound states—hydrogen-like atoms— is obtained. Kinetic equations are used to study the spectra of elementary excitations in the system when all its components are non-degenerate. It is shown that in such a system, in addition to the typical plasma waves, there are longitudinal waves of matter polarization and the transverse ones with a behavior characteristic of plasmon polaritons. The expressions for the dependence of the frequencies and Landau damping coefficients on the wave vector for all branches of the oscillations discovered are obtained. Numerical evaluation of the elementary perturbation parameters in the system on an example of a weakly ionized dilute gas of the 23Na atoms using the D2-line characteristics of the natrium atom is given. We note the possibility of using the results of the developed theory to describe the properties of a Bose condensate of photons in the diluted weakly ionized gas of hydrogen-like atoms.

Extending Quantum Chemistry of Bound States to Electronic Resonances

NASA Astrophysics Data System (ADS)

Jagau, Thomas-C.; Bravaya, Ksenia B.; Krylov, Anna I.

2017-05-01

Electronic resonances are metastable states with finite lifetime embedded in the ionization or detachment continuum. They are ubiquitous in chemistry, physics, and biology. Resonances play a central role in processes as diverse as DNA radiolysis, plasmonic catalysis, and attosecond spectroscopy. This review describes novel equation-of-motion coupled-cluster (EOM-CC) methods designed to treat resonances and bound states on an equal footing. Built on complex-variable techniques such as complex scaling and complex absorbing potentials that allow resonances to be associated with a single eigenstate of the molecular Hamiltonian rather than several continuum eigenstates, these methods extend electronic-structure tools developed for bound states to electronic resonances. Selected examples emphasize the formal advantages as well as the numerical accuracy of EOM-CC in the treatment of electronic resonances. Connections to experimental observables such as spectra and cross sections, as well as practical aspects of implementing complex-valued approaches, are also discussed.

The not-so-harmless axion

NASA Astrophysics Data System (ADS)

Dine, Michael; Fischler, Willy

1983-01-01

Cosmological aspects of a very weakly interacting axion are discussed. A solution to the problem of domain walls discussed by Sikivie is mentioned. Demanding that axions do not dominate the present energy density of the universe is shown to give an upper bound on the axion decay constant of at most 1012 GeV.

Effects of anisotropic interaction-induced properties of hydrogen-rare gas compounds on rototranslational Raman scattering spectra: Comprehensive theoretical and numerical analysis

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

Głaz, Waldemar, E-mail: glaz@kielich.amu.edu.pl; Bancewicz, Tadeusz; Godet, Jean-Luc

2016-07-21

A comprehensive study is presented of many aspects of the depolarized anisotropic collision induced (CI) component of light scattered by weakly bound compounds composed of a dihydrogen molecule and a rare gas (Rg) atom, H{sub 2}–Rg. The work continues a series of earlier projects marking the revival of interest in linear light scattering following the development of new highly advanced tools of quantum chemistry and other theoretical, computational, and experimental means of spectral analyses. Sophisticated ab initio computing procedures are applied in order to obtain the anisotropic polarizability component’s dependence on the H{sub 2}–Rg geometry. These data are then usedmore » to evaluate the CI spectral lines for all types of Rg atoms ranging from He to Xe (Rn excluded). Evolution of the properties of CI spectra with growing polarizability/masses of the complexes studied is observed. Special attention is given to the heaviest, Kr and Xe based, scatterers. The influence of specific factors shaping the spectral lines (e.g., bound and metastable contribution, potential anisotropy) is discussed. Also the share of pressure broadened allowed rotational transitions in the overall spectral profile is taken into account and the extent to which it is separable from the pure CI contribution is discussed. We finish with a brief comparison between the obtained results and available experimental data.« less

Time-resolved photoelectron imaging of iodide-nitromethane (I-·CH3NO2) photodissociation dynamics.

PubMed

Kunin, Alice; Li, Wei-Li; Neumark, Daniel M

2016-12-07

Femtosecond time-resolved photoelectron spectroscopy is used to probe the decay channels of iodide-nitromethane (I - ·CH 3 NO 2 ) binary clusters photoexcited at 3.56 eV, near the vertical detachment energy (VDE) of the cluster. The production of I - is observed, and its photoelectron signal exhibits a mono-exponential rise time of 21 ± 1 ps. Previous work has shown that excitation near the VDE of the I - ·CH 3 NO 2 complex transfers an electron from iodide to form a dipole-bound state of CH 3 NO 2 - that rapidly converts to a valence bound (VB) anion. The long appearance time for the I - fragment suggests that the VB anion decays by back transfer of the excess electron to iodide, reforming the I - ·CH 3 NO 2 anion and resulting in evaporation of iodide. Comparison of the measured lifetime to that predicted by RRKM theory suggests that the dissociation rate is limited by intramolecular vibrational energy redistribution in the re-formed anion between the high frequency CH 3 NO 2 vibrational modes and the much lower frequency intermolecular I - ·CH 3 NO 2 stretch and bends, the predominant modes involved in cluster dissociation to form I - . Evidence for a weak channel identified as HI + CH 2 NO 2 - is also observed.

Matrix-isolation studies on the radiation-induced chemistry in H₂O/CO₂ systems: reactions of oxygen atoms and formation of HOCO radical.

PubMed

Ryazantsev, Sergey V; Feldman, Vladimir I

2015-03-19

The radiation-induced transformations occurring upon X-ray irradiation of solid CO2/H2O/Ng systems (Ng = Ar, Kr, Xe) at 8-10 K and subsequent annealing up to 45 K were studied by Fourier transform infrared spectroscopy. The infrared (IR) spectra of deposited matrices revealed the presence of isolated monomers, dimers, and intermolecular H2O···CO2 complexes. Irradiation resulted in effective decomposition of matrix-isolated carbon dioxide and water yielding CO molecules and OH radicals, respectively. Annealing of the irradiated samples led to formation of O3, HO2, and a number of xenon hydrides of HXeY type (in the case of xenon matrices). The formation of these species was used for monitoring of the postirradiation thermally induced chemical reactions involving O and H atoms generated by radiolysis. It was shown that the radiolysis of CO2 in noble-gas matrices produced high yields of stabilized oxygen atoms. In all cases, the temperatures at which O atoms become mobile and react are lower than those of H atoms. Dynamics and reactivity of oxygen atoms was found to be independent of the precursor nature. In addition, the formation of HOCO radicals was observed in all the noble-gas matrices at remarkably low temperatures. The IR spectra of HOCO and DOCO were first characterized in krypton and xenon matrices. It was concluded that the formation of HOCO was mainly due to the radiation-induced evolution of the weakly bound H2O···CO2 complexes. This result indicates the significance of weak intermolecular interactions in the radiation-induced chemical processes in inert low-temperature media.

Stoichiometry and kinetics of mercury uptake by photosynthetic bacteria.

PubMed

Kis, Mariann; Sipka, Gábor; Maróti, Péter

2017-05-01

Mercury adsorption on the cell surface and intracellular uptake by bacteria represent the key first step in the production and accumulation of highly toxic mercury in living organisms. In this work, the biophysical characteristics of mercury bioaccumulation are studied in intact cells of photosynthetic bacteria by use of analytical (dithizone) assay and physiological photosynthetic markers (pigment content, fluorescence induction, and membrane potential) to determine the amount of mercury ions bound to the cell surface and taken up by the cell. It is shown that the Hg(II) uptake mechanism (1) has two kinetically distinguishable components, (2) includes co-opted influx through heavy metal transporters since the slow component is inhibited by Ca 2+ channel blockers, (3) shows complex pH dependence demonstrating the competition of ligand binding of Hg(II) ions with H + ions (low pH) and high tendency of complex formation of Hg(II) with hydroxyl ions (high pH), and (4) is not a passive but an energy-dependent process as evidenced by light activation and inhibition by protonophore. Photosynthetic bacteria can accumulate Hg(II) in amounts much (about 10 5 ) greater than their own masses by well-defined strong and weak binding sites with equilibrium binding constants in the range of 1 (μM) -1 and 1 (mM) -1 , respectively. The strong binding sites are attributed to sulfhydryl groups as the uptake is blocked by use of sulfhydryl modifying agents and their number is much (two orders of magnitude) smaller than the number of weak binding sites. Biofilms developed by some bacteria (e.g., Rvx. gelatinosus) increase the mercury binding capacity further by a factor of about five. Photosynthetic bacteria in the light act as a sponge of Hg(II) and can be potentially used for biomonitoring and bioremediation of mercury-contaminated aqueous cultures.

Inhibition of neutrophil migration by aggregated immunoglobulin attached to micropore membranes.

PubMed Central

Kemp, A S; Brown, S

1980-01-01

The effect of substrate-bound immunoglobulin on neutrophil migration was examined. Immunoglobulin aggregates bound to micropore membranes inhibited the neutrophil response to a chemotactic stimulus. This inhibition was reversed by the presence of aggregates in suspension suggesting competition between substrate-bound and free aggregates for neutrophil surface binding sites. The immobilization of neutrophils by substrate-bound aggregated immunoglobulin suggests a mechanism for the accumulation of neutrophils at sites of immune complex deposition and tissue-bound antibodies in vivo. PMID:7380477

Direct excitation luminescence spectroscopy of Eu(III) complexes of 1,4,7-tris(carbamoylmethyl)-1,4,7,10- tetraazacyclododecane derivatives and kinetic studies of their catalytic cleavage of an RNA analog.

PubMed

Nwe, Kido; Richard, John P; Morrow, Janet R

2007-11-28

The macrocycles 1,4,7-tris(carbamoylmethyl)-1,4,7,10-tetrazacyclododecane (1), 1,4,7-tris[(N-ethyl)carbamoylmethyl]-1,4,7,10-tetraazacyclododecane (2), 1,4,7-tris[(N,N-diethyl)carbamoylmethyl]-1,4,7,10-tetraazacyclododecane (3) and their Eu(III) complexes are prepared. Studies using direct Eu(III) excitation luminescence spectroscopy show that all three Eu(III) complexes exhibit only one predominant isomer with two bound waters under neutral to mildly basic conditions (Eu(X)(H(2)O)(2) for X = 1-3). There are no detectable ligand ionizations over the pH range 5.0-8.0 for Eu(3), 5.0-8.5 for Eu(2) or 5.0-9.5 for Eu(1). The three Eu(III) complexes show a linear dependence of second-order rate constants for the cleavage of 4-nitrophenyl-2-hydroxyethylphosphate (HpPNP) on pH in the range 6.5-8.0 for Eu(3), 7.0-8.5 for Eu(2) and 7.0-9.0 for Eu(1). This pH-rate profile is consistent with the Eu(III) complex-substrate complex being converted to the active form by loss of a proton and with Eu(III) water pK(a) values that are higher than 8.0 for Eu(3), 8.5 for Eu(2) and 9.0 for Eu(1). Inhibition studies show that Eu() binds strongly to the dianionic ligand methylphosphate (K(d) = 0.28 mM), and more weakly to diethylphosphate (K(d) = 7.5 mM), consistent with a catalytic role of the Eu(III) complexes in stabilizing the developing negative charge on the phosphorane transition state.

Redox electrodeposition polymers: adaptation of the redox potential of polymer-bound Os complexes for bioanalytical applications.

PubMed

Guschin, Dmitrii A; Castillo, John; Dimcheva, Nina; Schuhmann, Wolfgang

2010-10-01

The design of polymers carrying suitable ligands for coordinating Os complexes in ligand exchange reactions against labile chloro ligands is a strategy for the synthesis of redox polymers with bound Os centers which exhibit a wide variation in their redox potential. This strategy is applied to polymers with an additional variation of the properties of the polymer backbone with respect to pH-dependent solubility, monomer composition, hydrophilicity etc. A library of Os-complex-modified electrodeposition polymers was synthesized and initially tested with respect to their electron-transfer ability in combination with enzymes such as glucose oxidase, cellobiose dehydrogenase, and PQQ-dependent glucose dehydrogenase entrapped during the pH-induced deposition process. The different polymer-bound Os complexes in a library containing 50 different redox polymers allowed the statistical evaluation of the impact of an individual ligand to the overall redox potential of an Os complex. Using a simple linear regression algorithm prediction of the redox potential of Os complexes becomes feasible. Thus, a redox polymer can now be designed to optimally interact in electron-transfer reactions with a selected enzyme.

Three-color single molecule imaging shows WASP detachment from Arp2/3 complex triggers actin filament branch formation

PubMed Central

Smith, Benjamin A; Padrick, Shae B; Doolittle, Lynda K; Daugherty-Clarke, Karen; Corrêa, Ivan R; Xu, Ming-Qun; Goode, Bruce L; Rosen, Michael K; Gelles, Jeff

2013-01-01

During cell locomotion and endocytosis, membrane-tethered WASP proteins stimulate actin filament nucleation by the Arp2/3 complex. This process generates highly branched arrays of filaments that grow toward the membrane to which they are tethered, a conflict that seemingly would restrict filament growth. Using three-color single-molecule imaging in vitro we revealed how the dynamic associations of Arp2/3 complex with mother filament and WASP are temporally coordinated with initiation of daughter filament growth. We found that WASP proteins dissociated from filament-bound Arp2/3 complex prior to new filament growth. Further, mutations that accelerated release of WASP from filament-bound Arp2/3 complex proportionally accelerated branch formation. These data suggest that while WASP promotes formation of pre-nucleation complexes, filament growth cannot occur until it is triggered by WASP release. This provides a mechanism by which membrane-bound WASP proteins can stimulate network growth without restraining it. DOI: http://dx.doi.org/10.7554/eLife.01008.001 PMID:24015360

Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form

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

Yokoyama, Hideshi, E-mail: h-yokoya@u-shizuoka-ken.ac.jp; Tsuruta, Osamu; Akao, Naoya

2012-06-15

Highlights: Black-Right-Pointing-Pointer Structures of a metal-bound Helicobacter pylori neutrophil-activating protein were determined. Black-Right-Pointing-Pointer Two zinc ions were tetrahedrally coordinated by ferroxidase center (FOC) residues. Black-Right-Pointing-Pointer Two cadmium ions were coordinated in a trigonal-bipyramidal and octahedral manner. Black-Right-Pointing-Pointer The second metal ion was more weakly coordinated than the first at the FOC. Black-Right-Pointing-Pointer A zinc ion was found in one negatively-charged pore suitable as an ion path. -- Abstract: Helicobacter pylori neutrophil-activating protein (HP-NAP) is a Dps-like iron storage protein forming a dodecameric shell, and promotes adhesion of neutrophils to endothelial cells. The crystal structure of HP-NAP in a Zn{sup 2+}-more » or Cd{sup 2+}-bound form reveals the binding of two zinc or two cadmium ions and their bridged water molecule at the ferroxidase center (FOC). The two zinc ions are coordinated in a tetrahedral manner to the conserved residues among HP-NAP and Dps proteins. The two cadmium ions are coordinated in a trigonal-bipyramidal and distorted octahedral manner. In both structures, the second ion is more weakly coordinated than the first. Another zinc ion is found inside of the negatively-charged threefold-related pore, which is suitable for metal ions to pass through.« less

Estimation of Free Radical Ionization Energies by the Kinetic Method and the Relationship between the Kinetic Method and the Hammett Equation.

PubMed

Chen, G; Wong, P; Cooks, R G

1997-09-01

Substituted 1,2-diphenylethanes undergo competitive dissociations upon electron ionization (EI) to generate substituted benzyl cation and benzyl radical pairs. Application of the kinetic method to the previous reported EI mass spectra of these covalently bound precursor ions (data are taken from McLafferty et al. J. Am. Chem. Soc. 1970, 92, 6867)) is used to estimate the ionization energies of substituted benzyl free radicals. A correlation is observed between the Hammett σ constant of the substituents and the kinetic method parameter, ln(k(x)/k(H)), where k(x) is the rate of fragmentation to give the substituted product ion and k(H) is the rate to give the benzyl ion itself. Systems involving weakly bound cluster ions, including proton-bound dimers of meta- and para-substituted pyridines and meta- and para-substituted anilines, and electron-bound dimers of meta- and para-substituted nitrobenzenes, also show good correlations between the kinetic method parameter and the Hammett σ constant.

The participation of ribosomes in protein glycosylation. Interaction of the ribosome-UDP-N-acetyl-glucosamine complex with dolichol phosphate.

PubMed

Paszkiewicz-Gadek, A; Porowska, H; Gałasiński, W

1992-01-01

UDP-N-acetylglucosamine can be bound by pure ribosomes. The part of N-acetylglucosamine-1-P can be transferred from the complex ribosome-UDP-N-acetylglucosamine onto dolichol phosphate. Evidence is presented that N-acetylglucosamine bound to dolichol phosphate can be transferred to the nascent peptide synthesized on the ribosome.

Theoretical and computational studies of excitons in conjugated polymers

NASA Astrophysics Data System (ADS)

Barford, William; Bursill, Robert J.; Smith, Richard W.

2002-09-01

We present a theoretical and computational analysis of excitons in conjugated polymers. We use a tight-binding model of π-conjugated electrons, with 1/r interactions for large r. In both the weak-coupling limit (defined by W>>U) and the strong-coupling limit (defined by W<

Detection of Nucleic Acids in Complex Samples via Magnetic Microbead-assisted Catalyzed Hairpin Assembly and "DD-A" FRET.

PubMed

Fang, Hongmei; Xie, Nuli; Ou, Min; Huang, Jin; Li, Wenshan; Wang, Qing; Liu, Jianbo; Yang, Xiaohai; Wang, Kemin

2018-05-21

Nucleic acids, as one kind of significant biomarkers, have attracted tremendous attention and exhibited immense value in fundamental studies and clinical applications. In this work, we developed a fluorescent assay for detecting nucleic acids in complex samples based on magnetic microbead (MMB)-assisted catalyzed hairpin assembly (CHA) and donor donor-acceptor fluorescence resonance energy transfer ("DD-A" FRET) signaling mechanism. Three types of DNA hairpin probes were employed in this system, including Capture, H1 (double FAM-labelled probe as FRET donor) and H2 (TAMRA-labelled probe as FRET acceptor). Firstly, the Captures immobilized on MMBs bound to targets in complex samples, and the sequences in Captures that could trigger catalyzed hairpin assembly (CHA) were exposed. Then, target-enriched MMBs complexes were separated and resuspended in the reaction buffer containing H1 and H2. As a result, numerous H1-H2 duplexes were formed during CHA process, inducing an obvious FRET signal. In contrast, CHA could not be trigger and the FRET signal was weak while target was absent. With the aid of magnetic separation and "DD-A" FRET, it was demonstrated to effectively eliminate errors from background interference. Importantly, this strategy realized amplified detection in buffer, with detection limits of microRNA as low as 34 pM. Furthermore, this method was successfully applied to detect microRNA-21 in serum and cell culture media. The results showed that our method has the potential for biomedical research and clinical application.

Divalent Metal-Ion Complexes with Dipeptide Ligands Having Phe and His Side-Chain Anchors: Effects of Sequence, Metal Ion, and Anchor.

PubMed

Dunbar, Robert C; Berden, Giel; Martens, Jonathan K; Oomens, Jos

2015-09-24

Conformational preferences have been surveyed for divalent metal cation complexes with the dipeptide ligands AlaPhe, PheAla, GlyHis, and HisGly. Density functional theory results for a full set of complexes are presented, and previous experimental infrared spectra, supplemented by a number of newly recorded spectra obtained with infrared multiple photon dissociation spectroscopy, provide experimental verification of the preferred conformations in most cases. The overall structural features of these complexes are shown, and attention is given to comparisons involving peptide sequence, nature of the metal ion, and nature of the side-chain anchor. A regular progression is observed as a function of binding strength, whereby the weakly binding metal ions (Ba(2+) to Ca(2+)) transition from carboxylate zwitterion (ZW) binding to charge-solvated (CS) binding, while the stronger binding metal ions (Ca(2+) to Mg(2+) to Ni(2+)) transition from CS binding to metal-ion-backbone binding (Iminol) by direct metal-nitrogen bonds to the deprotonated amide nitrogens. Two new sequence-dependent reversals are found between ZW and CS binding modes, such that Ba(2+) and Ca(2+) prefer ZW binding in the GlyHis case but prefer CS binding in the HisGly case. The overall binding strength for a given metal ion is not strongly dependent on the sequence, but the histidine peptides are significantly more strongly bound (by 50-100 kJ mol(-1)) than the phenylalanine peptides.

Lipid nanocapsule functionalization by lipopeptides derived from human papillomavirus type-16 capsid for nucleic acid delivery into cancer cells.

PubMed

Weyland, M; Griveau, A; Bejaud, J; Benoit, J-P; Coursaget, P; Garcion, E

2013-10-01

Plasmid DNA (pDNA) and small interfering RNAs (siRNAs) are very useful tools for the treatment of cancer. However, pDNA and siRNAs efficacy is restricted by their negative charge and susceptibility to degradation by endonucleases that prevent them penetrating tissue and cellular barriers such as the plasma and endolysosomal membranes. Viral vectors have some advantages but their use is largely limited by their immunogenicity. On the other hand, synthetic nanoparticles have advantage of being relatively non-immunogenic but their ability to deliver nucleic acids remains less efficient than their viral counterparts. The present study is focussed on the development and evaluation of biomimetic lipid nanocapsules (LNCs) functionalized with a L1 papillomavirus type-16 capsid-derived lipopeptide on their surface, for transfection of U87MG glioma cells and Caco-2 colorectal adenocarcinoma cells with pDNA or siRNAs. Since the L1-peptide has been described as a nuclear localization signal able to complex with nucleic acids and bind to heparan sulfate on the cell surface, the structure and function of L1-peptide bound to LNCs (L1-LNCs) were investigated. Although L1-LNCs were shown to complex with both pDNA and siRNAs, the pDNA-L1-LNC complexes showed only weak transfection efficiency. In contrast, siRNA-L1-LNC complexes appeared as effective repressors of targeted messengers. Copyright © 2013 Elsevier B.V. All rights reserved.

Decay dynamics of nascent acetonitrile and nitromethane dipole-bound anions produced by intracluster charge-transfer

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

Yandell, Margaret A.; King, Sarah B.; Neumark, Daniel M., E-mail: dneumark@berkeley.edu

2014-05-14

Decay dynamics of nascent dipole bound states of acetonitrile and nitromethane are examined using time-resolved photoelectron imaging of iodide-acetonitrile (I{sup −}·CH{sub 3}CN) and iodide-nitromethane (I{sup −}·CH{sub 3}NO{sub 2}) complexes. Dipole-bound anions are created by UV-initiated electron transfer to the molecule of interest from the associated iodide ion at energies just below the vertical detachment energy of the halide-molecule complex. The acetonitrile anion is observed to decay biexponentially with time constants in the range of 4–900 ps. In contrast, the dipole bound state of nitromethane decays rapidly over 400 fs to form the valence bound anion. The nitromethane valence anion speciesmore » then decays biexponentially with time constants of 2 ps and 1200 ps. The biexponential decay dynamics in acetonitrile are interpreted as iodine atom loss and autodetachment from the excited dipole-bound anion, followed by slower autodetachment of the relaxed metastable ion, while the dynamics of the nitromethane system suggest that a dipole-bound anion to valence anion transition proceeds via intramolecular vibrational energy redistribution to nitro group modes in the vicinity of the iodine atom.« less

Decay dynamics of nascent acetonitrile and nitromethane dipole-bound anions produced by intracluster charge-transfer.

PubMed

Yandell, Margaret A; King, Sarah B; Neumark, Daniel M

2014-05-14

Decay dynamics of nascent dipole bound states of acetonitrile and nitromethane are examined using time-resolved photoelectron imaging of iodide-acetonitrile (I(-)·CH3CN) and iodide-nitromethane (I(-)·CH3NO2) complexes. Dipole-bound anions are created by UV-initiated electron transfer to the molecule of interest from the associated iodide ion at energies just below the vertical detachment energy of the halide-molecule complex. The acetonitrile anion is observed to decay biexponentially with time constants in the range of 4-900 ps. In contrast, the dipole bound state of nitromethane decays rapidly over 400 fs to form the valence bound anion. The nitromethane valence anion species then decays biexponentially with time constants of 2 ps and 1200 ps. The biexponential decay dynamics in acetonitrile are interpreted as iodine atom loss and autodetachment from the excited dipole-bound anion, followed by slower autodetachment of the relaxed metastable ion, while the dynamics of the nitromethane system suggest that a dipole-bound anion to valence anion transition proceeds via intramolecular vibrational energy redistribution to nitro group modes in the vicinity of the iodine atom.

Control of the Ability of Profilin to Bind and Facilitate Nucleotide Exchange from G-actin*

PubMed Central

Wen, Kuo-Kuang; McKane, Melissa; Houtman, Jon C. D.; Rubenstein, Peter A.

2008-01-01

A major factor in profilin regulation of actin cytoskeletal dynamics is its facilitation of G-actin nucleotide exchange. However, the mechanism of this facilitation is unknown. We studied the interaction of yeast (YPF) and human profilin 1 (HPF1) with yeast and mammalian skeletal muscle actins. Homologous pairs (YPF and yeast actin, HPF1 and muscle actin) bound more tightly to one another than heterologous pairs. However, with saturating profilin, HPF1 caused a faster etheno-ATP exchange with both yeast and muscle actins than did YPF. Based on the -fold change in ATP exchange rate/Kd, however, the homologous pairs are more efficient than the heterologous pairs. Thus, strength of binding of profilin to actin and nucleotide exchange rate are not tightly coupled. Actin/HPF interactions were entropically driven, whereas YPF interactions were enthalpically driven. Hybrid yeast actins containing subdomain 1 (sub1) or subdomain 1 and 2 (sub12) muscle actin residues bound more weakly to YPF than did yeast actin (Kd = 2 μm versus 0.6 μm). These hybrids bound even more weakly to HPF than did yeast actin (Kd = 5 μm versus 3.2 μm). sub1/YPF interactions were entropically driven, whereas the sub12/YPF binding was enthalpically driven. Compared with WT yeast actin, YPF binding to sub1 occurred with a 5 times faster koff and a 2 times faster kon. sub12 bound with a 3 times faster koff and a 1.5 times slower kon. Profilin controls the energetics of its interaction with nonhybrid actin, but interactions between actin subdomains 1 and 2 affect the topography of the profilin binding site. PMID:18223293

Thermal and FTIR spectroscopic analysis of the interactions of aniline adsorbed on to MCM-41 mesoporous material.

PubMed

Eimer, Griselda A; Gómez Costa, Marcos B; Pierella, Liliana B; Anunziata, Oscar A

2003-07-15

The adsorption of aniline on Na-AlMCM-41 synthesized by us has been characterized by infrared spectroscopy, temperature programmed desorption (TPD), and differential thermal analysis methods. Aniline would be mostly bound to the mesostructure through weak pi interactions. On the mesostructure containing adsorbed water, the co-adsorption of aniline could occur by weak hydrogen bonding through surface water molecules. For water, two possible modes of adsorption have been identified. Different associations between aniline and hydrated and nonhydrated mesostructures have been evaluated in order to favor the posterior in situ polymerization of adsorbed aniline.

Weakly dynamic dark energy via metric-scalar couplings with torsion

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

Sur, Sourav; Bhatia, Arshdeep Singh, E-mail: sourav.sur@gmail.com, E-mail: arshdeepsb@gmail.com

We study the dynamical aspects of dark energy in the context of a non-minimally coupled scalar field with curvature and torsion. Whereas the scalar field acts as the source of the trace mode of torsion, a suitable constraint on the torsion pseudo-trace provides a mass term for the scalar field in the effective action. In the equivalent scalar-tensor framework, we find explicit cosmological solutions representing dark energy in both Einstein and Jordan frames. We demand the dynamical evolution of the dark energy to be weak enough, so that the present-day values of the cosmological parameters could be estimated keeping themmore » within the confidence limits set for the standard LCDM model from recent observations. For such estimates, we examine the variations of the effective matter density and the dark energy equation of state parameters over different redshift ranges. In spite of being weakly dynamic, the dark energy component differs significantly from the cosmological constant, both in characteristics and features, for e.g. it interacts with the cosmological (dust) fluid in the Einstein frame, and crosses the phantom barrier in the Jordan frame. We also obtain the upper bounds on the torsion mode parameters and the lower bound on the effective Brans-Dicke parameter. The latter turns out to be fairly large, and in agreement with the local gravity constraints, which therefore come in support of our analysis.« less

Weakly dynamic dark energy via metric-scalar couplings with torsion

NASA Astrophysics Data System (ADS)

Sur, Sourav; Singh Bhatia, Arshdeep

2017-07-01

We study the dynamical aspects of dark energy in the context of a non-minimally coupled scalar field with curvature and torsion. Whereas the scalar field acts as the source of the trace mode of torsion, a suitable constraint on the torsion pseudo-trace provides a mass term for the scalar field in the effective action. In the equivalent scalar-tensor framework, we find explicit cosmological solutions representing dark energy in both Einstein and Jordan frames. We demand the dynamical evolution of the dark energy to be weak enough, so that the present-day values of the cosmological parameters could be estimated keeping them within the confidence limits set for the standard LCDM model from recent observations. For such estimates, we examine the variations of the effective matter density and the dark energy equation of state parameters over different redshift ranges. In spite of being weakly dynamic, the dark energy component differs significantly from the cosmological constant, both in characteristics and features, for e.g. it interacts with the cosmological (dust) fluid in the Einstein frame, and crosses the phantom barrier in the Jordan frame. We also obtain the upper bounds on the torsion mode parameters and the lower bound on the effective Brans-Dicke parameter. The latter turns out to be fairly large, and in agreement with the local gravity constraints, which therefore come in support of our analysis.

Apparent dynamic contact angle of an advancing gas--liquid meniscus

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

Kalliadasis, S.; Chang, H.

1994-01-01

The steady motion of an advancing meniscus in a gas-filled capillary tube involves a delicate balance of capillary, viscous, and intermolecular forces. The limit of small capillary numbers Ca (dimensionless speeds) is analyzed here with a matched asymptotic analysis that links the outer capillary region to the precursor film in front of the meniscus through a lubricating film. The meniscus shape in the outer region is constructed and the apparent dynamic contact angle [Theta] that the meniscus forms with the solid surface is derived as a function of the capillary number, the capillary radius, and the Hamaker's constant for intermolecularmore » forces, under conditions of weak gas--solid interaction, which lead to fast spreading of the precursor film and weak intermolecular forces relative to viscous forces within the lubricating film. The dependence on intermolecular forces is very weak and the contact angle expression has a tight upper bound tan [Theta]=7.48 Ca[sup 1/3] for thick films, which is independent of the Hamaker constant. This upper bound is in very good agreement with existing experimental data for wetting fluids in any capillary and for partially wetting fluids in a prewetted capillary. Significant correction to the Ca[sup 1/3] dependence occurs only at very low Ca, where the intermolecular forces become more important and tan [Theta] diverges slightly from the above asymptotic behavior toward lower values.« less

Stationary and oscillatory bound states of dissipative solitons created by third-order dispersion

NASA Astrophysics Data System (ADS)

Sakaguchi, Hidetsugu; Skryabin, Dmitry V.; Malomed, Boris A.

2018-06-01

We consider the model of fiber-laser cavities near the zero-dispersion point, based on the complex Ginzburg-Landau equation with the cubic-quintic nonlinearity, including the third-order dispersion (TOD) term. It is well known that this model supports stable dissipative solitons. We demonstrate that the same model gives rise to several families of robust bound states of the solitons, which exists only in the presence of the TOD. There are both stationary and dynamical bound states, with oscillating separation between the bound solitons. Stationary states are multistable, corresponding to different values of the separation. With the increase of the TOD coefficient, the bound state with the smallest separation gives rise the oscillatory state through the Hopf bifurcation. Further growth of TOD leads to a bifurcation transforming the oscillatory limit cycle into a strange attractor, which represents a chaotically oscillating dynamical bound state. Families of multistable three- and four-soliton complexes are found too, the ones with the smallest separation between the solitons again ending by a transition to oscillatory states through the Hopf bifurcation.

Stability of proton-bound clusters of alkyl alcohols, aldehydes and ketones in Ion Mobility Spectrometry.

PubMed

Jurado-Campos, Natividad; Garrido-Delgado, Rocío; Martínez-Haya, Bruno; Eiceman, Gary A; Arce, Lourdes

2018-08-01

Significant substances in emerging applications of ion mobility spectrometry such as breath analysis for clinical diagnostics and headspace analysis for food purity include low molar mass alcohols, ketones, aldehydes and esters which produce mobility spectra containing protonated monomers and proton-bound dimers. Spectra for all n- alcohols, aldehydes and ketones from carbon number three to eight exhibited protonated monomers and proton-bound dimers with ion drift times of 6.5-13.3 ms at ambient pressure and from 35° to 80 °C in nitrogen. Only n-alcohols from 1-pentanol to 1-octanol produced proton-bound trimers which were sufficiently stable to be observed at these temperatures and drift times of 12.8-16.3 ms. Polar functional groups were protected in compact structures in ab initio models for proton-bound dimers of alcohols, ketones and aldehydes. Only alcohols formed a V-shaped arrangement for proton-bound trimers strengthening ion stability and lifetime. In contrast, models for proton-bound trimers of aldehydes and ketones showed association of the third neutral through weak, non-specific, long-range interactions consistent with ion dissociation in the ion mobility drift tube before arriving at the detector. Collision cross sections derived from reduced mobility coefficients in nitrogen gas atmosphere support the predicted ion structures and approximate degrees of hydration. Copyright © 2018 Elsevier B.V. All rights reserved.

Arabidopsis SEPALLATA proteins differ in cooperative DNA-binding during the formation of floral quartet-like complexes

PubMed Central

Jetha, Khushboo; Theißen, Günter; Melzer, Rainer

2014-01-01

The SEPALLATA (SEP) genes of Arabidopsis thaliana encode MADS-domain transcription factors that specify the identity of all floral organs. The four Arabidopsis SEP genes function in a largely yet not completely redundant manner. Here, we analysed interactions of the SEP proteins with DNA. All of the proteins were capable of forming tetrameric quartet-like complexes on DNA fragments carrying two sequence elements termed CArG-boxes. Distances between the CArG-boxes for strong cooperative DNA-binding were in the range of 4–6 helical turns. However, SEP1 also bound strongly to CArG-box pairs separated by smaller or larger distances, whereas SEP2 preferred large and SEP4 preferred small inter-site distances for binding. Cooperative binding of SEP3 was comparatively weak for most of the inter-site distances tested. All SEP proteins constituted floral quartet-like complexes together with the floral homeotic proteins APETALA3 (AP3) and PISTILLATA (PI) on the target genes AP3 and SEP3. Our results suggest an important part of an explanation for why the different SEP proteins have largely, but not completely redundant functions in determining floral organ identity: they may bind to largely overlapping, but not identical sets of target genes that differ in the arrangement and spacing of the CArG-boxes in their cis-regulatory regions. PMID:25183521

Physical characteristics of lanthanide complexes that act as magnetization transfer (MT) contrast agents

NASA Astrophysics Data System (ADS)

Zhang, Shanrong; Sherry, A. Dean

2003-02-01

Rapid water exchange is normally considered a prerequisite for efficient Gd3+-based MRI contrast agents. Yet recent measures of exchange rates in some Gd3+ complexes have shown that water exchange can become limiting when such complexes are attached to larger macromolecular structures. A new class of lanthanide complexes that display unusually slow water exchange (bound water lifetimes (τM298) > 10 μs) has recently been reported. This apparent disadvantage may be taken advantage of by switching the metal ion from gadolinium(III) to a lanthanide that shifts the bound water resonance substantially away from bulk water. Given appropriate water exchange kinetics, one can then alter the intensity of the bulk water signal by selective presaturation of this highly shifted, Ln3+-bound water resonance. This provides the basis of a new method to alter MR image contrast in tissue. We have synthesized a variety of DOTA-tetra(amide) ligands to evaluate as potential magnetization transfer (MT) contrast agents and found that the bound water lifetimes in these complexes are sensitive to both ligand structure (a series of Eu3+ complexes have τM298 values that range from 1 to 1300 μs) and the identity of the paramagnetic Ln3+ cation (from 3 to 800 μs for a single ligand). This demonstrates that it may be possible either to fine-tune the ligand structure or to select proper lanthanide cation to create an optimal MT agent for any clinical imaging field.

Importance of lifetime effects in breakup and suppression of complete fusion in reactions of weakly bound nuclei

NASA Astrophysics Data System (ADS)

Cook, K. J.; Simpson, E. C.; Luong, D. H.; Kalkal, Sunil; Dasgupta, M.; Hinde, D. J.

2016-06-01

Background: Complete fusion cross sections in collisions of light weakly bound nuclei and high-Z targets show suppression of complete fusion at above-barrier energies. This has been interpreted as resulting from the breakup of the weakly bound nucleus prior to reaching the fusion barrier, reducing the probability of complete charge capture. Below-barrier studies of reactions of 9Be have found that the breakup of 8Be formed by neutron stripping dominates over direct breakup and that transfer-triggered breakup may account for the observed suppression of complete fusion. Purpose: This paper investigates how the above conclusions are affected by lifetimes of the resonant states that are populated prior to breakup. If the mean life of a populated resonance (above the breakup threshold) is much longer than the fusion time scale, then its breakup (decay) cannot suppress complete fusion. For short-lived resonances, the situation is more complex. This work explicitly includes the mean life of the short-lived 2+ resonance in 8Be in classical dynamical model calculations to determine its effect on energy and angular correlations of the breakup fragments and on model predictions of suppression of cross sections for complete fusion at above-barrier energies. Method: Previously performed coincidence measurements of breakup fragments produced in reactions of 9Be with 144Sm, 168Er, 186W, 196Pt, 208Pb, and 209Bi at energies below the barrier have been reanalyzed using an improved efficiency determination of the BALiN detector array. Predictions of breakup observables and of complete and incomplete fusion at energies above the fusion barrier are then made using the classical dynamical simulation code platypus, modified to include the effect of lifetimes of resonant states. Results: The agreement of the breakup observables is much improved when lifetime effects are included explicitly. Sensitivity to subzeptosecond lifetime is observed. The predicted suppression of complete fusion owing to breakup is nearly independent of Z and has an average value of ˜9 % . This is below the experimentally determined fusion suppression, which is typically ˜30 % in these systems. Conclusions: Inclusion of resonance lifetimes is essential to correctly reproduce breakup observables. This results in a larger fraction of nuclei remaining intact at the fusion-barrier radius compared with calculations that do not explicitly include lifetime effects. The more realistic treatment of breakup followed in this work leads to the conclusion that the suppression of complete fusion cannot be fully explained by breakup prior to reaching the fusion barrier. Only one-third of the observed fusion suppression can be attributed to the competing process of breakup. Other mechanisms that can suppress complete fusion must therefore be investigated. One of the possible candidates is cluster transfer that produces the same heavy targetlike nuclei as those formed by incomplete fusion.

Ligand binding phenomena that pertain to the metabolic function of renalase.

PubMed

Beaupre, Brett A; Roman, Joseph V; Hoag, Matthew R; Meneely, Kathleen M; Silvaggi, Nicholas R; Lamb, Audrey L; Moran, Graham R

2016-12-15

Renalase catalyzes the oxidation of isomers of β-NAD(P)H that carry the hydride in the 2 or 6 positions of the nicotinamide base to form β-NAD(P) + . This activity is thought to alleviate inhibition of multiple β-NAD(P)-dependent enzymes of primary and secondary metabolism by these isomers. Here we present evidence for a variety of ligand binding phenomena relevant to the function of renalase. We offer evidence of the potential for primary metabolism inhibition with structures of malate dehydrogenase and lactate dehydrogenase bound to the 6-dihydroNAD isomer. The previously observed preference of renalase from Pseudomonas for NAD-derived substrates over those derived from NADP is accounted for by the structure of the enzyme in complex with NADPH. We also show that nicotinamide nucleosides and mononucleotides reduced in the 2- and 6-positions are renalase substrates, but bind weakly. A seven-fold enhancement of acquisition (k red /K d ) for 6-dihydronicotinamide riboside was observed for human renalase in the presence of ADP. However, generally the addition of complement ligands, AMP for mononucleotide or ADP for nucleoside substrates, did not enhance the reductive half-reaction. Non-substrate nicotinamide nucleosides or nucleotides bind weakly suggesting that only β-NADH and β-NADPH compete with dinucleotide substrates for access to the active site. Copyright © 2016 Elsevier Inc. All rights reserved.

The binding of platinum hexahalides (Cl, Br and I) to hen egg-white lysozyme and the chemical transformation of the PtI{sub 6} octahedral complex to a PtI{sub 3} moiety bound to His15

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

Tanley, Simon W. M.; Starkey, Laurina-Victoria; Lamplough, Lucinda

The platinum hexahalides have an octahedral arrangement of six halogen atoms bound to a Pt centre, thus having an octahedral shape that could prove to be useful in interpreting poor electron-density maps. In a detailed characterization, PtI{sub 6} chemically transformed to a square-planar PtI{sub 3} complex bound to the N{sup δ} atom of His15 of HEWL was also observed, which was not observed for PtBr{sub 6} or PtCl{sub 6}. This study examines the binding and chemical stability of the platinum hexahalides K{sub 2}PtCl{sub 6}, K{sub 2}PtBr{sub 6} and K{sub 2}PtI{sub 6} when soaked into pre-grown hen egg-white lysozyme (HEWL) crystalsmore » as the protein host. Direct comparison of the iodo complex with the chloro and bromo complexes shows that the iodo complex is partly chemically transformed to a square-planar PtI{sub 3} complex bound to the N{sup δ} atom of His15, a chemical behaviour that is not exhibited by the chloro or bromo complexes. Each complex does, however, bind to HEWL in its octahedral form either at one site (PtI{sub 6}) or at two sites (PtBr{sub 6} and PtCl{sub 6}). As heavy-atom derivatives of a protein, the octahedral shape of the hexahalides could be helpful in cases of difficult-to-interpret electron-density maps as they would be recognisable ‘objects’.« less

Teacher-Student Relationship at University: An Important yet Under-Researched Field

ERIC Educational Resources Information Center

Hagenauer, Gerda; Volet, Simone E.

2014-01-01

This article reviews the extant research on the relationship between students and teachers in higher education across three main areas: the quality of this relationship, its consequences and its antecedents. The weaknesses and gaps in prior research are highlighted and the importance of addressing the multi-dimensional and context-bound nature of…

A Characterization of Banach Spaces Containing l1

PubMed Central

Rosenthal, Haskell P.

1974-01-01

It is proved that a Banach space contains a subspace isomorphic to l1 if (and only if) it has a bounded sequence with no weak-Cauchy subsequence. The proof yields that a sequence of subsets of a given set has a subsequence that is either convergent or Boolean independent. PMID:16592162

Oxidation of the Ru(0001) surface covered by weakly bound, ultrathin silicate films

DOE PAGES

Emmez, Emre; Anibal Boscoboinik, J.; Tenney, Samuel; ...

2015-06-30

Bilayer silicate films grown on metal substrates are weakly bound to the metal surfaces, which allows ambient gas molecules to intercalate the oxide/metal interface. In this work, we studied the interaction of oxygen with Ru(0001) supported ultrathin silicate and aluminosilicate films at elevated O 2 pressures (10 -5–10 mbar) and temperatures (450–923 K). The results show that the silicate films stay essentially intact under these conditions, and oxygen in the film does not exchange with oxygen in the ambient. O 2 molecules readily penetrate the film and dissociate on the underlying Ru surface underneath. Also, the silicate layer does howevermore » strongly passivate the Ru surface towards RuO 2(110) oxide formation that readily occurs on bare Ru(0001) under the same conditions. Lastly, the results indicate considerable spatial effects for oxidation reactions on metal surfaces in the confined space at the interface. Moreover, the aluminosilicate films completely suppress the Ru oxidation, providing some rationale for using crystalline aluminosilicates in anti-corrosion coatings.« less

Optical Lattice Clocks with Weakly Bound Molecules.

PubMed

Borkowski, Mateusz

2018-02-23

Optical molecular clocks promise unparalleled sensitivity to the temporal variation of the electron-to-proton mass ratio and insight into possible new physics beyond the standard model. We propose to realize a molecular clock with bosonic ^{174}Yb_{2} molecules, where the forbidden ^{1}S_{0}→^{3}P_{0} clock transition would be induced magnetically. The use of a bosonic species avoids possible complications due to the hyperfine structure present in fermionic species. While direct clock line photoassociation would be challenging, weakly bound ground state molecules could be produced by stimulated Raman adiabatic passage and used instead. The recent scattering measurements [L. Franchi, et al. New J. Phys. 19, 103037 (2017)NJOPFM1367-263010.1088/1367-2630/aa8fb4] enable us to determine the positions of target ^{1}S_{0}+^{3}P_{0} vibrational levels and calculate the Franck-Condon factors for clock transitions between ground and excited molecular states. The resulting magnetically induced Rabi frequencies are similar to those for atoms hinting that an experimental realization is feasible. A successful observation could pave the way towards Hz-level molecular spectroscopy.

Neutron whispering gallery

NASA Astrophysics Data System (ADS)

Nesvizhevsky, Valery V.; Voronin, Alexei Yu.; Cubitt, Robert; Protasov, Konstantin V.

2010-02-01

The `whispering gallery' effect has been known since ancient times for sound waves in air, later in water and more recently for a broad range of electromagnetic waves: radio, optics, Roentgen and so on. It consists of wave localization near a curved reflecting surface and is expected for waves of various natures, for instance, for atoms and neutrons. For matter waves, it would include a new feature: a massive particle would be settled in quantum states, with parameters depending on its mass. Here, we present for the first time the quantum whispering-gallery effect for cold neutrons. This phenomenon provides an example of an exactly solvable problem analogous to the `quantum bouncer'; it is complementary to the recently discovered gravitationally bound quantum states of neutrons . These two phenomena provide a direct demonstration of the weak equivalence principle for a massive particle in a pure quantum state. Deeply bound whispering-gallery states are long-living and weakly sensitive to surface potential; highly excited states are short-living and very sensitive to the wall potential shape. Therefore, they are a promising tool for studying fundamental neutron-matter interactions, quantum neutron optics and surface physics effects.

Gravitational mass of positron from LEP synchrotron losses.

PubMed

Kalaydzhyan, Tigran

2016-07-27

General relativity(GR) is the current description of gravity in modern physics. One of the cornerstones of GR, as well as Newton's theory of gravity, is the weak equivalence principle (WEP), stating that the trajectory of a freely falling test body is independent of its internal structure and composition. WEP is known to be valid for the normal matter with a high precision. However, due to the rarity of antimatter and weakness of the gravitational forces, the WEP has never been confirmed for antimatter. The current direct bounds on the ratio between the gravitational and inertial masses of the antihydrogen do not rule out a repulsive nature for the antimatter gravity. Here we establish an indirect bound of 0.13% on the difference between the gravitational and inertial masses of the positron (antielectron) from the analysis of synchrotron losses at the Large Electron-Positron collider (LEP). This serves as a confirmation of the conventional gravitational properties of antimatter without common assumptions such as, e.g., coupling of gravity to virtual particles, dynamics of distant astrophysical sources and the nature of absolute gravitational potentials.

Gravitational mass of positron from LEP synchrotron losses

PubMed Central

Kalaydzhyan, Tigran

2016-01-01

General relativity(GR) is the current description of gravity in modern physics. One of the cornerstones of GR, as well as Newton’s theory of gravity, is the weak equivalence principle (WEP), stating that the trajectory of a freely falling test body is independent of its internal structure and composition. WEP is known to be valid for the normal matter with a high precision. However, due to the rarity of antimatter and weakness of the gravitational forces, the WEP has never been confirmed for antimatter. The current direct bounds on the ratio between the gravitational and inertial masses of the antihydrogen do not rule out a repulsive nature for the antimatter gravity. Here we establish an indirect bound of 0.13% on the difference between the gravitational and inertial masses of the positron (antielectron) from the analysis of synchrotron losses at the Large Electron-Positron collider (LEP). This serves as a confirmation of the conventional gravitational properties of antimatter without common assumptions such as, e.g., coupling of gravity to virtual particles, dynamics of distant astrophysical sources and the nature of absolute gravitational potentials. PMID:27461548

Search for neutral color-octet weak-triplet scalar particles in proton-proton collisions at √s = 8 TeV

DOE PAGES

Khachatryan, Vardan

2015-09-29

A search for pair production of neutral color-octet weak-triplet scalar particles (Θ 0) is performed in processes where one Θ 0 decays to a pair of b quark jets and the other to a Z boson plus a jet, with the Z boson decaying to a pair of electrons or muons. The search is performed with data collected by the CMS experiment at the CERN LHC corresponding to an integrated luminosity of 19.7 fb –1 of proton-proton collisions at √s = 8 TeV. The number of observed events is found to be in agreement with the standard model predictions. Themore » 95% confidence level upper limit on the product of the cross section and branching fraction is obtained as a function of the Θ 0 mass. The 95% confidence level lower bounds on the Θ 0 mass are found to be 623 and 426 GeV, for two different octo-triplet theoretical scenarios. These are the first direct experimental bounds on particles predicted by the octo-triplet model.« less

Search for neutral color-octet weak-triplet scalar particles in proton-proton collisions at √{s}=8 TeV

NASA Astrophysics Data System (ADS)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Knünz, V.; König, A.; Krammer, M.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Schöfbeck, R.; Strauss, J.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Lauwers, J.; Luyckx, S.; Ochesanu, S.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; Daci, N.; De Bruyn, I.; Deroover, K.; Heracleous, N.; Keaveney, J.; Lowette, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Van Parijs, I.; Barria, P.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Dobur, D.; Fasanella, G.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Randleconde, A.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Zenoni, F.; Zhang, F.; Beernaert, K.; Benucci, L.; Cimmino, A.; Crucy, S.; Fagot, A.; Garcia, G.; Gul, M.; Mccartin, J.; Ocampo Rios, A. A.; Poyraz, D.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Tytgat, M.; Van Driessche, W.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bondu, O.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Mertens, A.; Nuttens, C.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Beliy, N.; Caebergs, T.; Hammad, G. H.; Aldá Júnior, W. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Dos Reis Martins, T.; Hensel, C.; Mora Herrera, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; De Souza Santos, A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Moon, C. S.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Genchev, V.; Hadjiiska, R.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Cheng, T.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Shaheen, S. M.; Tao, J.; Wang, C.; Wang, Z.; Zhang, H.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Zou, W.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Bodlak, M.; Finger, M.; Finger, M.; Ali, A.; Aly, R.; Aly, S.; Elgammal, S.; Ellithi Kamel, A.; Lotfy, A.; Mahmoud, M. A.; Masod, R.; Radi, A.; Calpas, B.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Pekkanen, J.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Machet, M.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Zghiche, A.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Chapon, E.; Charlot, C.; Dahms, T.; Davignon, O.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Lisniak, S.; Mastrolorenzo, L.; Miné, P.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Merlin, J. A.; Skovpen, K.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Bernet, C.; Boudoul, G.; Bouvier, E.; Brochet, S.; Carrillo Montoya, C. A.; Chasserat, J.; Chierici, R.; Contardo, D.; Courbon, B.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Laktineh, I. B.; Lethuillier, M.; Mirabito, L.; Pequegnot, A. L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Xiao, H.; Lomidze, D.; Autermann, C.; Beranek, S.; Edelhoff, M.; Feld, L.; Heister, A.; Kiesel, M. K.; Klein, K.; Lipinski, M.; Ostapchuk, A.; Preuten, M.; Raupach, F.; Sammet, J.; Schael, S.; Schulte, J. F.; Verlage, T.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Endres, M.; Erdmann, M.; Erdweg, S.; Esch, T.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Millet, P.; Olschewski, M.; Padeken, K.; Papacz, P.; Pook, T.; Radziej, M.; Reithler, H.; Rieger, M.; Scheuch, F.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Haj Ahmad, W.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Künsken, A.; Lingemann, J.; Nehrkorn, A.; Nowack, A.; Nugent, I. M.; Pistone, C.; Pooth, O.; Stahl, A.; Aldaya Martin, M.; Asin, I.; Bartosik, N.; Behnke, O.; Behrens, U.; Bell, A. J.; Borras, K.; Burgmeier, A.; Cakir, A.; Calligaris, L.; Campbell, A.; Choudhury, S.; Costanza, F.; Diez Pardos, C.; Dolinska, G.; Dooling, S.; Dorland, T.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Flucke, G.; Gallo, E.; Garay Garcia, J.; Geiser, A.; Gizhko, A.; Gunnellini, P.; Hauk, J.; Hempel, M.; Jung, H.; Kalogeropoulos, A.; Karacheban, O.; Kasemann, M.; Katsas, P.; Kieseler, J.; Kleinwort, C.; Korol, I.; Lange, W.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Mankel, R.; Marfin, I.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Naumann-Emme, S.; Nayak, A.; Ntomari, E.; Perrey, H.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Ribeiro Cipriano, P. M.; Roland, B.; Sahin, M. Ö.; Salfeld-Nebgen, J.; Saxena, P.; Schoerner-Sadenius, T.; Schröder, M.; Seitz, C.; Spannagel, S.; Trippkewitz, K. D.; Wissing, C.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Erfle, J.; Garutti, E.; Goebel, K.; Gonzalez, D.; Görner, M.; Haller, J.; Hoffmann, M.; Höing, R. S.; Junkes, A.; Klanner, R.; Kogler, R.; Lapsien, T.; Lenz, T.; Marchesini, I.; Marconi, D.; Nowatschin, D.; Ott, J.; Pantaleo, F.; Peiffer, T.; Perieanu, A.; Pietsch, N.; Poehlsen, J.; Rathjens, D.; Sander, C.; Schettler, H.; Schleper, P.; Schlieckau, E.; Schmidt, A.; Seidel, M.; Sola, V.; Stadie, H.; Steinbrück, G.; Tholen, H.; Troendle, D.; Usai, E.; Vanelderen, L.; Vanhoefer, A.; Akbiyik, M.; Barth, C.; Baus, C.; Berger, J.; Böser, C.; Butz, E.; Chwalek, T.; Colombo, F.; De Boer, W.; Descroix, A.; Dierlamm, A.; Feindt, M.; Frensch, F.; Giffels, M.; Gilbert, A.; Hartmann, F.; Husemann, U.; Kassel, F.; Katkov, I.; Kornmayer, A.; Lobelle Pardo, P.; Mozer, M. U.; Müller, T.; Müller, Th.; Plagge, M.; Quast, G.; Rabbertz, K.; Röcker, S.; Roscher, F.; Simonis, H. J.; Stober, F. M.; Ulrich, R.; Wagner-Kuhr, J.; Wayand, S.; Weiler, T.; Wöhrmann, C.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Markou, A.; Psallidas, A.; Topsis-Giotis, I.; Agapitos, A.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Tziaferi, E.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Loukas, N.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Strologas, J.; Bencze, G.; Hajdu, C.; Hazi, A.; Hidas, P.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Molnar, J.; Szillasi, Z.; Bartók, M.; Makovec, A.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Mal, P.; Mandal, K.; Sahoo, N.; Swain, S. K.; Bansal, S.; Beri, S. B.; Bhatnagar, V.; Chawla, R.; Gupta, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, A.; Kaur, M.; Kumar, R.; Mehta, A.; Mittal, M.; Nishu, N.; Singh, J. B.; Walia, G.; Kumar, Ashok; Kumar, Arun; Bhardwaj, A.; Choudhary, B. C.; Garg, R. B.; Kumar, A.; Malhotra, S.; Naimuddin, M.; Ranjan, K.; Sharma, R.; Sharma, V.; Banerjee, S.; Bhattacharya, S.; Chatterjee, K.; Dey, S.; Dutta, S.; Jain, Sa.; Jain, Sh.; Khurana, R.; Majumdar, N.; Modak, A.; Mondal, K.; Mukherjee, S.; Mukhopadhyay, S.; Roy, A.; Roy, D.; Roy Chowdhury, S.; Sarkar, S.; Sharan, M.; Abdulsalam, A.; Chudasama, R.; Dutta, D.; Jha, V.; Kumar, V.; Mohanty, A. K.; Pant, L. M.; Shukla, P.; Topkar, A.; Aziz, T.; Banerjee, S.; Bhowmik, S.; Chatterjee, R. M.; Dewanjee, R. K.; Dugad, S.; Ganguly, S.; Ghosh, S.; Guchait, M.; Gurtu, A.; Kole, G.; Kumar, S.; Mahakud, B.; Maity, M.; Majumder, G.; Mazumdar, K.; Mitra, S.; Mohanty, G. B.; Parida, B.; Sarkar, T.; Sudhakar, K.; Sur, N.; Sutar, B.; Wickramage, N.; Sharma, S.; Bakhshiansohi, H.; Behnamian, H.; Etesami, S. M.; Fahim, A.; Goldouzian, R.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Calabria, C.; Caputo, C.; Chhibra, S. S.; Colaleo, A.; Creanza, D.; Cristella, L.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; Miniello, G.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Ranieri, A.; Selvaggi, G.; Sharma, A.; Silvestris, L.; Venditti, R.; Verwilligen, P.; Abbiendi, G.; Battilana, C.; Benvenuti, A. C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Rossi, A. M.; Rovelli, T.; Siroli, G. 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M.; Lanza, G.; Lista, L.; Meola, S.; Merola, M.; Paolucci, P.; Sciacca, C.; Thyssen, F.; Azzi, P.; Bacchetta, N.; Bisello, D.; Carlin, R.; Carvalho Antunes De Oliveira, A.; Checchia, P.; Dall'Osso, M.; Dorigo, T.; Gasparini, F.; Gasparini, U.; Gozzelino, A.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Pazzini, J.; Pozzobon, N.; Ronchese, P.; Sgaravatto, M.; Simonetto, F.; Torassa, E.; Tosi, M.; Vanini, S.; Ventura, S.; Zanetti, M.; Zotto, P.; Zucchetta, A.; Zumerle, G.; Braghieri, A.; Gabusi, M.; Magnani, A.; Ratti, S. P.; Re, V.; Riccardi, C.; Salvini, P.; Vai, I.; Vitulo, P.; Alunni Solestizi, L.; Biasini, M.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Mantovani, G.; Menichelli, M.; Saha, A.; Santocchia, A.; Spiezia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Broccolo, G.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fedi, G.; Foà, L.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Serban, A. T.; Spagnolo, P.; Squillacioti, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; D'imperio, G.; Del Re, D.; Diemoz, M.; Gelli, S.; Jorda, C.; Longo, E.; Margaroli, F.; Meridiani, P.; Micheli, F.; Organtini, G.; Paramatti, R.; Preiato, F.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Soffi, L.; Traczyk, P.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bellan, R.; Biino, C.; Cartiglia, N.; Casasso, S.; Costa, M.; Covarelli, R.; Degano, A.; Demaria, N.; Finco, L.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Musich, M.; Obertino, M. M.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Romero, A.; Ruspa, M.; Sacchi, R.; Solano, A.; Staiano, A.; Tamponi, U.; Trapani, P. 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F.; Khatiwada, A.; Prosper, H.; Veeraraghavan, V.; Weinberg, M.; Bhopatkar, V.; Hohlmann, M.; Kalakhety, H.; Mareskas-palcek, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Kurt, P.; O'Brien, C.; Sandoval Gonzalez, I. D.; Silkworth, C.; Turner, P.; Varelas, N.; Wu, Z.; Zakaria, M.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Sen, S.; Snyder, C.; Tan, P.; Tiras, E.; Wetzel, J.; Yi, K.; Anderson, I.; Barnett, B. A.; Blumenfeld, B.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Nash, K.; Osherson, M.; Swartz, M.; Xiao, M.; Xin, Y.; Baringer, P.; Bean, A.; Benelli, G.; Bruner, C.; Gray, J.; Kenny, R. P.; Majumder, D.; Malek, M.; Murray, M.; Noonan, D.; Sanders, S.; Stringer, R.; Wang, Q.; Wood, J. S.; Chakaberia, I.; Ivanov, A.; Kaadze, K.; Khalil, S.; Makouski, M.; Maravin, Y.; Saini, L. K.; Skhirtladze, N.; Svintradze, I.; Lange, D.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Calvert, B.; Eno, S. C.; Ferraioli, C.; Gomez, J. A.; Hadley, N. J.; Jabeen, S.; Kellogg, R. G.; Kolberg, T.; Kunkle, J.; Lu, Y.; Mignerey, A. C.; Pedro, K.; Shin, Y. H.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Baty, A.; Bierwagen, K.; Brandt, S.; Busza, W.; Cali, I. A.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Klute, M.; Kovalskyi, D.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Mcginn, C.; Niu, X.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Stephans, G. S. F.; Sumorok, K.; Varma, M.; Velicanu, D.; Veverka, J.; Wang, J.; Wang, T. W.; Wyslouch, B.; Yang, M.; Zhukova, V.; Dahmes, B.; Finkel, A.; Gude, A.; Hansen, P.; Kalafut, S.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Fangmeier, C.; Gonzalez Suarez, R.; Kamalieddin, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Meier, F.; Monroy, J.; Ratnikov, F.; Siado, J. E.; Snow, G. R.; Alyari, M.; Dolen, J.; George, J.; Godshalk, A.; Iashvili, I.; Kaisen, J.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Teixeira De Lima, R.; Trocino, D.; Wang, R.-J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Trovato, M.; Velasco, M.; Won, S.; Brinkerhoff, A.; Dev, N.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Lynch, S.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Pearson, T.; Planer, M.; Ruchti, R.; Smith, G.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hart, A.; Hill, C.; Hughes, R.; Kotov, K.; Ling, T. Y.; Liu, B.; Luo, W.; Puigh, D.; Rodenburg, M.; Winer, B. L.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Palmer, C.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zuranski, A.; Barnes, V. E.; Benedetti, D.; Bortoletto, D.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Miller, D. H.; Neumeister, N.; Primavera, F.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Sun, J.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Zablocki, J.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Chen, Z.; Ecklund, K. M.; Geurts, F. J. M.; Guilbaud, M.; Li, W.; Michlin, B.; Northup, M.; Padley, B. P.; Redjimi, R.; Roberts, J.; Rorie, J.; Tu, Z.; Zabel, J.; Betchart, B.; Bodek, A.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Goldenzweig, P.; Han, J.; Harel, A.; Hindrichs, O.; Khukhunaishvili, A.; Petrillo, G.; Verzetti, M.; Vishnevskiy, D.; Demortier, L.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Lath, A.; Panwalkar, S.; Park, M.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Foerster, M.; Riley, G.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Castaneda Hernandez, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Flanagan, W.; Gilmore, J.; Kamon, T.; Krutelyov, V.; Montalvo, R.; Mueller, R.; Osipenkov, I.; Pakhotin, Y.; Patel, R.; Perloff, A.; Roe, J.; Rose, A.; Safonov, A.; Suarez, I.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Undleeb, S.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wolfe, E.; Wood, J.; Xia, F.; Clarke, C.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Christian, A.; Dasu, S.; Dodd, L.; Duric, S.; Friis, E.; Gomber, B.; Grothe, M.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Ruggles, T.; Sarangi, T.; Savin, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.

2015-09-01

A search for pair production of neutral color-octet weak-triplet scalar particles (Θ0) is performed in processes where one Θ0 decays to a pair of b quark jets and the other to a Z boson plus a jet, with the Z boson decaying to a pair of electrons or muons. The search is performed with data collected by the CMS experiment at the CERN LHC corresponding to an integrated luminosity of 19.7 fb-1 of proton-proton collisions at √{s}=8 TeV. The number of observed events is found to be in agreement with the standard model predictions. The 95% confidence level upper limit on the product of the cross section and branching fraction is obtained as a function of the Θ0 mass. The 95% confidence level lower bounds on the Θ0 mass are found to be 623 and 426 GeV, for two different octo-triplet theoretical scenarios. These are the first direct experimental bounds on particles predicted by the octo-triplet model. [Figure not available: see fulltext.

Optical Lattice Clocks with Weakly Bound Molecules

NASA Astrophysics Data System (ADS)

Borkowski, Mateusz

2018-02-01

Optical molecular clocks promise unparalleled sensitivity to the temporal variation of the electron-to-proton mass ratio and insight into possible new physics beyond the standard model. We propose to realize a molecular clock with bosonic 174Yb2 molecules, where the forbidden 1S0 →3P0 clock transition would be induced magnetically. The use of a bosonic species avoids possible complications due to the hyperfine structure present in fermionic species. While direct clock line photoassociation would be challenging, weakly bound ground state molecules could be produced by stimulated Raman adiabatic passage and used instead. The recent scattering measurements [L. Franchi, et al. New J. Phys. 19, 103037 (2017), 10.1088/1367-2630/aa8fb4] enable us to determine the positions of target 1S0 +3P0 vibrational levels and calculate the Franck-Condon factors for clock transitions between ground and excited molecular states. The resulting magnetically induced Rabi frequencies are similar to those for atoms hinting that an experimental realization is feasible. A successful observation could pave the way towards Hz-level molecular spectroscopy.

Optimizing the Readout of Lanthanide-DOTA Complexes for the Detection of Ligand-Bound Copper(I).

PubMed

Hanna, Jill R; Allan, Christopher; Lawrence, Charlotte; Meyer, Odile; Wilson, Neil D; Hulme, Alison N

2017-05-14

The CuAAC 'click' reaction was used to couple alkyne-functionalized lanthanide-DOTA complexes to a range of fluorescent antennae. Screening of the antenna components was aided by comparison of the luminescent output of the resultant sensors using data normalized to account for reaction conversion as assessed by IR. A maximum 82-fold enhanced signal:background luminescence output was achieved using a Eu(III)-DOTA complex coupled to a coumarin-azide, in a reaction which is specific to the presence of copper(I). This optimized complex provides a new lead design for lanthanide-DOTA complexes which can act as irreversible 'turn-on' catalytic sensors for the detection of ligand-bound copper(I).

Higher coordinate gold(I) complexes with the weak Lewis base tri(4-fluorophenyl) phosphine. Synthesis, structural, luminescence, and DFT studies

NASA Astrophysics Data System (ADS)

Agbeworvi, George; Assefa, Zerihun; Sykora, Richard E.; Taylor, Jared; Crawford, Carlos

2016-03-01

The structures and spectroscopic properties of two high coordinate gold(I) phosphine complexes with the TFFPP=tri(4-fluorophenyl)phosphine ligand are reported. Synthesis in a 1:3 metal to ligand ratio provided the compound [AuCl(TFFPP)3] (2) that crystallize in the P 1 bar space group, where the asymmetric unit consists of three independent molecules. In all three sites, two sets of bond angles display distinctly different ranges. The three P-Au-P angles have average values of 117.92°, 117.57°, and 114.78° for sites A, B, and C, with the corresponding P-Au-Cl angles of 98.31°, 99.05°, and 103.38°, respectively. The chloride ion coordinates as the fourth ligand, at the corresponding Au-Cl distance of 2.7337, 2.6825, and 2.6951 Å for the three sites. This distance is longer by 0.40-0.45 Å than the Au-Cl distance found in the mono TFFPP complex 1 (2.285 Å) indicating a weakening of the Au-Cl interaction as the coordination number increases. In compound 3, [Au(TFFPP)3]Cl·½CH2Cl2·H2O, the structure consists of three phosphine ligands bound to the gold(I) atom, but the Cl- exists as uncoordinated counter anion. The structural differences observed in the two complexes are attributable to crystal-packing effects caused by the introduction of H-bonding as well as enhanced intra and inter-molecular π-interaction in 3. The photoluminescence of the complexes compared with that of the ligand show ligand centered emission perturbed by the metal coordination. Theoretical DFT studies conducted on these complexes supports assignments of the electronic transitions observed in these systems.

a Chiral Tagging Strategy for Determining Absolute Configuration and Enantiomeric Excess by Molecular Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Caminati, Walther; Patterson, David; Thomas, Javix; Xu, Yunjie; West, Channing; Pate, Brooks

2017-06-01

The introduction of three wave mixing rotational spectroscopy by Patterson, Schnell, and Doyle [1,2] has expanded applications of molecular rotational spectroscopy into the field of chiral analysis. Chiral analysis of a molecule is the quantitative measurement of the relative abundances of all stereoisomers of the molecule and these include both diastereomers (with distinct molecular rotational spectra) and enantiomers (with equivalent molecular rotational spectra). This work adapts a common strategy in chiral analysis of enantiomers to molecular rotational spectroscopy. A "chiral tag" is attached to the molecule of interest by making a weakly bound complex in a pulsed jet expansion. When this tag molecule is enantiopure, it will create diastereomeric complexes with the two enantiomers of the molecule being analyzed and these can be differentiated by molecule rotational spectroscopy. Identifying the structure of this complex, with knowledge of the absolute configuration of the tag, establishes the absolute configuration of the molecule of interest. Furthermore, the diastereomer complex spectra can be used to determine the enantiomeric excess of the sample. The ability to perform chiral analysis will be illustrated by a study of solketal using propylene oxide as the tag. The possibility of using current methods of quantum chemistry to assign a specific structure to the chiral tag complex will be discussed. Finally, chiral tag rotational spectroscopy offers a "gold standard" method for determining the absolute configuration of the molecule through determination of the substitution structure of the complex. When this measurement is possible, rotational spectroscopy can deliver a quantitative three dimensional structure of the molecule with correct stereochemistry as the analysis output. [1] David Patterson, Melanie Schnell, John M. Doyle, Nature 497, 475 (2013). [2] David Patterson, John M. Doyle, Phys. Rev. Lett. 111, 023008 (2013).

Volume dependence of N-body bound states

NASA Astrophysics Data System (ADS)

König, Sebastian; Lee, Dean

2018-04-01

We derive the finite-volume correction to the binding energy of an N-particle quantum bound state in a cubic periodic volume. Our results are applicable to bound states with arbitrary composition and total angular momentum, and in any number of spatial dimensions. The only assumptions are that the interactions have finite range. The finite-volume correction is a sum of contributions from all possible breakup channels. In the case where the separation is into two bound clusters, our result gives the leading volume dependence up to exponentially small corrections. If the separation is into three or more clusters, there is a power-law factor that is beyond the scope of this work, however our result again determines the leading exponential dependence. We also present two independent methods that use finite-volume data to determine asymptotic normalization coefficients. The coefficients are useful to determine low-energy capture reactions into weakly bound states relevant for nuclear astrophysics. Using the techniques introduced here, one can even extract the infinite-volume energy limit using data from a single-volume calculation. The derived relations are tested using several exactly solvable systems and numerical examples. We anticipate immediate applications to lattice calculations of hadronic, nuclear, and cold atomic systems.

Exotic equilibria of Harary graphs and a new minimum degree lower bound for synchronization

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

Canale, Eduardo A., E-mail: ecanale@pol.una.py; Monzón, Pablo, E-mail: monzon@fing.edu.uy

2015-02-15

This work is concerned with stability of equilibria in the homogeneous (equal frequencies) Kuramoto model of weakly coupled oscillators. In 2012 [R. Taylor, J. Phys. A: Math. Theor. 45, 1–15 (2012)], a sufficient condition for almost global synchronization was found in terms of the minimum degree–order ratio of the graph. In this work, a new lower bound for this ratio is given. The improvement is achieved by a concrete infinite sequence of regular graphs. Besides, non standard unstable equilibria of the graphs studied in Wiley et al. [Chaos 16, 015103 (2006)] are shown to exist as conjectured in that work.

The weakly coupled fractional one-dimensional Schrödinger operator with index 1 < α <= 2

NASA Astrophysics Data System (ADS)

Hatzinikitas, Agapitos N.

2010-12-01

Considering the space fractional Weyl operator hat{P}^{α } on the separable Hilbert space H=L^2({R},dx) we determine the asymptotic behavior of both the free Green's function and its variation with respect to energy in one dimension for bound states. Later, we specify the Birman-Schwinger representation for the Schrödinger operator hat{H}_g=K_{α }hat{P}^{α }+ghat{V} and extract the finite-rank portion which is essential for the asymptotic expansion of the ground state. Finally, we determine necessary and sufficient conditions for there to be a bound state for small coupling constant g.

Energies and excited-state dynamics of 1Bu+, 1Bu- and 3Ag- states of carotenoids bound to LH2 antenna complexes from purple photosynthetic bacteria

NASA Astrophysics Data System (ADS)

Christiana, Rebecca; Miki, Takeshi; Kakitani, Yoshinori; Aoyagi, Shiho; Koyama, Yasushi; Limantara, Leenawaty

2009-10-01

Time-resolved pump-probe stimulated-emission and transient-absorption spectra were recorded after excitation with ˜30 fs pulses to the 1Bu+(0) and optically-forbidden diabatic levels of carotenoids, neurosporene, spheroidene and lycopene having n = 9-11 double bonds, bound to LH2 antenna complexes from Rhodobacter sphaeroides G1C, 2.4.1 and Rhodospirillum molischianum. The low-energy shift of stimulated emission from the covalent 1Bu-(0) and 3Ag-(0) levels slightly larger than that from the ionic 1Bu+(0) state suggests the polarization, whereas more efficient triplet generation suggests the twisting of the conjugated chain in Cars bound to the LH2 complexes, when compared to Cars free in solution.

Necessary and sufficient optimality conditions for classical simulations of quantum communication processes

NASA Astrophysics Data System (ADS)

Montina, Alberto; Wolf, Stefan

2014-07-01

We consider the process consisting of preparation, transmission through a quantum channel, and subsequent measurement of quantum states. The communication complexity of the channel is the minimal amount of classical communication required for classically simulating it. Recently, we reduced the computation of this quantity to a convex minimization problem with linear constraints. Every solution of the constraints provides an upper bound on the communication complexity. In this paper, we derive the dual maximization problem of the original one. The feasible points of the dual constraints, which are inequalities, give lower bounds on the communication complexity, as illustrated with an example. The optimal values of the two problems turn out to be equal (zero duality gap). By this property, we provide necessary and sufficient conditions for optimality in terms of a set of equalities and inequalities. We use these conditions and two reasonable but unproven hypotheses to derive the lower bound n ×2n -1 for a noiseless quantum channel with capacity equal to n qubits. This lower bound can have interesting consequences in the context of the recent debate on the reality of the quantum state.

Kinetics and thermochemistry of 2,5-dimethyltetrahydrofuran and related oxolanes: next next-generation biofuels.

PubMed

Simmie, John M

2012-05-10

The enthalpies of formation, entropies, specific heats at constant pressure, enthalpy functions, and all carbon-hydrogen and carbon-methyl bond dissociation energies have been computed using high-level methods for the cyclic ethers (oxolanes) tetrahydrofuran, 2-methyltetrahydrofuran, and 2,5-dimethyltetrahydrofuran. Barrier heights for hydrogen-abstraction reactions by hydrogen atoms and the methyl radical are also computed and shown to correlate with reaction energy change. The results show a pleasing consistency and considerably expands the available data for these important compounds. Abstraction by ȮH is accompanied by formation of both pre- and postreaction weakly bound complexes. The resulting radicals formed after abstraction undergo ring-opening reactions leading to readily recognizable intermediates, while competitive H-elimination reactions result in formation of dihydrofurans. Formation enthalpies of all 2,3- and 2,5-dihydrofurans and associated radicals are also reported. It is probable that the compounds at the center of this study will be relatively clean-burning biofuels, although formation of intermediate aldehydes might be problematic.

Potential bioavailability assessment, source apportionment and ecological risk of heavy metals in the sediment of Brisbane River estuary, Australia.

PubMed

Duodu, Godfred Odame; Goonetilleke, Ashantha; Ayoko, Godwin A

2017-04-15

A weak acid extraction was used to mobilize the loosely bound metals in estuary sediment samples. More than 30% of Ag, As, Ca, Cd, Co, Cu, Hg, Mn Ni, Pb and Zn were leached from the sediment showing that these metals are significantly present in the bioavailable form. PCA/APCS identified three sources of the metals, namely: lithogenic accounting for 72%, shipping related contributing 15% and traffic related representing 13% of the total load. Application of pollution index (PI) and modified pollution index (MPI) revealed that the sediment range from unpolluted to heavily polluted while ecological risk index (RI) classifies the sediment as posing low ecological risk modified ecological risk index (MRI) suggests considerable to very high ecological risk. To provide holistic insights into the ecological risks posed by metals, enrichment factor, MPI and MRI are recommended for the assessment of sediment in complex environments such as estuaries. Copyright © 2017 Elsevier Ltd. All rights reserved.

Theoretical studies on atmospheric chemistry of HFE-245mc and perfluoro-ethyl formate: Reaction with OH radicals, atmospheric fate of alkoxy radical and global warming potential

NASA Astrophysics Data System (ADS)

Lily, Makroni; Baidya, Bidisha; Chandra, Asit K.

2017-02-01

Theoretical studies have been performed on the kinetics, mechanism and thermochemistry of the hydrogen abstraction reactions of CF3CF2OCH3 (HFE-245mc) and CF3CF2OCHO with OH radical using DFT based M06-2X method. IRC calculation shows that both hydrogen abstraction reactions proceed via weakly bound hydrogen-bonded complex preceding to the formation of transition state. The rate coefficients calculated by canonical transition state theory along with Eckart's tunnelling correction at 298 K: k1(CF3CF2OCH3 + OH) = 1.09 × 10-14 and k2(CF3CF2OCHO + OH) = 1.03 × 10-14 cm3 molecule-1 s-1 are in very good agreement with the experimental values. The atmospheric implications of CF3CF2OCH3 and CF3CF2OCHO are also discussed.

The importance of structural softening for the evolution and architecture of passive margins

PubMed Central

Duretz, T.; Petri, B.; Mohn, G.; Schmalholz, S. M.; Schenker, F. L.; Müntener, O.

2016-01-01

Lithospheric extension can generate passive margins that bound oceans worldwide. Detailed geological and geophysical studies in present and fossil passive margins have highlighted the complexity of their architecture and their multi-stage deformation history. Previous modeling studies have shown the significant impact of coarse mechanical layering of the lithosphere (2 to 4 layer crust and mantle) on passive margin formation. We built upon these studies and design high-resolution (~100–300 m) thermo-mechanical numerical models that incorporate finer mechanical layering (kilometer scale) mimicking tectonically inherited heterogeneities. During lithospheric extension a variety of extensional structures arises naturally due to (1) structural softening caused by necking of mechanically strong layers and (2) the establishment of a network of weak layers across the deforming multi-layered lithosphere. We argue that structural softening in a multi-layered lithosphere is the main cause for the observed multi-stage evolution and architecture of magma-poor passive margins. PMID:27929057

Vibrational nonlinear optical properties of spatially confined weakly bound complexes.

PubMed

Zaleśny, Robert; Chołuj, Marta; Kozłowska, Justyna; Bartkowiak, Wojciech; Luis, Josep M

2017-09-13

This study focuses on the theoretical description of the influence of spatial confinement on the electronic and vibrational contributions to (hyper)polarizabilities of two dimeric hydrogen bonded systems, namely HCNHCN and HCNHNC. A two-dimensional analytical potential is employed to render the confining environment (e.g. carbon nanotube). Based on the results of the state-of-the-art calculations, performed at the CCSD(T)/aug-cc-pVTZ level of theory, we established that: (i) the influence of spatial confinement increases with increasing order of the electrical properties, (ii) the effect of spatial confinement is much larger in the case of the electronic than vibrational contribution (this holds for each order of the electrical properties) and (iii) the decrease in the static nuclear relaxation first hyperpolarizability upon the increase of confinement strength is mainly due to changes in the harmonic term, however, in the case of nuclear relaxation second hyperpolarizability the anharmonic terms contribute more to the drop of this property.

A non-ideal MHD model for structure formation

NASA Astrophysics Data System (ADS)

Karmakar, Pralay Kumar; Sarma, Pankaj

2018-02-01

The evolutionary initiation dynamics of triggered planetary structure formation is indeed a complex process yet to be well understood. We herein develop a theoretical classical model to see the gravitational fragmentation kinetics of the viscoelastic non-ideal magneto-hydro-dynamic (MHD) fabric. The inhomogeneous planetary disk is primarily composed of heavier dust grains (strongly correlated) together with relatively lighter electrons, ions and neutrals (weakly correlated) in a mean-fluidic approximation. A normal harmonic mode analysis results in a quadratic dispersion relation of a unique shape. It is demonstrated that the growth rate of the MHD fluctuations (magnetosonic) contributing to the planet formation rate, apart from the wave vector and its projection orientation, has a pure explicit dependency on the viscoelastic parameters. The analysis specifically shows that the effective generalized viscosity (χ) , viscoelastic relaxation time (τm) , and K-orientation (θ) play as destabilizing agencies against the non-local gravitational disk collapse. The relevancy is briefly indicated in the real astronomical context of bounded planetary structure formation and evolution.

The aqueous geochemistry of uranium in a drainage containing uraniferous organic-rich sediments, Lake Tahoe area, Nevada, USA

USGS Publications Warehouse

Zielinski, R.A.; Otton, J.K.; Wanty, R.B.; Pierson, C.T.

1988-01-01

Anomalously uraniferous waters occur in a small (4.2 km2) drainage in the west-central Carson Range, Nevada, on the eastern side of Lake Tahoe. The waters transport uranium from local U-rich soils and bedrock to organic-rich valley-fill sediments where it is concentrated, but weakly bound. The dissolved U and the U that is potentially available from coexisting sediments pose a threat to the quality of drinking water that is taken from the drainage. The U concentration in samples of 6 stream, 11 spring and 7 near-surface waters ranged from 0.1 V). Possible precipitation of U(IV) minerals is predicted under the more reducing conditions that are particularly likely in near-surface waters, but the inhibitory effects of sluggish kinetics or organic complexing are not considered. These combined results suggest that a process such as adsorption or ion exchange, rather than mineral saturation, is the most probable mechanism for uranium fixation in the sediments. -Authors

Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution

NASA Astrophysics Data System (ADS)

Wohlert, Jakob; Schnupf, Udo; Brady, John W.

2010-10-01

Multidimensional potentials of mean force for the interactions in aqueous solution of both anomers of D-glucopyranose with two planar aromatic molecules, indole and para-methyl-phenol, have been calculated using molecular dynamics simulations with umbrella sampling and were subsequently used to estimate binding free energies. Indole and para-methyl-phenol serve as models for the side chains of the amino acids tryptophan and tyrosine, respectively. In all cases, a weak affinity between the glucose molecules and the flat aromatic surfaces was found. The global minimum for these interactions was found to be for the case when the pseudoplanar face of β-D-glucopyranose is stacked against the planar surfaces of the aromatic residues. The calculated binding free energies are in good agreement with both experiment and previous simulations. The multidimensional free energy maps suggest a mechanism that could lend kinetic stability to the complexes formed by sugars bound to sugar-binding proteins.

On the global well-posedness of BV weak solutions to the Kuramoto-Sakaguchi equation

NASA Astrophysics Data System (ADS)

Amadori, Debora; Ha, Seung-Yeal; Park, Jinyeong

2017-01-01

The Kuramoto model is a prototype phase model describing the synchronous behavior of weakly coupled limit-cycle oscillators. When the number of oscillators is sufficiently large, the dynamics of Kuramoto ensemble can be effectively approximated by the corresponding mean-field equation, namely "the Kuramoto-Sakaguchi (KS) equation". This KS equation is a kind of scalar conservation law with a nonlocal flux function due to the mean-field interactions among oscillators. In this paper, we provide a unique global solvability of bounded variation (BV) weak solutions to the kinetic KS equation for identical oscillators using the method of front-tracking in hyperbolic conservation laws. Moreover, we also show that our BV weak solutions satisfy local-in-time L1-stability with respect to BV-initial data. For the ensemble of identical Kuramoto oscillators, we explicitly construct an exponentially growing BV weak solution generated from BV perturbation of incoherent state for any positive coupling strength. This implies the nonlinear instability of incoherent state in a positive coupling strength regime. We provide several numerical examples and compare them with our analytical results.

A calix[4]arene strapped calix[4]pyrrole: an ion-pair receptor displaying three different cesium cation recognition modes.

PubMed

Kim, Sung Kuk; Sessler, Jonathan L; Gross, Dustin E; Lee, Chang-Hee; Kim, Jong Seung; Lynch, Vincent M; Delmau, Laetitia H; Hay, Benjamin P

2010-04-28

An ion-pair receptor, the calix[4]pyrrole-calix[4]arene pseudodimer 2, bearing a strong anion-recognition site but not a weak cation-recognition site, has been synthesized and characterized by standard spectroscopic means and via single-crystal X-ray diffraction analysis. In 10% CD(3)OD in CDCl(3) (v/v), this new receptor binds neither the Cs(+) cation nor the F(-) anion when exposed to these species in the presence of other counterions; however, it forms a stable 1:1 solvent-separated CsF complex when exposed to these two ions in concert with one another in this same solvent mixture. In contrast to what is seen in the case of a previously reported crown ether "strapped" calixarene-calixpyrrole ion-pair receptor 1 (J. Am. Chem. Soc. 2008, 130, 13162-13166), where Cs(+) cation recognition takes place within the crown, in 2.CsF cation recognition takes place within the receptor cavity itself, as inferred from both single-crystal X-ray diffraction analyses and (1)H NMR spectroscopic studies. This binding mode is supported by calculations carried out using the MMFF94 force field model. In 10% CD(3)OD in CDCl(3) (v/v), receptor 2 shows selectivity for CsF over the Cs(+) salts of Cl(-), Br(-), and NO(3)(-) but will bind these other cesium salts in the absence of fluoride, both in solution and in the solid state. In the case of CsCl, an unprecedented 2:2 complex is observed in the solid state that is characterized by two different ion-pair binding modes. One of these consists of a contact ion pair with the cesium cation and chloride anion both being bound within the central binding pocket and in direct contact with one another. The other mode involves a chloride anion bound to the pyrrole NH protons of a calixpyrrole subunit and a cesium cation sandwiched between two cone shaped calix[4]pyrroles originating from separate receptor units. In contrast to what is seen for CsF and CsCl, single-crystal X-ray structural analyses and (1)H NMR spectroscopic studies reveal that receptor 2 forms a 1:1 complex with CsNO(3), with the ions bound in the form of a contact ion pair. Thus, depending on the counteranion, receptor 2 is able to stabilize three different ion-pair binding modes with Cs(+), namely solvent-bridged, contact, and host-separated.

A complex guided spectral transform Lanczos method for studying quantum resonance states

DOE PAGES

Yu, Hua-Gen

2014-12-28

A complex guided spectral transform Lanczos (cGSTL) algorithm is proposed to compute both bound and resonance states including energies, widths and wavefunctions. The algorithm comprises of two layers of complex-symmetric Lanczos iterations. A short inner layer iteration produces a set of complex formally orthogonal Lanczos (cFOL) polynomials. They are used to span the guided spectral transform function determined by a retarded Green operator. An outer layer iteration is then carried out with the transform function to compute the eigen-pairs of the system. The guided spectral transform function is designed to have the same wavefunctions as the eigenstates of the originalmore » Hamiltonian in the spectral range of interest. Therefore the energies and/or widths of bound or resonance states can be easily computed with their wavefunctions or by using a root-searching method from the guided spectral transform surface. The new cGSTL algorithm is applied to bound and resonance states of HO₂, and compared to previous calculations.« less

Flight control application of new stability robustness bounds for linear uncertain systems

NASA Technical Reports Server (NTRS)

Yedavalli, Rama K.

1993-01-01

This paper addresses the issue of obtaining bounds on the real parameter perturbations of a linear state-space model for robust stability. Based on Kronecker algebra, new, easily computable sufficient bounds are derived that are much less conservative than the existing bounds since the technique is meant for only real parameter perturbations (in contrast to specializing complex variation case to real parameter case). The proposed theory is illustrated with application to several flight control examples.

Iron-sulfur Proteins Are the Major Source of Protein-bound Dinitrosyl Iron Complexes Formed in Escherichia coli Cells under Nitric Oxide Stress

PubMed Central

Landry, Aaron P.; Duan, Xuewu; Huang, Hao; Ding, Huangen

2011-01-01

Protein-bound dinitrosyl iron complexes (DNICs) have been observed in prokaryotic and eukaryotic cells under nitric oxide (NO) stress. The identity of proteins that bind DNICs, however, still remains elusive. Here we demonstrate that iron-sulfur proteins are the major source of protein-bound DNICs formed in Escherichia coli cells under NO stress. Expression of recombinant iron-sulfur proteins, but not the proteins without iron-sulfur clusters, almost doubles the amount of protein-bound DNICs formed in E. coli cells after NO exposure. Purification of recombinant proteins from the NO-exposed E. coli cells further confirms that iron-sulfur proteins, but not the proteins without iron-sulfur clusters, are modified forming protein-bound DINCs. Deletion of the iron-sulfur cluster assembly proteins IscA and SufA to block the [4Fe-4S] cluster biogenesis in E. coli cells largely eliminates the NO-mediated formation of protein-bound DNICs, suggesting that iron-sulfur clusters are mainly responsible for the NO-mediated formation of protein-bound DNICs in cells. Furthermore, depletion of “chelatable iron pool” in the wild-type E. coli cells effectively removes iron-sulfur clusters from proteins and concomitantly diminishes the NO-mediated formation of protein-bound DNICs, indicating that iron-sulfur clusters in proteins constitute at least part of “chelatable iron pool” in cells. PMID:21420489

The interstellar formation and spectra of the noble gas, proton-bound HeHHe+, HeHNe+ and HeHAr+ complexes

NASA Astrophysics Data System (ADS)

Stephan, Cody J.; Fortenberry, Ryan C.

2017-07-01

The sheer interstellar abundance of helium makes any bound molecules or complexes containing it of potential interest for astrophysical observation. This work utilizes high-level and trusted quantum chemical techniques to predict the rotational, vibrational and rovibrational traits of HeHHe+, HeHNe+ and HeHAr+. The first two are shown to be strongly bound, while HeHAr+ is shown to be more of a van der Waals complex of argonium with a helium atom. In any case, the formation of HeHHe+ through reactions of HeH+ with HeH3+ is exothermic. HeHHe+ exhibits the quintessentially bright proton-shuttle motion present in all proton-bound complexes in the 7.4 micron range making it a possible target for telescopic observation at the mid-/far-Infrared crossover point and a possible tracer for the as-of-yet unobserved helium hydride cation. Furthermore, a similar mode in HeHNe+ can be observed to the blue of this close to 6.9 microns. The brightest mode of HeHAr+ is dimmed due the reduced interaction of the helium atom with the central proton, but this fundamental frequency can be found slightly to the red of the Ar-H stretch in the astrophysically detected argonium cation.

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

PubMed Central

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

Insight into Temperature Dependence of GTPase Activity in Human Guanylate Binding Protein-1

PubMed Central

Rahman, Safikur; Deep, Shashank; Sau, Apurba Kumar

2012-01-01

Interferon-γ induced human guanylate binding protein-1(hGBP1) belongs to a family of dynamin related large GTPases. Unlike all other GTPases, hGBP1 hydrolyzes GTP to a mixture of GDP and GMP with GMP being the major product at 37°C but GDP became significant when the hydrolysis reaction was carried out at 15°C. The hydrolysis reaction in hGBP1 is believed to involve with a number of catalytic steps. To investigate the effect of temperature in the product formation and on the different catalytic complexes of hGBP1, we carried out temperature dependent GTPase assays, mutational analysis, chemical and thermal denaturation studies. The Arrhenius plot for both GDP and GMP interestingly showed nonlinear behaviour, suggesting that the product formation from the GTP-bound enzyme complex is associated with at least more than one step. The negative activation energy for GDP formation and GTPase assay with external GDP together indicate that GDP formation occurs through the reversible dissociation of GDP-bound enzyme dimer to monomer, which further reversibly dissociates to give the product. Denaturation studies of different catalytic complexes show that unlike other complexes the free energy of GDP-bound hGBP1 decreases significantly at lower temperature. GDP formation is found to be dependent on the free energy of the GDP-bound enzyme complex. The decrease in the free energy of this complex at low temperature compared to at high is the reason for higher GDP formation at low temperature. Thermal denaturation studies also suggest that the difference in the free energy of the GTP-bound enzyme dimer compared to its monomer plays a crucial role in the product formation; higher stability favours GMP but lower favours GDP. Thus, this study provides the first thermodynamic insight into the effect of temperature in the product formation of hGBP1. PMID:22859948

Unmatter Plasma revisited

NASA Astrophysics Data System (ADS)

Smarandache, Florentin

2017-10-01

Unmmatter Plasma is a novel form of plasma, exclusively made of matter and its antimatter counterpart. The electron-positron beam plasma was generated in the laboratory in the beginning of 2015. This experimental fact shows that unmatter, a new form of matter that is formed by matter and antimatter bind together (mathematically predicted since 2004) really exists. That is the electron-positron plasma experiment of 2015 is the experimentum crucis verifying the mathematically predicted unmatter. Unmatter is formed by combinations of matter and antimatter that bind together, or by long-range mixture of matter and antimatter forming a weakly-coupled phase. Binding and bound state means that the interaction is sufficiently strong to tie together the particles of a system, therefore hindering them from becoming free. For example, a usual liquid is a bound state of molecules, while a gas is an un-bounded where the molecules can move freely in successive collisions.

The entropic cost of quantum generalized measurements

NASA Astrophysics Data System (ADS)

Mancino, Luca; Sbroscia, Marco; Roccia, Emanuele; Gianani, Ilaria; Somma, Fabrizia; Mataloni, Paolo; Paternostro, Mauro; Barbieri, Marco

2018-03-01

Landauer's principle introduces a symmetry between computational and physical processes: erasure of information, a logically irreversible operation, must be underlain by an irreversible transformation dissipating energy. Monitoring micro- and nano-systems needs to enter into the energetic balance of their control; hence, finding the ultimate limits is instrumental to the development of future thermal machines operating at the quantum level. We report on the experimental investigation of a lower bound to the irreversible entropy associated to generalized quantum measurements on a quantum bit. We adopted a quantum photonics gate to implement a device interpolating from the weakly disturbing to the fully invasive and maximally informative regime. Our experiment prompted us to introduce a bound taking into account both the classical result of the measurement and the outcoming quantum state; unlike previous investigation, our entropic bound is based uniquely on measurable quantities. Our results highlight what insights the information-theoretic approach provides on building blocks of quantum information processors.

Strong-Coupling Effects and Shear Viscosity in an Ultracold Fermi Gas

NASA Astrophysics Data System (ADS)

Kagamihara, D.; Ohashi, Y.

2017-06-01

We theoretically investigate the shear viscosity η , as well as the entropy density s, in the normal state of an ultracold Fermi gas. Including pairing fluctuations within the framework of a T-matrix approximation, we calculate these quantities in the Bardeen-Cooper-Schrieffer (BCS)-Bose-Einstein condensation (BEC) crossover region. We also evaluate η / s, to compare it with the lower bound of this ratio, conjectured by Kovtun, Son, and Starinets (KSS bound). In the weak-coupling BCS side, we show that the shear viscosity η is remarkably suppressed near the superfluid phase transition temperature Tc, due to the so-called pseudogap phenomenon. In the strong-coupling BEC side, we find that, within the neglect of the vertex corrections, one cannot correctly describe η . We also show that η / s decreases with increasing the interaction strength, to become very close to the KSS bound, \\hbar /4π kB, on the BEC side.

Large time behavior of entropy solutions to one-dimensional unipolar hydrodynamic model for semiconductor devices

NASA Astrophysics Data System (ADS)

Huang, Feimin; Li, Tianhong; Yu, Huimin; Yuan, Difan

2018-06-01

We are concerned with the global existence and large time behavior of entropy solutions to the one-dimensional unipolar hydrodynamic model for semiconductors in the form of Euler-Poisson equations in a bounded interval. In this paper, we first prove the global existence of entropy solution by vanishing viscosity and compensated compactness framework. In particular, the solutions are uniformly bounded with respect to space and time variables by introducing modified Riemann invariants and the theory of invariant region. Based on the uniform estimates of density, we further show that the entropy solution converges to the corresponding unique stationary solution exponentially in time. No any smallness condition is assumed on the initial data and doping profile. Moreover, the novelty in this paper is about the unform bound with respect to time for the weak solutions of the isentropic Euler-Poisson system.

Systematics of intermediate-energy single-nucleon removal cross sections

NASA Astrophysics Data System (ADS)

Tostevin, J. A.; Gade, A.

2014-11-01

There is now a large and increasing body of experimental data and theoretical analyses for reactions that remove a single nucleon from an intermediate-energy beam of neutron- or proton-rich nuclei. In each such measurement, one obtains the inclusive cross section for the population of all bound final states of the mass A -1 reaction residue. These data, from different regions of the nuclear chart, and that involve weakly and strongly bound nucleons, are compared with theoretical expectations. These calculations include an approximate treatment of the reaction dynamics and shell-model descriptions of the projectile initial state, the bound final states of the residues, and the single-particle strengths computed from their overlap functions. The results are discussed in the light of recent data, more exclusive tests of the eikonal dynamical description, and calculations that take input from more microscopic nuclear structure models.

Zero-point energy effects in anion solvation shells.

PubMed

Habershon, Scott

2014-05-21

By comparing classical and quantum-mechanical (path-integral-based) molecular simulations of solvated halide anions X(-) [X = F, Cl, Br and I], we identify an ion-specific quantum contribution to anion-water hydrogen-bond dynamics; this effect has not been identified in previous simulation studies. For anions such as fluoride, which strongly bind water molecules in the first solvation shell, quantum simulations exhibit hydrogen-bond dynamics nearly 40% faster than the corresponding classical results, whereas those anions which form a weakly bound solvation shell, such as iodide, exhibit a quantum effect of around 10%. This observation can be rationalized by considering the different zero-point energy (ZPE) of the water vibrational modes in the first solvation shell; for strongly binding anions, the ZPE of bound water molecules is larger, giving rise to faster dynamics in quantum simulations. These results are consistent with experimental investigations of anion-bound water vibrational and reorientational motion.

Microscopic Chain Motion in Polymer Nanocomposites with Dynamically Asymmetric Interphases

PubMed Central

Senses, Erkan; Faraone, Antonio; Akcora, Pinar

2016-01-01

Dynamics of the interphase region between matrix and bound polymers on nanoparticles is important to understand the macroscopic rheological properties of nanocomposites. Here, we present neutron scattering investigations on nanocomposites with dynamically asymmetric interphases formed by a high-glass transition temperature polymer, poly(methyl methacrylate), adsorbed on nanoparticles and a low-glass transition temperature miscible matrix, poly(ethylene oxide). By taking advantage of selective isotope labeling of the chains, we studied the role of interfacial polymer on segmental and collective dynamics of the matrix chains from subnanoseconds to 100 nanoseconds. Our results show that the Rouse relaxation remains unchanged in a weakly attractive composite system while the dynamics significantly slows down in a strongly attractive composite. More importantly, the chains disentangle with a remarkable increase of the reptation tube size when the bound polymer is vitreous. The glassy and rubbery states of the bound polymer as temperature changes underpin the macroscopic stiffening of nanocomposites. PMID:27457056

Josephson Radiation from Gapless Andreev Bound States in HgTe-Based Topological Junctions

NASA Astrophysics Data System (ADS)

Deacon, R. S.; Wiedenmann, J.; Bocquillon, E.; Domínguez, F.; Klapwijk, T. M.; Leubner, P.; Brüne, C.; Hankiewicz, E. M.; Tarucha, S.; Ishibashi, K.; Buhmann, H.; Molenkamp, L. W.

2017-04-01

Frequency analysis of the rf emission of oscillating Josephson supercurrent is a powerful passive way of probing properties of topological Josephson junctions. In particular, measurements of the Josephson emission enable the detection of topological gapless Andreev bound states that give rise to emission at half the Josephson frequency fJ rather than conventional emission at fJ. Here, we report direct measurement of rf emission spectra on Josephson junctions made of HgTe-based gate-tunable topological weak links. The emission spectra exhibit a clear signal at half the Josephson frequency fJ/2 . The linewidths of emission lines indicate a coherence time of 0.3-4 ns for the fJ/2 line, much shorter than for the fJ line (3-4 ns). These observations strongly point towards the presence of topological gapless Andreev bound states and pave the way for a future HgTe-based platform for topological quantum computation.

Hydrogen exchange mass spectrometry of functional membrane-bound chemotaxis receptor complexes.

PubMed

Koshy, Seena S; Eyles, Stephen J; Weis, Robert M; Thompson, Lynmarie K

2013-12-10

The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (∼2 Å) piston displacement of one helix of the periplasmic and transmembrane domains toward the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) measurements of global exchange of the CF demonstrate that the CF exhibits significantly slower exchange in functional complexes than in solution. Because the exchange rates in functional complexes are comparable to those of other proteins with similar structures, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system.

Hydrogen Exchange Mass Spectrometry of Functional Membrane-bound Chemotaxis Receptor Complexes

PubMed Central

Koshy, Seena S.; Eyles, Stephen J.; Weis, Robert M.; Thompson, Lynmarie K.

2014-01-01

The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (~2 Å) piston displacement of one helix of the periplasmic and transmembrane domains towards the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen exchange mass spectrometry (HDX-MS) measurements of global exchange of CF demonstrate that CF exhibits significantly slower exchange in functional complexes than in solution. Since the exchange rates in functional complexes are comparable to that of other proteins of similar structure, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements, by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system. PMID:24274333

Modeling of magnitude distributions by the generalized truncated exponential distribution

NASA Astrophysics Data System (ADS)

Raschke, Mathias

2015-01-01

The probability distribution of the magnitude can be modeled by an exponential distribution according to the Gutenberg-Richter relation. Two alternatives are the truncated exponential distribution (TED) and the cutoff exponential distribution (CED). The TED is frequently used in seismic hazard analysis although it has a weak point: when two TEDs with equal parameters except the upper bound magnitude are mixed, then the resulting distribution is not a TED. Inversely, it is also not possible to split a TED of a seismic region into TEDs of subregions with equal parameters except the upper bound magnitude. This weakness is a principal problem as seismic regions are constructed scientific objects and not natural units. We overcome it by the generalization of the abovementioned exponential distributions: the generalized truncated exponential distribution (GTED). Therein, identical exponential distributions are mixed by the probability distribution of the correct cutoff points. This distribution model is flexible in the vicinity of the upper bound magnitude and is equal to the exponential distribution for smaller magnitudes. Additionally, the exponential distributions TED and CED are special cases of the GTED. We discuss the possible ways of estimating its parameters and introduce the normalized spacing for this purpose. Furthermore, we present methods for geographic aggregation and differentiation of the GTED and demonstrate the potential and universality of our simple approach by applying it to empirical data. The considerable improvement by the GTED in contrast to the TED is indicated by a large difference between the corresponding values of the Akaike information criterion.

A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch: General Architecture of the Metalloinsertion Binding Mode†

PubMed Central

Zeglis, Brian M.; Pierre, Valérie C.; Kaiser, Jens T.; Barton, Jacqueline K.

2009-01-01

Two crystal structures are determined for Δ-Rh(bpy)2(chrysi)3+ (chrysi = 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5′-CGGAAATTACCG-3′ containing two adenosine-adenosine mismatches (italics) through metalloinsertion. Diffraction quality crystals with two different space groups (P3221 and P43212) were obtained under very similar crystallization conditions. In both structures, the bulky rhodium complex inserts into the two mismatched sites from the minor groove side, ejecting the mismatched bases into the major groove. The conformational changes are localized to the mismatched site; the metal complex replaces the mismatched base pair without an increase in base pair rise. The expansive metal complex is accommodated in the duplex by a slight opening in the phosphodiester backbone; all sugars retain a C2′-endo puckering, and flanking base pairs neither stretch nor shear. The structures differ, however, in that in one of the structures, an additional metal complex is bound by intercalation from the major groove at the central 5′-AT-3′ step. We conclude that this additional metal complex is intercalated into this central step because of crystal packing forces. The structures described here of Δ-Rh(bpy)2(chrysi)3+ bound to thermodynamically destabilized AA mismatches share critical features with binding by metalloinsertion in two other oligonucleotides containing different single base mismatches. These results underscore the generality of the metalloinsertion as a new mode of non-covalent binding by small molecules with a DNA duplex. PMID:19374348

Ionization of doped helium nanodroplets: Complexes of C60 with water clusters

NASA Astrophysics Data System (ADS)

Denifl, S.; Zappa, F.; Mähr, I.; Mauracher, A.; Probst, M.; Urban, J.; Mach, P.; Bacher, A.; Bohme, D. K.; Echt, O.; Märk, T. D.; Scheier, P.

2010-06-01

Water clusters are known to undergo an autoprotonation reaction upon ionization by photons or electron impact, resulting in the formation of (H2O)nH3O+. Ejection of OH cannot be quenched by near-threshold ionization; it is only partly quenched when clusters are complexed with inert gas atoms. Mass spectra recorded by electron ionization of water-doped helium droplets show that the helium matrix also fails to quench OH loss. The situation changes drastically when helium droplets are codoped with C60. Charged C60-water complexes are predominantly unprotonated; C60(H2O)4+ and (C60)2(H2O)4+ appear with enhanced abundance. Another intense ion series is due to C60(H2O)nOH+; dehydrogenation is proposed to be initiated by charge transfer between the primary He+ ion and C60. The resulting electronically excited C60+∗ leads to the formation of a doubly charged C60-water complex either via emission of an Auger electron from C60+∗, or internal Penning ionization of the attached water complex, followed by charge separation within {C60(H2O)n}2+. This mechanism would also explain previous observations of dehydrogenation reactions in doped helium droplets. Mass-analyzed ion kinetic energy scans reveal spontaneous (unimolecular) dissociation of C60(H2O)n+. In addition to the loss of single water molecules, a prominent reaction channel yields bare C60+ for sizes n=3, 4, or 6. Ab initio Hartree-Fock calculations for C60-water complexes reveal negligible charge transfer within neutral complexes. Cationic complexes are well described as water clusters weakly bound to C60+. For n=3, 4, or 6, fissionlike desorption of the entire water complex from C60(H2O)n+ energetically competes with the evaporation of a single water molecule.

Reliable and efficient a posteriori error estimation for adaptive IGA boundary element methods for weakly-singular integral equations

PubMed Central

Feischl, Michael; Gantner, Gregor; Praetorius, Dirk

2015-01-01

We consider the Galerkin boundary element method (BEM) for weakly-singular integral equations of the first-kind in 2D. We analyze some residual-type a posteriori error estimator which provides a lower as well as an upper bound for the unknown Galerkin BEM error. The required assumptions are weak and allow for piecewise smooth parametrizations of the boundary, local mesh-refinement, and related standard piecewise polynomials as well as NURBS. In particular, our analysis gives a first contribution to adaptive BEM in the frame of isogeometric analysis (IGABEM), for which we formulate an adaptive algorithm which steers the local mesh-refinement and the multiplicity of the knots. Numerical experiments underline the theoretical findings and show that the proposed adaptive strategy leads to optimal convergence. PMID:26085698

Pulmonary function and dysfunction in multiple sclerosis.

PubMed

Smeltzer, S C; Utell, M J; Rudick, R A; Herndon, R M

1988-11-01

Pulmonary function was studied in 25 patients with clinically definite multiple sclerosis with a range of motor impairment. Forced vital capacity (FVC), maximal voluntary ventilation (MVV), and maximal expiratory pressure (MEP) were normal in the ambulatory patients (mean greater than or equal to 80% predicted) but reduced in bedridden patients (mean, 38.5%, 31.6%, and 36.3% predicted; FCV, MVV, and MEP, respectively) and wheelchair-bound patients with upper extremity involvement (mean, 69.4%, 50.4%, and 62.6% predicted; FVC, MVV, and MEP, respectively). Forced vital capacity, MVV, and MEP correlated with Kurtzke Expanded Disability Status scores (tau = -0.72, -0.70, and -0.65) and expiratory muscle weakness occurred most frequently. These findings demonstrate that marked expiratory weakness develops in severely paraparetic patients with multiple sclerosis and the weakness increases as the upper extremities become increasingly involved.

Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the transforming ability of bound DNA.

PubMed Central

Khanna, M; Stotzky, G

1992-01-01

The equilibrium adsorption and binding of DNA from Bacillus subtilis on the clay mineral montmorillonite, the ability of bound DNA to transform competent cells, and the resistance of bound DNA to degradation by DNase I are reported. Maximum adsorption of DNA on the clay occurred after 90 min of contact and was followed by a plateau. Adsorption was pH dependent and was greatest at pH 1.0 (19.9 micrograms of DNA mg of clay-1) and least at pH 9.0 (10.7 micrograms of DNA mg of clay-1). The transformation frequency increased as the pH at which the clay-DNA complexes were prepared increased, and there was no transformation by clay-DNA complexes prepared at pH 1. After extensive washing with deionized distilled water (pH 5.5) or DNA buffer (pH 7.5), 21 and 28%, respectively, of the DNA remained bound. Bound DNA was capable of transforming competent cells (as was the desorbed DNA), indicating that adsorption, desorption, and binding did not alter the transforming ability of the DNA. Maximum transformation by bound DNA occurred at 37 degrees C (the other temperatures evaluated were 0, 25, and 45 degrees C). DNA bound on montmorillonite was protected against degradation by DNase, supporting the concept that "cryptic genes" may persist in the environment when bound on particulates. The concentration of DNase required to inhibit transformation by bound DNA was higher than that required to inhibit transformation by comparable amounts of free DNA, and considerably more bound than free DNase was required to inhibit transformation by the same amount of free DNA. Similarly, when DNA and DNase were bound on the same or separate samples of montmorillonite, the bound DNA was protected from the activity of DNase. PMID:1622268

Regulation of branched-chain amino acid catabolism in rat models for spontaneous type 2 diabetes mellitus.

PubMed

Kuzuya, Teiji; Katano, Yoshiaki; Nakano, Isao; Hirooka, Yoshiki; Itoh, Akihiro; Ishigami, Masatoshi; Hayashi, Kazuhiko; Honda, Takashi; Goto, Hidemi; Fujita, Yuko; Shikano, Rie; Muramatsu, Yuji; Bajotto, Gustavo; Tamura, Tomohiro; Tamura, Noriko; Shimomura, Yoshiharu

2008-08-15

The branched-chain alpha-keto acid dehydrogenase (BCKDH) complex is the most important regulatory enzyme in branched-chain amino acid (BCAA) catabolism. We examined the regulation of hepatic BCKDH complex activity in spontaneous type 2 diabetes Otsuka Long-Evans Tokushima Fatty (OLETF) rats and Zucker diabetic fatty rats. Hepatic BCKDH complex activity in these rats was significantly lower than in corresponding control rats. The amount of BCKDH complex in OLETF rats corresponded to the total activity of the complex. Activity and abundance of the bound form of BCKDH kinase, which is responsible for inactivation of the complex, showed an inverse correlation to BCKDH complex activity in OLETF rats. Dietary supplementation of 5% BCAAs for 10 weeks markedly increased BCKDH complex activity, and decreased the activity and bound form of BCKDH kinase in the rats. These results suggest that BCAA catabolism in type 2 diabetes is downregulated and enhanced by BCAA supplementation.

Increases in Global and Domain Specific Self-Esteem Following a 10 Day Developmental Voyage

ERIC Educational Resources Information Center

Grocott, Andrew C.; Hunter, John A.

2009-01-01

Although positive effects are often reported, research assessing the impact of Adventure Education and Outward Bound programmes on self-esteem is fraught with methodological weaknesses pertaining to an emphasis on scales assessing global self-esteem, a lack of follow-up measures to assess the potential long-term benefits of such programmes and…

Precise control of molecular dynamics with a femtosecond frequency comb.

PubMed

Pe'er, Avi; Shapiro, Evgeny A; Stowe, Matthew C; Shapiro, Moshe; Ye, Jun

2007-03-16

We present a general and highly efficient scheme for performing narrow-band Raman transitions between molecular vibrational levels using a coherent train of weak pump-dump pairs of shaped ultrashort pulses. The use of weak pulses permits an analytic description within the framework of coherent control in the perturbative regime, while coherent accumulation of many pulse pairs enables near unity transfer efficiency with a high spectral selectivity, thus forming a powerful combination of pump-dump control schemes and the precision of the frequency comb. Simulations verify the feasibility and robustness of this concept, with the aim to form deeply bound, ultracold molecules.

BOUNDARY VALUE PROBLEM INVOLVING THE p-LAPLACIAN ON THE SIERPIŃSKI GASKET

NASA Astrophysics Data System (ADS)

Priyadarshi, Amit; Sahu, Abhilash

In this paper, we study the following boundary value problem involving the weak p-Laplacian. -Δpu=λa(x)|u|q-1u + b(x)|u|l-1uin 𝒮∖𝒮 0; u=0on 𝒮0, where 𝒮 is the Sierpiński gasket in ℝ2, 𝒮0 is its boundary, λ > 0, p > 1, 0 < q < p - 1 < l and a,b : 𝒮→ ℝ are bounded nonnegative functions. We will show the existence of at least two nontrivial weak solutions to the above problem for a certain range of λ using the analysis of fibering maps on suitable subsets.

Continuous quantum measurement with independent detector cross correlations.

PubMed

Jordan, Andrew N; Büttiker, Markus

2005-11-25

We investigate the advantages of using two independent, linear detectors for continuous quantum measurement. For single-shot measurement, the detection process may be quantum limited if the detectors are twins. For weak continuous measurement, cross correlations allow a violation of the Korotkov-Averin bound for the detector's signal-to-noise ratio. The joint weak measurement of noncommuting observables is also investigated, and we find the cross correlation changes sign as a function of frequency, reflecting a crossover from incoherent relaxation to coherent, out of phase oscillations. Our results are applied to a double quantum-dot charge qubit, simultaneously measured by two quantum point contacts.

The bound states of ultracold KRb molecules

NASA Astrophysics Data System (ADS)

Julienne, Paul; Hanna, Thomas

2009-03-01

Recently ultracold vibrational ground state ^40K^87Rb polar molecules have been made using magnetoassociation of two cold atoms to a weakly bound Feshbach molecule, followed by a two-color optical STIRAP process to transfer molecules to the molecular ground state [1]. We have used accurate potential energy curves for the singlet and triplet states of the KRb molecule [2] with coupled channels calculations to calculate all of the bound states of the ^40K^87Rb molecule as a function of magnetic field from the cold atom collision threshold to the v=0 ground state. We have also developed approximate models for understanding the changing properties of the molecular bound states as binding energy increases. Some overall conclusions from these calculations will be presented. [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231--235. [2] A. Pashov, O. Docenko, M. Tamanis, R. Ferber, H. Kn"ockel, and E. Tiemann, Phys. Rev. A, 2007, 76, 022511.

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

Blennow, Mattias; Herrero-Garcia, Juan; Schwetz, Thomas, E-mail: emb@kth.se, E-mail: juhg@kth.se, E-mail: schwetz@fysik.su.se

We show that a positive signal in a dark matter (DM) direct detection experiment can be used to place a lower bound on the DM capture rate in the Sun, independent of the DM halo. For a given particle physics model and DM mass we obtain a lower bound on the capture rate independent of the local DM density, velocity distribution, galactic escape velocity, as well as the scattering cross section. We illustrate this lower bound on the capture rate by assuming that upcoming direct detection experiments will soon obtain a significant signal. When comparing the lower bound on themore » capture rate with limits on the high-energy neutrino flux from the Sun from neutrino telescopes, we can place upper limits on the branching fraction of DM annihilation channels leading to neutrinos. With current data from IceCube and Super-Kamiokande non-trivial limits can be obtained for spin-dependent interactions and direct annihilations into neutrinos. In some cases also annihilations into ττ or b b start getting constrained. For spin-independent interactions current constraints are weak, but they may become interesting for data from future neutrino telescopes.« less

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

Blennow, Mattias; Herrero-Garcia, Juan; Schwetz, Thomas

We show that a positive signal in a dark matter (DM) direct detection experiment can be used to place a lower bound on the DM capture rate in the Sun, independent of the DM halo. For a given particle physics model and DM mass we obtain a lower bound on the capture rate independent of the local DM density, velocity distribution, galactic escape velocity, as well as the scattering cross section. We illustrate this lower bound on the capture rate by assuming that upcoming direct detection experiments will soon obtain a significant signal. When comparing the lower bound on themore » capture rate with limits on the high-energy neutrino flux from the Sun from neutrino telescopes, we can place upper limits on the branching fraction of DM annihilation channels leading to neutrinos. With current data from IceCube and Super-Kamiokande non-trivial limits can be obtained for spin-dependent interactions and direct annihilations into neutrinos. In some cases also annihilations into ττ or bb start getting constrained. For spin-independent interactions current constraints are weak, but they may become interesting for data from future neutrino telescopes.« less

Theory of space-charge polarization for determining ionic constants of electrolytic solutions

NASA Astrophysics Data System (ADS)

Sawada, Atsushi

2007-06-01

A theoretical expression of the complex dielectric constant attributed to space-charge polarization has been derived under an electric field calculated using Poisson's equation considering the effects of bound charges on ions. The frequency dependence of the complex dielectric constant of chlorobenzene solutions doped with tetrabutylammonium tetraphenylborate (TBATPB) has been analyzed using the theoretical expression, and the impact of the bound charges on the complex dielectric constant has been clarified quantitatively in comparison with a theory that does not consider the effect of the bound charges. The Stokes radius of TBA +(=TPB-) determined by the present theory shows a good agreement with that determined by conductometry in the past; hence, the present theory should be applicable to the direct determination of the mobility of ion species in an electrolytic solution without the need to measure ionic limiting equivalent conductance and transport number.

Macrocyclic metal complexes for metalloenzyme mimicry and sensor development.

PubMed

Joshi, Tanmaya; Graham, Bim; Spiccia, Leone

2015-08-18

Examples of proteins that incorporate one or more metal ions within their structure are found within a broad range of classes, including oxidases, oxidoreductases, reductases, proteases, proton transport proteins, electron transfer/transport proteins, storage proteins, lyases, rusticyanins, metallochaperones, sporulation proteins, hydrolases, endopeptidases, luminescent proteins, iron transport proteins, oxygen storage/transport proteins, calcium binding proteins, and monooxygenases. The metal coordination environment therein is often generated from residues inherent to the protein, small exogenous molecules (e.g., aqua ligands) and/or macrocyclic porphyrin units found, for example, in hemoglobin, myoglobin, cytochrome C, cytochrome C oxidase, and vitamin B12. Thus, there continues to be considerable interest in employing macrocyclic metal complexes to construct low-molecular weight models for metallobiosites that mirror essential features of the coordination environment of a bound metal ion without inclusion of the surrounding protein framework. Herein, we review and appraise our research exploring the application of the metal complexes formed by two macrocyclic ligands, 1,4,7-triazacyclononane (tacn) and 1,4,7,10-tetraazacyclododecane (cyclen), and their derivatives in biological inorganic chemistry. Taking advantage of the kinetic inertness and thermodynamic stability of their metal complexes, these macrocyclic scaffolds have been employed in the development of models that aid the understanding of metal ion-binding natural systems, and complexes with potential applications in biomolecule sensing, diagnosis, and therapy. In particular, the focus has been on "coordinatively unsaturated" metal complexes that incorporate a kinetically inert and stable metal-ligand moiety, but which also contain one or more weakly bound ligands, allowing for the reversible binding of guest molecules via the formation and dissociation of coordinate bonds. With regards to mimicking metallobiosites, examples are presented from our work on tacn-based complexes developed as simplified structural models for multimetallic enzyme sites. In particular, structural comparisons are made between multinuclear copper(II) complexes formed by such ligands and multicopper enzymes featuring type-2 and type-3 copper centers, such as ascorbate oxidase (AO) and laccase (Lc). Likewise, with the aid of relevant examples, we highlight the importance of cooperativity between either multiple metal centers or a metal center and a proximal auxiliary unit appended to the macrocyclic ligand in achieving efficient phosphate ester cleavage. Finally, the critical importance of the Zn(II)-imido and Zn(II)-phosphate interactions in Zn-cyclen-based systems for delivering highly sensitive electrochemical and fluorescent chemosensors is also showcased. The Account additionally highlights some of the factors that limit the performance of these synthetic nucleases and the practical application of the biosensors, and then identifies some avenues for the development of more effective macrocyclic constructs in the future.

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.

PubMed

Tyzack, Jonathan D; Fernando, Laurent; Ribeiro, Antonio J M; Borkakoti, Neera; Thornton, Janet M

2018-04-03

There are numerous applications that use the structures of protein-ligand complexes from the PDB, such as 3D pharmacophore identification, virtual screening, and fragment-based drug design. The structures underlying these applications are potentially much more informative if they contain biologically relevant bound ligands, with high similarity to the cognate ligands. We present a study of ligand-enzyme complexes that compares the similarity of bound and cognate ligands, enabling the best matches to be identified. We calculate the molecular similarity scores using a method called PARITY (proportion of atoms residing in identical topology), which can conveniently be combined to give a similarity score for all cognate reactants or products in the reaction. Thus, we generate a rank-ordered list of related PDB structures, according to the biological similarity of the ligands bound in the structures. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural mechanism of JH delivery in hemolymph by JHBP of silkworm, Bombyx mori

PubMed Central

Suzuki, Rintaro; Fujimoto, Zui; Shiotsuki, Takahiro; Tsuchiya, Wataru; Momma, Mitsuru; Tase, Akira; Miyazawa, Mitsuhiro; Yamazaki, Toshimasa

2011-01-01

Juvenile hormone (JH) plays crucial roles in many aspects of the insect life. All the JH actions are initiated by transport of JH in the hemolymph as a complex with JH-binding protein (JHBP) to target tissues. Here, we report structural mechanism of JH delivery by JHBP based upon the crystal and solution structures of apo and JH-bound JHBP. In solution, apo-JHBP exists in equilibrium of multiple conformations with different orientations of the gate helix for the hormone-binding pocket ranging from closed to open forms. JH-binding to the gate-open form results in the fully closed JHBP-JH complex structure where the bound JH is completely buried inside the protein. JH-bound JHBP opens the gate helix to release the bound hormone likely by sensing the less polar environment at the membrane surface of target cells. This is the first report that provides structural insight into JH signaling. PMID:22355650

On the Complexity of Delaying an Adversary’s Project

DTIC Science & Technology

2005-01-01

interdiction models for such problems and show that the resulting problem com- plexities run the gamut : polynomially solvable, weakly NP-complete, strongly...problems and show that the resulting problem complexities run the gamut : polynomially solvable, weakly NP-complete, strongly NP-complete or NP-hard. We

W-Z-top-quark bags

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

Crichigno, Marcos P.; Shuryak, Edward; Flambaum, Victor V.

2010-10-01

We discuss a new family of multiquanta-bound states in the standard model which exist due to the mutual Higgs-based attraction of the heaviest members of the standard model, namely, gauge quanta W, Z, and (anti)top quarks, t, t. We use a self-consistent mean-field approximation, up to a rather large particle number N. In this paper we do not focus on weakly bound, nonrelativistic bound states, but rather on 'bags' in which the Higgs vacuum expectation value is significantly modified or depleted. The minimal number N above which such states appear strongly depends on the ratio of the Higgs mass tomore » the masses of W, Z, t, t: For a light Higgs mass, m{sub H{approx}}50 GeV, bound states start from N{approx}O(10), but for a ''realistic'' Higgs mass, m{sub H{approx}}100 GeV, one finds metastable/bound W, Z bags only for N{approx}O(1000). We also found that in the latter case pure top bags disappear for all N, although top quarks can still be well bound to the W bags. Anticipating the cosmological applications (discussed in the following Article [Phys. Rev. D 82, 073019]) of these bags as 'doorway states' for baryosynthesis, we also consider here the existence of such metastable bags at finite temperatures, when standard-model parameters such as Higgs, gauge, and top masses are significantly modified.« less

Bounding the space of holographic CFTs with chaos

DOE PAGES

Perlmutter, Eric

2016-10-13

In this study, thermal states of quantum systems with many degrees of freedom are subject to a bound on the rate of onset of chaos, including a bound on the Lyapunov exponent, λ L ≤ 2π/β. We harness this bound to constrain the space of putative holographic CFTs and their would-be dual theories of AdS gravity. First, by studying out-of-time-order four-point functions, we discuss how λ L = 2π/β in ordinary two-dimensional holographic CFTs is related to properties of the OPE at strong coupling. We then rule out the existence of unitary, sparse two-dimensional CFTs with large central charge andmore » a set of higher spin currents of bounded spin; this implies the inconsistency of weakly coupled AdS 3 higher spin gravities without infinite towers of gauge fields, such as the SL(N) theories. This fits naturally with the structure of higher-dimensional gravity, where finite towers of higher spin fields lead to acausality. On the other hand, unitary CFTs with classical W ∞[λ] symmetry, dual to 3D Vasiliev or hs[λ] higher spin gravities, do not violate the chaos bound, instead exhibiting no chaos: λ L = 0. Independently, we show that such theories violate unitarity for |λ| > 2. These results encourage a tensionless string theory interpretation of the 3D Vasiliev theory.« less

The Development and Study of Surface Bound Ruthenium Organometallic Complexes

NASA Astrophysics Data System (ADS)

Abbott, Geoffrey Reuben

The focus of this project has been on the use of mono-diimine ruthenium organometallic complexes, of the general structure [H(Ru)(CO)(L)2(L') 2][PF6] (L=PPh3, DPPENE and L'=Bpy, DcBpy, MBpyC, Phen, AminoPhen) bound to surfaces as luminescent probes. Both biological and inorganic/organic hybrid surfaces have been studied. The complexes were characterized both bound and unbound using standard analytical techniques such as NMR, IR and X-ray crystallography, as well as through several photophysical methods as well. Initially the study focused on how the photophyscial properties of the complexes were affected by incorporation into biological membranes. It was found that by conjugating the probes to a more rigid cholesterol moiety that luminescence was conserved, compared to conjugation with a far more flexible lipid moiety, where luminescence was either lost or reduced. Both the cholesterol and lipid conjugates were able to insert into a lipid membrane, and in the more rigid environment some of the lipid conjugates regained some of their luminescence, but often blue shifted and reduced, depending on the conjugation site. Silica Polyamine Composites (SPCs) were a hybrid material developed in the Rosenberg Lab as useful metal separation materials, that could be easily modified, and had several benefits over current commercially available polymers, or inorganic materials. These SPCs also provided an opportunity for the development of a heterogeneous platform for luminescent complexes as either catalysts or sensors. Upon binding of the luminescent Ru complexes to the surface no loss, or major change in luminescence was seen, however, when bound to the rigid surface a significant increase in excited state lifetime was measured. It is likely that through binding and interacting with the surface that the complexes lost non-radiative decay pathways, resulting in the increase in lifetime, however, these interactions do not seem to affect the energy level of the MLCT band in a large way. With a better understanding of the effects of surface binding on the complexes, the study turned to possible applications, as either sensors or catalysts. Recently the bound complexes have been found to be very useful as toxic metal sensors, as the free amines left on the surface could bind toxic metal ions in close proximity leading to either a quenching or enhancement of the luminescence of the complexes, depending on the metal ion. This process was determined to be a static process, requiring the toxic metal to remain bound to the surface in order to affect the luminescence of the Ru complex. The quenching is thought to be due to a metal-centered electron-transfer reaction, in which the excited-state electron is transferred from the Ru to the toxic metal, but relaxes back to the Ru center. The enhancement of luminescence is due to the external heavy-atom effect, in which heavier atoms mixes MLCT singlet state with the triplet state through spin-orbit coupling.

Interrelationship between flexoelectricity and strain gradient elasticity in ferroelectric nanofilms: A phase field study

NASA Astrophysics Data System (ADS)

Jiang, Limei; Xu, Xiaofei; Zhou, Yichun

2016-12-01

With the development of the integrated circuit technology and decreasing of the device size, ferroelectric films used in nano ferroelectric devices become thinner and thinner. Along with the downscaling of the ferroelectric film, there is an increasing influence of two strain gradient related terms. One is the strain gradient elasticity and the other one is flexoelectricity. To investigate the interrelationship between flexoelectricity and strain gradient elasticity and their combined effect on the domain structure in ferroelectric nanofilms, a phase field model of flexoelectricity and strain gradient elasticity on the ferroelectric domain evolution is developed based on Mindlin's theory of strain-gradient elasticity. Weak form is derived and implemented in finite element formulations for numerically solving the model equations. The simulation results show that upper bounds for flexoelectric coefficients can be enhanced by increasing strain gradient elasticity coefficients. While a large flexoelectricity that exceeds the upper bound can induce a transition from a ferroelectric state to a modulated/incommensurate state, a large enough strain gradient elasticity may lead to a conversion from an incommensurate state to a ferroelectric state. Strain gradient elasticity and the flexoelectricity have entirely opposite effects on polarization. The observed interrelationship between the strain gradient elasticity and flexoelectricity is rationalized by an analytical solution of the proposed theoretical model. The model proposed in this paper could help us understand the mechanism of phenomena observed in ferroelectric nanofilms under complex electromechanical loads and provide some guides on the practical application of ferroelectric nanofilms.

Actin-interacting Protein 1 Promotes Disassembly of Actin-depolymerizing Factor/Cofilin-bound Actin Filaments in a pH-dependent Manner.

PubMed

Nomura, Kazumi; Hayakawa, Kimihide; Tatsumi, Hitoshi; Ono, Shoichiro

2016-03-04

Actin-interacting protein 1 (AIP1) is a conserved WD repeat protein that promotes disassembly of actin filaments when actin-depolymerizing factor (ADF)/cofilin is present. Although AIP1 is known to be essential for a number of cellular events involving dynamic rearrangement of the actin cytoskeleton, the regulatory mechanism of the function of AIP1 is unknown. In this study, we report that two AIP1 isoforms from the nematode Caenorhabditis elegans, known as UNC-78 and AIPL-1, are pH-sensitive in enhancement of actin filament disassembly. Both AIP1 isoforms only weakly enhance disassembly of ADF/cofilin-bound actin filaments at an acidic pH but show stronger disassembly activity at neutral and basic pH values. However, a severing-defective mutant of UNC-78 shows pH-insensitive binding to ADF/cofilin-decorated actin filaments, suggesting that the process of filament severing or disassembly, but not filament binding, is pH-dependent. His-60 of AIP1 is located near the predicted binding surface for the ADF/cofilin-actin complex, and an H60K mutation of AIP1 partially impairs its pH sensitivity, suggesting that His-60 is involved in the pH sensor for AIP1. These biochemical results suggest that pH-dependent changes in AIP1 activity might be a novel regulatory mechanism of actin filament dynamics. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

A Point Mutation in the Exon Junction Complex Factor Y14 Disrupts Its Function in mRNA Cap Binding and Translation Enhancement*

PubMed Central

Chuang, Tzu-Wei; Lee, Kuo-Ming; Lou, Yuan-Chao; Lu, Chia-Chen; Tarn, Woan-Yuh

2016-01-01

Eukaryotic mRNA biogenesis involves a series of interconnected steps mediated by RNA-binding proteins. The exon junction complex core protein Y14 is required for nonsense-mediated mRNA decay (NMD) and promotes translation. Moreover, Y14 binds the cap structure of mRNAs and inhibits the activity of the decapping enzyme Dcp2. In this report, we show that an evolutionarily conserved tryptophan residue (Trp-73) of Y14 is critical for its binding to the mRNA cap structure. A Trp-73 mutant (W73V) bound weakly to mRNAs and failed to protect them from degradation. However, this mutant could still interact with the NMD and mRNA degradation factors and retained partial NMD activity. In addition, we found that the W73V mutant could not interact with translation initiation factors. Overexpression of W73V suppressed reporter mRNA translation in vitro and in vivo and reduced the level of a set of nascent proteins. These results reveal a residue of Y14 that confers cap-binding activity and is essential for Y14-mediated enhancement of translation. Finally, we demonstrated that Y14 may selectively and differentially modulate protein biosynthesis. PMID:26887951

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

McLellan, Jason S.; Chen, Man; Chang, Jung-San

Respiratory syncytial virus (RSV) is a major cause of pneumonia and bronchiolitis in infants and elderly people. Currently there is no effective vaccine against RSV, but passive prophylaxis with neutralizing antibodies reduces hospitalizations. To investigate the mechanism of antibody-mediated RSV neutralization, we undertook structure-function studies of monoclonal antibody 101F, which binds a linear epitope in the RSV fusion glycoprotein. Crystal structures of the 101F antigen-binding fragment in complex with peptides from the fusion glycoprotein defined both the extent of the linear epitope and the interactions of residues that are mutated in antibody escape variants. The structure allowed for modeling ofmore » 101F in complex with trimers of the fusion glycoprotein, and the resulting models suggested that 101F may contact additional surfaces located outside the linear epitope. This hypothesis was supported by surface plasmon resonance experiments that demonstrated 101F bound the peptide epitope {approx}16,000-fold more weakly than the fusion glycoprotein. The modeling also showed no substantial clashes between 101F and the fusion glycoprotein in either the pre- or postfusion state, and cell-based assays indicated that 101F neutralization was not associated with blocking virus attachment. Collectively, these results provide a structural basis for RSV neutralization by antibodies that target a major antigenic site on the fusion glycoprotein.« less

[1,10]Phenanthroline based cyanine dyes as fluorescent probes for ribonucleic acids in live cells

NASA Astrophysics Data System (ADS)

Kovalska, Vladyslava; Kuperman, Marina; Varzatskii, Oleg; Kryvorotenko, Dmytro; Kinski, Elisa; Schikora, Margot; Janko, Christina; Alexiou, Christoph; Yarmoluk, Sergiy; Mokhir, Andriy

2017-12-01

A series of monomethine, trimethine- and styrylcyanine dyes based on a [1,10]phenanthroline moiety was synthesized, characterized and investigated as potential fluorescent probes for nucleic acids in cell free settings and in cells. The dyes were found to be weakly fluorescent in the unbound state, whereas upon the binding to dsDNA or RNA their emission intensity raised up to 50 times (for monomethine benzothiazole derivative FT1 complexed with RNA). The strongest fluorescence intensity in assemblies with dsDNA and RNA was observed for the trimethine benzothiazole derivative FT4. The quantum yield of FT4 fluorescence in its complex with dsDNA was found to be 1.5% and the binding constant (K b) was estimated to be 7.9 × 104 M-1 that is a typical value for intercalating molecules. The FT4 dye was found to be cell membrane permeable. It stains RNA rich components—the nucleoli and most probably the cytoplasmic RNA. FT4 bound to RNAs delivers a very strong fluorescence signal, which makes this easily accessible dye a potentially useful alternative to known RNA stains, e.g. expensive SYTO® 83. The advantage of FT4 is its easy synthetic access including no chromatographic purification steps, which will be reflected in its substantially lower price.

Quantum mechanical characterization of the He4ICl weakly bound complex.

PubMed

Valdés, Álvaro; Prosmiti, Rita

2013-08-15

Vibrational calculations are performed for the 12-dimensional He4ICl van der Waals complex using the multiconfiguration time-dependent Hartree (MCTDH) method. The potential energy surface of the cluster is represented as a sum of the triatomic He-ICl ab initio parametrized terms plus the He-He interactions. The topology of the potential presents higher anisotropy compared to the one with a homonuclear dopant, and this is clearly reflected in the structure and energetics of the low-lying conformers of the system. In order to take advantage of the MCTDH method, natural potential fits are employed for the potential energy operator, and also, a mode combination scheme is introduced in order to speed up the computations. Zero-point energy, binding energies, and vibrationally averaged structures of different isomers of the He4ICl cluster are obtained. The present results predict that the (3,1,0) structure, involving three He atoms in the near T-shaped and one He atom in the linear configurations, to be the most stable one in accord with recent experimental findings. Comparisons with previous theoretical and experimental data are presented, and the stability of the high-order conformers is discussed in connection with the multiple minima (global and local) of the underlying potential surface.

The nucleotide-free state of heterotrimeric G proteins α-subunit adopts a highly stable conformation.

PubMed

Andhirka, Sai Krishna; Vignesh, Ravichandran; Aradhyam, Gopala Krishna

2017-08-01

Deciphering the mechanism of activation of heterotrimeric G proteins by their cognate receptors continues to be an intriguing area of research. The recently solved crystal structure of the ternary complex captured the receptor-bound α-subunit in an open conformation, without bound nucleotide has improved our understanding of the activation process. Despite these advancements, the mechanism by which the receptor causes GDP release from the α-subunit remains elusive. To elucidate the mechanism of activation, we studied guanine nucleotide-induced structural stability of the α-subunit (in response to thermal/chaotrope-mediated stress). Inherent stabilities of the inactive (GDP-bound) and active (GTP-bound) forms contribute antagonistically to the difference in conformational stability whereas the GDP-bound protein is able to switch to a stable intermediate state, GTP-bound protein loses this ability. Partial perturbation of the protein fold reveals the underlying influence of the bound nucleotide providing an insight into the mechanism of activation. An extra stable, pretransition intermediate, 'empty pocket' state (conformationally active-state like) in the unfolding pathway of GDP-bound protein mimics a gating system - the activation process having to overcome this stable intermediate state. We demonstrate that a relatively more complex conformational fold of the GDP-bound protein is at the core of the gating system. We report capturing this threshold, 'metastable empty pocket' conformation (the gate) of α-subunit of G protein and hypothesize that the receptor activates the G protein by enabling it to achieve this structure through mild structural perturbation. © 2017 Federation of European Biochemical Societies.

Streptococcal inhibitor of complement (SIC) inhibits the membrane attack complex by preventing uptake of C567 onto cell membranes

PubMed Central

Fernie-King, Barbara A; Seilly, David J; Willers, Christine; Würzner, Reinhard; Davies, Alexandra; Lachmann, Peter J

2001-01-01

Streptococcal inhibitor of complement (SIC) was first described in 1996 as a putative inhibitor of the membrane attack complex of complement (MAC). SIC is a 31 000 MW protein secreted in large quantities by the virulent Streptococcus pyogenes strains M1 and M57, and is encoded by a gene which is extremely variable. In order to study further the interactions of SIC with the MAC, we have made a recombinant form of SIC (rSIC) in Escherichia coli and purified native M1 SIC which was used to raise a polyclonal antibody. SIC prevented reactive lysis of guinea pig erythrocytes by the MAC at a stage prior to C5b67 complexes binding to cell membranes, presumably by blocking the transiently expressed membrane insertion site on C7. The ability of SIC and clusterin (another putative fluid phase complement inhibitor) to inhibit complement lysis was compared, and found to be equally efficient. In parallel, by enzyme-linked immunosorbent assay both SIC and rSIC bound strongly to C5b67 and C5b678 complexes and to a lesser extent C5b-9, but only weakly to individual complement components. The implications of these data for virulence of SIC-positive streptococci are discussed, in light of the fact that Gram-positive organisms are already protected against complement lysis by the presence of their peptidoglycan cell walls. We speculate that MAC inhibition may not be the sole function of SIC. PMID:11454069

Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal.

PubMed Central

Oikonomakos, N. G.; Zographos, S. E.; Tsitsanou, K. E.; Johnson, L. N.; Acharya, K. R.

1996-01-01

It has been established that phosphate analogues can activate glycogen phosphorylase reconstituted with pyridoxal in place of the natural cofactor pyridoxal 5'-phosphate (Change YC. McCalmont T, Graves DJ. 1983. Biochemistry 22:4987-4993). Pyridoxal phosphorylase b has been studied by kinetic, ultracentrifugation, and X-ray crystallographic experiments. In solution, the catalytically active species of pyridoxal phosphorylase b adopts a conformation that is more R-state-like than that of native phosphorylase b, but an inactive dimeric species of the enzyme can be stabilized by activator phosphite in combination with the T-state inhibitor glucose. Co-crystals of pyridoxal phosphorylase b complexed with either phosphite, phosphate, or fluorophosphate, the inhibitor glucose, and the weak activator IMP were grown in space group P4(3)2(1)2, with native-like unit cell dimensions, and the structures of the complexes have been refined to give crystallographic R factors of 18.5-19.2%, for data between 8 and 2.4 A resolution. The anions bind tightly at the catalytic site in a similar but not identical position to that occupied by the cofactor 5'-phosphate group in the native enzyme (phosphorus to phosphorus atoms distance = 1.2 A). The structural results show that the structures of the pyridoxal phosphorylase b-anion-glucose-IMP complexes are overall similar to the glucose complex of native T-state phosphorylase b. Structural comparisons suggest that the bound anions, in the position observed in the crystal, might have a structural role for effective catalysis. PMID:8976550

Sorption of Sr, Co and Zn on illite: Batch experiments and modelling including Co in-diffusion measurements on compacted samples

NASA Astrophysics Data System (ADS)

Montoya, V.; Baeyens, B.; Glaus, M. A.; Kupcik, T.; Marques Fernandes, M.; Van Laer, L.; Bruggeman, C.; Maes, N.; Schäfer, T.

2018-02-01

Experimental investigations on the uptake of divalent cations (Sr, Co and Zn) onto illite (Illite du Puy, Le-Puy-en-Velay, France) were carried out by three different international research groups (Institute for Nuclear Waste Disposal, KIT (Germany), Group Waste & Disposal, SCK-CEN, (Belgium) and Laboratory for Waste Management, PSI (Switzerland)) in the framework of the European FP7 CatClay project. The dependence of solid-liquid distribution ratios (Rd values) on pH at trace metal conditions (sorption edges) and on the metal ion concentration (sorption isotherms) was determined in dilute suspensions of homo-ionic Na-illite (Na-IdP) under controlled N2 atmosphere. The experimental results were modelled using the 2 Site Protolysis Non Electrostatic Surface Complexation and Cation Exchange (2SPNE SC/CE) sorption model. The sorption of Sr depends strongly on ionic strength, while a rather weak pH dependence is observed in a pH range between 3 and 11. The data were modelled with cation exchange reactions, taking into account competition with H, K, Ca, Mg and Al, and surface complexation on weak amphotheric edge sites at higher pH values. The sorption of Co on Na-IdP, however, is strongly pH dependent. Cation exchange on the planar sites and surface complexation on strong and weak amphoteric edge sites were used to describe the Co sorption data. Rd values for Co derived from in-diffusion measurements on compacted Na-IdP samples (bulk-dry density of 1700 kg m-3) between pH 5.0 and 9.0 are in good agreement with the batch sorption data. The equivalence of both approaches to measure sorption was thus confirmed for the present test system. In addition, the results highlight the importance of both major and minor surface species for the diffusive transport behaviour of strongly sorbing metal cations. While surface complexes at the edge sites determine largely the Rd value, the diffusive flux may be governed by those species bound to the planar sites, even at low fractional occupancies. The pH dependent sorption determined for trace Zn concentrations showed large Rd values across the entire pH range with almost no dependence on the background electrolyte concentration. Additional sorption experiments carried out at substantial fractional Zn loadings demonstrated that the selectivity for the exchange of Na+ for Zn2+ at the planar sites could not explain the large Rd values measured at low pH and trace Zn concentrations. This suggests that another mechanism is ruling Zn uptake under these conditions.

Constraining the noncommutative spectral action via astrophysical observations.

PubMed

Nelson, William; Ochoa, Joseph; Sakellariadou, Mairi

2010-09-03

The noncommutative spectral action extends our familiar notion of commutative spaces, using the data encoded in a spectral triple on an almost commutative space. Varying a rather simple action, one can derive all of the standard model of particle physics in this setting, in addition to a modified version of Einstein-Hilbert gravity. In this Letter we use observations of pulsar timings, assuming that no deviation from general relativity has been observed, to constrain the gravitational sector of this theory. While the bounds on the coupling constants remain rather weak, they are comparable to existing bounds on deviations from general relativity in other settings and are likely to be further constrained by future observations.

Orphan Spins in the S=5/2 Antiferromagnet CaFe_{2}O_{4}.

PubMed

Stock, C; Rodriguez, E E; Lee, N; Demmel, F; Fouquet, P; Laver, M; Niedermayer, Ch; Su, Y; Nemkovski, K; Green, M A; Rodriguez-Rivera, J A; Kim, J W; Zhang, L; Cheong, S-W

2017-12-22

CaFe_{2}O_{4} is an anisotropic S=5/2 antiferromagnet with two competing A (↑↑↓↓) and B (↑↓↑↓) magnetic order parameters separated by static antiphase boundaries at low temperatures. Neutron diffraction and bulk susceptibility measurements, show that the spins near these boundaries are weakly correlated and a carry an uncompensated ferromagnetic moment that can be tuned with a magnetic field. Spectroscopic measurements find these spins are bound with excitation energies less than the bulk magnetic spin waves and resemble the spectra from isolated spin clusters. Localized bound orphaned spins separate the two competing magnetic order parameters in CaFe_{2}O_{4}.

Orphan Spins in the S =5/2 Antiferromagnet CaFe2O4

NASA Astrophysics Data System (ADS)

Stock, C.; Rodriguez, E. E.; Lee, N.; Demmel, F.; Fouquet, P.; Laver, M.; Niedermayer, Ch.; Su, Y.; Nemkovski, K.; Green, M. A.; Rodriguez-Rivera, J. A.; Kim, J. W.; Zhang, L.; Cheong, S.-W.

2017-12-01

CaFe2O4 is an anisotropic S =5/2 antiferromagnet with two competing A (↑↑↓↓) and B (↑↓↑↓) magnetic order parameters separated by static antiphase boundaries at low temperatures. Neutron diffraction and bulk susceptibility measurements, show that the spins near these boundaries are weakly correlated and a carry an uncompensated ferromagnetic moment that can be tuned with a magnetic field. Spectroscopic measurements find these spins are bound with excitation energies less than the bulk magnetic spin waves and resemble the spectra from isolated spin clusters. Localized bound orphaned spins separate the two competing magnetic order parameters in CaFe2 O4 .

Cosmological bounds on neutrino statistics

NASA Astrophysics Data System (ADS)

de Salas, P. F.; Gariazzo, S.; Laveder, M.; Pastor, S.; Pisanti, O.; Truong, N.

2018-03-01

We consider the phenomenological implications of the violation of the Pauli exclusion principle for neutrinos, focusing on cosmological observables such as the spectrum of Cosmic Microwave Background anisotropies, Baryon Acoustic Oscillations and the primordial abundances of light elements. Neutrinos that behave (at least partly) as bosonic particles have a modified equilibrium distribution function that implies a different influence on the evolution of the Universe that, in the case of massive neutrinos, can not be simply parametrized by a change in the effective number of neutrinos. Our results show that, despite the precision of the available cosmological data, only very weak bounds can be obtained on neutrino statistics, disfavouring a more bosonic behaviour at less than 2σ.

Methane mobility in carbon nanotubes

NASA Astrophysics Data System (ADS)

Bienfait, M.; Asmussen, B.; Johnson, M.; Zeppenfeld, P.

2000-07-01

Quasi-elastic neutron scattering has been used to characterize the diffusivity of CH 4 molecules condensed in single-wall carbon nanotubes. It is shown that the two sites of adsorption, previously observed by adsorption volumetry and calorimetry measurements, correspond to a solid-like phase for the more strongly bound site at T<120 K and to a liquid-like component for the more weakly bound site at 70< T<120 K. The diffusion coefficients of the mobile molecules range between 3×10 -7 to 15×10 -7 cm 2 s -1. The fraction of this viscous liquid diminishes as the temperature is decreased; the adsorbate is fully solidified at 50 K and below.

Detection of gear cracks in a complex gearbox of wind turbines using supervised bounded component analysis of vibration signals collected from multi-channel sensors

NASA Astrophysics Data System (ADS)

Li, Zhixiong; Yan, Xinping; Wang, Xuping; Peng, Zhongxiao

2016-06-01

In the complex gear transmission systems, in wind turbines a crack is one of the most common failure modes and can be fatal to the wind turbine power systems. A single sensor may suffer with issues relating to its installation position and direction, resulting in the collection of weak dynamic responses of the cracked gear. A multi-channel sensor system is hence applied in the signal acquisition and the blind source separation (BSS) technologies are employed to optimally process the information collected from multiple sensors. However, literature review finds that most of the BSS based fault detectors did not address the dependence/correlation between different moving components in the gear systems; particularly, the popular used independent component analysis (ICA) assumes mutual independence of different vibration sources. The fault detection performance may be significantly influenced by the dependence/correlation between vibration sources. In order to address this issue, this paper presents a new method based on the supervised order tracking bounded component analysis (SOTBCA) for gear crack detection in wind turbines. The bounded component analysis (BCA) is a state of art technology for dependent source separation and is applied limitedly to communication signals. To make it applicable for vibration analysis, in this work, the order tracking has been appropriately incorporated into the BCA framework to eliminate the noise and disturbance signal components. Then an autoregressive (AR) model built with prior knowledge about the crack fault is employed to supervise the reconstruction of the crack vibration source signature. The SOTBCA only outputs one source signal that has the closest distance with the AR model. Owing to the dependence tolerance ability of the BCA framework, interfering vibration sources that are dependent/correlated with the crack vibration source could be recognized by the SOTBCA, and hence, only useful fault information could be preserved in the reconstructed signal. The crack failure thus could be precisely identified by the cyclic spectral correlation analysis. A series of numerical simulations and experimental tests have been conducted to illustrate the advantages of the proposed SOTBCA method for fatigue crack detection. Comparisons to three representative techniques, i.e. Erdogan's BCA (E-BCA), joint approximate diagonalization of eigen-matrices (JADE), and FastICA, have demonstrated the effectiveness of the SOTBCA. Hence the proposed approach is suitable for accurate gear crack detection in practical applications.

Wave Tank Studies of Strong Modulation of Wind Ripples Due To Long Waves

NASA Astrophysics Data System (ADS)

Ermakov, S.; Sergievskaya, I.; Shchegolkov, Yu.

Modulation of wind capillary-gravity ripples due to long waves has been studied in wave tank experiment at low wind speeds using Ka-band radar. The experiments were carried out both for clean water and the water surface covered with surfactant films. It is obtained that the modulation of radar signals is quite strong and can increase with surfactant concentration and fetch. It is shown that the hydrodynamic Modulation Transfer Function (MTF) calculated for free wind ripples and taking into account the kinematic (straining) effect, variations of the wind stress and variations of surfactant concentration strongly underestimates experimental MTF-values. The effect of strong modulation is assumed to be connected with nonlinear harmonics of longer dm-cm- scale waves - bound waves ("parasitic ripples"). The intensity of bound waves depends strongly on the amplitude of decimetre-scale waves, therefore even weak modulation of the dm-scale waves due to long waves results to strong ("cascade") modulation of bound waves. Modulation of the system of "free/bound waves" is estimated using results of wave tank studies of bound waves generation and is shown to be in quali- tative agreement with experiment. This work was supported by MOD, UK via DERA Winfrith (Project ISTC 1774P) and by RFBR (Project 02-05-65102).

Blood coagulation reactions on nanoscale membrane surfaces

NASA Astrophysics Data System (ADS)

Pureza, Vincent S.

Blood coagulation requires the assembly of several membrane-bound protein complexes composed of regulatory and catalytic subunits. The biomembranes involved in these reactions not only provide a platform for these procoagulant proteins, but can also affect their function. Increased exposure of acidic phospholipids on the outer leaflet of the plasma membrane can dramatically modulate the catalytic efficiencies of such membrane-bound enzymes. Under physiologic conditions, however, these phospholipids spontaneously cluster into a patchwork of membrane microdomains upon which membrane binding proteins may preferentially assemble. As a result, the membrane composition surrounding these proteins is largely unknown. Through the development and use of a nanometer-scale bilayer system that provides rigorous control of the phospholipid membrane environment, I investigated the role of phosphatidylserine, an acidic phospholipid, in the direct vicinity (within nanometers) of two critical membrane-bound procoagulant protein complexes and their respective natural substrates. Here, I present how the assembly and function of the tissue factor˙factor VIIa and factor Va˙factor Xa complexes, the first and final cofactor˙enzyme complexes of the blood clotting cascade, respectively, are mediated by changes in their immediate phospholipid environments.

Single-molecule FRET studies of the cooperative and non-cooperative binding kinetics of the bacteriophage T4 single-stranded DNA binding protein (gp32) to ssDNA lattices at replication fork junctions

PubMed Central

Lee, Wonbae; Gillies, John P.; Jose, Davis; Israels, Brett A.; von Hippel, Peter H.; Marcus, Andrew H.

2016-01-01

Gene 32 protein (gp32) is the single-stranded (ss) DNA binding protein of the bacteriophage T4. It binds transiently and cooperatively to ssDNA sequences exposed during the DNA replication process and regulates the interactions of the other sub-assemblies of the replication complex during the replication cycle. We here use single-molecule FRET techniques to build on previous thermodynamic studies of gp32 binding to initiate studies of the dynamics of the isolated and cooperative binding of gp32 molecules within the replication complex. DNA primer/template (p/t) constructs are used as models to determine the effects of ssDNA lattice length, gp32 concentration, salt concentration, binding cooperativity and binding polarity at p/t junctions. Hidden Markov models (HMMs) and transition density plots (TDPs) are used to characterize the dynamics of the multi-step assembly pathway of gp32 at p/t junctions of differing polarity, and show that isolated gp32 molecules bind to their ssDNA targets weakly and dissociate quickly, while cooperatively bound dimeric or trimeric clusters of gp32 bind much more tightly, can ‘slide’ on ssDNA sequences, and exhibit binding dynamics that depend on p/t junction polarities. The potential relationships of these binding dynamics to interactions with other components of the T4 DNA replication complex are discussed. PMID:27694621

DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA.

PubMed

Keyamura, Kenji; Katayama, Tsutomu

2011-08-19

Chromosomal replication is initiated from the replication origin oriC in Escherichia coli by the active ATP-bound form of DnaA protein. The regulatory inactivation of DnaA (RIDA) system, a complex of the ADP-bound Hda and the DNA-loaded replicase clamp, represses extra initiations by facilitating DnaA-bound ATP hydrolysis, yielding the inactive ADP-bound form of DnaA. However, the mechanisms involved in promoting the DnaA-Hda interaction have not been determined except for the involvement of an interaction between the AAA+ domains of the two. This study revealed that DnaA Leu-422 and Pro-423 residues within DnaA domain IV, including a typical DNA-binding HTH motif, are specifically required for RIDA-dependent ATP hydrolysis in vitro and that these residues support efficient interaction with the DNA-loaded clamp·Hda complex and with Hda in vitro. Consistently, substitutions of these residues caused accumulation of ATP-bound DnaA in vivo and oriC-dependent inhibition of cell growth. Leu-422 plays a more important role in these activities than Pro-423. By contrast, neither of these residues is crucial for DNA replication from oriC, although they are highly conserved in DnaA orthologues. Structural analysis of a DnaA·Hda complex model suggested that these residues make contact with residues in the vicinity of the Hda AAA+ sensor I that participates in formation of a nucleotide-interacting surface. Together, the results show that functional DnaA-Hda interactions require a second interaction site within DnaA domain IV in addition to the AAA+ domain and suggest that these interactions are crucial for the formation of RIDA complexes that are active for DnaA-ATP hydrolysis.

DnaA Protein DNA-binding Domain Binds to Hda Protein to Promote Inter-AAA+ Domain Interaction Involved in Regulatory Inactivation of DnaA*

PubMed Central

Keyamura, Kenji; Katayama, Tsutomu

2011-01-01

Chromosomal replication is initiated from the replication origin oriC in Escherichia coli by the active ATP-bound form of DnaA protein. The regulatory inactivation of DnaA (RIDA) system, a complex of the ADP-bound Hda and the DNA-loaded replicase clamp, represses extra initiations by facilitating DnaA-bound ATP hydrolysis, yielding the inactive ADP-bound form of DnaA. However, the mechanisms involved in promoting the DnaA-Hda interaction have not been determined except for the involvement of an interaction between the AAA+ domains of the two. This study revealed that DnaA Leu-422 and Pro-423 residues within DnaA domain IV, including a typical DNA-binding HTH motif, are specifically required for RIDA-dependent ATP hydrolysis in vitro and that these residues support efficient interaction with the DNA-loaded clamp·Hda complex and with Hda in vitro. Consistently, substitutions of these residues caused accumulation of ATP-bound DnaA in vivo and oriC-dependent inhibition of cell growth. Leu-422 plays a more important role in these activities than Pro-423. By contrast, neither of these residues is crucial for DNA replication from oriC, although they are highly conserved in DnaA orthologues. Structural analysis of a DnaA·Hda complex model suggested that these residues make contact with residues in the vicinity of the Hda AAA+ sensor I that participates in formation of a nucleotide-interacting surface. Together, the results show that functional DnaA-Hda interactions require a second interaction site within DnaA domain IV in addition to the AAA+ domain and suggest that these interactions are crucial for the formation of RIDA complexes that are active for DnaA-ATP hydrolysis. PMID:21708944

Scholarisation, Apprenticeship and Social Differentiation. Analysis of the Non-Industrial Craft Sector in Morocco

ERIC Educational Resources Information Center

Gerard, Etienne

2012-01-01

The article approaches the question of the schooling processes in the particular environment of the Moroccan craftsmen of Fez. It shows that the weak schooling of the children is bound to the representations and to the ways of transmission of craft industry knowledge. Schooling is, indeed, the object of tensions between a school system of western…

Gravitational mass of positron from LEP synchrotron losses

DOE PAGES

Kalaydzhyan, Tigran

2016-07-27

General relativity(GR) is the current description of gravity in modern physics. One of the cornerstones of GR, as well as Newton’s theory of gravity, is the weak equivalence principle (WEP), stating that the trajectory of a freely falling test body is independent of its internal structure and composition. WEP is known to be valid for the normal matter with a high precision. However, due to the rarity of antimatter and weakness of the gravitational forces, the WEP has never been confirmed for antimatter. The current direct bounds on the ratio between the gravitational and inertial masses of the antihydrogen domore » not rule out a repulsive nature for the antimatter gravity. Here we establish an indirect bound of 0.13% on the difference between the gravitational and inertial masses of the positron (antielectron) from the analysis of synchrotron losses at the Large Electron-Positron collider (LEP). As a result, this serves as a confirmation of the conventional gravitational properties of antimatter without common assumptions such as, e.g., coupling of gravity to virtual particles, dynamics of distant astrophysical sources and the nature of absolute gravitational potentials.« less

Dynamic-Stark-effect-induced coherent mixture of virtual paths in laser-dressed helium: energetic electron impact excitation

NASA Astrophysics Data System (ADS)

Agueny, Hicham; Makhoute, Abdelkader; Dubois, Alain

2017-06-01

We theoretically investigate quantum virtual path interference caused by the dynamic Stark effect in bound-bound electronic transitions. The effect is studied in an intermediate resonant region and in connection with the energetic electron impact excitation of a helium atom embedded in a weak low-frequency laser field. The process under investigation is dealt with via a Born-Floquet approach. Numerical calculations show a resonant feature in laser-assisted cross sections. The latter is found to be sensitive to the intensity of the laser field dressing. We show that this feature is a signature of quantum beats which result from the coherent mixture of different quantum virtual pathways, and that excitation may follow in order to end up with a common final channel. This mixture arises from the dynamic Stark effect, which produces a set of avoided crossings in laser-dressed states. The effect allows one to coherently control quantum virtual path interference by varying the intensity of the laser field dressing. Our findings suggest that the combination of an energetic electron and a weak laser field is a useful tool for the coherent control of nonadiabatic transitions in an intermediate resonant region.

Binding the diproton in stars: anthropic limits on the strength of gravity

NASA Astrophysics Data System (ADS)

Barnes, Luke A.

2015-12-01

We calculate the properties and investigate the stability of stars that burn via strong (and electromagnetic) interactions, and compare their properties with those that, as in our Universe, include a rate-limiting weak interaction. It has been suggested that, if the diproton were bound, stars would burn ~1018 times brighter and faster via strong interactions, resulting in a universe that would fail to support life. By considering the representative case of a star in our Universe with initially equal numbers of protons and deuterons, we find that stable, "strong-burning" stars adjust their central densities and temperatures to have familiar surface temperatures, luminosities and lifetimes. There is no "diproton disaster". In addition, strong-burning stars are stable in a much larger region of the parameter space of fundamental constants, specifically the strength of electromagnetism and gravity. The strongest anthropic bound on stars in such universes is not their stability, as is the case for stars limited by the weak interaction, but rather their lifetime. Regardless of the strength of electromagnetism, all stars burn out in mere millions of years unless the gravitational coupling constant is extremely small, αGlesssim 10-30.

Accurate predictions of spectroscopic and molecular properties of 27 Λ-S and 73 Ω states of AsS radical

NASA Astrophysics Data System (ADS)

Shi, Deheng; Song, Ziyue; Niu, Xianghong; Sun, Jinfeng; Zhu, Zunlue

2016-01-01

The PECs are calculated for the 27 Λ-S states and their corresponding 73 Ω states of AsS radical. Of these Λ-S states, only the 22Δ and 54Π states are replulsive. The 12Σ+, 22Σ+, 42Π, 34Δ, 34Σ+, and 44Π states possess double wells. The 32Σ+ state possesses three wells. The A2Π, 32Π, 12Φ, 24Π, 34Π, 24Δ, 34Δ, 16Σ+, and 16Π states are inverted with the SO coupling effect included. The 14Σ+, 24Σ+, 24Σ-, 24Δ, 14Φ, 16Σ+, and 16Π states, the second wells of 12Σ+, 34Σ+, 42Π, 44Π, and 34Δ states, and the third well of 32Σ+ state are very weakly-bound states. The PECs are extrapolated to the CBS limit. The effect of SO coupling on the PECs is discussed. The spectroscopic parameters are evaluated, and compared with available measurements and other theoretical ones. The vibrational properties of several weakly-bound states are determined. The spectroscopic properties reported here can be expected to be reliably predicted ones.

Vibronic transitions in the alkali-metal (Li, Na, K, Rb) - alkaline-earth-metal (Ca, Sr) series: A systematic analysis of de-excitation mechanisms based on the graphical mapping of Frank-Condon integrals

NASA Astrophysics Data System (ADS)

Pototschnig, Johann V.; Meyer, Ralf; Hauser, Andreas W.; Ernst, Wolfgang E.

2017-02-01

Research on ultracold molecules has seen a growing interest recently in the context of high-resolution spectroscopy and quantum computation. After forming weakly bound molecules from atoms in cold collisions, the preparation of molecules in low vibrational levels of the ground state is experimentally challenging, and typically achieved by population transfer using excited electronic states. Accurate potential energy surfaces are needed for a correct description of processes such as the coherent de-excitation from the highest and therefore weakly bound vibrational levels in the electronic ground state via couplings to electronically excited states. This paper is dedicated to the vibrational analysis of potentially relevant electronically excited states in the alkali-metal (Li, Na, K, Rb)- alkaline-earth metal (Ca,Sr) diatomic series. Graphical maps of Frank-Condon overlap integrals are presented for all molecules of the group. By comparison to overlap graphics produced for idealized potential surfaces, we judge the usability of the selected states for future experiments on laser-enhanced molecular formation from mixtures of quantum degenerate gases.

Generalization of the Hartree-Fock approach to collision processes

NASA Astrophysics Data System (ADS)

Hahn, Yukap

1997-06-01

The conventional Hartree and Hartree-Fock approaches for bound states are generalized to treat atomic collision processes. All the single-particle orbitals, for both bound and scattering states, are determined simultaneously by requiring full self-consistency. This generalization is achieved by introducing two Ansäauttze: (a) the weak asymptotic boundary condition, which maintains the correct scattering energy and target orbitals with correct number of nodes, and (b) square integrable amputated scattering functions to generate self-consistent field (SCF) potentials for the target orbitals. The exact initial target and final-state asymptotic wave functions are not required and thus need not be specified a priori, as they are determined simultaneously by the SCF iterations. To check the asymptotic behavior of the solution, the theory is applied to elastic electron-hydrogen scattering at low energies. The solution is found to be stable and the weak asymptotic condition is sufficient to produce the correct scattering amplitudes. The SCF potential for the target orbital shows the strong penetration by the projectile electron during the collision, but the exchange term tends to restore the original form. Potential applicabilities of this extension are discussed, including the treatment of ionization and shake-off processes.

Charge renormalization at the large-D limit for N-electron atoms and weakly bound systems

NASA Astrophysics Data System (ADS)

Kais, S.; Bleil, R.

1995-05-01

We develop a systematic way to determine an effective nuclear charge ZRD such that the Hartree-Fock results will be significantly closer to the exact energies by utilizing the analytically known large-D limit energies. This method yields an expansion for the effective nuclear charge in powers of (1/D), which we have evaluated to the first order. This first order approximation to the desired effective nuclear charge has been applied to two-electron atoms with Z=2-20, and weakly bound systems such as H-. The errors for the two-electron atoms when compared with exact results were reduced from ˜0.2% for Z=2 to ˜0.002% for large Z. Although usual Hartree-Fock calculations for H- show this to be unstable, our results reduce the percent error of the Hartree-Fock energy from 7.6% to 1.86% and predicts the anion to be stable. For N-electron atoms (N=3-18, Z=3-28), using only the zeroth order approximation for the effective charge significantly reduces the error of Hartree-Fock calculations and recovers more than 80% of the correlation energy.

[Study of "bound insulin" of the blood sera of blood/donors and patients with diabetes mellitus by circular dichroism].

PubMed

Gracheva, N K; Kharitonenkov, I G

1978-01-01

Circular dichroism was applied to the study of the structure of the insulin-transferrin complexes ("bound insulin") isolated from the blood sera of donors and patients suffering from diabetes mellitus of moderate severity. There proved to be a considerable (in comparison with the normal) reduction of the alpha-helix areas in the "bound insulin"molecule of the patients. A comparative study of the circular dichroism spectra in the area of absorption of aromatic amino acids permitted to suppose that the structural changes of the molecule of a complex isolated from the blood sera of patients could not be explained by alterations in the area of the aromatic amino acids.

Tunneling Time and Weak Measurement in Strong Field Ionization.

PubMed

Zimmermann, Tomáš; Mishra, Siddhartha; Doran, Brent R; Gordon, Daniel F; Landsman, Alexandra S

2016-06-10

Tunneling delays represent a hotly debated topic, with many conflicting definitions and little consensus on when and if such definitions accurately describe the physical observables. Here, we relate these different definitions to distinct experimental observables in strong field ionization, finding that two definitions, Larmor time and Bohmian time, are compatible with the attoclock observable and the resonance lifetime of a bound state, respectively. Both of these definitions are closely connected to the theory of weak measurement, with Larmor time being the weak measurement value of tunneling time and Bohmian trajectory corresponding to the average particle trajectory, which has been recently reconstructed using weak measurement in a two-slit experiment [S. Kocsis, B. Braverman, S. Ravets, M. J. Stevens, R. P. Mirin, L. K. Shalm, and A. M. Steinberg, Science 332, 1170 (2011)]. We demonstrate a big discrepancy in strong field ionization between the Bohmian and weak measurement values of tunneling time, and we suggest this arises because the tunneling time is calculated for a small probability postselected ensemble of electrons. Our results have important implications for the interpretation of experiments in attosecond science, suggesting that tunneling is unlikely to be an instantaneous process.

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

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark

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)more » 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.« less

Pre-folding IkappaBalpha alters control of NF-kappaB signaling.

PubMed

Truhlar, Stephanie M E; Mathes, Erika; Cervantes, Carla F; Ghosh, Gourisankar; Komives, Elizabeth A

2008-06-27

Transcription complex components frequently show coupled folding and binding but the functional significance of this mode of molecular recognition is unclear. IkappaBalpha binds to and inhibits the transcriptional activity of NF-kappaB via its ankyrin repeat (AR) domain. The beta-hairpins in ARs 5-6 in IkappaBalpha are weakly-folded in the free protein, and their folding is coupled to NF-kappaB binding. Here, we show that introduction of two stabilizing mutations in IkappaBalpha AR 6 causes ARs 5-6 to fold cooperatively to a conformation similar to that in NF-kappaB-bound IkappaBalpha. Free IkappaBalpha is degraded by a proteasome-dependent but ubiquitin-independent mechanism, and this process is slower for the pre-folded mutants both in vitro and in cells. Interestingly, the pre-folded mutants bind NF-kappaB more weakly, as shown by both surface plasmon resonance and isothermal titration calorimetry in vitro and immunoprecipitation experiments from cells. One consequence of the weaker binding is that resting cells containing these mutants show incomplete inhibition of NF-kappaB activation; they have significant amounts of nuclear NF-kappaB. Additionally, the weaker binding combined with the slower rate of degradation of the free protein results in reduced levels of nuclear NF-kappaB upon stimulation. These data demonstrate clearly that the coupled folding and binding of IkappaBalpha is critical for its precise control of NF-kappaB transcriptional activity.

Monitoring Ras Interactions with the Nucleotide Exchange Factor Son of Sevenless (Sos) Using Site-specific NMR Reporter Signals and Intrinsic Fluorescence*

PubMed Central

Vo, Uybach; Vajpai, Navratna; Flavell, Liz; Bobby, Romel; Breeze, Alexander L.; Embrey, Kevin J.; Golovanov, Alexander P.

2016-01-01

The activity of Ras is controlled by the interconversion between GTP- and GDP-bound forms partly regulated by the binding of the guanine nucleotide exchange factor Son of Sevenless (Sos). The details of Sos binding, leading to nucleotide exchange and subsequent dissociation of the complex, are not completely understood. Here, we used uniformly 15N-labeled Ras as well as [13C]methyl-Met,Ile-labeled Sos for observing site-specific details of Ras-Sos interactions in solution. Binding of various forms of Ras (loaded with GDP and mimics of GTP or nucleotide-free) at the allosteric and catalytic sites of Sos was comprehensively characterized by monitoring signal perturbations in the NMR spectra. The overall affinity of binding between these protein variants as well as their selected functional mutants was also investigated using intrinsic fluorescence. The data support a positive feedback activation of Sos by Ras·GTP with Ras·GTP binding as a substrate for the catalytic site of activated Sos more weakly than Ras·GDP, suggesting that Sos should actively promote unidirectional GDP → GTP exchange on Ras in preference of passive homonucleotide exchange. Ras·GDP weakly binds to the catalytic but not to the allosteric site of Sos. This confirms that Ras·GDP cannot properly activate Sos at the allosteric site. The novel site-specific assay described may be useful for design of drugs aimed at perturbing Ras-Sos interactions. PMID:26565026

Weak bases and formation of a less soluble lauryl sulfate salt/complex in sodium lauryl sulfate (SLS) containing media.

PubMed

Bhattachar, Shobha N; Risley, Donald S; Werawatganone, Pornpen; Aburub, Aktham

2011-06-30

This work reports on the solubility of two weakly basic model compounds in media containing sodium lauryl sulfate (SLS). Results clearly show that the presence of SLS in the media (e.g. simulated gastric fluid or dissolution media) can result in an underestimation of solubility of some weak bases. We systematically study this phenomenon and provide evidence (chromatography and pXRD) for the first time that the decrease in solubility is likely due to formation of a less soluble salt/complex between the protonated form of the weak base and lauryl sulfate anion. Copyright © 2011 Elsevier B.V. All rights reserved.

A new order-theoretic characterisation of the polytime computable functions☆

PubMed Central

Avanzini, Martin; Eguchi, Naohi; Moser, Georg

2015-01-01

We propose a new order-theoretic characterisation of the class of polytime computable functions. To this avail we define the small polynomial path order (sPOP⁎ for short). This termination order entails a new syntactic method to analyse the innermost runtime complexity of term rewrite systems fully automatically: for any rewrite system compatible with sPOP⁎ that employs recursion up to depth d, the (innermost) runtime complexity is polynomially bounded of degree d. This bound is tight. Thus we obtain a direct correspondence between a syntactic (and easily verifiable) condition of a program and the asymptotic worst-case complexity of the program. PMID:26412933

Combined effects of π-π stacking and hydrogen bonding on the (N1) acidity of uracil and hydrolysis of 2'-deoxyuridine.

PubMed

Kellie, Jennifer L; Navarro-Whyte, Lex; Carvey, Matthew T; Wetmore, Stacey D

2012-03-01

M06-2X/6-31+G(d,p) is used to study the simultaneous effects of π-π stacking interactions with phenylalanine (modeled as benzene) and hydrogen bonding with small molecules (HF, H(2)O, and NH(3)) on the N1 acidity of uracil and the hydrolytic deglycosylation of 2'-deoxyuridine (dU) (facilitated by fully (OH(-)) or partially (HCOO(-)···H(2)O) activated water). When phenylalanine is complexed with isolated uracil, the proton affinity of all acceptor sites significantly increases (by up to 28 kJ mol(-1)), while the N1 acidity slightly decreases (by ~6 kJ mol(-1)). When small molecules are hydrogen bound to uracil, addition of the phenylalanine ring can increase or decrease the acidity of uracil depending on the number and nature (acidity) of the molecules bound. Furthermore, a strong correlation between the effects of π-π stacking on the acidity of U and the dU deglycosylation reaction energetics is found, where the hydrolysis barrier can increase or decrease depending on the nature and number of small molecules bound, the nucleophile considered (which dictates the negative charge on U in the transition state), and the polarity of the (bulk) environment. These findings emphasize that the catalytic (or anticatalytic) role of the active-site aromatic amino acid residues is highly dependent on the situation under consideration. In the case of uracil-DNA glycosylase (UNG), which catalyzes the hydrolytic excision of uracil from DNA, the type of discrete hydrogen-bonding interactions with U, the nature of the nucleophile, and the anticipated weak, nonpolar environment in the active site suggest that phenylalanine will be slightly anticatalytic in the chemical step, and therefore experimentally observed contributions to catalysis may entirely result from associated structural changes that occur prior to deglycosylation.

A Study of Strong Stability of Distributed Systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Cataltepe, Tayfun

1989-01-01

The strong stability of distributed systems is studied and the problem of characterizing strongly stable semigroups of operators associated with distributed systems is addressed. Main emphasis is on contractive systems. Three different approaches to characterization of strongly stable contractive semigroups are developed. The first one is an operator theoretical approach. Using the theory of dilations, it is shown that every strongly stable contractive semigroup is related to the left shift semigroup on an L(exp 2) space. Then, a decomposition for the state space which identifies strongly stable and unstable states is introduced. Based on this decomposition, conditions for a contractive semigroup to be strongly stable are obtained. Finally, extensions of Lyapunov's equation for distributed parameter systems are investigated. Sufficient conditions for weak and strong stabilities of uniformly bounded semigroups are obtained by relaxing the equivalent norm condition on the right hand side of the Lyanupov equation. These characterizations are then applied to the problem of feedback stabilization. First, it is shown via the state space decomposition that under certain conditions a contractive system (A,B) can be strongly stabilized by the feedback -B(*). Then, application of the extensions of the Lyapunov equation results in sufficient conditions for weak, strong, and exponential stabilizations of contractive systems by the feedback -B(*). Finally, it is shown that for a contractive system, the first derivative of x with respect to time = Ax + Bu (where B is any linear bounded operator), there is a related linear quadratic regulator problem and a corresponding steady state Riccati equation which always has a bounded nonnegative solution.

A Lorentz model for weak magnetic field bioeffects: part I--thermal noise is an essential component of AC/DC effects on bound ion trajectory.

PubMed

Muehsam, David J; Pilla, Arthur A

2009-09-01

We have previously employed the Lorentz-Langevin model to describe the effects of weak exogenous magnetic fields via the classical Lorentz force on a charged ion bound in a harmonic oscillator potential, in the presence of thermal noise forces. Previous analyses predicted that microT-range fields give rise to a rotation of the oscillator orientation at the Larmor frequency and bioeffects were based upon the assumption that the classical trajectory of the bound charge itself could modulate a biochemical process. Here, it is shown that the thermal component of the motion follows the Larmor trajectory. The results show that the Larmor frequency is independent of the thermal noise strength, and the motion retains the form of a coherent oscillator throughout the binding lifetime, rather than devolving into a random walk. Thermal equilibration results in a continual increase in the vibrational amplitude of the rotating oscillator towards the steady-state amplitude, but does not affect the Larmor orbit. Thus, thermal noise contributes to, rather than inhibits, the effect of the magnetic field upon reactivity. Expressions are derived for the ensemble average of position and the velocity of the thermal component of the oscillator motion. The projection of position and velocity onto a Cartesian axis measures the nonuniformity of the Larmor trajectory and is illustrated for AC and combined AC/DC magnetic fields, suggesting a means of interpreting resonance phenomena. It is noted that the specific location and height of resonances are dependent upon binding lifetime and initial AC phase.

On degenerate coupled transport processes in porous media with memory phenomena

NASA Astrophysics Data System (ADS)

Beneš, Michal; Pažanin, Igor

2018-06-01

In this paper we prove the existence of weak solutions to degenerate parabolic systems arising from the fully coupled moisture movement, solute transport of dissolved species and heat transfer through porous materials. Physically relevant mixed Dirichlet-Neumann boundary conditions and initial conditions are considered. Existence of a global weak solution of the problem is proved by means of semidiscretization in time, proving necessary uniform estimates and by passing to the limit from discrete approximations. Degeneration occurs in the nonlinear transport coefficients which are not assumed to be bounded below and above by positive constants. Degeneracies in transport coefficients are overcome by proving suitable a-priori $L^{\\infty}$-estimates based on De Giorgi and Moser iteration technique.

Particle physics on ice: constraints on neutrino interactions far above the weak scale.

PubMed

Anchordoqui, Luis A; Feng, Jonathan L; Goldberg, Haim

2006-01-20

Ultrahigh energy cosmic rays and neutrinos probe energies far above the weak scale. Their usefulness might appear to be limited by astrophysical uncertainties; however, by simultaneously considering up- and down-going events, one may disentangle particle physics from astrophysics. We show that present data from the AMANDA experiment in the South Pole ice already imply an upper bound on neutrino cross sections at energy scales that will likely never be probed at man-made accelerators. The existing data also place an upper limit on the neutrino flux valid for any neutrino cross section. In the future, similar analyses of IceCube data will constrain neutrino properties and fluxes at the theta(10%) level.

Achieving metrological precision limits through postselection

NASA Astrophysics Data System (ADS)

Alves, G. Bié; Pimentel, A.; Hor-Meyll, M.; Walborn, S. P.; Davidovich, L.; Filho, R. L. de Matos

2017-01-01

Postselection strategies have been proposed with the aim of amplifying weak signals, which may help to overcome detection thresholds associated with technical noise in high-precision measurements. Here we use an optical setup to experimentally explore two different postselection protocols for the estimation of a small parameter: a weak-value amplification procedure and an alternative method that does not provide amplification but nonetheless is shown to be more robust for the sake of parameter estimation. Each technique leads approximately to the saturation of quantum limits for the estimation precision, expressed by the Cramér-Rao bound. For both situations, we show that parameter estimation is improved when the postselection statistics are considered together with the measurement device.

Complement activating properties of complexes containing rheumatoid factor in synovial fluids and sera from patients with rheumatoid arthritis.

PubMed Central

Elson, C J; Carter, S D; Cottrell, B J; Scott, D G; Bacon, P A; Wallington, T B

1985-01-01

The relationship between complexes containing rheumatoid factor and complexes activating complement was examined in synovial fluids and sera from patients with rheumatoid arthritis (RA). In each case this was performed by quantifying the amount of rheumatoid factor bound by solid phase Fab'2 anti-C3 and/or solid phase conglutinin. Both anti-C3 coated and conglutinin coated microtitre plates bound high levels of complexes containing rheumatoid factor from sera of RA patients with vasculitis. Unexpectedly, these complexes were detected in synovial fluids from only a minority of RA patients with synovitis. However, RA synovial fluids did contain other complexes as shown by the presence of complement consuming activity, C1q binding material and immunoglobulin attaching to conglutinin. It is considered that in RA synovial fluids the complexes containing RF and those activating complement are not necessarily the same whilst in vasculitic sera the complexes containing rheumatoid factor also activate complement. PMID:3978872

The Cramér-Rao Bounds and Sensor Selection for Nonlinear Systems with Uncertain Observations.

PubMed

Wang, Zhiguo; Shen, Xiaojing; Wang, Ping; Zhu, Yunmin

2018-04-05

This paper considers the problems of the posterior Cramér-Rao bound and sensor selection for multi-sensor nonlinear systems with uncertain observations. In order to effectively overcome the difficulties caused by uncertainty, we investigate two methods to derive the posterior Cramér-Rao bound. The first method is based on the recursive formula of the Cramér-Rao bound and the Gaussian mixture model. Nevertheless, it needs to compute a complex integral based on the joint probability density function of the sensor measurements and the target state. The computation burden of this method is relatively high, especially in large sensor networks. Inspired by the idea of the expectation maximization algorithm, the second method is to introduce some 0-1 latent variables to deal with the Gaussian mixture model. Since the regular condition of the posterior Cramér-Rao bound is unsatisfied for the discrete uncertain system, we use some continuous variables to approximate the discrete latent variables. Then, a new Cramér-Rao bound can be achieved by a limiting process of the Cramér-Rao bound of the continuous system. It avoids the complex integral, which can reduce the computation burden. Based on the new posterior Cramér-Rao bound, the optimal solution of the sensor selection problem can be derived analytically. Thus, it can be used to deal with the sensor selection of a large-scale sensor networks. Two typical numerical examples verify the effectiveness of the proposed methods.

Weak Links: Stabilizers of Complex Systems from Proteins to Social Networks

NASA Astrophysics Data System (ADS)

Csermely, Peter

Why do women stabilize our societies? Why can we enjoy and understand Shakespeare? Why are fruitflies uniform? Why do omnivorous eating habits aid our survival? Why is Mona Lisa's smile beautiful? -- Is there any answer to these questions? This book shows that the statement: "weak links stabilize complex systems" holds the answers to all of the surprising questions above. The author (recipientof several distinguished science communication prizes) uses weak (low affinity, low probability) interactions as a thread to introduce a vast varietyof networks from proteins to ecosystems.

Interactions between HIV-1 Reverse Transcriptase and the Downstream Template Strand in Stable Complexes with Primer-Template

PubMed Central

Rutvisuttinunt, Wiriya; Meyer, Peter R.; Scott, Walter A.

2008-01-01

Background Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) forms stable ternary complexes in which RT is bound tightly at fixed positions on the primer-template (P/T). We have probed downstream interactions between RT and the template strand in the complex containing the incoming dNTP (+1 dNTP•RT•P/T complex) and in the complex containing the pyrophosphate analog, foscarnet (foscarnet•RT•P/T complex). Methods and Results UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP). Furthermore, formation of the +1 dNTP•RT•P/T complex on a biotin-containing template inhibited binding of streptavidin when biotin was in the +2 position on the template but not when the biotin was in the +3 position. Streptavidin pre-bound to a biotin residue in the template caused RT to stall two to three nucleotides upstream from the biotin residue. The downstream border of the complex formed by the stalled RT was mapped by digestion with exonuclease RecJF. UV-induced cross-linking of the complex formed by the pyrophosphate analog, foscarnet, with RT and P/T occurred preferentially with bromodeoxyuridine in the +1 position on the template in keeping with the location of RT one base upstream in the foscarnet•RT•P/T complex (i.e., in the pre-translocation position). Conclusions For +1 dNTP•RT•P/T and foscarnet•RT•P/T stable complexes, tight interactions were observed between RT and the first unpaired template nucleotide following the bound dNTP or the primer terminus, respectively. PMID:18974785

Conformational heterogeneity within the Michaelis complex of lactate dehydrogenase†

PubMed Central

Deng, Hua; Vu, Dung V.; Clinch, Keith; Desamero, Ruel; Dyer, R. Brian; Callender, Robert

2011-01-01

A series of isotope edited IR measurements, both static as well as temperature jump relaxation spectroscopy, are performed on lactate dehydrogenase (LDH) to determine the ensemble of structures available to its Michaelis complex. There clearly has been a substantial reduction in the number of states available to the pyruvate substrate (as modeled by the substrate mimic, oxamate) and NADH when bound to protein compared to dissolved in solution, as determined by the bandwidths and positions of the critical C2=O band of bound substrate mimic and the C4-H stretch of NADH reduced nicotinamide group. Moreover, it is found that a strong ionic bond (characterized by a signature IR band discovered in this study) is formed between the carboxyl group of bound pyruvate with (presumably) Arg171, forming a strong ‘anchor’ within the protein matrix. However, conformational heterogeneity within the Michaelis complex is found that has an impact on both catalytic efficiency and thermodynamics of the enzyme. PMID:21568287

Global synchronization of complex dynamical networks through digital communication with limited data rate.

PubMed

Wang, Yan-Wu; Bian, Tao; Xiao, Jiang-Wen; Wen, Changyun

2015-10-01

This paper studies the global synchronization of complex dynamical network (CDN) under digital communication with limited bandwidth. To realize the digital communication, the so-called uniform-quantizer-sets are introduced to quantize the states of nodes, which are then encoded and decoded by newly designed encoders and decoders. To meet the requirement of the bandwidth constraint, a scaling function is utilized to guarantee the quantizers having bounded inputs and thus achieving bounded real-time quantization levels. Moreover, a new type of vector norm is introduced to simplify the expression of the bandwidth limit. Through mathematical induction, a sufficient condition is derived to ensure global synchronization of the CDNs. The lower bound on the sum of the real-time quantization levels is analyzed for different cases. Optimization method is employed to relax the requirements on the network topology and to determine the minimum of such lower bound for each case, respectively. Simulation examples are also presented to illustrate the established results.

Syntaxin1a variants lacking an N-peptide or bearing the LE mutation bind to Munc18a in a closed conformation

DOE PAGES

Colbert, Karen N.; Hattendorf, Douglas A.; Weiss, Thomas M.; ...

2013-07-15

In neurons, soluble N-ethylmaleimide–sensitive factor attachment receptor (SNARE) proteins drive the fusion of synaptic vesicles to the plasma membrane through the formation of a four-helix SNARE complex. Members of the Sec1/Munc18 protein family regulate membrane fusion through interactions with the syntaxin family of SNARE proteins. The neuronal protein Munc18a interacts with a closed conformation of the SNARE protein syntaxin1a (Syx1a) and with an assembled SNARE complex containing Syx1a in an open conformation. The N-peptide of Syx1a (amino acids 1–24) has been implicated in the transition of Munc18a-bound Syx1a to Munc18a-bound SNARE complex, but the underlying mechanism is not understood. Inmore » addition, we report the X-ray crystal structures of Munc18a bound to Syx1a with and without its native N-peptide (Syx1aΔN), along with small-angle X-ray scattering (SAXS) data for Munc18a bound to Syx1a, Syx1aΔN, and Syx1a L165A/E166A (LE), a mutation thought to render Syx1a in a constitutively open conformation. We show that all three complexes adopt the same global structure, in which Munc18a binds a closed conformation of Syx1a. We also identify a possible structural connection between the Syx1a N-peptide and SNARE domain that might be important for the transition of closed-to-open Syx1a in SNARE complex assembly. Although the role of the N-peptide in Munc18a-mediated SNARE complex assembly remains unclear, our results demonstrate that the N-peptide and LE mutation have no effect on the global conformation of the Munc18a–Syx1a complex.« less

Gossip and Distributed Kalman Filtering: Weak Consensus Under Weak Detectability

NASA Astrophysics Data System (ADS)

Kar, Soummya; Moura, José M. F.

2011-04-01

The paper presents the gossip interactive Kalman filter (GIKF) for distributed Kalman filtering for networked systems and sensor networks, where inter-sensor communication and observations occur at the same time-scale. The communication among sensors is random; each sensor occasionally exchanges its filtering state information with a neighbor depending on the availability of the appropriate network link. We show that under a weak distributed detectability condition: 1. the GIKF error process remains stochastically bounded, irrespective of the instability properties of the random process dynamics; and 2. the network achieves \\emph{weak consensus}, i.e., the conditional estimation error covariance at a (uniformly) randomly selected sensor converges in distribution to a unique invariant measure on the space of positive semi-definite matrices (independent of the initial state.) To prove these results, we interpret the filtered states (estimates and error covariances) at each node in the GIKF as stochastic particles with local interactions. We analyze the asymptotic properties of the error process by studying as a random dynamical system the associated switched (random) Riccati equation, the switching being dictated by a non-stationary Markov chain on the network graph.

Controlling quantum memory-assisted entropic uncertainty in non-Markovian environments

NASA Astrophysics Data System (ADS)

Zhang, Yanliang; Fang, Maofa; Kang, Guodong; Zhou, Qingping

2018-03-01

Quantum memory-assisted entropic uncertainty relation (QMA EUR) addresses that the lower bound of Maassen and Uffink's entropic uncertainty relation (without quantum memory) can be broken. In this paper, we investigated the dynamical features of QMA EUR in the Markovian and non-Markovian dissipative environments. It is found that dynamical process of QMA EUR is oscillation in non-Markovian environment, and the strong interaction is favorable for suppressing the amount of entropic uncertainty. Furthermore, we presented two schemes by means of prior weak measurement and posterior weak measurement reversal to control the amount of entropic uncertainty of Pauli observables in dissipative environments. The numerical results show that the prior weak measurement can effectively reduce the wave peak values of the QMA-EUA dynamic process in non-Markovian environment for long periods of time, but it is ineffectual on the wave minima of dynamic process. However, the posterior weak measurement reversal has an opposite effects on the dynamic process. Moreover, the success probability entirely depends on the quantum measurement strength. We hope that our proposal could be verified experimentally and might possibly have future applications in quantum information processing.

Entanglement-Assisted Weak Value Amplification

NASA Astrophysics Data System (ADS)

Pang, Shengshi; Dressel, Justin; Brun, Todd A.

2014-07-01

Large weak values have been used to amplify the sensitivity of a linear response signal for detecting changes in a small parameter, which has also enabled a simple method for precise parameter estimation. However, producing a large weak value requires a low postselection probability for an ancilla degree of freedom, which limits the utility of the technique. We propose an improvement to this method that uses entanglement to increase the efficiency. We show that by entangling and postselecting n ancillas, the postselection probability can be increased by a factor of n while keeping the weak value fixed (compared to n uncorrelated attempts with one ancilla), which is the optimal scaling with n that is expected from quantum metrology. Furthermore, we show the surprising result that the quantum Fisher information about the detected parameter can be almost entirely preserved in the postselected state, which allows the sensitive estimation to approximately saturate the relevant quantum Cramér-Rao bound. To illustrate this protocol we provide simple quantum circuits that can be implemented using current experimental realizations of three entangled qubits.

Higgs gravitational interaction, weak boson scattering, and Higgs inflation in Jordan and Einstein frames

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

Ren, Jing; Xianyu, Zhong-Zhi; He, Hong-Jian, E-mail: jingren2004@gmail.com, E-mail: xianyuzhongzhi@gmail.com, E-mail: hjhe@tsinghua.edu.cn

2014-06-01

We study gravitational interaction of Higgs boson through the unique dimension-4 operator ξH{sup †}HR, with H  the Higgs doublet and R  the Ricci scalar curvature. We analyze the effect of this dimensionless nonminimal coupling ξ  on weak gauge boson scattering in both Jordan and Einstein frames. We explicitly establish the longitudinal-Goldstone equivalence theorem with nonzero ξ coupling in both frames, and analyze the unitarity constraints. We study the ξ-induced weak boson scattering cross sections at O(1−30) TeV scales, and propose to probe the Higgs-gravity coupling via weak boson scattering experiments at the LHC (14 TeV) and the next generation ppmore » colliders (50-100 TeV). We further extend our study to Higgs inflation, and quantitatively derive the perturbative unitarity bounds via coupled channel analysis, under large field background at the inflation scale. We analyze the unitarity constraints on the parameter space in both the conventional Higgs inflation and the improved models in light of the recent BICEP2 data.« less

An Investigation of Human-Computer Interaction Approaches Beneficial to Weak Learners in Complex Animation Learning

ERIC Educational Resources Information Center

Yeh, Yu-Fang

2016-01-01

Animation is one of the useful contemporary educational technologies in teaching complex subjects. There is a growing interest in proper use of learner-technology interaction to promote learning quality for different groups of learner needs. The purpose of this study is to investigate if an interaction approach supports weak learners, who have…

SHARP ENTRYWISE PERTURBATION BOUNDS FOR MARKOV CHAINS.

PubMed

Thiede, Erik; VAN Koten, Brian; Weare, Jonathan

For many Markov chains of practical interest, the invariant distribution is extremely sensitive to perturbations of some entries of the transition matrix, but insensitive to others; we give an example of such a chain, motivated by a problem in computational statistical physics. We have derived perturbation bounds on the relative error of the invariant distribution that reveal these variations in sensitivity. Our bounds are sharp, we do not impose any structural assumptions on the transition matrix or on the perturbation, and computing the bounds has the same complexity as computing the invariant distribution or computing other bounds in the literature. Moreover, our bounds have a simple interpretation in terms of hitting times, which can be used to draw intuitive but rigorous conclusions about the sensitivity of a chain to various types of perturbations.

Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog

PubMed Central

Zhao, Xiaodong; Copeland, Daniel M.; Soares, Alexei S.; West, Ann H.

2008-01-01

Summary The crystal structure of the yeast SLN1 response regulator domain bound to both a phosphoryl analog (BeF3−) and Mg2+ ion in complex with its downstream phosphorelay signaling partner YPD1 has been determined at a resolution of 1.70 Å. Comparisons between the beryllium fluoride-activated complex and the unliganded (or apo) complex determined previously reveal modest but important differences. The SLN1-R1•Mg2+•BeF3− structure from the complex provides evidence for the first time that the mechanism of phosphorylation-induced activation is highly conserved between bacterial response regulator domains and this example from a eukaryotic organism. Residues in and around the active site undergo slight rearrangements in order to form bonds to the essential divalent cation and fluorine atoms of BeF3−. Two conserved switch-like residues (Thr 1173 and Phe 1192) occupy distinctly different positions in the apo- versus BeF3−-bound structures consistent with the “Y-T” coupling mechanism proposed for activation of CheY and other bacterial response regulators. Several loop regions and the α4-β5-α5 surface of the SLN1-R1 domain undergo subtle conformational changes (∼1-3 Å displacements relative to the apo-structure) that lead to significant changes in terms of contacts that are formed with YPD1. Detailed structural comparisons of protein-protein interactions in the apo- and BeF3−-bound complexes suggest at least a two-state equilibrium model for formation of a transient encounter complex, in which phosphorylation of the response regulator promotes the formation of a phosphotransfer-competent complex. In the BeF3−-activated complex, the position of His 64 from YPD1 is within ideal distance and near linear geometry with Asp 1144 from the SLN1-R1 domain for phosphotransfer to occur. The ground state structure presented here suggests that phosphoryl transfer will likely proceed through an associative mechanism involving formation of a pentacoordinate phosphorus intermediate. PMID:18076904

Kinetically inert Cu in coastal waters.

PubMed

Kogut, Megan B; Voelker, Bettina M

2003-02-01

Many studies have shown that Cu and other metals in natural waters are mostly bound by unidentified compounds interpreted to be strong ligands reversibly complexing a given metal. However, commonly applied analytical techniques are not capable of distinguishing strongly but reversibly complexed metal from metal bound in kinetically inert compounds. In this work, we use a modified competitive ligand exchange adsorptive cathodic stripping voltammetry method combined with size fractionation to show that most if not all of the apparently very strongly (log K > or = 13) bound Cu in samples from five New England coastal waters (1-18 nM, 10-60% of total Cu) is actually present as kinetically inert compounds. In three of the five samples examined by ultrafiltration, a significant portion of the 0.2-microm-filtrable inert Cu was retained by a 0.02-microm-pore size filter, suggesting that at least some of the Cu was kinetically inert because it was physically sequestered in colloidal material. The rest of the ambient Cu, and Cu added in titrations, were reversibly bound in complexes that could be modeled as having conditional stability constants of 10(10)-10(13). The Cu-binding ability of these complexes was equivalent to that of seawater containing reasonable concentrations of humic substances from terrestrial sources, approximately 0.15-0.45 mg of C/L. Both the inert compounds and the reversible ligands were important for determining [Cu2+] at ambient Cu levels in our samples.

Transformation of glucocorticoid receptors bound to the antagonist RU 486: Effects of alkaline phosphatase

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

Gruol, D.J.; Wolfe, K.A.

1990-08-28

RU 486 is a synthetic steroid that binds avidly to glucocorticoid receptors without promoting their transformation into activated transcription factors. A significant part of this behavior has been shown to be due to a failure of the RU 486 bound receptor to be efficiently released from a larger (sedimenting at 8-9 S) multimeric complex containing the 90-kDa heat shock protein. The studies have found that in vitro at 15{degree}C the RU 486-receptor was slowly released from the 8-9S complex and converted into a DNA binding protein by a process that could be blocked by sodium fluoride. Moreover, this transition wasmore » significantly accelerated by treatment with alkaline phosphatase. High-resolution anion-exchange chromatography showed that the profile of receptor subspecies released from the 8-9S complex was different for the RU 486 bound receptor when compared to the receptor occupied by the agonist triamcinolone acetonide. Production of the earliest eluting receptor form (peak A) was inhibited with RU 486. Treatment of the Ru 486-receptor with alkaline phosphatase increased the formation of the peak A subspecies as well as the capacity of receptor to bind DNA-cellulose. Taken together, the results indicate that phosphorylation of the receptor or a tightly bound factor contributes to defining the capacity with which individual steroids can promote dissociation of the 8-9S complex and conversion of the glucocorticoid receptor into a DNA-binding protein.« less

Merging Galaxy Clusters: A Case Study of ZwCl 2341.1+0000 and the Development of a New Forward Modeled Lensing Technique

NASA Astrophysics Data System (ADS)

Benson, Bryant Joseph

Context: Galaxy clusters are the most massive gravitationally bound structures in the universe and are formed through the process of hierarchical clustering, in which smaller systems undergo a series of mergers to form ever larger clusters. Because of the masses involved, mergers between these giants provide a unique laboratory for observing many interesting astrophysical processes. These merging systems also act as large dark matter colliders, because the dark matter halos of the clusters involved pass through each other during of the merger. This offers us a means to observe if dark matter-dark matter collisions result in momentum exchange beyond what occurs from gravity alone. Such observations can help us to unravel some of the mysteries behind dark matter, such as does it interact with itself through mechanisms beyond gravity, and how strong are those interactions. Answers to questions like these are what will eventually allow us to discover what dark matter really is. However, the extremely long time scales for these mergers (˜several billion years) make each observation a single snapshot in the long merger history, and we must infer many of the details necessary for understanding the full merger process. Furthermore, current weak lensing analyses lack the precision required to detect a signal from self-interacting dark matter. Uncertain weak lensing mass and position estimates also yield large uncertainties in the dynamical reconstruction of the merger scenarios. Need: In order to better model the dynamics of merging galaxy cluster systems, and to potentially measure any signal from self-interacting dark matter, we need to obtain more precise measurements on the masses and positions of the dark matter halos involved. Gravitational lensing offers a robust method for mapping the mass in these clusters because it directly measures the gravitational field, and does not depend on the dynamical state of the system that has been disturbed in the merger process. Of the lensing methods, weak gravitational lensing is the only way that we can probe a wide field and measure the total mass of the cluster. However, the precision of conventional weak lensing techniques is currently limited by shape noise (uncertainty in the shear due to the dispersion in the intrinsic shapes and orientations of unlensed galaxies). A possible avenue forward is to eliminate shape noise as a source of uncertainty in shear measurements via a technique to be described below. This would eliminate the largest source of uncertainty in weak lensing analyses, and enable us to obtain mass and position estimates of dark matter halos with a much higher level of precision. Task: In this dissertation we perform statistical clustering, conventional weak lensing analyses, and dynamical reconstruction on the merging galaxy cluster system ZwCl 2341.1+0000 in order to test the capabilities of the dynamical modeling on a complex, multiple merger. We use targeted optical spectroscopy to identify cluster member galaxies, which we then use to model the galaxy substructures. We also obtain a dynamical mass estimate using the galaxy velocity dispersions, and perform weak lensing analyses in the forms of aperture densitometry to place an upper bound on the total cluster mass, and multiple NFW profile halo fitting to approximate the masses and positions of the individual dark matter halos present in the merger. The masses, positions, and line of sight velocities of those clusters are then used to constrain the parameters describing the best fit merger scenario, with radio relic positions and polarization used to further tighten those constraints. We also develop a new method for obtaining weak lensing data from individual source galaxies in the form of shear measurements that are independent of shape noise, and direct measurements of the convergence. We accomplish this by simultaneously modeling the pre-lensing velocity and intensity profiles of a lensed, rotating disk galaxy, and the lensing transform required to distort those into the lensed profiles we observe. We test this method with a host of idealized simulations to characterize its capabilities in a best-case scenario and forecast the possible improvements it can bring to the precision of weak lensing analyses on galaxy clusters. (Abstract shortened by ProQuest.).

Phase-space mass bound for fermionic dark matter from dwarf spheroidal galaxies

NASA Astrophysics Data System (ADS)

Di Paolo, Chiara; Nesti, Fabrizio; Villante, Francesco L.

2018-04-01

We reconsider the lower bound on the mass of a fermionic dark matter (DM) candidate resulting from the existence of known small dwarf spheroidal galaxies, in the hypothesis that their DM halo is constituted by degenerate fermions, with phase-space density limited by the Pauli exclusion principle. By relaxing the common assumption that the DM halo scale radius is tied to that of the luminous stellar component and by marginalizing on the unknown stellar velocity dispersion anisotropy, we prove that observations lead to rather weak constraints on the DM mass, which could be as low as tens of eV. In this scenario, however, the DM haloes would be quite large and massive, so that a bound stems from the requirement that the time of orbital decay due to dynamical friction in the hosting Milky Way DM halo is longer than their lifetime. The smallest and nearest satellites Segue I and Willman I lead to a final lower bound of m ≳ 100 eV, still weaker than previous estimates but robust and independent on the model of DM formation and decoupling. We thus show that phase-space constraints do not rule out the possibility of sub-keV fermionic DM.

ϕ 3 theory with F4 flavor symmetry in 6 - 2 ɛ dimensions: 3-loop renormalization and conformal bootstrap

NASA Astrophysics Data System (ADS)

Pang, Yi; Rong, Junchen; Su, Ning

2016-12-01

We consider ϕ 3 theory in 6 - 2 ɛ with F 4 global symmetry. The beta function is calculated up to 3 loops, and a stable unitary IR fixed point is observed. The anomalous dimensions of operators quadratic or cubic in ϕ are also computed. We then employ conformal bootstrap technique to study the fixed point predicted from the perturbative approach. For each putative scaling dimension of ϕ (Δ ϕ ), we obtain the corresponding upper bound on the scaling dimension of the second lowest scalar primary in the 26 representation ( Δ 26 2nd ) which appears in the OPE of ϕ × ϕ. In D = 5 .95, we observe a sharp peak on the upper bound curve located at Δ ϕ equal to the value predicted by the 3-loop computation. In D = 5, we observe a weak kink on the upper bound curve at ( Δ ϕ , Δ 26 2nd ) = (1.6, 4).

Discovering protein complexes in protein interaction networks via exploring the weak ties effect

PubMed Central

2012-01-01

Background Studying protein complexes is very important in biological processes since it helps reveal the structure-functionality relationships in biological networks and much attention has been paid to accurately predict protein complexes from the increasing amount of protein-protein interaction (PPI) data. Most of the available algorithms are based on the assumption that dense subgraphs correspond to complexes, failing to take into account the inherence organization within protein complex and the roles of edges. Thus, there is a critical need to investigate the possibility of discovering protein complexes using the topological information hidden in edges. Results To provide an investigation of the roles of edges in PPI networks, we show that the edges connecting less similar vertices in topology are more significant in maintaining the global connectivity, indicating the weak ties phenomenon in PPI networks. We further demonstrate that there is a negative relation between the weak tie strength and the topological similarity. By using the bridges, a reliable virtual network is constructed, in which each maximal clique corresponds to the core of a complex. By this notion, the detection of the protein complexes is transformed into a classic all-clique problem. A novel core-attachment based method is developed, which detects the cores and attachments, respectively. A comprehensive comparison among the existing algorithms and our algorithm has been made by comparing the predicted complexes against benchmark complexes. Conclusions We proved that the weak tie effect exists in the PPI network and demonstrated that the density is insufficient to characterize the topological structure of protein complexes. Furthermore, the experimental results on the yeast PPI network show that the proposed method outperforms the state-of-the-art algorithms. The analysis of detected modules by the present algorithm suggests that most of these modules have well biological significance in context of complexes, suggesting that the roles of edges are critical in discovering protein complexes. PMID:23046740

Study of Omega-proton correlations in heavy-ion collisions

NASA Astrophysics Data System (ADS)

Han, Yifei; STAR Collaboration

2015-10-01

Recently the STAR experiment at RHIC measured Lambda-Lambda correlations from Au+Au collisions at √{sNN} = 200 GeV to search for the H particle (uuddss). The correlation strength indicated that the Lambda-Lambda interaction is weak and is unlikely to be attractive enough to form a bound state. A recent lattice QCD calculation predicted a possible di-baryon bound state with Omega-nucleon. Thus, we will extend the correlation measurements to Omega-proton, which could potentially be a sensitive approach to search for such a state. We will present the Omega-proton correlations based on data collected by STAR in Au+Au collisions at √{sNN} =200 GeV, and discuss the physics implications. for the STAR collaboration.

Backscattering measurement of 6He on 209Bi: Critical interaction distance

NASA Astrophysics Data System (ADS)

Guimarães, V.; Kolata, J. J.; Aguilera, E. F.; Howard, A.; Roberts, A.; Becchetti, F. D.; Torres-Isea, R. O.; Riggins, A.; Febrarro, M.; Scarduelli, V.; de Faria, P. N.; Monteiro, D. S.; Huiza, J. F. P.; Arazi, A.; Hinnefeld, J.; Moro, A. M.; Rossi, E. S.; Morcelle, V.; Barioni, A.

2016-06-01

An elastic backscattering experiment has been performed at energies below the Coulomb barrier to investigate static and dynamic effects in the interaction of 6He with 209Bi. The measured cross sections are presented in terms of the d σ /d σR u t h ratio, as a function of the distance of closest approach on a Rutherford trajectory. The data are compared with a three-body CDCC calculation and good agreement is observed. In addition, the critical distance of interaction was extracted. A larger value was obtained for the exotic 6He nucleus as compared with the weakly bound 6Li and 9Be nuclei and the tightly bound 4He12C, and 16O nuclei.

NASA Astrophysics Data System (ADS)

Morcelle, V.; Lichtenthäler, R.; Lépine-Szily, A.; Guimarães, V.; Pires, K. C. C.; Lubian, J.; Mendes Junior, D. R.; de Faria, P. N.; Kolata, J. J.; Becchetti, F. D.; Jiang, H.; Aguilera, E. F.; Lizcano, D.; Martinez-Quiroz, E.; Garcia, H.

2017-01-01

We present 8B 27Al elastic scattering angular distributions for the proton-halo nucleus 8B at two energies above the Coulomb barrier, namely Elab=15.3 and 21.7 MeV. The experiments were performed in the Radioactive Ion Beams in Brasil facility (RIBRAS) in São Paulo, and in the TwinSol facility at the University of Notre Dame, USA. The angular distributions were measured in the angular range of 15-80 degrees. Optical model and continuum discretized coupled channels calculations were performed, and the total reaction cross sections were derived. A comparison of the 8B+27Al total reaction cross sections with similar systems including exotic, weakly bound, and tightly bound projectiles impinging on the same target is presented.

Long-Time Behavior and Critical Limit of Subcritical SQG Equations in Scale-Invariant Sobolev Spaces

NASA Astrophysics Data System (ADS)

Coti Zelati, Michele

2018-02-01

We consider the subcritical SQG equation in its natural scale-invariant Sobolev space and prove the existence of a global attractor of optimal regularity. The proof is based on a new energy estimate in Sobolev spaces to bootstrap the regularity to the optimal level, derived by means of nonlinear lower bounds on the fractional Laplacian. This estimate appears to be new in the literature and allows a sharp use of the subcritical nature of the L^∞ bounds for this problem. As a by-product, we obtain attractors for weak solutions as well. Moreover, we study the critical limit of the attractors and prove their stability and upper semicontinuity with respect to the strength of the diffusion.

Solubility of lead and copper in biochar-amended small arms range soils: influence of soil organic carbon and pH.

PubMed

Uchimiya, Minori; Bannon, Desmond I

2013-08-14

Biochar is often considered a strong heavy metal stabilizing agent. However, biochar in some cases had no effects on, or increased the soluble concentrations of, heavy metals in soil. The objective of this study was to determine the factors causing some biochars to stabilize and others to dissolve heavy metals in soil. Seven small arms range soils with known total organic carbon (TOC), cation exchange capacity, pH, and total Pb and Cu contents were first screened for soluble Pb and Cu concentrations. Over 2 weeks successive equilibrations using weak acid (pH 4.5 sulfuric acid) and acetate buffer (0.1 M at pH 4.9), Alaska soil containing disproportionately high (31.6%) TOC had nearly 100% residual (insoluble) Pb and Cu. This soil was then compared with sandy soils from Maryland containing significantly lower (0.5-2.0%) TOC in the presence of 10 wt % (i) plant biochar activated to increase the surface-bound carboxyl and phosphate ligands (PS450A), (ii) manure biochar enriched with soluble P (BL700), and (iii) unactivated plant biochars produced at 350 °C (CH350) and 700 °C (CH500) and by flash carbonization (corn). In weak acid, the pH was set by soil and biochar, and the biochars increasingly stabilized Pb with repeated extractions. In pH 4.9 acetate buffer, PS450A and BL700 stabilized Pb, and only PS450A stabilized Cu. Surface ligands of PS450A likely complexed and stabilized Pb and Cu even under acidic pH in the presence of competing acetate ligand. Oppositely, unactivated plant biochars (CH350, CH500, and corn) mobilized Pb and Cu in sandy soils; the putative mechanism is the formation of soluble complexes with biochar-borne dissolved organic carbon. In summary, unactivated plant biochars can inadvertently increase dissolved Pb and Cu concentrations of sandy, low TOC soils when used to stabilize other contaminants.

Why are SiX5(-) and GeX5(-) (X = F, Cl) stable but not CF5(-) and CCl5(-)?

PubMed

Marchaj, Marzena; Freza, Sylwia; Skurski, Piotr

2012-03-01

The possible existence of the CF(5)(-), CCl(5)(-), SiF(5)(-), SiCl(5)(-), GeF(5)(-), and GeCl(5)(-) anions has been investigated using ab initio methods. The species containing Si and Ge as central atoms were found to adopt the D(3h)-symmetry trigonal bipyramidal equilibrium structures whose thermodynamic stabilities were confirmed by examining the most probable fragmentation channels. The ab initio re-examination of the electronic stabilities of the SiF(5)(-), SiCl(5)(-), GeF(5)(-), and GeCl(5)(-) anions [using the OVGF(full) method with the 6-311+G(3df) basis set] led to the very large vertical electron detachment (VDE) energies of 9.316 eV (SiF(5)(-)) and 9.742 eV (GeF(5)(-)), whereas smaller VDEs of 6.196 and 6.452 eV were predicted for the SiCl(5)(-) and GeCl(5)(-) species, respectively. By contrast, the high-symmetry and structurally compact anionic CF(5)(-) and CCl(5)(-) systems cannot exist due to the strongly repulsive potential predicted for the X(-) (F(-) or Cl(-)) approaching the CX(4) (CF(4) or CCl(4)). The formation of weakly bound CX(4)···X(-) (CF(4)···F(-) and CCl(4)···Cl(-)) anionic complexes (consisting of pseudotetrahedral neutral CX(4) with the weakly tethered X(-)) might be expected at low temperatures (approaching 0 K), whereas neither CX(5)(-) (CF(5)(-), CCl(5)(-)) systems nor CX(4)···X(-) (CF(4)···F(-) and CCl(4)···Cl(-)) complexes can exist in the elevated temperatures (above 0K) due to their susceptibility to the fragmentation (leading to the X(-) loss). © 2012 American Chemical Society

Silica-coated gold nanorods as saturable absorber for bound-state pulse generation in a fiber laser with near-zero dispersion

NASA Astrophysics Data System (ADS)

Wang, Xude; Luo, Aiping; Luo, Zhichao; Liu, Meng; Zou, Feng; Zhu, Yanfang; Xue, Jianping; Xu, Wencheng

2017-11-01

We presented a bound-state operation in a fiber laser with near-zero anomalous dispersion based on a silica-coated gold nanorods (GNRs@SiO2) saturable absorber (SA). Using a balanced twin detector measurement technique, the modulation depth and nonsaturable loss of the GNRs@SiO2 SA were measured to be approximately 3.5% and 39.3%, respectively. By virtue of the highly nonlinear effect of the GNRs@SiO2 SA, the bound-state pulses could be easily observed. Besides the lower-order bound-state pulses with two, three, and four solitons, the higher-order bound states with up to 12 solitons were also obtained in the laser cavity. The pulse profiles of the higher-order bound states were further reconstructed theoretically. The experimental results would give further insight towards understanding the complex nonlinear dynamics of bound-state pulses in fiber lasers.

Localization behavior at bound Bi complex states in GaA s 1 - x B i x

DOE PAGES

Alberi, K.; Christian, T. M.; Fluegel, B.; ...

2017-07-01

While bismuth-related states are known to localize carriers in GaAs 1-xBi x alloys, the localization behavior of distinct Bi pair, triplet and cluster states bound above the valence band is less well understood. We probe localization at three different Bi complex states in dilute GaAs 1-xBi x alloys using magneto-photoluminescence and time-resolved photoluminescence spectroscopy. The mass of electrons Coulomb-bound to holes trapped at Bi pair states is found to increase relative to the average electron mass in the alloy. This increase is attributed to enhanced local compressive strain in the immediate vicinity of the pairs. The dependence of energy transfermore » between these states on composition is also explored.« less

Dissociation of branched-chain alpha-keto acid dehydrogenase kinase (BDK) from branched-chain alpha-keto acid dehydrogenase complex (BCKDC) by BDK inhibitors.

PubMed

Murakami, Taro; Matsuo, Masayuki; Shimizu, Ayako; Shimomura, Yoshiharu

2005-02-01

Branched-chain alpha-keto acid dehydrogenase kinase (BDK) phosphorylates and inactivates the branched-chain alpha-keto acid dehydrogenase complex (BCKDC), which is the rate-limiting enzyme in the branched-chain amino acid catabolism. BDK has been believed to be bound to the BCKDC. However, recent our studies demonstrated that protein-protein interaction between BDK and BCKDC is one of the factors to regulate BDK activity. Furthermore, only the bound form of BDK appears to have its activity. In the present study, we examined effects of BDK inhibitors on the amount of BDK bound to the BCKDC using rat liver extracts. The bound form of BDK in the extracts of liver from low protein diet-fed rats was measured by an immunoprecipitation pull down assay with or without BDK inhibitors. Among the BDK inhibitors. alpha-ketoisocaproate, alpha-chloroisocaproate, and a-ketoisovalerate released the BDK from the complex. Furthermore, the releasing effect of these inhibitors on the BDK appeared to depend on their inhibition constants. On the other hand, clofibric acid and thiamine pyrophosphate had no effect on the protein-protein interaction between two enzymes. These results suggest that the dissociation of the BDK from the BCKDC is one of the mechanisms responsible for the action of some inhibitors to BDK.

The interaction of Dirac particles with non-abelian gauge fields and gravity - bound states

NASA Astrophysics Data System (ADS)

Finster, Felix; Smoller, Joel; Yau, Shing-Tung

2000-09-01

We consider a spherically symmetric, static system of a Dirac particle interacting with classical gravity and an SU(2) Yang-Mills field. The corresponding Einstein-Dirac-Yang-Mills equations are derived. Using numerical methods, we find different types of soliton-like solutions of these equations and discuss their properties. Some of these solutions are stable even for arbitrarily weak gravitational coupling.

A STUDY OF THE INFLUENCES OF THE FATHER'S JOB AND SOCIAL STATUS ON THE OCCUPATIONAL AND SOCIAL GOALS OF YOUTH. FINAL REPORT.

ERIC Educational Resources Information Center

GRINDER, ROBERT E.

THE MAJOR EMPHASIS OF THE STUDY WAS UPON THE HYPOTHESIS THAT, AMONG ADOLESCENT BOYS, STRONG ORIENTATION TOWARD THE FATHER AND DISINTEREST IN THE YOUTH CULTURE WILL PREDICT INVOLVEMENT IN THE COLLEGE-BOUND HIGH SCHOOL PROGRAM, AND CONVERSELY, WEAK ORIENTATION TOWARD THE FATHER AND HIGH INVOLVEMENT IN THE YOUTH CULTURE WILL PREDICT POTENTIAL DROPOUT…

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

PubMed Central

Seeliger, Daniel; de Groot, Bert L.

2010-01-01

Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 Å backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 Å backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available. PMID:20066034

Effects of sediment composition on inorganic mercury partitioning, speciation and bioavailability in oxic surficial sediments.

PubMed

Zhong, Huan; Wang, Wen-Xiong

2008-01-01

Artificially prepared sediments were used to assess the effects of sediment composition on inorganic Hg partitioning, speciation and bioavailability. Organic coating in sediment greatly increased the Hg partitioning and the amount of bioavailable Hg bound with the clay and the Fe and Mn oxides, but had little effect on that bound with the quartz and calcium carbonate as a result of weaker binding of humic acids and fulvic acids. The clay content increased the concentration of Hg in the sediments but inhibited the gut juice extraction due to the strong binding of Hg-organic matter (OM) complexes. Most Hg in the sediments was complexed by OM (mainly distributed in the organo-complexed phase and the strongly complexed phase), and the Hg-OM complexes (especially Hg in the strongly complexed phase) in sediments contributed much to gut juice extraction. Redistribution of Hg-OM complexes between sediments and gut juices may occur during gut juice extraction and modify Hg bioavailability and speciation in sediments.

Nitrogen-doped carbon-supported cobalt-iron oxygen reduction catalyst

DOEpatents

Zelenay, Piotr; Wu, Gang

2014-04-29

A Fe--Co hybrid catalyst for oxygen reaction reduction was prepared by a two part process. The first part involves reacting an ethyleneamine with a cobalt-containing precursor to form a cobalt-containing complex, combining the cobalt-containing complex with an electroconductive carbon supporting material, heating the cobalt-containing complex and carbon supporting material under conditions suitable to convert the cobalt-containing complex and carbon supporting material into a cobalt-containing catalyst support. The second part of the process involves polymerizing an aniline in the presence of said cobalt-containing catalyst support and an iron-containing compound under conditions suitable to form a supported, cobalt-containing, iron-bound polyaniline species, and subjecting said supported, cobalt-containing, iron bound polyaniline species to conditions suitable for producing a Fe--Co hybrid catalyst.

Static and kinetic studies of calmodulin and melittin complex.

PubMed

Itakura, M; Iio, T

1992-08-01

Ca2+ binding to calmodulin triggers conformational change of the protein which induces exposure of hydrophobic surfaces. Melittin has been believed to bind to Ca(2+)-bound calmodulin through the exposed hydrophobic surfaces. However, tryptophan fluorescence measurements and gel chromatography experiments with the melittin-calmodulin system revealed that melittin bound to calmodulin at zero salt concentration even in the absence of Ca2+; addition of salt removed melittin from Ca(2+)-free calmodulin. This means not only the hydrophobic interaction but also the electrostatic interaction contributes to the melittin-calmodulin binding. The fluorescence stopped-flow studies of the dissociation reaction of melittin-calmodulin complex revealed that Ca2+ removal from the complex induced a conformational change of calmodulin, resulting in reduction of the hydrophobic interaction between melittin and calmodulin, but the electrostatic interaction kept melittin still bound to calmodulin for a subsecond lag period, after which melittin dissociated from calmodulin. The fluorescence stopped-flow experiments on the dissociation reaction of complex of melittin and tryptic fragment(s) of calmodulin revealed that the lag period of the melittin dissociation reaction was attributable to the interaction between the C-terminal half of calmodulin and the C-terminal region of melittin.